WorldWideScience

Sample records for fully automated 3d

  1. 3D model assisted fully automated scanning laser Doppler vibrometer measurements

    Sels, Seppe; Ribbens, Bart; Bogaerts, Boris; Peeters, Jeroen; Vanlanduit, Steve

    2017-12-01

    In this paper, a new fully automated scanning laser Doppler vibrometer (LDV) measurement technique is presented. In contrast to existing scanning LDV techniques which use a 2D camera for the manual selection of sample points, we use a 3D Time-of-Flight camera in combination with a CAD file of the test object to automatically obtain measurements at pre-defined locations. The proposed procedure allows users to test prototypes in a shorter time because physical measurement locations are determined without user interaction. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. The proposed method is illustrated with vibration measurements of an unmanned aerial vehicle

  2. 3D camera assisted fully automated calibration of scanning laser Doppler vibrometers

    Sels, Seppe; Ribbens, Bart; Mertens, Luc; Vanlanduit, Steve

    2016-01-01

    Scanning laser Doppler vibrometers (LDV) are used to measure full-field vibration shapes of products and structures. In most commercially available scanning laser Doppler vibrometer systems the user manually draws a grid of measurement locations on a 2D camera image of the product. The determination of the correct physical measurement locations can be a time consuming and diffcult task. In this paper we present a new methodology for product testing and quality control that integrates 3D imaging techniques with vibration measurements. This procedure allows to test prototypes in a shorter period because physical measurements locations will be located automatically. The proposed methodology uses a 3D time-of-flight camera to measure the location and orientation of the test-object. The 3D image of the time-of-flight camera is then matched with the 3D-CAD model of the object in which measurement locations are pre-defined. A time of flight camera operates strictly in the near infrared spectrum. To improve the signal to noise ratio in the time-of-flight measurement, a time-of-flight camera uses a band filter. As a result of this filter, the laser spot of most laser vibrometers is invisible in the time-of-flight image. Therefore a 2D RGB-camera is used to find the laser-spot of the vibrometer. The laser spot is matched to the 3D image obtained by the time-of-flight camera. Next an automatic calibration procedure is used to aim the laser at the (pre)defined locations. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. Secondly the orientation of the CAD model is known with respect to the laser beam. This information can be used to find the direction of the measured vibration relatively to the surface of the object. With this direction, the vibration measurements can be compared more precisely with numerical

  3. 3D camera assisted fully automated calibration of scanning laser Doppler vibrometers

    Sels, Seppe, E-mail: Seppe.Sels@uantwerpen.be; Ribbens, Bart; Mertens, Luc; Vanlanduit, Steve [Op3Mech Research Group, University of Antwerp, Salesianenlaan 90, 2660 Antwerp (Belgium)

    2016-06-28

    Scanning laser Doppler vibrometers (LDV) are used to measure full-field vibration shapes of products and structures. In most commercially available scanning laser Doppler vibrometer systems the user manually draws a grid of measurement locations on a 2D camera image of the product. The determination of the correct physical measurement locations can be a time consuming and diffcult task. In this paper we present a new methodology for product testing and quality control that integrates 3D imaging techniques with vibration measurements. This procedure allows to test prototypes in a shorter period because physical measurements locations will be located automatically. The proposed methodology uses a 3D time-of-flight camera to measure the location and orientation of the test-object. The 3D image of the time-of-flight camera is then matched with the 3D-CAD model of the object in which measurement locations are pre-defined. A time of flight camera operates strictly in the near infrared spectrum. To improve the signal to noise ratio in the time-of-flight measurement, a time-of-flight camera uses a band filter. As a result of this filter, the laser spot of most laser vibrometers is invisible in the time-of-flight image. Therefore a 2D RGB-camera is used to find the laser-spot of the vibrometer. The laser spot is matched to the 3D image obtained by the time-of-flight camera. Next an automatic calibration procedure is used to aim the laser at the (pre)defined locations. Another benefit from this methodology is that it incorporates automatic mapping between a CAD model and the vibration measurements. This mapping can be used to visualize measurements directly on a 3D CAD model. Secondly the orientation of the CAD model is known with respect to the laser beam. This information can be used to find the direction of the measured vibration relatively to the surface of the object. With this direction, the vibration measurements can be compared more precisely with numerical

  4. UT simulation using a fully automated 3D hybrid model: Application to planar backwall breaking defects inspection

    Imperiale, Alexandre; Chatillon, Sylvain; Darmon, Michel; Leymarie, Nicolas; Demaldent, Edouard

    2018-04-01

    The high frequency models gathered in the CIVA software allow fast computations and provide satisfactory quantitative predictions in a wide range of situations. However, the domain of validity of these models is limited since they do not accurately predict the ultrasound response in configurations involving subwavelength complex phenomena. In addition, when modelling backwall breaking defects inspection, an important challenge remains to capture the propagation of the creeping waves that are generated at the critical angle. Hybrid models combining numerical and asymptotic methods have already been shown to be an effective strategy to overcome these limitations in 2D [1]. However, 3D simulations remain a crucial issue for industrial applications because of the computational cost of the numerical solver. A dedicated three dimensional high order finite element model combined with a domain decomposition method has been recently proposed to tackle 3D limitations [2]. In this communication, we will focus on the specific case of planar backwall breaking defects, with an adapted coupling strategy in order to efficiently model the propagation of creeping waves. Numerical and experimental validations will be proposed on various configurations.

  5. Automated 3-D Radiation Mapping

    Tarpinian, J. E.

    1991-01-01

    This work describes an automated radiation detection and imaging system which combines several state-of-the-art technologies to produce a portable but very powerful visualization tool for planning work in radiation environments. The system combines a radiation detection system, a computerized radiation imaging program, and computerized 3-D modeling to automatically locate and measurements are automatically collected and imaging techniques are used to produce colored, 'isodose' images of the measured radiation fields. The isodose lines from the images are then superimposed over the 3-D model of the area. The final display shows the various components in a room and their associated radiation fields. The use of an automated radiation detection system increases the quality of radiation survey obtained measurements. The additional use of a three-dimensional display allows easier visualization of the area and associated radiological conditions than two-dimensional sketches

  6. Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain.

    Bian, Wei; Li, Yan; Crane, Jason C; Nelson, Sarah J

    2018-02-01

    To implement a fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging (MRSI). The PRESS selected volume and outer-volume suppression bands were predefined on the MNI152 standard template image. The template image was aligned to the subject T 1 -weighted image during a scan, and the resulting transformation was then applied to the predefined prescription. To evaluate the method, H-1 MRSI data were obtained in repeat scan sessions from 20 healthy volunteers. In each session, datasets were acquired twice without repositioning. The overlap ratio of the prescribed volume in the two sessions was calculated and the reproducibility of inter- and intrasession metabolite peak height and area ratios was measured by the coefficient of variation (CoV). The CoVs from intra- and intersession were compared by a paired t-test. The average overlap ratio of the automatically prescribed selection volumes between two sessions was 97.8%. The average voxel-based intersession CoVs were less than 0.124 and 0.163 for peak height and area ratios, respectively. Paired t-test showed no significant difference between the intra- and intersession CoVs. The proposed method provides a time efficient method to prescribe 3D PRESS MRSI with reproducible imaging positioning and metabolite measurements. Magn Reson Med 79:636-642, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  7. Histograms of Oriented 3D Gradients for Fully Automated Fetal Brain Localization and Robust Motion Correction in 3 T Magnetic Resonance Images.

    Serag, Ahmed; Macnaught, Gillian; Denison, Fiona C; Reynolds, Rebecca M; Semple, Scott I; Boardman, James P

    2017-01-01

    Fetal brain magnetic resonance imaging (MRI) is a rapidly emerging diagnostic imaging tool. However, automated fetal brain localization is one of the biggest obstacles in expediting and fully automating large-scale fetal MRI processing. We propose a method for automatic localization of fetal brain in 3 T MRI when the images are acquired as a stack of 2D slices that are misaligned due to fetal motion. First, the Histogram of Oriented Gradients (HOG) feature descriptor is extended from 2D to 3D images. Then, a sliding window is used to assign a score to all possible windows in an image, depending on the likelihood of it containing a brain, and the window with the highest score is selected. In our evaluation experiments using a leave-one-out cross-validation strategy, we achieved 96% of complete brain localization using a database of 104 MRI scans at gestational ages between 34 and 38 weeks. We carried out comparisons against template matching and random forest based regression methods and the proposed method showed superior performance. We also showed the application of the proposed method in the optimization of fetal motion correction and how it is essential for the reconstruction process. The method is robust and does not rely on any prior knowledge of fetal brain development.

  8. Histograms of Oriented 3D Gradients for Fully Automated Fetal Brain Localization and Robust Motion Correction in 3 T Magnetic Resonance Images

    Ahmed Serag

    2017-01-01

    Full Text Available Fetal brain magnetic resonance imaging (MRI is a rapidly emerging diagnostic imaging tool. However, automated fetal brain localization is one of the biggest obstacles in expediting and fully automating large-scale fetal MRI processing. We propose a method for automatic localization of fetal brain in 3 T MRI when the images are acquired as a stack of 2D slices that are misaligned due to fetal motion. First, the Histogram of Oriented Gradients (HOG feature descriptor is extended from 2D to 3D images. Then, a sliding window is used to assign a score to all possible windows in an image, depending on the likelihood of it containing a brain, and the window with the highest score is selected. In our evaluation experiments using a leave-one-out cross-validation strategy, we achieved 96% of complete brain localization using a database of 104 MRI scans at gestational ages between 34 and 38 weeks. We carried out comparisons against template matching and random forest based regression methods and the proposed method showed superior performance. We also showed the application of the proposed method in the optimization of fetal motion correction and how it is essential for the reconstruction process. The method is robust and does not rely on any prior knowledge of fetal brain development.

  9. Fully 3D GPU PET reconstruction

    Herraiz, J.L., E-mail: joaquin@nuclear.fis.ucm.es [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Espana, S. [Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States); Cal-Gonzalez, J. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain); Vaquero, J.J. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Desco, M. [Departmento de Bioingenieria e Ingenieria Espacial, Universidad Carlos III, Madrid (Spain); Unidad de Medicina y Cirugia Experimental, Hospital General Universitario Gregorio Maranon, Madrid (Spain); Udias, J.M. [Grupo de Fisica Nuclear, Departmento Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid (Spain)

    2011-08-21

    Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.

  10. Fully 3D GPU PET reconstruction

    Herraiz, J.L.; Espana, S.; Cal-Gonzalez, J.; Vaquero, J.J.; Desco, M.; Udias, J.M.

    2011-01-01

    Fully 3D iterative tomographic image reconstruction is computationally very demanding. Graphics Processing Unit (GPU) has been proposed for many years as potential accelerators in complex scientific problems, but it has not been used until the recent advances in the programmability of GPUs that the best available reconstruction codes have started to be implemented to be run on GPUs. This work presents a GPU-based fully 3D PET iterative reconstruction software. This new code may reconstruct sinogram data from several commercially available PET scanners. The most important and time-consuming parts of the code, the forward and backward projection operations, are based on an accurate model of the scanner obtained with the Monte Carlo code PeneloPET and they have been massively parallelized on the GPU. For the PET scanners considered, the GPU-based code is more than 70 times faster than a similar code running on a single core of a fast CPU, obtaining in both cases the same images. The code has been designed to be easily adapted to reconstruct sinograms from any other PET scanner, including scanner prototypes.

  11. Fully 3D refraction correction dosimetry system

    Manjappa, Rakesh; Makki, S Sharath; Kanhirodan, Rajan; Kumar, Rajesh; Vasu, Ram Mohan

    2016-01-01

    The irradiation of selective regions in a polymer gel dosimeter results in an increase in optical density and refractive index (RI) at those regions. An optical tomography-based dosimeter depends on rayline path through the dosimeter to estimate and reconstruct the dose distribution. The refraction of light passing through a dose region results in artefacts in the reconstructed images. These refraction errors are dependant on the scanning geometry and collection optics. We developed a fully 3D image reconstruction algorithm, algebraic reconstruction technique-refraction correction (ART-rc) that corrects for the refractive index mismatches present in a gel dosimeter scanner not only at the boundary, but also for any rayline refraction due to multiple dose regions inside the dosimeter. In this study, simulation and experimental studies have been carried out to reconstruct a 3D dose volume using 2D CCD measurements taken for various views. The study also focuses on the effectiveness of using different refractive-index matching media surrounding the gel dosimeter. Since the optical density is assumed to be low for a dosimeter, the filtered backprojection is routinely used for reconstruction. We carry out the reconstructions using conventional algebraic reconstruction (ART) and refractive index corrected ART (ART-rc) algorithms. The reconstructions based on FDK algorithm for cone-beam tomography has also been carried out for comparison. Line scanners and point detectors, are used to obtain reconstructions plane by plane. The rays passing through dose region with a RI mismatch does not reach the detector in the same plane depending on the angle of incidence and RI. In the fully 3D scanning setup using 2D array detectors, light rays that undergo refraction are still collected and hence can still be accounted for in the reconstruction algorithm. It is found that, for the central region of the dosimeter, the usable radius using ART-rc algorithm with water as RI matched

  12. Fully 3D refraction correction dosimetry system.

    Manjappa, Rakesh; Makki, S Sharath; Kumar, Rajesh; Vasu, Ram Mohan; Kanhirodan, Rajan

    2016-02-21

    The irradiation of selective regions in a polymer gel dosimeter results in an increase in optical density and refractive index (RI) at those regions. An optical tomography-based dosimeter depends on rayline path through the dosimeter to estimate and reconstruct the dose distribution. The refraction of light passing through a dose region results in artefacts in the reconstructed images. These refraction errors are dependant on the scanning geometry and collection optics. We developed a fully 3D image reconstruction algorithm, algebraic reconstruction technique-refraction correction (ART-rc) that corrects for the refractive index mismatches present in a gel dosimeter scanner not only at the boundary, but also for any rayline refraction due to multiple dose regions inside the dosimeter. In this study, simulation and experimental studies have been carried out to reconstruct a 3D dose volume using 2D CCD measurements taken for various views. The study also focuses on the effectiveness of using different refractive-index matching media surrounding the gel dosimeter. Since the optical density is assumed to be low for a dosimeter, the filtered backprojection is routinely used for reconstruction. We carry out the reconstructions using conventional algebraic reconstruction (ART) and refractive index corrected ART (ART-rc) algorithms. The reconstructions based on FDK algorithm for cone-beam tomography has also been carried out for comparison. Line scanners and point detectors, are used to obtain reconstructions plane by plane. The rays passing through dose region with a RI mismatch does not reach the detector in the same plane depending on the angle of incidence and RI. In the fully 3D scanning setup using 2D array detectors, light rays that undergo refraction are still collected and hence can still be accounted for in the reconstruction algorithm. It is found that, for the central region of the dosimeter, the usable radius using ART-rc algorithm with water as RI matched

  13. Fully Resolved Simulations of 3D Printing

    Tryggvason, Gretar; Xia, Huanxiong; Lu, Jiacai

    2017-11-01

    Numerical simulations of Fused Deposition Modeling (FDM) (or Fused Filament Fabrication) where a filament of hot, viscous polymer is deposited to ``print'' a three-dimensional object, layer by layer, are presented. A finite volume/front tracking method is used to follow the injection, cooling, solidification and shrinking of the filament. The injection of the hot melt is modeled using a volume source, combined with a nozzle, modeled as an immersed boundary, that follows a prescribed trajectory. The viscosity of the melt depends on the temperature and the shear rate and the polymer becomes immobile as its viscosity increases. As the polymer solidifies, the stress is found by assuming a hyperelastic constitutive equation. The method is described and its accuracy and convergence properties are tested by grid refinement studies for a simple setup involving two short filaments, one on top of the other. The effect of the various injection parameters, such as nozzle velocity and injection velocity are briefly examined and the applicability of the approach to simulate the construction of simple multilayer objects is shown. The role of fully resolved simulations for additive manufacturing and their use for novel processes and as the ``ground truth'' for reduced order models is discussed.

  14. Automation of 3D cell culture using chemically defined hydrogels.

    Rimann, Markus; Angres, Brigitte; Patocchi-Tenzer, Isabel; Braum, Susanne; Graf-Hausner, Ursula

    2014-04-01

    Drug development relies on high-throughput screening involving cell-based assays. Most of the assays are still based on cells grown in monolayer rather than in three-dimensional (3D) formats, although cells behave more in vivo-like in 3D. To exemplify the adoption of 3D techniques in drug development, this project investigated the automation of a hydrogel-based 3D cell culture system using a liquid-handling robot. The hydrogel technology used offers high flexibility of gel design due to a modular composition of a polymer network and bioactive components. The cell inert degradation of the gel at the end of the culture period guaranteed the harmless isolation of live cells for further downstream processing. Human colon carcinoma cells HCT-116 were encapsulated and grown in these dextran-based hydrogels, thereby forming 3D multicellular spheroids. Viability and DNA content of the cells were shown to be similar in automated and manually produced hydrogels. Furthermore, cell treatment with toxic Taxol concentrations (100 nM) had the same effect on HCT-116 cell viability in manually and automated hydrogel preparations. Finally, a fully automated dose-response curve with the reference compound Taxol showed the potential of this hydrogel-based 3D cell culture system in advanced drug development.

  15. A Fully Inkjet Printed 3D Honeycomb Inspired Patch Antenna

    McKerricher, Garret; Titterington, Don; Shamim, Atif

    2015-01-01

    by inkjet printing in this work. This is the first demonstration of a fully 3D Multijet printing process with integrated polymer and metal. A 2.4 GHz patch antenna is successfully fabricated with good performance proving the viability of the process

  16. AUTOMATED CELL SEGMENTATION WITH 3D FLUORESCENCE MICROSCOPY IMAGES.

    Kong, Jun; Wang, Fusheng; Teodoro, George; Liang, Yanhui; Zhu, Yangyang; Tucker-Burden, Carol; Brat, Daniel J

    2015-04-01

    A large number of cell-oriented cancer investigations require an effective and reliable cell segmentation method on three dimensional (3D) fluorescence microscopic images for quantitative analysis of cell biological properties. In this paper, we present a fully automated cell segmentation method that can detect cells from 3D fluorescence microscopic images. Enlightened by fluorescence imaging techniques, we regulated the image gradient field by gradient vector flow (GVF) with interpolated and smoothed data volume, and grouped voxels based on gradient modes identified by tracking GVF field. Adaptive thresholding was then applied to voxels associated with the same gradient mode where voxel intensities were enhanced by a multiscale cell filter. We applied the method to a large volume of 3D fluorescence imaging data of human brain tumor cells with (1) small cell false detection and missing rates for individual cells; and (2) trivial over and under segmentation incidences for clustered cells. Additionally, the concordance of cell morphometry structure between automated and manual segmentation was encouraging. These results suggest a promising 3D cell segmentation method applicable to cancer studies.

  17. An automated 3D reconstruction method of UAV images

    Liu, Jun; Wang, He; Liu, Xiaoyang; Li, Feng; Sun, Guangtong; Song, Ping

    2015-10-01

    In this paper a novel fully automated 3D reconstruction approach based on low-altitude unmanned aerial vehicle system (UAVs) images will be presented, which does not require previous camera calibration or any other external prior knowledge. Dense 3D point clouds are generated by integrating orderly feature extraction, image matching, structure from motion (SfM) and multi-view stereo (MVS) algorithms, overcoming many of the cost, time limitations of rigorous photogrammetry techniques. An image topology analysis strategy is introduced to speed up large scene reconstruction by taking advantage of the flight-control data acquired by UAV. Image topology map can significantly reduce the running time of feature matching by limiting the combination of images. A high-resolution digital surface model of the study area is produced base on UAV point clouds by constructing the triangular irregular network. Experimental results show that the proposed approach is robust and feasible for automatic 3D reconstruction of low-altitude UAV images, and has great potential for the acquisition of spatial information at large scales mapping, especially suitable for rapid response and precise modelling in disaster emergency.

  18. 3D Architecture Viewpoints on Service Automation

    Gu, Q.; Cuadrado, F.; Lago, P.; Duenas, J.C.

    2013-01-01

    Service-oriented architecture is an emerging paradigm for the execution of business-oriented as well as technical infrastructure processes by means of services. Automating the execution of services is of paramount importance in order to fulfill the needs of companies. However we have found that

  19. A Fully Inkjet Printed 3D Honeycomb Inspired Patch Antenna

    McKerricher, Garret

    2015-07-16

    The ability to inkjet print three-dimensional objects with integrated conductive metal provides many opportunities for fabrication of radio frequency electronics and electronics in general. Both a plastic material and silver conductor are deposited by inkjet printing in this work. This is the first demonstration of a fully 3D Multijet printing process with integrated polymer and metal. A 2.4 GHz patch antenna is successfully fabricated with good performance proving the viability of the process. The inkjet printed plastic surface is very smooth, with less than 100 nm root mean square roughness. The printed silver nanoparticles are laser sintered to achieve adequate conductivity of 1e6 S/m while keeping the process below 80oC and avoiding damage to the polymer. The antenna is designed with a honeycomb substrate which minimizes material consumption. This reduces the weight, dielectric constant and dielectric loss which are all around beneficial. The antenna is entirely inkjet printed including the ground plane conductor and achieves an impressive 81% efficiency. The honeycomb substrate weighs twenty times less than a solid substrate. For comparison the honeycomb antenna provides an efficiency nearly 15% greater than a similarly fabricated antenna with a solid substrate.

  20. Towards dense volumetric pancreas segmentation in CT using 3D fully convolutional networks

    Roth, Holger; Oda, Masahiro; Shimizu, Natsuki; Oda, Hirohisa; Hayashi, Yuichiro; Kitasaka, Takayuki; Fujiwara, Michitaka; Misawa, Kazunari; Mori, Kensaku

    2018-03-01

    Pancreas segmentation in computed tomography imaging has been historically difficult for automated methods because of the large shape and size variations between patients. In this work, we describe a custom-build 3D fully convolutional network (FCN) that can process a 3D image including the whole pancreas and produce an automatic segmentation. We investigate two variations of the 3D FCN architecture; one with concatenation and one with summation skip connections to the decoder part of the network. We evaluate our methods on a dataset from a clinical trial with gastric cancer patients, including 147 contrast enhanced abdominal CT scans acquired in the portal venous phase. Using the summation architecture, we achieve an average Dice score of 89.7 +/- 3.8 (range [79.8, 94.8])% in testing, achieving the new state-of-the-art performance in pancreas segmentation on this dataset.

  1. Automated Prescription of Oblique Brain 3D MRSI

    Ozhinsky, Eugene; Vigneron, Daniel B.; Chang, Susan M.; Nelson, Sarah J.

    2012-01-01

    Two major difficulties encountered in implementing Magnetic Resonance Spectroscopic Imaging (MRSI) in a clinical setting are limited coverage and difficulty in prescription. The goal of this project was to completely automate the process of 3D PRESS MRSI prescription, including placement of the selection box, saturation bands and shim volume, while maximizing the coverage of the brain. The automated prescription technique included acquisition of an anatomical MRI image, optimization of the ob...

  2. Automated full-3D digitization system for documentation of paintings

    Karaszewski, Maciej; Adamczyk, Marcin; Sitnik, Robert; Michoński, Jakub; Załuski, Wojciech; Bunsch, Eryk; Bolewicki, Paweł

    2013-05-01

    In this paper, a fully automated 3D digitization system for documentation of paintings is presented. It consists of a specially designed frame system for secure fixing of painting, a custom designed, structured light-based, high-resolution measurement head with no IR and UV emission. This device is automatically positioned in two axes (parallel to the surface of digitized painting) with additional manual positioning in third, perpendicular axis. Manual change of observation angle is also possible around two axes to re-measure even partially shadowed areas. The whole system is built in a way which provides full protection of digitized object (moving elements cannot reach its vicinity) and is driven by computer-controlled, highly precise servomechanisms. It can be used for automatic (without any user attention) and fast measurement of the paintings with some limitation to their properties: maximum size of the picture is 2000mm x 2000mm (with deviation of flatness smaller than 20mm) Measurement head is automatically calibrated by the system and its possible working volume starts from 50mm x 50mm x 20mm (10000 points per square mm) and ends at 120mm x 80mm x 60mm (2500 points per square mm). The directional measurements obtained with this system are automatically initially aligned due to the measurement head's position coordinates known from servomechanisms. After the whole painting is digitized, the measurements are fine-aligned with color-based ICP algorithm to remove any influence of possible inaccuracy of positioning devices. We present exemplary digitization results along with the discussion about the opportunities of analysis which appear for such high-resolution, 3D computer models of paintings.

  3. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  4. PIXIE3D: An efficient, fully implicit, parallel, 3D extended MHD code for fusion plasma modeling

    Chacon, L.

    2007-01-01

    PIXIE3D is a modern, parallel, state-of-the-art extended MHD code that employs fully implicit methods for efficiency and accuracy. It features a general geometry formulation, and is therefore suitable for the study of many magnetic fusion configurations of interest. PIXIE3D advances the state of the art in extended MHD modeling in two fundamental ways. Firstly, it employs a novel conservative finite volume scheme which is remarkably robust and stable, and demands very small physical and/or numerical dissipation. This is a fundamental requirement when one wants to study fusion plasmas with realistic conductivities. Secondly, PIXIE3D features fully-implicit time stepping, employing Newton-Krylov methods for inverting the associated nonlinear systems. These methods have been shown to be scalable and efficient when preconditioned properly. Novel preconditioned ideas (so-called physics based), which were prototypes in the context of reduced MHD, have been adapted for 3D primitive-variable resistive MHD in PIXIE3D, and are currently being extended to Hall MHD. PIXIE3D is fully parallel, employing PETSc for parallelism. PIXIE3D has been thoroughly benchmarked against linear theory and against other available extended MHD codes on nonlinear test problems (such as the GEM reconnection challenge). We are currently in the process of extending such comparisons to fusion-relevant problems in realistic geometries. In this talk, we will describe both the spatial discretization approach and the preconditioning strategy employed for extended MHD in PIXIE3D. We will report on recent benchmarking studies between PIXIE3D and other 3D extended MHD codes, and will demonstrate its usefulness in a variety of fusion-relevant configurations such as Tokamaks and Reversed Field Pinches. (Author)

  5. Improving automated 3D reconstruction methods via vision metrology

    Toschi, Isabella; Nocerino, Erica; Hess, Mona; Menna, Fabio; Sargeant, Ben; MacDonald, Lindsay; Remondino, Fabio; Robson, Stuart

    2015-05-01

    This paper aims to provide a procedure for improving automated 3D reconstruction methods via vision metrology. The 3D reconstruction problem is generally addressed using two different approaches. On the one hand, vision metrology (VM) systems try to accurately derive 3D coordinates of few sparse object points for industrial measurement and inspection applications; on the other, recent dense image matching (DIM) algorithms are designed to produce dense point clouds for surface representations and analyses. This paper strives to demonstrate a step towards narrowing the gap between traditional VM and DIM approaches. Efforts are therefore intended to (i) test the metric performance of the automated photogrammetric 3D reconstruction procedure, (ii) enhance the accuracy of the final results and (iii) obtain statistical indicators of the quality achieved in the orientation step. VM tools are exploited to integrate their main functionalities (centroid measurement, photogrammetric network adjustment, precision assessment, etc.) into the pipeline of 3D dense reconstruction. Finally, geometric analyses and accuracy evaluations are performed on the raw output of the matching (i.e. the point clouds) by adopting a metrological approach. The latter is based on the use of known geometric shapes and quality parameters derived from VDI/VDE guidelines. Tests are carried out by imaging the calibrated Portable Metric Test Object, designed and built at University College London (UCL), UK. It allows assessment of the performance of the image orientation and matching procedures within a typical industrial scenario, characterised by poor texture and known 3D/2D shapes.

  6. Chest wall segmentation in automated 3D breast ultrasound scans.

    Tan, Tao; Platel, Bram; Mann, Ritse M; Huisman, Henkjan; Karssemeijer, Nico

    2013-12-01

    In this paper, we present an automatic method to segment the chest wall in automated 3D breast ultrasound images. Determining the location of the chest wall in automated 3D breast ultrasound images is necessary in computer-aided detection systems to remove automatically detected cancer candidates beyond the chest wall and it can be of great help for inter- and intra-modal image registration. We show that the visible part of the chest wall in an automated 3D breast ultrasound image can be accurately modeled by a cylinder. We fit the surface of our cylinder model to a set of automatically detected rib-surface points. The detection of the rib-surface points is done by a classifier using features representing local image intensity patterns and presence of rib shadows. Due to attenuation of the ultrasound signal, a clear shadow is visible behind the ribs. Evaluation of our segmentation method is done by computing the distance of manually annotated rib points to the surface of the automatically detected chest wall. We examined the performance on images obtained with the two most common 3D breast ultrasound devices in the market. In a dataset of 142 images, the average mean distance of the annotated points to the segmented chest wall was 5.59 ± 3.08 mm. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Automated Prescription of Oblique Brain 3D MRSI

    Ozhinsky, Eugene; Vigneron, Daniel B.; Chang, Susan M.; Nelson, Sarah J.

    2012-01-01

    Two major difficulties encountered in implementing Magnetic Resonance Spectroscopic Imaging (MRSI) in a clinical setting are limited coverage and difficulty in prescription. The goal of this project was to completely automate the process of 3D PRESS MRSI prescription, including placement of the selection box, saturation bands and shim volume, while maximizing the coverage of the brain. The automated prescription technique included acquisition of an anatomical MRI image, optimization of the oblique selection box parameters, optimization of the placement of OVS saturation bands, and loading of the calculated parameters into a customized 3D MRSI pulse sequence. To validate the technique and compare its performance with existing protocols, 3D MRSI data were acquired from 6 exams from 3 healthy volunteers. To assess the performance of the automated 3D MRSI prescription for patients with brain tumors, the data were collected from 16 exams from 8 subjects with gliomas. This technique demonstrated robust coverage of the tumor, high consistency of prescription and very good data quality within the T2 lesion. PMID:22692829

  8. Automated building of organometallic complexes from 3D fragments.

    Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

    2014-07-28

    A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry.

  9. Fully automated parallel oligonucleotide synthesizer

    Lebl, M.; Burger, Ch.; Ellman, B.; Heiner, D.; Ibrahim, G.; Jones, A.; Nibbe, M.; Thompson, J.; Mudra, Petr; Pokorný, Vít; Poncar, Pavel; Ženíšek, Karel

    2001-01-01

    Roč. 66, č. 8 (2001), s. 1299-1314 ISSN 0010-0765 Institutional research plan: CEZ:AV0Z4055905 Keywords : automated oligonucleotide synthesizer Subject RIV: CC - Organic Chemistry Impact factor: 0.778, year: 2001

  10. Automating 3D reconstruction using a probabilistic grammar

    Xiong, Hanwei; Xu, Jun; Xu, Chenxi; Pan, Ming

    2015-10-01

    3D reconstruction of objects from point clouds with a laser scanner is still a laborious task in many applications. Automating 3D process is an ongoing research topic and suffers from the complex structure of the data. The main difficulty is due to lack of knowledge of real world objects structure. In this paper, we accumulate such structure knowledge by a probabilistic grammar learned from examples in the same category. The rules of the grammar capture compositional structures at different levels, and a feature dependent probability function is attached for every rule. The learned grammar can be used to parse new 3D point clouds, organize segment patches in a hierarchal way, and assign them meaningful labels. The parsed semantics can be used to guide the reconstruction algorithms automatically. Some examples are given to explain the method.

  11. Free and open-source automated 3-D microscope.

    Wijnen, Bas; Petersen, Emily E; Hunt, Emily J; Pearce, Joshua M

    2016-11-01

    Open-source technology not only has facilitated the expansion of the greater research community, but by lowering costs it has encouraged innovation and customizable design. The field of automated microscopy has continued to be a challenge in accessibility due the expense and inflexible, noninterchangeable stages. This paper presents a low-cost, open-source microscope 3-D stage. A RepRap 3-D printer was converted to an optical microscope equipped with a customized, 3-D printed holder for a USB microscope. Precision measurements were determined to have an average error of 10 μm at the maximum speed and 27 μm at the minimum recorded speed. Accuracy tests yielded an error of 0.15%. The machine is a true 3-D stage and thus able to operate with USB microscopes or conventional desktop microscopes. It is larger than all commercial alternatives, and is thus capable of high-depth images over unprecedented areas and complex geometries. The repeatability is below 2-D microscope stages, but testing shows that it is adequate for the majority of scientific applications. The open-source microscope stage costs less than 3-9% of the closest proprietary commercial stages. This extreme affordability vastly improves accessibility for 3-D microscopy throughout the world. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  12. Automated Identification of Fiducial Points on 3D Torso Images

    Manas M. Kawale

    2013-01-01

    Full Text Available Breast reconstruction is an important part of the breast cancer treatment process for many women. Recently, 2D and 3D images have been used by plastic surgeons for evaluating surgical outcomes. Distances between different fiducial points are frequently used as quantitative measures for characterizing breast morphology. Fiducial points can be directly marked on subjects for direct anthropometry, or can be manually marked on images. This paper introduces novel algorithms to automate the identification of fiducial points in 3D images. Automating the process will make measurements of breast morphology more reliable, reducing the inter- and intra-observer bias. Algorithms to identify three fiducial points, the nipples, sternal notch, and umbilicus, are described. The algorithms used for localization of these fiducial points are formulated using a combination of surface curvature and 2D color information. Comparison of the 3D coordinates of automatically detected fiducial points and those identified manually, and geodesic distances between the fiducial points are used to validate algorithm performance. The algorithms reliably identified the location of all three of the fiducial points. We dedicate this article to our late colleague and friend, Dr. Elisabeth K. Beahm. Elisabeth was both a talented plastic surgeon and physician-scientist; we deeply miss her insight and her fellowship.

  13. Esophagus segmentation in CT via 3D fully convolutional neural network and random walk.

    Fechter, Tobias; Adebahr, Sonja; Baltas, Dimos; Ben Ayed, Ismail; Desrosiers, Christian; Dolz, Jose

    2017-12-01

    Precise delineation of organs at risk is a crucial task in radiotherapy treatment planning for delivering high doses to the tumor while sparing healthy tissues. In recent years, automated segmentation methods have shown an increasingly high performance for the delineation of various anatomical structures. However, this task remains challenging for organs like the esophagus, which have a versatile shape and poor contrast to neighboring tissues. For human experts, segmenting the esophagus from CT images is a time-consuming and error-prone process. To tackle these issues, we propose a random walker approach driven by a 3D fully convolutional neural network (CNN) to automatically segment the esophagus from CT images. First, a soft probability map is generated by the CNN. Then, an active contour model (ACM) is fitted to the CNN soft probability map to get a first estimation of the esophagus location. The outputs of the CNN and ACM are then used in conjunction with a probability model based on CT Hounsfield (HU) values to drive the random walker. Training and evaluation were done on 50 CTs from two different datasets, with clinically used peer-reviewed esophagus contours. Results were assessed regarding spatial overlap and shape similarity. The esophagus contours generated by the proposed algorithm showed a mean Dice coefficient of 0.76 ± 0.11, an average symmetric square distance of 1.36 ± 0.90 mm, and an average Hausdorff distance of 11.68 ± 6.80, compared to the reference contours. These results translate to a very good agreement with reference contours and an increase in accuracy compared to existing methods. Furthermore, when considering the results reported in the literature for the publicly available Synapse dataset, our method outperformed all existing approaches, which suggests that the proposed method represents the current state-of-the-art for automatic esophagus segmentation. We show that a CNN can yield accurate estimations of esophagus location, and that

  14. Developments towards a fully automated AMS system

    Steier, P.; Puchegger, S.; Golser, R.; Kutschera, W.; Priller, A.; Rom, W.; Wallner, A.; Wild, E.

    2000-01-01

    The possibilities of computer-assisted and automated accelerator mass spectrometry (AMS) measurements were explored. The goal of these efforts is to develop fully automated procedures for 'routine' measurements at the Vienna Environmental Research Accelerator (VERA), a dedicated 3-MV Pelletron tandem AMS facility. As a new tool for automatic tuning of the ion optics we developed a multi-dimensional optimization algorithm robust to noise, which was applied for 14 C and 10 Be. The actual isotope ratio measurements are performed in a fully automated fashion and do not require the presence of an operator. Incoming data are evaluated online and the results can be accessed via Internet. The system was used for 14 C, 10 Be, 26 Al and 129 I measurements

  15. Automated reconstruction of 3D models from real environments

    Sequeira, V.; Ng, K.; Wolfart, E.; Gonçalves, J. G. M.; Hogg, D.

    This paper describes an integrated approach to the construction of textured 3D scene models of building interiors from laser range data and visual images. This approach has been implemented in a collection of algorithms and sensors within a prototype device for 3D reconstruction, known as the EST (Environmental Sensor for Telepresence). The EST can take the form of a push trolley or of an autonomous mobile platform. The Autonomous EST (AEST) has been designed to provide an integrated solution for automating the creation of complete models. Embedded software performs several functions, including triangulation of the range data, registration of video texture, registration and integration of data acquired from different capture points. Potential applications include facilities management for the construction industry and creating reality models to be used in general areas of virtual reality, for example, virtual studios, virtualised reality for content-related applications (e.g., CD-ROMs), social telepresence, architecture and others. The paper presents the main components of the EST/AEST, and presents some example results obtained from the prototypes. The reconstructed model is encoded in VRML format so that it is possible to access and view the model via the World Wide Web.

  16. Automated curved planar reformation of 3D spine images

    Vrtovec, Tomaz; Likar, Bostjan; Pernus, Franjo

    2005-01-01

    Traditional techniques for visualizing anatomical structures are based on planar cross-sections from volume images, such as images obtained by computed tomography (CT) or magnetic resonance imaging (MRI). However, planar cross-sections taken in the coordinate system of the 3D image often do not provide sufficient or qualitative enough diagnostic information, because planar cross-sections cannot follow curved anatomical structures (e.g. arteries, colon, spine, etc). Therefore, not all of the important details can be shown simultaneously in any planar cross-section. To overcome this problem, reformatted images in the coordinate system of the inspected structure must be created. This operation is usually referred to as curved planar reformation (CPR). In this paper we propose an automated method for CPR of 3D spine images, which is based on the image transformation from the standard image-based to a novel spine-based coordinate system. The axes of the proposed spine-based coordinate system are determined on the curve that represents the vertebral column, and the rotation of the vertebrae around the spine curve, both of which are described by polynomial models. The optimal polynomial parameters are obtained in an image analysis based optimization framework. The proposed method was qualitatively and quantitatively evaluated on five CT spine images. The method performed well on both normal and pathological cases and was consistent with manually obtained ground truth data. The proposed spine-based CPR benefits from reduced structural complexity in favour of improved feature perception of the spine. The reformatted images are diagnostically valuable and enable easier navigation, manipulation and orientation in 3D space. Moreover, reformatted images may prove useful for segmentation and other image analysis tasks

  17. Fully 3D iterative scatter-corrected OSEM for HRRT PET using a GPU

    Kim, Kyung Sang; Ye, Jong Chul, E-mail: kssigari@kaist.ac.kr, E-mail: jong.ye@kaist.ac.kr [Bio-Imaging and Signal Processing Lab., Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 335 Gwahak-no, Yuseong-gu, Daejon 305-701 (Korea, Republic of)

    2011-08-07

    Accurate scatter correction is especially important for high-resolution 3D positron emission tomographies (PETs) such as high-resolution research tomograph (HRRT) due to large scatter fraction in the data. To address this problem, a fully 3D iterative scatter-corrected ordered subset expectation maximization (OSEM) in which a 3D single scatter simulation (SSS) is alternatively performed with a 3D OSEM reconstruction was recently proposed. However, due to the computational complexity of both SSS and OSEM algorithms for a high-resolution 3D PET, it has not been widely used in practice. The main objective of this paper is, therefore, to accelerate the fully 3D iterative scatter-corrected OSEM using a graphics processing unit (GPU) and verify its performance for an HRRT. We show that to exploit the massive thread structures of the GPU, several algorithmic modifications are necessary. For SSS implementation, a sinogram-driven approach is found to be more appropriate compared to a detector-driven approach, as fast linear interpolation can be performed in the sinogram domain through the use of texture memory. Furthermore, a pixel-driven backprojector and a ray-driven projector can be significantly accelerated by assigning threads to voxels and sinograms, respectively. Using Nvidia's GPU and compute unified device architecture (CUDA), the execution time of a SSS is less than 6 s, a single iteration of OSEM with 16 subsets takes 16 s, and a single iteration of the fully 3D scatter-corrected OSEM composed of a SSS and six iterations of OSEM takes under 105 s for the HRRT geometry, which corresponds to acceleration factors of 125x and 141x for OSEM and SSS, respectively. The fully 3D iterative scatter-corrected OSEM algorithm is validated in simulations using Geant4 application for tomographic emission and in actual experiments using an HRRT.

  18. Automated robust generation of compact 3D statistical shape models

    Vrtovec, Tomaz; Likar, Bostjan; Tomazevic, Dejan; Pernus, Franjo

    2004-05-01

    Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.

  19. Maximum likelihood reconstruction in fully 3D PET via the SAGE algorithm

    Ollinger, J.M.; Goggin, A.S.

    1996-01-01

    The SAGE and ordered subsets algorithms have been proposed as fast methods to compute penalized maximum likelihood estimates in PET. We have implemented both for use in fully 3D PET and completed a preliminary evaluation. The technique used to compute the transition matrix is fully described. The evaluation suggests that the ordered subsets algorithm converges much faster than SAGE, but that it stops short of the optimal solution

  20. Automated 3D ultrasound measurement of the angle of progression in labor.

    Montaguti, Elisa; Rizzo, Nicola; Pilu, Gianluigi; Youssef, Aly

    2018-01-01

    To assess the feasibility and reliability of an automated technique for the assessment of the angle of progression (AoP) in labor by using three-dimensional (3D) ultrasound. AoP was assessed by using 3D transperineal ultrasound by two operators in 52 women in active labor to evaluate intra- and interobserver reproducibility. Furthermore, intermethod agreement between automated and manual techniques on 3D images, and between automated technique on 3D vs 2D images were evaluated. Automated measurements were feasible in all cases. Automated measurements were considered acceptable in 141 (90.4%) out of the 156 on the first assessments and in all 156 after repeating measurements for unacceptable evaluations. The automated technique on 3D images demonstrated good intra- and interobserver reproducibility. The 3D-automated technique showed a very good agreement with the 3D manual technique. Notably, AoP calculated with the 3D automated technique were significantly wider in comparison with those measured manually on 3D images (133 ± 17° vs 118 ± 21°, p = 0.013). The assessment of the angle of progression through 3D ultrasound is highly reproducible. However, automated software leads to a systematic overestimation of AoP in comparison with the standard manual technique thus hindering its use in clinical practice in its present form.

  1. Automating the production planning of a 3D printing factory

    Adan, I.J.B.F.; Pogromskiy, A.Y.; Freens, J.P.N.; Ploegmakers, H.; Yilmaz, L.; Chan, W.K.V.; Moon, I.; Roeder, T.M.K.; Macal, C.; Rossetti, M.D.

    2015-01-01

    To increase a 3D printer's throughput and decrease the print objects' lead times, composing good batches for 3D printers in high-volume 3D printing environments is of great importance. Since manual planners cannot oversee the whole production planning, they tend to make sub-optimal decisions. This

  2. Fast implementations of reconstruction-based scatter compensation in fully 3D SPECT image reconstruction

    Kadrmas, Dan J.; Karimi, Seemeen S.; Frey, Eric C.; Tsui, Benjamin M.W.

    1998-01-01

    Accurate scatter compensation in SPECT can be performed by modelling the scatter response function during the reconstruction process. This method is called reconstruction-based scatter compensation (RBSC). It has been shown that RBSC has a number of advantages over other methods of compensating for scatter, but using RBSC for fully 3D compensation has resulted in prohibitively long reconstruction times. In this work we propose two new methods that can be used in conjunction with existing methods to achieve marked reductions in RBSC reconstruction times. The first method, coarse-grid scatter modelling, significantly accelerates the scatter model by exploiting the fact that scatter is dominated by low-frequency information. The second method, intermittent RBSC, further accelerates the reconstruction process by limiting the number of iterations during which scatter is modelled. The fast implementations were evaluated using a Monte Carlo simulated experiment of the 3D MCAT phantom with 99m Tc tracer, and also using experimentally acquired data with 201 Tl tracer. Results indicated that these fast methods can reconstruct, with fully 3D compensation, images very similar to those obtained using standard RBSC methods, and in reconstruction times that are an order of magnitude shorter. Using these methods, fully 3D iterative reconstruction with RBSC can be performed well within the realm of clinically realistic times (under 10 minutes for 64x64x24 image reconstruction). (author)

  3. Low Voltage CMOS Fully Differential Current Feedback Amplifier with Controllable 3-dB Bandwidth

    Madian, A.H.; Mahmoud, S.A.; Ashour, M.A.; Soliman, A.M.

    2008-01-01

    This paper presents a new CMOS fully differential current feedback operational amplifier with controllable 3-dB bandwidth suitable for analog data processing and acquisition applications. The FDCFOA has the advantage of a wide range controllable 3-dB bandwidth (∼57 MHz to 500 MHz) without changing the feedback resistance this guarantee the stability of the circuit. The FDCFOA has a standby current of 320μA. PSpice simulations of the FDCFOA block were given using 0.25μm CMOS technology from AMI MOSIS and dual supply voltages ±0.75 V

  4. Motion correction in neurological fan beam SPECT using motion tracking and fully 3D reconstruction

    Fulton, R.R.; Hutton, B.; Eberl, S.; Meikle, S.; Braun, M.; Westmead Hospital, Westmead, NSW; University of Technology, Sydney, NSW

    1998-01-01

    Full text: We have previously proposed the use of fully three-dimensional (3D) reconstruction and continuous monitoring of head position to correct for motion artifacts in neurological SPECT and PET. Knowledge of the motion during acquisition provided by a head tracking system can be used to reposition the projection data in space in such a way as to negate motion effects during reconstruction. The reconstruction algorithm must deal with variations in the projection geometry resulting from differences in the timing and nature of motion between patients. Rotational movements about any axis other than the camera's axis of rotation give rise to projection geometries which necessitate the use of a fully 3D reconstruction algorithm. Our previous work with computer simulations assuming parallel hole collimation demonstrated the feasibility of correcting for motion. We have now refined our iterative 3D reconstruction algorithm to support fan beam data and attenuation correction, and developed a practical head tracking system for use on a Trionix Triad SPECT system. The correction technique has been tested in fan beam SPECT studies of the 3D Hoffman brain phantom. Arbitrary movements were applied to the phantom during acquisition and recorded by the head tracker which monitored the position and orientation of the phantom throughout the study. 3D reconstruction was then performed using the motion data provided by the tracker. The accuracy of correction was assessed by comparing the corrected images with a motion free study acquired immediately beforehand, visually and by calculating mean squared error (MSE). Motion correction reduced distortion perceptibly and, depending on the motions applied, improved MSE by up to an order of magnitude. 3D reconstruction of the 128x128x128 data set took 20 minutes on a SUN Ultra 1 workstation. The results of these phantom experiments suggest that the technique can effectively compensate for head motion under clinical SPECT imaging

  5. Pragmatic fully 3D image reconstruction for the MiCES mouse imaging PET scanner

    Lee, Kisung; Kinahan, Paul E; Fessler, Jeffrey A; Miyaoka, Robert S; Janes, Marie; Lewellen, Tom K

    2004-01-01

    We present a pragmatic approach to image reconstruction for data from the micro crystal elements system (MiCES) fully 3D mouse imaging positron emission tomography (PET) scanner under construction at the University of Washington. Our approach is modelled on fully 3D image reconstruction used in clinical PET scanners, which is based on Fourier rebinning (FORE) followed by 2D iterative image reconstruction using ordered-subsets expectation-maximization (OSEM). The use of iterative methods allows modelling of physical effects (e.g., statistical noise, detector blurring, attenuation, etc), while FORE accelerates the reconstruction process by reducing the fully 3D data to a stacked set of independent 2D sinograms. Previous investigations have indicated that non-stationary detector point-spread response effects, which are typically ignored for clinical imaging, significantly impact image quality for the MiCES scanner geometry. To model the effect of non-stationary detector blurring (DB) in the FORE+OSEM(DB) algorithm, we have added a factorized system matrix to the ASPIRE reconstruction library. Initial results indicate that the proposed approach produces an improvement in resolution without an undue increase in noise and without a significant increase in the computational burden. The impact on task performance, however, remains to be evaluated

  6. Automated 3D reconstruction of interiors with multiple scan views

    Sequeira, Vitor; Ng, Kia C.; Wolfart, Erik; Goncalves, Joao G. M.; Hogg, David C.

    1998-12-01

    This paper presents two integrated solutions for realistic 3D model acquisition and reconstruction; an early prototype, in the form of a push trolley, and a later prototype in the form of an autonomous robot. The systems encompass all hardware and software required, from laser and video data acquisition, processing and output of texture-mapped 3D models in VRML format, to batteries for power supply and wireless network communications. The autonomous version is also equipped with a mobile platform and other sensors for the purpose of automatic navigation. The applications for such a system range from real estate and tourism (e.g., showing a 3D computer model of a property to a potential buyer or tenant) or as tool for content creation (e.g., creating 3D models of heritage buildings or producing broadcast quality virtual studios). The system can also be used in industrial environments as a reverse engineering tool to update the design of a plant, or as a 3D photo-archive for insurance purposes. The system is Internet compatible: the photo-realistic models can be accessed via the Internet and manipulated interactively in 3D using a common Web browser with a VRML plug-in. Further information and example reconstructed models are available on- line via the RESOLV web-page at http://www.scs.leeds.ac.uk/resolv/.

  7. A Fully Automated Penumbra Segmentation Tool

    Nagenthiraja, Kartheeban; Ribe, Lars Riisgaard; Hougaard, Kristina Dupont

    2012-01-01

    Introduction: Perfusion- and diffusion weighted MRI (PWI/DWI) is widely used to select patients who are likely to benefit from recanalization therapy. The visual identification of PWI-DWI-mismatch tissue depends strongly on the observer, prompting a need for software, which estimates potentially...... salavageable tissue, quickly and accurately. We present a fully Automated Penumbra Segmentation (APS) algorithm using PWI and DWI images. We compare automatically generated PWI-DWI mismatch mask to mask outlined manually by experts, in 168 patients. Method: The algorithm initially identifies PWI lesions......) at 600∙10-6 mm2/sec. Due to the nature of thresholding, the ADC mask overestimates the DWI lesion volume and consequently we initialized level-set algorithm on DWI image with ADC mask as prior knowledge. Combining the PWI and inverted DWI mask then yield the PWI-DWI mismatch mask. Four expert raters...

  8. Analysis of 3D stacked fully functional CMOS Active Pixel Sensor detectors

    Passeri, D; Servoli, L; Meroli, S

    2009-01-01

    The IC technology trend is to move from 3D flexible configurations (package on package, stacked dies) to real 3D ICs. This is mainly due to i) the increased electrical performances and ii) the cost of 3D integration which may be cheaper than to keep shrinking 2D circuits. Perspective advantages for particle tracking and vertex detectors applications in High Energy Physics can be envisaged: in this work, we will focus on the capabilities of the state-of-the-art vertical scale integration technologies, allowing for the fabrication of very compact, fully functional, multiple layers CMOS Active Pixel Sensor (APS) detectors. The main idea is to exploit the features of the 3D technologies for the fabrication of a ''stack'' of very thin and precisely aligned CMOS APS layers, leading to a single, integrated, multi-layers pixel sensor. The adoption of multiple-layers single detectors can dramatically reduce the mass of conventional, separated detectors (thus reducing multiple scattering issues), at the same time allowing for very precise measurements of particle trajectory and momentum. As a proof of concept, an extensive device and circuit simulation activity has been carried out, aiming at evaluate the suitability of such a kind of CMOS active pixel layers for particle tracking purposes.

  9. A new fully automated TLD badge reader

    Kannan, S.; Ratna, P.; Kulkarni, M.S.

    2003-01-01

    At present personnel monitoring in India is being carried out using a number of manual and semiautomatic TLD badge Readers and the BARC TL dosimeter badge designed during 1970. Of late the manual TLD badge readers are almost completely replaced by semiautomatic readers with a number of performance improvements like use of hot gas heating to reduce the readout time considerably. PC based design with storage of glow curve for every dosimeter, on-line dose computation and printout of dose reports, etc. However the semiautomatic system suffers from the lack of a machine readable ID code on the badge and the physical design of the dosimeter card not readily compatible for automation. This paper describes a fully automated TLD badge Reader developed in the RSS Division, using a new TLD badge with machine readable ID code. The new PC based reader has a built-in reader for reading the ID code, in the form of an array of holes, on the dosimeter card. The reader has a number of self-diagnostic features to ensure a high degree of reliability. (author)

  10. Fully 3D PET image reconstruction using a fourier preconditioned conjugate-gradient algorithm

    Fessler, J.A.; Ficaro, E.P.

    1996-01-01

    Since the data sizes in fully 3D PET imaging are very large, iterative image reconstruction algorithms must converge in very few iterations to be useful. One can improve the convergence rate of the conjugate-gradient (CG) algorithm by incorporating preconditioning operators that approximate the inverse of the Hessian of the objective function. If the 3D cylindrical PET geometry were not truncated at the ends, then the Hessian of the penalized least-squares objective function would be approximately shift-invariant, i.e. G'G would be nearly block-circulant, where G is the system matrix. We propose a Fourier preconditioner based on this shift-invariant approximation to the Hessian. Results show that this preconditioner significantly accelerates the convergence of the CG algorithm with only a small increase in computation

  11. Automated Finger Spelling by Highly Realistic 3D Animation

    Adamo-Villani, Nicoletta; Beni, Gerardo

    2004-01-01

    We present the design of a new 3D animation tool for self-teaching (signing and reading) finger spelling the first basic component in learning any sign language. We have designed a highly realistic hand with natural animation of the finger motions. Smoothness of motion (in real time) is achieved via programmable blending of animation segments. The…

  12. Automation of 3D micro object handling process

    Gegeckaite, Asta; Hansen, Hans Nørgaard

    2007-01-01

    Most of the micro objects in industrial production are handled with manual labour or in semiautomatic stations. Manual labour usually makes handling and assembly operations highly flexible, but slow, relatively imprecise and expensive. Handling of 3D micro objects poses special challenges due to ...

  13. 3D vision system for intelligent milking robot automation

    Akhloufi, M. A.

    2013-12-01

    In a milking robot, the correct localization and positioning of milking teat cups is of very high importance. The milking robots technology has not changed since a decade and is based primarily on laser profiles for teats approximate positions estimation. This technology has reached its limit and does not allow optimal positioning of the milking cups. Also, in the presence of occlusions, the milking robot fails to milk the cow. These problems, have economic consequences for producers and animal health (e.g. development of mastitis). To overcome the limitations of current robots, we have developed a new system based on 3D vision, capable of efficiently positioning the milking cups. A prototype of an intelligent robot system based on 3D vision for real-time positioning of a milking robot has been built and tested under various conditions on a synthetic udder model (in static and moving scenarios). Experimental tests, were performed using 3D Time-Of-Flight (TOF) and RGBD cameras. The proposed algorithms permit the online segmentation of teats by combing 2D and 3D visual information. The obtained results permit the teat 3D position computation. This information is then sent to the milking robot for teat cups positioning. The vision system has a real-time performance and monitors the optimal positioning of the cups even in the presence of motion. The obtained results, with both TOF and RGBD cameras, show the good performance of the proposed system. The best performance was obtained with RGBD cameras. This latter technology will be used in future real life experimental tests.

  14. Fully 3D printed integrated reactor array for point-of-care molecular diagnostics.

    Kadimisetty, Karteek; Song, Jinzhao; Doto, Aoife M; Hwang, Young; Peng, Jing; Mauk, Michael G; Bushman, Frederic D; Gross, Robert; Jarvis, Joseph N; Liu, Changchun

    2018-06-30

    Molecular diagnostics that involve nucleic acid amplification tests (NAATs) are crucial for prevention and treatment of infectious diseases. In this study, we developed a simple, inexpensive, disposable, fully 3D printed microfluidic reactor array that is capable of carrying out extraction, concentration and isothermal amplification of nucleic acids in variety of body fluids. The method allows rapid molecular diagnostic tests for infectious diseases at point of care. A simple leak-proof polymerization strategy was developed to integrate flow-through nucleic acid isolation membranes into microfluidic devices, yielding a multifunctional diagnostic platform. Static coating technology was adopted to improve the biocompatibility of our 3D printed device. We demonstrated the suitability of our device for both end-point colorimetric qualitative detection and real-time fluorescence quantitative detection. We applied our diagnostic device to detection of Plasmodium falciparum in plasma samples and Neisseria meningitides in cerebrospinal fluid (CSF) samples by loop-mediated, isothermal amplification (LAMP) within 50 min. The detection limits were 100 fg for P. falciparum and 50 colony-forming unit (CFU) for N. meningitidis per reaction, which are comparable to that of benchtop instruments. This rapid and inexpensive 3D printed device has great potential for point-of-care molecular diagnosis of infectious disease in resource-limited settings. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Correction of head motion artifacts in SPECT with fully 3-D OS-EM reconstruction

    Fulton, R.R.

    1998-01-01

    Full text: A method which relies on continuous monitoring of head position has been developed to correct for head motion in SPECT studies of the brain. Head position and orientation are monitored during data acquisition by an inexpensive head tracking system (ADL-1, Shooting Star Technology, Rosedale, British Colombia). Motion correction involves changing the projection geometry to compensate for motion (using data from the head tracker), and reconstructing with a fully 3-D OS-EM algorithm. The reconstruction algorithm can accommodate any number of movements and any projection geometry. A single iteration of 3-D OS-EM using all available projections provides a satisfactory 3-D reconstruction, essentially free of motion artifacts. The method has been validated in studies of the 3-D Hoffman brain phantom. Multiple 36- degree acquisitions, each with the phantom in a different position, were performed on a Trionix triple head camera. Movements were simulated by combining projections from the different acquisitions. Accuracy was assessed by comparison with a motion-free reconstruction, visually and by calculating mean squared error (MSE). Motion correction reduced distortion perceptibly and, depending on the motions applied, improved MSE by up to an order of magnitude. Three-dimensional reconstruction of the 128 x 128 x 128 data set took 2- minutes on a SUN Ultra 1 workstation. This motion correction technique can be retro-fitted to existing SPECT systems and could be incorporated in future SPECT camera designs. It appears to be applicable in PET as well as SPECT, to be able to correct for any head movements, and to have the potential to improve the accuracy of tomographic brain studies under clinical imaging conditions

  16. Global fully kinetic models of planetary magnetospheres with iPic3D

    Gonzalez, D.; Sanna, L.; Amaya, J.; Zitz, A.; Lembege, B.; Markidis, S.; Schriver, D.; Walker, R. J.; Berchem, J.; Peng, I. B.; Travnicek, P. M.; Lapenta, G.

    2016-12-01

    We report on the latest developments of our approach to model planetary magnetospheres, mini magnetospheres and the Earth's magnetosphere with the fully kinetic, electromagnetic particle in cell code iPic3D. The code treats electrons and multiple species of ions as full kinetic particles. We review: 1) Why a fully kinetic model and in particular why kinetic electrons are needed for capturing some of the most important aspects of the physics processes of planetary magnetospheres. 2) Why the energy conserving implicit method (ECIM) in its newest implementation [1] is the right approach to reach this goal. We consider the different electron scales and study how the new IECIM can be tuned to resolve only the electron scales of interest while averaging over the unresolved scales preserving their contribution to the evolution. 3) How with modern computing planetary magnetospheres, mini magnetosphere and eventually Earth's magnetosphere can be modeled with fully kinetic electrons. The path from petascale to exascale for iPiC3D is outlined based on the DEEP-ER project [2], using dynamic allocation of different processor architectures (Xeon and Xeon Phi) and innovative I/O technologies.Specifically results from models of Mercury are presented and compared with MESSENGER observations and with previous hybrid (fluid electrons and kinetic ions) simulations. The plasma convection around the planets includes the development of hydrodynamic instabilities at the flanks, the presence of the collisionless shocks, the magnetosheath, the magnetopause, reconnection zones, the formation of the plasma sheet and the magnetotail, and the variation of ion/electron plasma flows when crossing these frontiers. Given the full kinetic nature of our approach we focus on detailed particle dynamics and distribution at locations that can be used for comparison with satellite data. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint ar

  17. A Moving 3D Laser Scanner for Automated Underbridge Inspection

    Marco Tarabini

    2017-12-01

    Full Text Available Recent researches have proven that the underbridge geometry can be reconstructed by mounting a 3D laser scanner on a motorized cart travelling on a walkway located under the bridge. The walkway is moved by a truck and the accuracy of the bridge model depends on the accuracy of the trajectory of the scanning head with respect to a fixed reference system. In this paper, we describe a vision-based measurement system that can be used to identify the relative motion of the cart that moves the 3D laser scanner with respect to the walkway. The orientation of the walkway with respect to the bridge is determined using inclinometers and a camera that detect the position of a laser spot, while the position of the truck with respect to the bridge is measured using a conventional odometer. The accuracy of the proposed system was initially evaluated by numerical simulations and successively verified by experiments in laboratory conditions. The complete system has then been tested by comparing the geometry of buildings reconstructed using the proposed system with the geometry obtained with a static scan. Results showed that the error is less than 6 mm; given the satisfying quality of the point clouds obtained, it is also possible to detect small defects on the surface.

  18. Automated quality characterization of 3D printed bone scaffolds

    Tzu-Liang Bill Tseng

    2014-07-01

    Full Text Available Optimization of design is an important step in obtaining tissue engineering scaffolds with appropriate shapes and inner microstructures. Different shapes and sizes of scaffolds are modeled using UGS NX 6.0 software with variable pore sizes. The quality issue we are concerned is the scaffold porosity, which is mainly caused by the fabrication inaccuracies. Bone scaffolds are usually characterized using a scanning electron microscope, but this study presents a new automated inspection and classification technique. Due to many numbers and size variations for the pores, the manual inspection of the fabricated scaffolds tends to be error-prone and costly. Manual inspection also raises the chance of contamination. Thus, non-contact, precise inspection is preferred. In this study, the critical dimensions are automatically measured by the vision camera. The measured data are analyzed to classify the quality characteristics. The automated inspection and classification techniques developed in this study are expected to improve the quality of the fabricated scaffolds and reduce the overall cost of manufacturing.

  19. Fully Printed 3D Cube Cantor Fractal Rectenna for Ambient RF Energy Harvesting Application

    Bakytbekov, Azamat

    2017-11-01

    Internet of Things (IoT) is a new emerging paradigm which requires billions of wirelessly connected devices that communicate with each other in a complex radio-frequency (RF) environment. Considering the huge number of devices, recharging batteries or replacing them becomes impractical in real life. Therefore, harvesting ambient RF energy for powering IoT devices can be a practical solution to achieve self-charging operation. The antenna for the RF energy harvesting application must work on multiple frequency bands (multiband or wideband) to capture as much power as possible from ambient; it should be compact and small in size so that it can be integrated with IoT devices; and it should be low cost, considering the huge number of devices. This thesis presents a fully printed 3D cube Cantor fractal RF energy harvesting unit, which meets the above-mentioned criteria. The multiband Cantor fractal antenna has been designed and implemented on a package of rectifying circuits using additive manufacturing (combination of 3D inkjet printing of plastic substrate and 2D metallic screen printing of silver paste) for the first time for RF energy harvesting application. The antenna, which is in a Cantor fractal shape, is folded on five faces of a 3D cube where the bottom face accommodates rectifying circuit with matching network. The rectenna (rectifying antenna) harvests RF power from GSM900, GSM1800, and 3G at 2100 MHz frequency. Indoor and outdoor field tests of the RF energy harvester have been conducted in the IMPACT lab and the King Abdullah University of Science and Technology (KAUST) campus territory, and 252.4 mV of maximum output voltage is harvested.

  20. 3D Assembly Group Analysis for Cognitive Automation

    Christian Brecher

    2012-01-01

    Full Text Available A concept that allows the cognitive automation of robotic assembly processes is introduced. An assembly cell comprised of two robots was designed to verify the concept. For the purpose of validation a customer-defined part group consisting of Hubelino bricks is assembled. One of the key aspects for this process is the verification of the assembly group. Hence a software component was designed that utilizes the Microsoft Kinect to perceive both depth and color data in the assembly area. This information is used to determine the current state of the assembly group and is compared to a CAD model for validation purposes. In order to efficiently resolve erroneous situations, the results are interactively accessible to a human expert. The implications for an industrial application are demonstrated by transferring the developed concepts to an assembly scenario for switch-cabinet systems.

  1. A parallel code named NEPTUNE for 3D fully electromagnetic and pic simulations

    Dong Ye; Yang Wenyuan; Chen Jun; Zhao Qiang; Xia Fang; Ma Yan; Xiao Li; Sun Huifang; Chen Hong; Zhou Haijing; Mao Zeyao; Dong Zhiwei

    2010-01-01

    A parallel code named NEPTUNE for 3D fully electromagnetic and particle-in-cell (PIC) simulations is introduced, which could run on the Linux system with hundreds to thousand CPUs. NEPTUNE is suitable to simulate entire 3D HPM devices; many HPM devices are simulated and designed by using it. In NEPTUNE code, the electromagnetic fields are updated by using the finite-difference in time domain (FDTD) method of solving Maxwell equations and the particles are moved by using Buneman-Boris advance method of solving relativistic Newton-Lorentz equation. Electromagnetic fields and particles are coupled by using liner weighing interpolation PIC method, and the electric filed components are corrected by using Boris method of solve Poisson equation in order to ensure charge-conservation. NEPTUNE code could construct many complicated geometric structures, such as arbitrary axial-symmetric structures, plane transforming structures, slow-wave-structures, coupling holes, foils, and so on. The boundary conditions used in NEPTUNE code are introduced in brief, including perfectly electric conductor boundary, external wave boundary, and particle boundary. Finally, some typical HPM devices are simulated and test by using NEPTUNE code, including MILO, RBWO, VCO, and RKA. The simulation results are with correct and credible physical images, and the parallel efficiencies are also given. (authors)

  2. 3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study.

    Dolz, Jose; Desrosiers, Christian; Ben Ayed, Ismail

    2018-04-15

    This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during inference. We address the problem via small kernels, allowing deeper architectures. We further model both local and global context by embedding intermediate-layer outputs in the final prediction, which encourages consistency between features extracted at different scales and embeds fine-grained information directly in the segmentation process. Our model is efficiently trained end-to-end on a graphics processing unit (GPU), in a single stage, exploiting the dense inference capabilities of fully CNNs. We performed comprehensive experiments over two publicly available datasets. First, we demonstrate a state-of-the-art performance on the ISBR dataset. Then, we report a large-scale multi-site evaluation over 1112 unregistered subject datasets acquired from 17 different sites (ABIDE dataset), with ages ranging from 7 to 64 years, showing that our method is robust to various acquisition protocols, demographics and clinical factors. Our method yielded segmentations that are highly consistent with a standard atlas-based approach, while running in a fraction of the time needed by atlas-based methods and avoiding registration/normalization steps. This makes it convenient for massive multi-site neuroanatomical imaging studies. To the best of our knowledge, our work is the first to study subcortical structure segmentation on such large-scale and heterogeneous data. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms.

    Kristin Verena Kaltdorf

    2017-01-01

    Full Text Available Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i in embryonic Danio rerio 4 and 8 days past fertilization (dpf and (ii to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ wild-type and its septin mutant (unc-59(e261. We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261 on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement. This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter. Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles and specificity (true vesicles as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual

  4. Ankle-Foot Orthosis Made by 3D Printing Technique and Automated Design Software

    Yong Ho Cha

    2017-01-01

    Full Text Available We described 3D printing technique and automated design software and clinical results after the application of this AFO to a patient with a foot drop. After acquiring a 3D modelling file of a patient’s lower leg with peroneal neuropathy by a 3D scanner, we loaded this file on the automated orthosis software and created the “STL” file. The designed AFO was printed using a fused filament fabrication type 3D printer, and a mechanical stress test was performed. The patient alternated between the 3D-printed and conventional AFOs for 2 months. There was no crack or damage, and the shape and stiffness of the AFO did not change after the durability test. The gait speed increased after wearing the conventional AFO (56.5 cm/sec and 3D-printed AFO (56.5 cm/sec compared to that without an AFO (42.2 cm/sec. The patient was more satisfied with the 3D-printed AFO than the conventional AFO in terms of the weight and ease of use. The 3D-printed AFO exhibited similar functionality as the conventional AFO and considerably satisfied the patient in terms of the weight and ease of use. We suggest the possibility of the individualized AFO with 3D printing techniques and automated design software.

  5. PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.

    Lee, Woonghee; Kim, Jin Hae; Westler, William M; Markley, John L

    2011-06-15

    PONDEROSA (Peak-picking Of Noe Data Enabled by Restriction of Shift Assignments) accepts input information consisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C-edited and/or (15)N-edited) spectra, and returns assignments of NOESY crosspeaks, distance and angle constraints, and a reliable NMR structure represented by a family of conformers. PONDEROSA incorporates and integrates external software packages (TALOS+, STRIDE and CYANA) to carry out different steps in the structure determination. PONDEROSA implements internal functions that identify and validate NOESY peak assignments and assess the quality of the calculated three-dimensional structure of the protein. The robustness of the analysis results from PONDEROSA's hierarchical processing steps that involve iterative interaction among the internal and external modules. PONDEROSA supports a variety of input formats: SPARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star). To demonstrate the utility of PONDEROSA, we used the package to determine 3D structures of two proteins: human ubiquitin and Escherichia coli iron-sulfur scaffold protein variant IscU(D39A). The automatically generated structural constraints and ensembles of conformers were as good as or better than those determined previously by much less automated means. The program, in the form of binary code along with tutorials and reference manuals, is available at http://ponderosa.nmrfam.wisc.edu/.

  6. Fully digital 1-D, 2-D and 3-D multiscroll chaos as hardware pseudo random number generators

    Mansingka, Abhinav S.; Radwan, Ahmed Gomaa; Salama, Khaled N.

    2012-01-01

    This paper introduces the first fully digital implementation of 1-D, 2-D and 3-D multiscroll chaos using the sawtooth nonlinearity in a 3rd order ODE with the Euler approximation. Systems indicate chaotic behaviour through phase space boundedness

  7. Advanced 3-D Ultrasound Imaging: 3-D Synthetic Aperture Imaging using Fully Addressed and Row-Column Addressed 2-D Transducer Arrays

    Bouzari, Hamed

    the important diagnostic information in a noninvasive manner. Diagnostic and therapeutic decisions often require accurate estimates of e.g., organ, cyst, or tumor volumes. 3-D ultrasound imaging can provide these measurements without relying on the geometrical assumptions and operator-dependent skills involved...... is one of the factors for the widespread use of ultrasound imaging. The high price tag on the high quality 3-D scanners is limiting their market share. Row-column addressing of 2-D transducer arrays is a low cost alternative to fully addressed 2-D arrays, for 3-D ultrasound imaging. Using row....... Based on a set of acoustical measurements the center frequency, bandwidth, surface pressure, sensitivity, and acoustical cross-talks were evaluated and discussed. The imaging quality assessments were carried out based on Field II simulations as well as phantom measurements. Moreover, an analysis...

  8. LV challenge LKEB contribution : fully automated myocardial contour detection

    Wijnhout, J.S.; Hendriksen, D.; Assen, van H.C.; Geest, van der R.J.

    2009-01-01

    In this paper a contour detection method is described and evaluated on the evaluation data sets of the Cardiac MR Left Ventricle Segmentation Challenge as part of MICCAI 2009s 3D Segmentation Challenge for Clinical Applications. The proposed method, using 2D AAM and 3D ASM, performs a fully

  9. On the unsteady wake dynamics behind a circular disk using fully 3D proper orthogonal decomposition

    Yang, Jianzhi; Liu, Minghou; Gu, Hailin; Yao, Mengyun [Department of Thermal Science and Energy Engineering, University of Science and Technology of China, Hefei, Anhui 230027 (China); Wu, Guang, E-mail: mhliu@ustc.edu.cn [Technical Services Engineer, ANSYS, Inc (United States)

    2017-02-15

    In the present work, the wakes behind a circular disk at various transitional regimes are numerically explored using fully 3D proper orthogonal decomposition (POD). The Reynolds numbers considered in this study (Re = 152, 170, 300 and 3000) cover four transitional states, i.e. the reflectional-symmetry-breaking (RSB) mode, the standing wave (SW) mode, a weakly chaotic state, and a higher-Reynolds-number state. Through analysis of the spatial POD modes at different wake states, it is found that a planar-symmetric vortex shedding mode characterized by the first mode pair is persistent in all the states. When the wake develops into a weakly chaotic state, a new vortex shedding mode characterized by the second mode pair begins to appear and completely forms at the higher-Reynolds-number state of Re = 3000, i.e. planar-symmetry-breaking vortex shedding mode. On the other hand, the coherent structure at Re = 3000 extracted from the first two POD modes shows a good resemblance to the wake configuration in the SW mode, while the coherent structure reconstructed from the first four POD modes shows a good resemblance to the wake configuration in the RSB mode. The present results indicate that the dynamics or flow instabilities observed at transitional RSB and SW modes are still preserved in a higher-Reynolds-number regime. (paper)

  10. AUTOMATED FEATURE BASED TLS DATA REGISTRATION FOR 3D BUILDING MODELING

    K. Kitamura; N. Kochi; S. Kaneko

    2012-01-01

    In this paper we present a novel method for the registration of point cloud data obtained using terrestrial laser scanner (TLS). The final goal of our investigation is the automated reconstruction of CAD drawings and the 3D modeling of objects surveyed by TLS. Because objects are scanned from multiple positions, individual point cloud need to be registered to the same coordinate system. We propose in this paper an automated feature based registration procedure. Our proposed method does not re...

  11. Automated Extraction of 3D Trees from Mobile LiDAR Point Clouds

    Y. Yu

    2014-06-01

    Full Text Available This paper presents an automated algorithm for extracting 3D trees directly from 3D mobile light detection and ranging (LiDAR data. To reduce both computational and spatial complexities, ground points are first filtered out from a raw 3D point cloud via blockbased elevation filtering. Off-ground points are then grouped into clusters representing individual objects through Euclidean distance clustering and voxel-based normalized cut segmentation. Finally, a model-driven method is proposed to achieve the extraction of 3D trees based on a pairwise 3D shape descriptor. The proposed algorithm is tested using a set of mobile LiDAR point clouds acquired by a RIEGL VMX-450 system. The results demonstrate the feasibility and effectiveness of the proposed algorithm.

  12. pynoddy 1.0: an experimental platform for automated 3-D kinematic and potential field modelling

    Florian Wellmann, J.; Thiele, Sam T.; Lindsay, Mark D.; Jessell, Mark W.

    2016-03-01

    We present a novel methodology for performing experiments with subsurface structural models using a set of flexible and extensible Python modules. We utilize the ability of kinematic modelling techniques to describe major deformational, tectonic, and magmatic events at low computational cost to develop experiments testing the interactions between multiple kinematic events, effect of uncertainty regarding event timing, and kinematic properties. These tests are simple to implement and perform, as they are automated within the Python scripting language, allowing the encapsulation of entire kinematic experiments within high-level class definitions and fully reproducible results. In addition, we provide a link to geophysical potential-field simulations to evaluate the effect of parameter uncertainties on maps of gravity and magnetics. We provide relevant fundamental information on kinematic modelling and our implementation, and showcase the application of our novel methods to investigate the interaction of multiple tectonic events on a pre-defined stratigraphy, the effect of changing kinematic parameters on simulated geophysical potential fields, and the distribution of uncertain areas in a full 3-D kinematic model, based on estimated uncertainties in kinematic input parameters. Additional possibilities for linking kinematic modelling to subsequent process simulations are discussed, as well as additional aspects of future research. Our modules are freely available on github, including documentation and tutorial examples, and we encourage the contribution to this project.

  13. Automated 3D closed surface segmentation: application to vertebral body segmentation in CT images.

    Liu, Shuang; Xie, Yiting; Reeves, Anthony P

    2016-05-01

    A fully automated segmentation algorithm, progressive surface resolution (PSR), is presented in this paper to determine the closed surface of approximately convex blob-like structures that are common in biomedical imaging. The PSR algorithm was applied to the cortical surface segmentation of 460 vertebral bodies on 46 low-dose chest CT images, which can be potentially used for automated bone mineral density measurement and compression fracture detection. The target surface is realized by a closed triangular mesh, which thereby guarantees the enclosure. The surface vertices of the triangular mesh representation are constrained along radial trajectories that are uniformly distributed in 3D angle space. The segmentation is accomplished by determining for each radial trajectory the location of its intersection with the target surface. The surface is first initialized based on an input high confidence boundary image and then resolved progressively based on a dynamic attraction map in an order of decreasing degree of evidence regarding the target surface location. For the visual evaluation, the algorithm achieved acceptable segmentation for 99.35 % vertebral bodies. Quantitative evaluation was performed on 46 vertebral bodies and achieved overall mean Dice coefficient of 0.939 (with max [Formula: see text] 0.957, min [Formula: see text] 0.906 and standard deviation [Formula: see text] 0.011) using manual annotations as the ground truth. Both visual and quantitative evaluations demonstrate encouraging performance of the PSR algorithm. This novel surface resolution strategy provides uniform angular resolution for the segmented surface with computation complexity and runtime that are linearly constrained by the total number of vertices of the triangular mesh representation.

  14. Automated quantitative 3D analysis of aorta size, morphology, and mural calcification distributions

    Kurugol, Sila, E-mail: sila.kurugol@childrens.harvard.edu; Come, Carolyn E.; Diaz, Alejandro A.; Ross, James C.; Washko, George R.; San Jose Estepar, Raul [Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115 (United States); Kinney, Greg L.; Black-Shinn, Jennifer L.; Hokanson, John E. [Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado 80045 (United States); Budoff, Matthew J. [Los Angeles Biomedical Research Center at Harbor and UCLA Medical Center, Torrance, California 90502 (United States)

    2015-09-15

    Purpose: The purpose of this work is to develop a fully automated pipeline to compute aorta morphology and calcification measures in large cohorts of CT scans that can be used to investigate the potential of these measures as imaging biomarkers of cardiovascular disease. Methods: The first step of the automated pipeline is aorta segmentation. The algorithm the authors propose first detects an initial aorta boundary by exploiting cross-sectional circularity of aorta in axial slices and aortic arch in reformatted oblique slices. This boundary is then refined by a 3D level-set segmentation that evolves the boundary to the location of nearby edges. The authors then detect the aortic calcifications with thresholding and filter out the false positive regions due to nearby high intensity structures based on their anatomical location. The authors extract the centerline and oblique cross sections of the segmented aortas and compute the aorta morphology and calcification measures of the first 2500 subjects from COPDGene study. These measures include volume and number of calcified plaques and measures of vessel morphology such as average cross-sectional area, tortuosity, and arch width. Results: The authors computed the agreement between the algorithm and expert segmentations on 45 CT scans and obtained a closest point mean error of 0.62 ± 0.09 mm and a Dice coefficient of 0.92 ± 0.01. The calcification detection algorithm resulted in an improved true positive detection rate of 0.96 compared to previous work. The measurements of aorta size agreed with the measurements reported in previous work. The initial results showed associations of aorta morphology with calcification and with aging. These results may indicate aorta stiffening and unwrapping with calcification and aging. Conclusions: The authors have developed an objective tool to assess aorta morphology and aortic calcium plaques on CT scans that may be used to provide information about the presence of cardiovascular

  15. From 3D Bioprinters to a fully integrated Organ Biofabrication Line

    Passamai, V. E.; Dernowsek, J. A.; Nogueira, J.; Lara, V.; Vilalba, F.; Mironov, V. A.; Rezende, R. A.; da Silva, J. V.

    2016-04-01

    About 30 years ago, the 3D printing technique appeared. From that time on, engineers in medical science field started to look at 3D printing as a partner. Firstly, biocompatible and biodegradable 3D structures for cell seeding called “scaffolds” were fabricated for in vitro and in vivo animal trials. The advances proved to be of great importance, but, the use of scaffolds faces some limitations, such as low homogeneity and low density of cell aggregates. In the last decade, 3D bioprinting technology emerged as a promising approach to overcome these limitations and as one potential solution to the challenge of organ fabrication, to obtain very similar 3D human tissues, not only for transplantation, but also for drug discovery, disease research and to decrease the usage of animals in laboratory experimentation. 3D bioprinting allowed the fabrication of 3D alive structures with higher and controllable cell density and homogeneity. Other advantage of biofabrication is that the tissue constructs are solid scaffold-free. This paper presents the 3D bioprinting technology; equipment development, stages and components of a complex Organ Bioprinting Line (OBL) and the importance of developing a Virtual OBL.

  16. A Fully Automated Approach to Spike Sorting.

    Chung, Jason E; Magland, Jeremy F; Barnett, Alex H; Tolosa, Vanessa M; Tooker, Angela C; Lee, Kye Y; Shah, Kedar G; Felix, Sarah H; Frank, Loren M; Greengard, Leslie F

    2017-09-13

    Understanding the detailed dynamics of neuronal networks will require the simultaneous measurement of spike trains from hundreds of neurons (or more). Currently, approaches to extracting spike times and labels from raw data are time consuming, lack standardization, and involve manual intervention, making it difficult to maintain data provenance and assess the quality of scientific results. Here, we describe an automated clustering approach and associated software package that addresses these problems and provides novel cluster quality metrics. We show that our approach has accuracy comparable to or exceeding that achieved using manual or semi-manual techniques with desktop central processing unit (CPU) runtimes faster than acquisition time for up to hundreds of electrodes. Moreover, a single choice of parameters in the algorithm is effective for a variety of electrode geometries and across multiple brain regions. This algorithm has the potential to enable reproducible and automated spike sorting of larger scale recordings than is currently possible. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. A simple and low-cost fully 3D-printed non-planar emulsion generator

    Zhang, Jiaming

    2015-12-23

    Droplet-based microfluidic devices provide a powerful platform for material, chemical and biological applications based on droplet templates. The technique traditionally utilized to fabricate microfluidic emulsion generators, i.e. soft-lithography, is complex and expensive for producing three-dimensional (3D) structures. The emergent 3D printing technology provides an attractive alternative due to its simplicity and low-cost. Recently a handful of studies have already demonstrated droplet production through 3D-printed microfluidic devices. However, these devices invariably use purely two-dimensional (2D) flow structures. Herein we apply 3D printing technology to fabricate simple and low-cost 3D miniaturized fluidic devices for droplet generation (single emulsion) and droplet-in-droplet (double emulsion) without need for surface treatment of the channel walls. This is accomplished by varying the channel diameters at the junction, so the inner liquid does not touch the outer walls. This 3D-printed emulsion generator has been successfully tested over a range of conditions. We also formulate and demonstrate, for the first time, uniform scaling laws for the emulsion drop sizes generated in different regimes, by incorporating the dynamic contact angle effects during the drop formation. Magnetically responsive microspheres are also produced with our emulsion templates, demonstrating the potential applications of this 3D emulsion generator in chemical and material engineering.

  18. Objective and subjective comparison of standard 2-D and fully 3-D reconstructed data on a PET/CT system.

    Strobel, Klaus; Rüdy, Matthias; Treyer, Valerie; Veit-Haibach, Patrick; Burger, Cyrill; Hany, Thomas F

    2007-07-01

    The relative advantage of fully 3-D versus 2-D mode for whole-body imaging is currently the focus of considerable expert debate. The nature of 3-D PET acquisition for FDG PET/CT theoretically allows a shorter scan time and improved efficiency of FDG use than in the standard 2-D acquisition. We therefore objectively and subjectively compared standard 2-D and fully 3-D reconstructed data for FDG PET/CT on a research PET/CT system. In a total of 36 patients (mean 58.9 years, range 17.3-78.9 years; 21 male, 15 female) referred for known or suspected malignancy, FDG PET/CT was performed using a research PET/CT system with advanced detector technology with improved sensitivity and spatial resolution. After 45 min uptake, a low-dose CT (40 mAs) from head to thigh was performed followed by 2-D PET (emission 3 min per field) and 3-D PET (emission 1.5 min per field) with both seven slices overlap to cover the identical anatomical region. Acquisition time was therefore 50% less (seven fields; 21 min vs. 10.5 min). PET data was acquired in a randomized fashion, so in 50% of the cases 2-D data was acquired first. CT data was used for attenuation correction. 2-D (OSEM) and 3-D PET images were iteratively reconstructed. Subjective analysis of 2-D and 3-D images was performed by two readers in a blinded, randomized fashion evaluating the following criteria: sharpness of organs (liver, chest wall/lung), overall image quality and detectability and dignity of each identified lesion. Objective analysis of PET data was investigated measuring maximum standard uptake value with lean body mass (SUV(max,LBM)) of identified lesions. On average, per patient, the SUV(max) was 7.86 (SD 7.79) for 2-D and 6.96 (SD 5.19) for 3-D. On a lesion basis, the average SUV(max) was 7.65 (SD 7.79) for 2-D and 6.75 (SD 5.89) for 3-D. The absolute difference on a paired t-test of SUV 3-D-2-D based on each measured lesion was significant with an average of -0.956 (P=0.002) and an average of -0.884 on a

  19. Novel fully integrated computer system for custom footwear: from 3D digitization to manufacturing

    Houle, Pascal-Simon; Beaulieu, Eric; Liu, Zhaoheng

    1998-03-01

    This paper presents a recently developed custom footwear system, which integrates 3D digitization technology, range image fusion techniques, a 3D graphical environment for corrective actions, parametric curved surface representation and computer numerical control (CNC) machining. In this system, a support designed with the help of biomechanics experts can stabilize the foot in a correct and neutral position. The foot surface is then captured by a 3D camera using active ranging techniques. A software using a library of documented foot pathologies suggests corrective actions on the orthosis. Three kinds of deformations can be achieved. The first method uses previously scanned pad surfaces by our 3D scanner, which can be easily mapped onto the foot surface to locally modify the surface shape. The second kind of deformation is construction of B-Spline surfaces by manipulating control points and modifying knot vectors in a 3D graphical environment to build desired deformation. The last one is a manual electronic 3D pen, which may be of different shapes and sizes, and has an adjustable 'pressure' information. All applied deformations should respect a G1 surface continuity, which ensure that the surface can accustom a foot. Once the surface modification process is completed, the resulting data is sent to manufacturing software for CNC machining.

  20. Silhouette-based approach of 3D image reconstruction for automated image acquisition using robotic arm

    Azhar, N.; Saad, W. H. M.; Manap, N. A.; Saad, N. M.; Syafeeza, A. R.

    2017-06-01

    This study presents the approach of 3D image reconstruction using an autonomous robotic arm for the image acquisition process. A low cost of the automated imaging platform is created using a pair of G15 servo motor connected in series to an Arduino UNO as a main microcontroller. Two sets of sequential images were obtained using different projection angle of the camera. The silhouette-based approach is used in this study for 3D reconstruction from the sequential images captured from several different angles of the object. Other than that, an analysis based on the effect of different number of sequential images on the accuracy of 3D model reconstruction was also carried out with a fixed projection angle of the camera. The effecting elements in the 3D reconstruction are discussed and the overall result of the analysis is concluded according to the prototype of imaging platform.

  1. Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors

    Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

    2016-01-01

    study, we used the structure prediction tools PIGS and I-TASSER for creating the 3D models and the TM-align algorithm to superpose them. The innovation of the current methodology resides in the usage of methods adapted from 3D content-based search methodologies to determine the local structural...... determine it are extremely laborious and demanding. Hence, the ability to gain insight into the structure of Igs at large relies on the availability of tools and algorithms for producing accurate Ig structural models based on their primary sequence alone. These models can then be used to determine...... to achieve an optimal solution to this task yet their results were hindered mainly due to the lack of efficient clustering methods based on the similarity of 3D structure descriptors. Here, we present a novel workflow for robust Ig 3D modeling and automated clustering. We validated our protocol in chronic...

  2. Automated prescription of oblique brain 3D magnetic resonance spectroscopic imaging.

    Ozhinsky, Eugene; Vigneron, Daniel B; Chang, Susan M; Nelson, Sarah J

    2013-04-01

    Two major difficulties encountered in implementing Magnetic Resonance Spectroscopic Imaging (MRSI) in a clinical setting are limited coverage and difficulty in prescription. The goal of this project was to automate completely the process of 3D PRESS MRSI prescription, including placement of the selection box, saturation bands and shim volume, while maximizing the coverage of the brain. The automated prescription technique included acquisition of an anatomical MRI image, optimization of the oblique selection box parameters, optimization of the placement of outer-volume suppression saturation bands, and loading of the calculated parameters into a customized 3D MRSI pulse sequence. To validate the technique and compare its performance with existing protocols, 3D MRSI data were acquired from six exams from three healthy volunteers. To assess the performance of the automated 3D MRSI prescription for patients with brain tumors, the data were collected from 16 exams from 8 subjects with gliomas. This technique demonstrated robust coverage of the tumor, high consistency of prescription and very good data quality within the T2 lesion. Copyright © 2012 Wiley Periodicals, Inc.

  3. A 3D network of helicates fully assembled by pi-stacking interactions.

    Vázquez, Miguel; Taglietti, Angelo; Gatteschi, Dante; Sorace, Lorenzo; Sangregorio, Claudio; González, Ana M; Maneiro, Marcelino; Pedrido, Rosa M; Bermejo, Manuel R

    2003-08-07

    The neutral dinuclear dihelicate [Cu2(L)2] x 2CH3CN (1) forms a unique 3D network in the solid state due to pi-stacking interactions, which are responsible for intermolecular antiferromagnetic coupling between Cu(II) ions.

  4. High-Precision Phenotyping of Grape Bunch Architecture Using Fast 3D Sensor and Automation

    Florian Rist

    2018-03-01

    Full Text Available Wine growers prefer cultivars with looser bunch architecture because of the decreased risk for bunch rot. As a consequence, grapevine breeders have to select seedlings and new cultivars with regard to appropriate bunch traits. Bunch architecture is a mosaic of different single traits which makes phenotyping labor-intensive and time-consuming. In the present study, a fast and high-precision phenotyping pipeline was developed. The optical sensor Artec Spider 3D scanner (Artec 3D, L-1466, Luxembourg was used to generate dense 3D point clouds of grapevine bunches under lab conditions and an automated analysis software called 3D-Bunch-Tool was developed to extract different single 3D bunch traits, i.e., the number of berries, berry diameter, single berry volume, total volume of berries, convex hull volume of grapes, bunch width and bunch length. The method was validated on whole bunches of different grapevine cultivars and phenotypic variable breeding material. Reliable phenotypic data were obtained which show high significant correlations (up to r2 = 0.95 for berry number compared to ground truth data. Moreover, it was shown that the Artec Spider can be used directly in the field where achieved data show comparable precision with regard to the lab application. This non-invasive and non-contact field application facilitates the first high-precision phenotyping pipeline based on 3D bunch traits in large plant sets.

  5. High-Precision Phenotyping of Grape Bunch Architecture Using Fast 3D Sensor and Automation.

    Rist, Florian; Herzog, Katja; Mack, Jenny; Richter, Robert; Steinhage, Volker; Töpfer, Reinhard

    2018-03-02

    Wine growers prefer cultivars with looser bunch architecture because of the decreased risk for bunch rot. As a consequence, grapevine breeders have to select seedlings and new cultivars with regard to appropriate bunch traits. Bunch architecture is a mosaic of different single traits which makes phenotyping labor-intensive and time-consuming. In the present study, a fast and high-precision phenotyping pipeline was developed. The optical sensor Artec Spider 3D scanner (Artec 3D, L-1466, Luxembourg) was used to generate dense 3D point clouds of grapevine bunches under lab conditions and an automated analysis software called 3D-Bunch-Tool was developed to extract different single 3D bunch traits, i.e., the number of berries, berry diameter, single berry volume, total volume of berries, convex hull volume of grapes, bunch width and bunch length. The method was validated on whole bunches of different grapevine cultivars and phenotypic variable breeding material. Reliable phenotypic data were obtained which show high significant correlations (up to r² = 0.95 for berry number) compared to ground truth data. Moreover, it was shown that the Artec Spider can be used directly in the field where achieved data show comparable precision with regard to the lab application. This non-invasive and non-contact field application facilitates the first high-precision phenotyping pipeline based on 3D bunch traits in large plant sets.

  6. Fully Soft 3D-Printed Electroactive Fluidic Valve for Soft Hydraulic Robots.

    Zatopa, Alex; Walker, Steph; Menguc, Yigit

    2018-06-01

    Soft robots are designed to utilize their compliance and contortionistic abilities to both interact safely with their environment and move through it in ways a rigid robot cannot. To more completely achieve this, the robot should be made of as many soft components as possible. Here we present a completely soft hydraulic control valve consisting of a 3D-printed photopolymer body with electrorheological (ER) fluid as a working fluid and gallium-indium-tin liquid metal alloy as electrodes. This soft 3D-printed ER valve weighs less than 10 g and allows for onboard actuation control, furthering the goal of an entirely soft controllable robot. The soft ER valve pressure-holding capabilities were tested under unstrained conditions, cyclic valve activation, and the strained conditions of bending, twisting, stretching, and indentation. It was found that the max holding pressure of the valve when 5 kV was applied across the electrodes was 264 kPa, and that the holding pressure deviated less than 15% from the unstrained max holding pressure under all strain conditions except for indentation, which had a 60% max pressure increase. In addition, a soft octopus-like robot was designed, 3D printed, and assembled, and a soft ER valve was used to stop the fluid flow, build pressure in the robot, and actuate six tentacle-like soft bending actuators.

  7. 3D printed fluidics with embedded analytic functionality for automated reaction optimisation

    Andrew J. Capel; Andrew Wright; Matthew J. Harding; George W. Weaver; Yuqi Li; Russell A. Harris; Steve Edmondson; Ruth D. Goodridge; Steven D. R. Christie

    2017-01-01

    Additive manufacturing or ‘3D printing’ is being developed as a novel manufacturing process for the production of bespoke micro and milli-scale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting, to create multi-functional fluidic devices with embedded reaction moni...

  8. Automated Identification and Localization of Hematopoietic Stem Cells in 3D Intravital Microscopy Data

    Reema A. Khorshed

    2015-07-01

    Full Text Available Measuring three-dimensional (3D localization of hematopoietic stem cells (HSCs within the bone marrow microenvironment using intravital microscopy is a rapidly expanding research theme. This approach holds the key to understanding the detail of HSC-niche interactions, which are critical for appropriate stem cell function. Due to the complex tissue architecture of the bone marrow and to the progressive introduction of scattering and signal loss at increasing imaging depths, there is no ready-made software to handle efficient segmentation and unbiased analysis of the data. To address this, we developed an automated image analysis tool that simplifies and standardizes the biological interpretation of 3D HSC microenvironment images. The algorithm identifies HSCs and measures their localization relative to surrounding osteoblast cells and bone collagen. We demonstrate here the effectiveness, consistency, and accuracy of the proposed approach compared to current manual analysis and its wider applicability to analyze other 3D bone marrow components.

  9. Framework for Automated GD&T Inspection Using 3D Scanner

    Pathak, Vimal Kumar; Singh, Amit Kumar; Sivadasan, M.; Singh, N. K.

    2018-04-01

    Geometric Dimensioning and Tolerancing (GD&T) is a typical dialect that helps designers, production faculty and quality monitors to convey design specifications in an effective and efficient manner. GD&T has been practiced since the start of machine component assembly but without overly naming it. However, in recent times industries have started increasingly emphasizing on it. One prominent area where most of the industries struggle with is quality inspection. Complete inspection process is mostly human intensive. Also, the use of conventional gauges and templates for inspection purpose highly depends on skill of workers and quality inspectors. In industries, the concept of 3D scanning is not new but is used only for creating 3D drawings or modelling of physical parts. However, the potential of 3D scanning as a powerful inspection tool is hardly explored. This study is centred on designing a procedure for automated inspection using 3D scanner. Linear, geometric and dimensional inspection of the most popular test bar-stepped bar, as a simple example was also carried out as per the new framework. The new generation engineering industries would definitely welcome this automated inspection procedure being quick and reliable with reduced human intervention.

  10. Automated 3D Damaged Cavity Model Builder for Lower Surface Acreage Tile on Orbiter

    Belknap, Shannon; Zhang, Michael

    2013-01-01

    The 3D Automated Thermal Tool for Damaged Acreage Tile Math Model builder was developed to perform quickly and accurately 3D thermal analyses on damaged lower surface acreage tiles and structures beneath the damaged locations on a Space Shuttle Orbiter. The 3D model builder created both TRASYS geometric math models (GMMs) and SINDA thermal math models (TMMs) to simulate an idealized damaged cavity in the damaged tile(s). The GMMs are processed in TRASYS to generate radiation conductors between the surfaces in the cavity. The radiation conductors are inserted into the TMMs, which are processed in SINDA to generate temperature histories for all of the nodes on each layer of the TMM. The invention allows a thermal analyst to create quickly and accurately a 3D model of a damaged lower surface tile on the orbiter. The 3D model builder can generate a GMM and the correspond ing TMM in one or two minutes, with the damaged cavity included in the tile material. A separate program creates a configuration file, which would take a couple of minutes to edit. This configuration file is read by the model builder program to determine the location of the damage, the correct tile type, tile thickness, structure thickness, and SIP thickness of the damage, so that the model builder program can build an accurate model at the specified location. Once the models are built, they are processed by the TRASYS and SINDA.

  11. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    Lee, Woonghee; Petit, Chad M.; Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L.

    2016-01-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  12. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States); Petit, Chad M. [University of Alabama at Birmingham, Department of Biochemistry and Molecular Genetics (United States); Cornilescu, Gabriel; Stark, Jaime L.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-06-15

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27–98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models.

  13. Cardiac imaging: working towards fully-automated machine analysis & interpretation.

    Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

    2017-03-01

    Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered: This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary: Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation.

  14. Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

    Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

    2002-01-01

    The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

  15. FAFNER - a fully 3-D neutral beam injection code using Monte Carlo methods

    Lister, G.G.

    1985-01-01

    A computer code is described which models the injection of fast neutral particles into 3-dimensional toroidal plasmas and follows the paths of the resulting fast ions until they are either lost to the system or fully thermalised. A comprehensive model for the neutral beam injection system is included. The code is written especially for the use on the CRAY-1 computer: in particular, the modular nature of the program should enable the most time consuming sections of the program to be vectorised for each particular experiment to be modelled. The effects of plasma contamination by possible injection of impurities, such as oxygen, with the beams are also included. The code may also be readily adapted to plasmas for which a 1 or 2-dimensional description is adequate. It has also been constructed with a view to ready coupling with a transport or equilibrium code. (orig.)

  16. Fully anisotropic goal-oriented mesh adaptation for 3D steady Euler equations

    Loseille, A.; Dervieux, A.; Alauzet, F.

    2010-04-01

    This paper studies the coupling between anisotropic mesh adaptation and goal-oriented error estimate. The former is very well suited to the control of the interpolation error. It is generally interpreted as a local geometric error estimate. On the contrary, the latter is preferred when studying approximation errors for PDEs. It generally involves non local error contributions. Consequently, a full and strong coupling between both is hard to achieve due to this apparent incompatibility. This paper shows how to achieve this coupling in three steps. First, a new a priori error estimate is proved in a formal framework adapted to goal-oriented mesh adaptation for output functionals. This estimate is based on a careful analysis of the contributions of the implicit error and of the interpolation error. Second, the error estimate is applied to the set of steady compressible Euler equations which are solved by a stabilized Galerkin finite element discretization. A goal-oriented error estimation is derived. It involves the interpolation error of the Euler fluxes weighted by the gradient of the adjoint state associated with the observed functional. Third, rewritten in the continuous mesh framework, the previous estimate is minimized on the set of continuous meshes thanks to a calculus of variations. The optimal continuous mesh is then derived analytically. Thus, it can be used as a metric tensor field to drive the mesh adaptation. From a numerical point of view, this method is completely automatic, intrinsically anisotropic, and does not depend on any a priori choice of variables to perform the adaptation. 3D examples of steady flows around supersonic and transsonic jets are presented to validate the current approach and to demonstrate its efficiency.

  17. Fully automated MR liver volumetry using watershed segmentation coupled with active contouring.

    Huynh, Hieu Trung; Le-Trong, Ngoc; Bao, Pham The; Oto, Aytek; Suzuki, Kenji

    2017-02-01

    Our purpose is to develop a fully automated scheme for liver volume measurement in abdominal MR images, without requiring any user input or interaction. The proposed scheme is fully automatic for liver volumetry from 3D abdominal MR images, and it consists of three main stages: preprocessing, rough liver shape generation, and liver extraction. The preprocessing stage reduced noise and enhanced the liver boundaries in 3D abdominal MR images. The rough liver shape was revealed fully automatically by using the watershed segmentation, thresholding transform, morphological operations, and statistical properties of the liver. An active contour model was applied to refine the rough liver shape to precisely obtain the liver boundaries. The liver volumes calculated by the proposed scheme were compared to the "gold standard" references which were estimated by an expert abdominal radiologist. The liver volumes computed by using our developed scheme excellently agreed (Intra-class correlation coefficient was 0.94) with the "gold standard" manual volumes by the radiologist in the evaluation with 27 cases from multiple medical centers. The running time was 8.4 min per case on average. We developed a fully automated liver volumetry scheme in MR, which does not require any interaction by users. It was evaluated with cases from multiple medical centers. The liver volumetry performance of our developed system was comparable to that of the gold standard manual volumetry, and it saved radiologists' time for manual liver volumetry of 24.7 min per case.

  18. Automated 3D-Objectdocumentation on the Base of an Image Set

    Sebastian Vetter

    2011-12-01

    Full Text Available Digital stereo-photogrammetry allows users an automatic evaluation of the spatial dimension and the surface texture of objects. The integration of image analysis techniques simplifies the automation of evaluation of large image sets and offers a high accuracy [1]. Due to the substantial similarities of stereoscopic image pairs, correlation techniques provide measurements of subpixel precision for corresponding image points. With the help of an automated point search algorithm in image sets identical points are used to associate pairs of images to stereo models and group them. The found identical points in all images are basis for calculation of the relative orientation of each stereo model as well as defining the relation of neighboured stereo models. By using proper filter strategies incorrect points are removed and the relative orientation of the stereo model can be made automatically. With the help of 3D-reference points or distances at the object or a defined distance of camera basis the stereo model is orientated absolute. An adapted expansion- and matching algorithm offers the possibility to scan the object surface automatically. The result is a three dimensional point cloud; the scan resolution depends on image quality. With the integration of the iterative closest point- algorithm (ICP these partial point clouds are fitted to a total point cloud. In this way, 3D-reference points are not necessary. With the help of the implemented triangulation algorithm a digital surface models (DSM can be created. The texturing can be made automatically by the usage of the images that were used for scanning the object surface. It is possible to texture the surface model directly or to generate orthophotos automatically. By using of calibrated digital SLR cameras with full frame sensor a high accuracy can be reached. A big advantage is the possibility to control the accuracy and quality of the 3d-objectdocumentation with the resolution of the images. The

  19. Algorithms of control parameters selection for automation of FDM 3D printing process

    Kogut Paweł

    2017-01-01

    Full Text Available The paper presents algorithms of control parameters selection of the Fused Deposition Modelling (FDM technology in case of an open printing solutions environment and 3DGence ONE printer. The following parameters were distinguished: model mesh density, material flow speed, cooling performance, retraction and printing speeds. These parameters are independent in principle printing system, but in fact to a certain degree that results from the selected printing equipment features. This is the first step for automation of the 3D printing process in FDM technology.

  20. Fully digital 1-D, 2-D and 3-D multiscroll chaos as hardware pseudo random number generators

    Mansingka, Abhinav S.

    2012-10-07

    This paper introduces the first fully digital implementation of 1-D, 2-D and 3-D multiscroll chaos using the sawtooth nonlinearity in a 3rd order ODE with the Euler approximation. Systems indicate chaotic behaviour through phase space boundedness and positive Lyapunov exponent. Low-significance bits form a PRNG and pass all tests in the NIST SP. 800-22 suite without post-processing. Real-time control of the number of scrolls allows distinct output streams with 2-D and 3-D multiscroll chaos enabling greater controllability. The proposed PRNGs are experimentally verified on a Xilinx Virtex 4 FPGA with logic utilization less than 1.25%, throughput up to 5.25 Gbits/s and up to 512 distinct output streams with low cross-correlation.

  1. Study of Shortwave Spectra in Fully 3D Environment: Synergy Between Scanning Radars and Spectral Radiation Measurements

    Wiscombe, Warren J.

    2012-01-01

    The main theme for our research is the understanding and closure of the surface spectral shortwave radiation problem in fully 3D cloud situations by combining the new ARM scanning radars, shortwave spectrometers, and microwave radiometers with the arsenal of radiative transfer tools developed by our group. In particular, we define first a large number of cloudy test cases spanning all 3D possibilities not just the customary uniform-overcast ones. Second, for each case, we define a "Best Estimate of Clouds That Affect Shortwave Radiation" using all relevant ARM instruments, notably the new scanning radars, and contribute this to the ARM Archive. Third, we test the ASR-signature radiative transfer model RRTMG_SW for those cases, focusing on the near-IR because of long-standing problems in this spectral region, and work with the developers to improve RRTMG_SW in order to increase its penetration into the modeling community.

  2. Implementation of a Monte Carlo simulation environment for fully 3D PET on a high-performance parallel platform

    Zaidi, H; Morel, Christian

    1998-01-01

    This paper describes the implementation of the Eidolon Monte Carlo program designed to simulate fully three-dimensional (3D) cylindrical positron tomographs on a MIMD parallel architecture. The original code was written in Objective-C and developed under the NeXTSTEP development environment. Different steps involved in porting the software on a parallel architecture based on PowerPC 604 processors running under AIX 4.1 are presented. Basic aspects and strategies of running Monte Carlo calculations on parallel computers are described. A linear decrease of the computing time was achieved with the number of computing nodes. The improved time performances resulting from parallelisation of the Monte Carlo calculations makes it an attractive tool for modelling photon transport in 3D positron tomography. The parallelisation paradigm used in this work is independent from the chosen parallel architecture

  3. 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors.

    Narayanaswamy, Arunachalam; Wang, Yu; Roysam, Badrinath

    2011-09-01

    The accuracy and reliability of automated neurite tracing systems is ultimately limited by image quality as reflected in the signal-to-noise ratio, contrast, and image variability. This paper describes a novel combination of image processing methods that operate on images of neurites captured by confocal and widefield microscopy, and produce synthetic images that are better suited to automated tracing. The algorithms are based on the curvelet transform (for denoising curvilinear structures and local orientation estimation), perceptual grouping by scalar voting (for elimination of non-tubular structures and improvement of neurite continuity while preserving branch points), adaptive focus detection, and depth estimation (for handling widefield images without deconvolution). The proposed methods are fast, and capable of handling large images. Their ability to handle images of unlimited size derives from automated tiling of large images along the lateral dimension, and processing of 3-D images one optical slice at a time. Their speed derives in part from the fact that the core computations are formulated in terms of the Fast Fourier Transform (FFT), and in part from parallel computation on multi-core computers. The methods are simple to apply to new images since they require very few adjustable parameters, all of which are intuitive. Examples of pre-processing DIADEM Challenge images are used to illustrate improved automated tracing resulting from our pre-processing methods.

  4. Fully automated MRI-guided robotics for prostate brachytherapy

    Stoianovici, D.; Vigaru, B.; Petrisor, D.; Muntener, M.; Patriciu, A.; Song, D.

    2008-01-01

    The uncertainties encountered in the deployment of brachytherapy seeds are related to the commonly used ultrasound imager and the basic instrumentation used for the implant. An alternative solution is under development in which a fully automated robot is used to place the seeds according to the dosimetry plan under direct MRI-guidance. Incorporation of MRI-guidance creates potential for physiological and molecular image-guided therapies. Moreover, MRI-guided brachytherapy is also enabling for re-estimating dosimetry during the procedure, because with the MRI the seeds already implanted can be localised. An MRI compatible robot (MrBot) was developed. The robot is designed for transperineal percutaneous prostate interventions, and customised for fully automated MRI-guided brachytherapy. With different end-effectors, the robot applies to other image-guided interventions of the prostate. The robot is constructed of non-magnetic and dielectric materials and is electricity free using pneumatic actuation and optic sensing. A new motor (PneuStep) was purposely developed to set this robot in motion. The robot fits alongside the patient in closed-bore MRI scanners. It is able to stay fully operational during MR imaging without deteriorating the quality of the scan. In vitro, cadaver, and animal tests showed millimetre needle targeting accuracy, and very precise seed placement. The robot tested without any interference up to 7T. The robot is the first fully automated robot to function in MRI scanners. Its first application is MRI-guided seed brachytherapy. It is capable of automated, highly accurate needle placement. Extensive testing is in progress prior to clinical trials. Preliminary results show that the robot may become a useful image-guided intervention instrument. (author)

  5. A Fully Automated High-Throughput Zebrafish Behavioral Ototoxicity Assay.

    Todd, Douglas W; Philip, Rohit C; Niihori, Maki; Ringle, Ryan A; Coyle, Kelsey R; Zehri, Sobia F; Zabala, Leanne; Mudery, Jordan A; Francis, Ross H; Rodriguez, Jeffrey J; Jacob, Abraham

    2017-08-01

    Zebrafish animal models lend themselves to behavioral assays that can facilitate rapid screening of ototoxic, otoprotective, and otoregenerative drugs. Structurally similar to human inner ear hair cells, the mechanosensory hair cells on their lateral line allow the zebrafish to sense water flow and orient head-to-current in a behavior called rheotaxis. This rheotaxis behavior deteriorates in a dose-dependent manner with increased exposure to the ototoxin cisplatin, thereby establishing itself as an excellent biomarker for anatomic damage to lateral line hair cells. Building on work by our group and others, we have built a new, fully automated high-throughput behavioral assay system that uses automated image analysis techniques to quantify rheotaxis behavior. This novel system consists of a custom-designed swimming apparatus and imaging system consisting of network-controlled Raspberry Pi microcomputers capturing infrared video. Automated analysis techniques detect individual zebrafish, compute their orientation, and quantify the rheotaxis behavior of a zebrafish test population, producing a powerful, high-throughput behavioral assay. Using our fully automated biological assay to test a standardized ototoxic dose of cisplatin against varying doses of compounds that protect or regenerate hair cells may facilitate rapid translation of candidate drugs into preclinical mammalian models of hearing loss.

  6. A fully 3D approach for metal artifact reduction in computed tomography

    Kratz, Bärbel; Weyers, Imke; Buzug, Thorsten M.

    2012-01-01

    Purpose: In computed tomography imaging metal objects in the region of interest introduce inconsistencies during data acquisition. Reconstructing these data leads to an image in spatial domain including star-shaped or stripe-like artifacts. In order to enhance the quality of the resulting image the influence of the metal objects can be reduced. Here, a metal artifact reduction (MAR) approach is proposed that is based on a recomputation of the inconsistent projection data using a fully three-dimensional Fourier-based interpolation. The success of the projection space restoration depends sensitively on a sensible continuation of neighboring structures into the recomputed area. Fortunately, structural information of the entire data is inherently included in the Fourier space of the data. This can be used for a reasonable recomputation of the inconsistent projection data. Methods: The key step of the proposed MAR strategy is the recomputation of the inconsistent projection data based on an interpolation using nonequispaced fast Fourier transforms (NFFT). The NFFT interpolation can be applied in arbitrary dimension. The approach overcomes the problem of adequate neighborhood definitions on irregular grids, since this is inherently given through the usage of higher dimensional Fourier transforms. Here, applications up to the third interpolation dimension are presented and validated. Furthermore, prior knowledge may be included by an appropriate damping of the transform during the interpolation step. This MAR method is applicable on each angular view of a detector row, on two-dimensional projection data as well as on three-dimensional projection data, e.g., a set of sequential acquisitions at different spatial positions, projection data of a spiral acquisition, or cone-beam projection data. Results: Results of the novel MAR scheme based on one-, two-, and three-dimensional NFFT interpolations are presented. All results are compared in projection data space and spatial

  7. 3D printed fluidics with embedded analytic functionality for automated reaction optimisation

    Andrew J. Capel

    2017-01-01

    Full Text Available Additive manufacturing or ‘3D printing’ is being developed as a novel manufacturing process for the production of bespoke micro- and milliscale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting, to create multifunctional fluidic devices with embedded reaction monitoring capability. The selectively laser melted parts are the first published examples of multifunctional 3D printed metal fluidic devices. These devices allow high temperature and pressure chemistry to be performed in solvent systems destructive to the majority of devices manufactured via stereolithography, polymer jetting and fused deposition modelling processes previously utilised for this application. These devices were integrated with commercially available flow chemistry, chromatographic and spectroscopic analysis equipment, allowing automated online and inline optimisation of the reaction medium. This set-up allowed the optimisation of two reactions, a ketone functional group interconversion and a fused polycyclic heterocycle formation, via spectroscopic and chromatographic analysis.

  8. 3D printed fluidics with embedded analytic functionality for automated reaction optimisation

    Capel, Andrew J; Wright, Andrew; Harding, Matthew J; Weaver, George W; Li, Yuqi; Harris, Russell A; Edmondson, Steve; Goodridge, Ruth D

    2017-01-01

    Additive manufacturing or ‘3D printing’ is being developed as a novel manufacturing process for the production of bespoke micro- and milliscale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting, to create multifunctional fluidic devices with embedded reaction monitoring capability. The selectively laser melted parts are the first published examples of multifunctional 3D printed metal fluidic devices. These devices allow high temperature and pressure chemistry to be performed in solvent systems destructive to the majority of devices manufactured via stereolithography, polymer jetting and fused deposition modelling processes previously utilised for this application. These devices were integrated with commercially available flow chemistry, chromatographic and spectroscopic analysis equipment, allowing automated online and inline optimisation of the reaction medium. This set-up allowed the optimisation of two reactions, a ketone functional group interconversion and a fused polycyclic heterocycle formation, via spectroscopic and chromatographic analysis. PMID:28228852

  9. 3D printed fluidics with embedded analytic functionality for automated reaction optimisation.

    Capel, Andrew J; Wright, Andrew; Harding, Matthew J; Weaver, George W; Li, Yuqi; Harris, Russell A; Edmondson, Steve; Goodridge, Ruth D; Christie, Steven D R

    2017-01-01

    Additive manufacturing or '3D printing' is being developed as a novel manufacturing process for the production of bespoke micro- and milliscale fluidic devices. When coupled with online monitoring and optimisation software, this offers an advanced, customised method for performing automated chemical synthesis. This paper reports the use of two additive manufacturing processes, stereolithography and selective laser melting, to create multifunctional fluidic devices with embedded reaction monitoring capability. The selectively laser melted parts are the first published examples of multifunctional 3D printed metal fluidic devices. These devices allow high temperature and pressure chemistry to be performed in solvent systems destructive to the majority of devices manufactured via stereolithography, polymer jetting and fused deposition modelling processes previously utilised for this application. These devices were integrated with commercially available flow chemistry, chromatographic and spectroscopic analysis equipment, allowing automated online and inline optimisation of the reaction medium. This set-up allowed the optimisation of two reactions, a ketone functional group interconversion and a fused polycyclic heterocycle formation, via spectroscopic and chromatographic analysis.

  10. Increasing the automation of a 2D-3D registration system.

    Varnavas, Andreas; Carrell, Tom; Penney, Graeme

    2013-02-01

    Routine clinical use of 2D-3D registration algorithms for Image Guided Surgery remains limited. A key aspect for routine clinical use of this technology is its degree of automation, i.e., the amount of necessary knowledgeable interaction between the clinicians and the registration system. Current image-based registration approaches usually require knowledgeable manual interaction during two stages: for initial pose estimation and for verification of produced results. We propose four novel techniques, particularly suited to vertebra-based registration systems, which can significantly automate both of the above stages. Two of these techniques are based upon the intraoperative "insertion" of a virtual fiducial marker into the preoperative data. The remaining two techniques use the final registration similarity value between multiple CT vertebrae and a single fluoroscopy vertebra. The proposed methods were evaluated with data from 31 operations (31 CT scans, 419 fluoroscopy images). Results show these methods can remove the need for manual vertebra identification during initial pose estimation, and were also very effective for result verification, producing a combined true positive rate of 100% and false positive rate equal to zero. This large decrease in required knowledgeable interaction is an important contribution aiming to enable more widespread use of 2D-3D registration technology.

  11. Automated 3D-Printed Unibody Immunoarray for Chemiluminescence Detection of Cancer Biomarker Proteins

    Tang, C. K.; Vaze, A.; Rusling, J. F.

    2017-01-01

    A low cost three-dimensional (3D) printed clear plastic microfluidic device was fabricated for fast, low cost automated protein detection. The unibody device features three reagent reservoirs, an efficient 3D network for passive mixing, and an optically transparent detection chamber housing a glass capture antibody array for measuring chemiluminescence output with a CCD camera. Sandwich type assays were built onto the glass arrays using a multi-labeled detection antibody-polyHRP (HRP = horseradish peroxidase). Total assay time was ~30 min in a complete automated assay employing a programmable syringe pump so that the protocol required minimal operator intervention. The device was used for multiplexed detection of prostate cancer biomarker proteins prostate specific antigen (PSA) and platelet factor 4 (PF-4). Detection limits of 0.5 pg mL−1 were achieved for these proteins in diluted serum with log dynamic ranges of four orders of magnitude. Good accuracy vs ELISA was validated by analyzing human serum samples. This prototype device holds good promise for further development as a point-of-care cancer diagnostics tool. PMID:28067370

  12. Fully porous 3D printed titanium femoral stem to reduce stress-shielding following total hip arthroplasty.

    Arabnejad, Sajad; Johnston, Burnett; Tanzer, Michael; Pasini, Damiano

    2017-08-01

    Current hip replacement femoral implants are made of fully solid materials which all have stiffness considerably higher than that of bone. This mechanical mismatch can cause significant bone resorption secondary to stress shielding, which can lead to serious complications such as peri-prosthetic fracture during or after revision surgery. In this work, a high strength fully porous material with tunable mechanical properties is introduced for use in hip replacement design. The implant macro geometry is based off of a short stem taper-wedge implant compatible with minimally invasive hip replacement surgery. The implant micro-architecture is fine-tuned to locally mimic bone tissue properties which results in minimum bone resorption secondary to stress shielding. We present a systematic approach for the design of a 3D printed fully porous hip implant that encompasses the whole activity spectrum of implant development, from concept generation, multiscale mechanics of porous materials, material architecture tailoring, to additive manufacturing, and performance assessment via in vitro experiments in composite femurs. We show that the fully porous implant with an optimized material micro-structure can reduce the amount of bone loss secondary to stress shielding by 75% compared to a fully solid implant. This result also agrees with those of the in vitro quasi-physiological experimental model and the corresponding finite element model for both the optimized fully porous and fully solid implant. These studies demonstrate the merit and the potential of tuning material architecture to achieve a substantial reduction of bone resorption secondary to stress shielding. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:1774-1783, 2017. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  13. Multimodality 3D Superposition and Automated Whole Brain Tractography: Comprehensive Printing of the Functional Brain.

    Konakondla, Sanjay; Brimley, Cameron J; Sublett, Jesna Mathew; Stefanowicz, Edward; Flora, Sarah; Mongelluzzo, Gino; Schirmer, Clemens M

    2017-09-29

    Whole brain tractography using diffusion tensor imaging (DTI) sequences can be used to map cerebral connectivity; however, this can be time-consuming due to the manual component of image manipulation required, calling for the need for a standardized, automated, and accurate fiber tracking protocol with automatic whole brain tractography (AWBT). Interpreting conventional two-dimensional (2D) images, such as computed tomography (CT) and magnetic resonance imaging (MRI), as an intraoperative three-dimensional (3D) environment is a difficult task with recognized inter-operator variability. Three-dimensional printing in neurosurgery has gained significant traction in the past decade, and as software, equipment, and practices become more refined, trainee education, surgical skills, research endeavors, innovation, patient education, and outcomes via valued care is projected to improve. We describe a novel multimodality 3D superposition (MMTS) technique, which fuses multiple imaging sequences alongside cerebral tractography into one patient-specific 3D printed model. Inferences on cost and improved outcomes fueled by encouraging patient engagement are explored.

  14. The design of 3D scaffold for tissue engineering using automated scaffold design algorithm.

    Mahmoud, Shahenda; Eldeib, Ayman; Samy, Sherif

    2015-06-01

    Several progresses have been introduced in the field of bone regenerative medicine. A new term tissue engineering (TE) was created. In TE, a highly porous artificial extracellular matrix or scaffold is required to accommodate cells and guide their growth in three dimensions. The design of scaffolds with desirable internal and external structure represents a challenge for TE. In this paper, we introduce a new method known as automated scaffold design (ASD) for designing a 3D scaffold with a minimum mismatches for its geometrical parameters. The method makes use of k-means clustering algorithm to separate the different tissues and hence decodes the defected bone portions. The segmented portions of different slices are registered to construct the 3D volume for the data. It also uses an isosurface rendering technique for 3D visualization of the scaffold and bones. It provides the ability to visualize the transplanted as well as the normal bone portions. The proposed system proves good performance in both the segmentation results and visualizations aspects.

  15. Towards automated electron holographic tomography for 3D mapping of electrostatic potentials

    Wolf, Daniel, E-mail: Daniel.Wolf@Triebenberg.de [Triebenberg Laboratory, Institute of Structure Physics, Technische Universitaet Dresden, 01062 Dresden (Germany); Lubk, Axel; Lichte, Hannes [Triebenberg Laboratory, Institute of Structure Physics, Technische Universitaet Dresden, 01062 Dresden (Germany); Friedrich, Heiner [Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Sorbonnelaan 16, 3584 CA, Utrecht (Netherlands)

    2010-04-15

    Electron-holographic tomography (EHT), that is, the combination of off-axis electron holography with electron tomography, was successfully applied for the quantitative 3D mapping of electrostatic potentials at the nanoscale. Here we present the first software package (THOMAS) for semi-automated acquisition of holographic tilt series, a prerequisite for efficient data collection. Using THOMAS, the acquisition time for a holographic tilt series, consisting of object and reference holograms, is reduced by a factor of five on average, compared to the previous, completely manual approaches. Moreover, the existing software packages for retrieving amplitude and phase information from electron holograms have been extended, now including a one-step procedure for holographic tilt series reconstruction. Furthermore, a modified SIRT algorithm (WSIRT) was implemented for the quantitative 3D reconstruction of the electrostatic potential from the aligned phase tilt series. Finally, the application of EHT to a polystyrene latex sphere test-specimen and a pn-doped Ge 'needle'-shaped specimen are presented, illustrating the quantitative character of EHT. For both specimens the mean inner potential (MIP) values were accurately determined from the reconstructed 3D potential. For the Ge specimen, additionally the 'built-in' voltage across the pn junction of 0.5 V was obtained.

  16. Automated segmentation and geometrical modeling of the tricuspid aortic valve in 3D echocardiographic images.

    Pouch, Alison M; Wang, Hongzhi; Takabe, Manabu; Jackson, Benjamin M; Sehgal, Chandra M; Gorman, Joseph H; Gorman, Robert C; Yushkevich, Paul A

    2013-01-01

    The aortic valve has been described with variable anatomical definitions, and the consistency of 2D manual measurement of valve dimensions in medical image data has been questionable. Given the importance of image-based morphological assessment in the diagnosis and surgical treatment of aortic valve disease, there is considerable need to develop a standardized framework for 3D valve segmentation and shape representation. Towards this goal, this work integrates template-based medial modeling and multi-atlas label fusion techniques to automatically delineate and quantitatively describe aortic leaflet geometry in 3D echocardiographic (3DE) images, a challenging task that has been explored only to a limited extent. The method makes use of expert knowledge of aortic leaflet image appearance, generates segmentations with consistent topology, and establishes a shape-based coordinate system on the aortic leaflets that enables standardized automated measurements. In this study, the algorithm is evaluated on 11 3DE images of normal human aortic leaflets acquired at mid systole. The clinical relevance of the method is its ability to capture leaflet geometry in 3DE image data with minimal user interaction while producing consistent measurements of 3D aortic leaflet geometry.

  17. AUTOMATED RECONSTRUCTION OF WALLS FROM AIRBORNE LIDAR DATA FOR COMPLETE 3D BUILDING MODELLING

    Y. He

    2012-07-01

    Full Text Available Automated 3D building model generation continues to attract research interests in photogrammetry and computer vision. Airborne Light Detection and Ranging (LIDAR data with increasing point density and accuracy has been recognized as a valuable source for automated 3D building reconstruction. While considerable achievements have been made in roof extraction, limited research has been carried out in modelling and reconstruction of walls, which constitute important components of a full building model. Low point density and irregular point distribution of LIDAR observations on vertical walls render this task complex. This paper develops a novel approach for wall reconstruction from airborne LIDAR data. The developed method commences with point cloud segmentation using a region growing approach. Seed points for planar segments are selected through principle component analysis, and points in the neighbourhood are collected and examined to form planar segments. Afterwards, segment-based classification is performed to identify roofs, walls and planar ground surfaces. For walls with sparse LIDAR observations, a search is conducted in the neighbourhood of each individual roof segment to collect wall points, and the walls are then reconstructed using geometrical and topological constraints. Finally, walls which were not illuminated by the LIDAR sensor are determined via both reconstructed roof data and neighbouring walls. This leads to the generation of topologically consistent and geometrically accurate and complete 3D building models. Experiments have been conducted in two test sites in the Netherlands and Australia to evaluate the performance of the proposed method. Results show that planar segments can be reliably extracted in the two reported test sites, which have different point density, and the building walls can be correctly reconstructed if the walls are illuminated by the LIDAR sensor.

  18. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    Carlos Morón

    2015-05-01

    Full Text Available This paper describes a new low-cost means to detect and locate mechanical impacts (collisions on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

  19. BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.

    Wan, Yinan; Long, Fuhui; Qu, Lei; Xiao, Hang; Hawrylycz, Michael; Myers, Eugene W; Peng, Hanchuan

    2015-10-01

    Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

  20. Automation of Hessian-Based Tubularity Measure Response Function in 3D Biomedical Images.

    Dzyubak, Oleksandr P; Ritman, Erik L

    2011-01-01

    The blood vessels and nerve trees consist of tubular objects interconnected into a complex tree- or web-like structure that has a range of structural scale 5 μm diameter capillaries to 3 cm aorta. This large-scale range presents two major problems; one is just making the measurements, and the other is the exponential increase of component numbers with decreasing scale. With the remarkable increase in the volume imaged by, and resolution of, modern day 3D imagers, it is almost impossible to make manual tracking of the complex multiscale parameters from those large image data sets. In addition, the manual tracking is quite subjective and unreliable. We propose a solution for automation of an adaptive nonsupervised system for tracking tubular objects based on multiscale framework and use of Hessian-based object shape detector incorporating National Library of Medicine Insight Segmentation and Registration Toolkit (ITK) image processing libraries.

  1. FULLY AUTOMATED IMAGE ORIENTATION IN THE ABSENCE OF TARGETS

    C. Stamatopoulos

    2012-07-01

    Full Text Available Automated close-range photogrammetric network orientation has traditionally been associated with the use of coded targets in the object space to allow for an initial relative orientation (RO and subsequent spatial resection of the images. Over the past decade, automated orientation via feature-based matching (FBM techniques has attracted renewed research attention in both the photogrammetry and computer vision (CV communities. This is largely due to advances made towards the goal of automated relative orientation of multi-image networks covering untargetted (markerless objects. There are now a number of CV-based algorithms, with accompanying open-source software, that can achieve multi-image orientation within narrow-baseline networks. From a photogrammetric standpoint, the results are typically disappointing as the metric integrity of the resulting models is generally poor, or even unknown, while the number of outliers within the image matching and triangulation is large, and generally too large to allow relative orientation (RO via the commonly used coplanarity equations. On the other hand, there are few examples within the photogrammetric research field of automated markerless camera calibration to metric tolerances, and these too are restricted to narrow-baseline, low-convergence imaging geometry. The objective addressed in this paper is markerless automatic multi-image orientation, maintaining metric integrity, within networks that incorporate wide-baseline imagery. By wide-baseline we imply convergent multi-image configurations with convergence angles of up to around 90°. An associated aim is provision of a fast, fully automated process, which can be performed without user intervention. For this purpose, various algorithms require optimisation to allow parallel processing utilising multiple PC cores and graphics processing units (GPUs.

  2. Towards Automated Large-Scale 3D Phenotyping of Vineyards under Field Conditions

    Johann Christian Rose

    2016-12-01

    Full Text Available In viticulture, phenotypic data are traditionally collected directly in the field via visual and manual means by an experienced person. This approach is time consuming, subjective and prone to human errors. In recent years, research therefore has focused strongly on developing automated and non-invasive sensor-based methods to increase data acquisition speed, enhance measurement accuracy and objectivity and to reduce labor costs. While many 2D methods based on image processing have been proposed for field phenotyping, only a few 3D solutions are found in the literature. A track-driven vehicle consisting of a camera system, a real-time-kinematic GPS system for positioning, as well as hardware for vehicle control, image storage and acquisition is used to visually capture a whole vine row canopy with georeferenced RGB images. In the first post-processing step, these images were used within a multi-view-stereo software to reconstruct a textured 3D point cloud of the whole grapevine row. A classification algorithm is then used in the second step to automatically classify the raw point cloud data into the semantic plant components, grape bunches and canopy. In the third step, phenotypic data for the semantic objects is gathered using the classification results obtaining the quantity of grape bunches, berries and the berry diameter.

  3. Hepatic vessel segmentation for 3D planning of liver surgery experimental evaluation of a new fully automatic algorithm.

    Conversano, Francesco; Franchini, Roberto; Demitri, Christian; Massoptier, Laurent; Montagna, Francesco; Maffezzoli, Alfonso; Malvasi, Antonio; Casciaro, Sergio

    2011-04-01

    The aim of this study was to identify the optimal parameter configuration of a new algorithm for fully automatic segmentation of hepatic vessels, evaluating its accuracy in view of its use in a computer system for three-dimensional (3D) planning of liver surgery. A phantom reproduction of a human liver with vessels up to the fourth subsegment order, corresponding to a minimum diameter of 0.2 mm, was realized through stereolithography, exploiting a 3D model derived from a real human computed tomographic data set. Algorithm parameter configuration was experimentally optimized, and the maximum achievable segmentation accuracy was quantified for both single two-dimensional slices and 3D reconstruction of the vessel network, through an analytic comparison of the automatic segmentation performed on contrast-enhanced computed tomographic phantom images with actual model features. The optimal algorithm configuration resulted in a vessel detection sensitivity of 100% for vessels > 1 mm in diameter, 50% in the range 0.5 to 1 mm, and 14% in the range 0.2 to 0.5 mm. An average area overlap of 94.9% was obtained between automatically and manually segmented vessel sections, with an average difference of 0.06 mm(2). The average values of corresponding false-positive and false-negative ratios were 7.7% and 2.3%, respectively. A robust and accurate algorithm for automatic extraction of the hepatic vessel tree from contrast-enhanced computed tomographic volume images was proposed and experimentally assessed on a liver model, showing unprecedented sensitivity in vessel delineation. This automatic segmentation algorithm is promising for supporting liver surgery planning and for guiding intraoperative resections. Copyright © 2011 AUR. Published by Elsevier Inc. All rights reserved.

  4. Modular high power diode lasers with flexible 3D multiplexing arrangement optimized for automated manufacturing

    Könning, Tobias; Bayer, Andreas; Plappert, Nora; Faßbender, Wilhelm; Dürsch, Sascha; Küster, Matthias; Hubrich, Ralf; Wolf, Paul; Köhler, Bernd; Biesenbach, Jens

    2018-02-01

    A novel 3-dimensional arrangement of mirrors is used to re-arrange beams from 1-D and 2-D high power diode laser arrays. The approach allows for a variety of stacking geometries, depending on individual requirements. While basic building blocks, including collimating optics, always remain the same, most adaptations can be realized by simple rearrangement of a few optical components. Due to fully automated alignment processes, the required changes can be realized in software by changing coordinates, rather than requiring customized mechanical components. This approach minimizes development costs due to its flexibility, while reducing overall product cost by using similar building blocks for a variety of products and utilizing a high grade of automation. The modules can be operated with industrial grade water, lowering overall system and maintenance cost. Stackable macro coolers are used as the smallest building block of the system. Each cooler can hold up to five diode laser bars. Micro optical components, collimating the beam, are mounted directly to the cooler. All optical assembly steps are fully automated. Initially, the beams from all laser bars propagate in the same direction. Key to the concept is an arrangement of deflectors, which re-arrange the beams into a 2-D array of the desired shape and high fill factor. Standard multiplexing techniques like polarization- or wavelengths-multiplexing have been implemented as well. A variety of fiber coupled modules ranging from a few hundred watts of optical output power to multiple kilowatts of power, as well as customized laser spot geometries like uniform line sources, have been realized.

  5. Fully Automated Deep Learning System for Bone Age Assessment.

    Lee, Hyunkwang; Tajmir, Shahein; Lee, Jenny; Zissen, Maurice; Yeshiwas, Bethel Ayele; Alkasab, Tarik K; Choy, Garry; Do, Synho

    2017-08-01

    Skeletal maturity progresses through discrete phases, a fact that is used routinely in pediatrics where bone age assessments (BAAs) are compared to chronological age in the evaluation of endocrine and metabolic disorders. While central to many disease evaluations, little has changed to improve the tedious process since its introduction in 1950. In this study, we propose a fully automated deep learning pipeline to segment a region of interest, standardize and preprocess input radiographs, and perform BAA. Our models use an ImageNet pretrained, fine-tuned convolutional neural network (CNN) to achieve 57.32 and 61.40% accuracies for the female and male cohorts on our held-out test images. Female test radiographs were assigned a BAA within 1 year 90.39% and within 2 years 98.11% of the time. Male test radiographs were assigned 94.18% within 1 year and 99.00% within 2 years. Using the input occlusion method, attention maps were created which reveal what features the trained model uses to perform BAA. These correspond to what human experts look at when manually performing BAA. Finally, the fully automated BAA system was deployed in the clinical environment as a decision supporting system for more accurate and efficient BAAs at much faster interpretation time (<2 s) than the conventional method.

  6. Fully Automated Lipid Pool Detection Using Near Infrared Spectroscopy

    Elżbieta Pociask

    2016-01-01

    Full Text Available Background. Detecting and identifying vulnerable plaque, which is prone to rupture, is still a challenge for cardiologist. Such lipid core-containing plaque is still not identifiable by everyday angiography, thus triggering the need to develop a new tool where NIRS-IVUS can visualize plaque characterization in terms of its chemical and morphologic characteristic. The new tool can lead to the development of new methods of interpreting the newly obtained data. In this study, the algorithm to fully automated lipid pool detection on NIRS images is proposed. Method. Designed algorithm is divided into four stages: preprocessing (image enhancement, segmentation of artifacts, detection of lipid areas, and calculation of Lipid Core Burden Index. Results. A total of 31 NIRS chemograms were analyzed by two methods. The metrics, total LCBI, maximal LCBI in 4 mm blocks, and maximal LCBI in 2 mm blocks, were calculated to compare presented algorithm with commercial available system. Both intraclass correlation (ICC and Bland-Altman plots showed good agreement and correlation between used methods. Conclusions. Proposed algorithm is fully automated lipid pool detection on near infrared spectroscopy images. It is a tool developed for offline data analysis, which could be easily augmented for newer functions and projects.

  7. Automated bone segmentation from large field of view 3D MR images of the hip joint

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

    2013-01-01

    Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head–neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone–cartilage interfaces for potential cartilage segmentation. (paper)

  8. Automated bone segmentation from large field of view 3D MR images of the hip joint

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S.; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

    2013-10-01

    Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation.

  9. Automated 3D ultrasound elastography of the breast: a phantom validation study

    Hendriks, Gijs A. G. M.; Holländer, Branislav; Menssen, Jan; Milkowski, Andy; Hansen, Hendrik H. G.; de Korte, Chris L.

    2016-04-01

    In breast cancer screening, the automated breast volume scanner (ABVS) was introduced as an alternative for mammography since the latter technique is less suitable for women with dense breasts. Although clinical studies show promising results, clinicians report two disadvantages: long acquisition times (>90 s) introducing breathing artefacts, and high recall rates due to detection of many small lesions of uncertain malignant potential. Technical improvements for faster image acquisition and better discrimination between benign and malignant lesions are thus required. Therefore, the aim of this study was to investigate if 3D ultrasound elastography using plane-wave imaging is feasible. Strain images of a breast elastography phantom were acquired by an ABVS-mimicking device that allowed axial and elevational movement of the attached transducer. Pre- and post-deformation volumes were acquired with different constant speeds (between 1.25 and 40.0 mm s-1) and by three protocols: Go-Go (pre- and post-volumes with identical start and end positions), Go-Return (similar to Go-Go with opposite scanning directions) and Control (pre- and post-volumes acquired per position, this protocol can be seen as reference). Afterwards, 2D and 3D cross-correlation and strain algorithms were applied to the acquired volumes and the results were compared. The Go-Go protocol was shown to be superior with better strain image quality (CNRe and SNRe) than Go-Return and to be similar as Control. This can be attributed to applying opposite mechanical forces to the phantom during the Go-Return protocol, leading to out-of-plane motion. This motion was partly compensated by using 3D cross-correlation. However, the quality was still inferior to Go-Go. Since these results were obtained in a phantom study with controlled deformations, the effect of possible uncontrolled in vivo tissue motion artefacts has to be addressed in future studies. In conclusion, it seems feasible to implement 3D ultrasound

  10. Automated 3D ultrasound elastography of the breast: a phantom validation study

    Hendriks, Gijs A G M; Holländer, Branislav; Menssen, Jan; Hansen, Hendrik H G; De Korte, Chris L; Milkowski, Andy

    2016-01-01

    In breast cancer screening, the automated breast volume scanner (ABVS) was introduced as an alternative for mammography since the latter technique is less suitable for women with dense breasts. Although clinical studies show promising results, clinicians report two disadvantages: long acquisition times (>90 s) introducing breathing artefacts, and high recall rates due to detection of many small lesions of uncertain malignant potential. Technical improvements for faster image acquisition and better discrimination between benign and malignant lesions are thus required. Therefore, the aim of this study was to investigate if 3D ultrasound elastography using plane-wave imaging is feasible. Strain images of a breast elastography phantom were acquired by an ABVS-mimicking device that allowed axial and elevational movement of the attached transducer. Pre- and post-deformation volumes were acquired with different constant speeds (between 1.25 and 40.0 mm s −1 ) and by three protocols: Go–Go (pre- and post-volumes with identical start and end positions), Go–Return (similar to Go–Go with opposite scanning directions) and Control (pre- and post-volumes acquired per position, this protocol can be seen as reference). Afterwards, 2D and 3D cross-correlation and strain algorithms were applied to the acquired volumes and the results were compared. The Go–Go protocol was shown to be superior with better strain image quality (CNR e and SNR e ) than Go–Return and to be similar as Control. This can be attributed to applying opposite mechanical forces to the phantom during the Go–Return protocol, leading to out-of-plane motion. This motion was partly compensated by using 3D cross-correlation. However, the quality was still inferior to Go–Go. Since these results were obtained in a phantom study with controlled deformations, the effect of possible uncontrolled in vivo tissue motion artefacts has to be addressed in future studies. In conclusion, it seems feasible to

  11. Using a 3D profiler and infrared camera to monitor oven loading in fully cooked meat operations

    Stewart, John; Giorges, Aklilu

    2009-05-01

    Ensuring meat is fully cooked is an important food safety issue for operations that produce "ready to eat" products. In order to kill harmful pathogens like Salmonella, all of the product must reach a minimum threshold temperature. Producers typically overcook the majority of the product to ensure meat in the most difficult scenario reaches the desired temperature. A difficult scenario can be caused by an especially thick piece of meat or by a surge of product into the process. Overcooking wastes energy, degrades product quality, lowers the maximum throughput rate of the production line and decreases product yield. At typical production rates of 6000lbs/hour, these losses from overcooking can have a significant cost impact on producers. A wide area 3D camera coupled with a thermal camera was used to measure the thermal mass variability of chicken breasts in a cooking process. Several types of variability are considered including time varying thermal mass (mass x temperature / time), variation in individual product geometry and variation in product temperature. The automatic identification of product arrangement issues that affect cooking such as overlapping product and folded products is also addressed. A thermal model is used along with individual product geometry and oven cook profiles to predict the percentage of product that will be overcooked and to identify products that may not fully cook in a given process.

  12. Fully automated gynecomastia quantification from low-dose chest CT

    Liu, Shuang; Sonnenblick, Emily B.; Azour, Lea; Yankelevitz, David F.; Henschke, Claudia I.; Reeves, Anthony P.

    2018-02-01

    Gynecomastia is characterized by the enlargement of male breasts, which is a common and sometimes distressing condition found in over half of adult men over the age of 44. Although the majority of gynecomastia is physiologic or idiopathic, its occurrence may also associate with an extensive variety of underlying systemic disease or drug toxicity. With the recent large-scale implementation of annual lung cancer screening using low-dose chest CT (LDCT), gynecomastia is believed to be a frequent incidental finding on LDCT. A fully automated system for gynecomastia quantification from LDCT is presented in this paper. The whole breast region is first segmented using an anatomyorientated approach based on the propagation of pectoral muscle fronts in the vertical direction. The subareolar region is then localized, and the fibroglandular tissue within it is measured for the assessment of gynecomastia. The presented system was validated using 454 breast regions from non-contrast LDCT scans of 227 adult men. The ground truth was established by an experienced radiologist by classifying each breast into one of the five categorical scores. The automated measurements have been demonstrated to achieve promising performance for the gynecomastia diagnosis with the AUC of 0.86 for the ROC curve and have statistically significant Spearman correlation r=0.70 (p early detection as well as the treatment of both gynecomastia and the underlying medical problems, if any, that cause gynecomastia.

  13. A new method for automated discontinuity trace mapping on rock mass 3D surface model

    Li, Xiaojun; Chen, Jianqin; Zhu, Hehua

    2016-04-01

    This paper presents an automated discontinuity trace mapping method on a 3D surface model of rock mass. Feature points of discontinuity traces are first detected using the Normal Tensor Voting Theory, which is robust to noisy point cloud data. Discontinuity traces are then extracted from feature points in four steps: (1) trace feature point grouping, (2) trace segment growth, (3) trace segment connection, and (4) redundant trace segment removal. A sensitivity analysis is conducted to identify optimal values for the parameters used in the proposed method. The optimal triangular mesh element size is between 5 cm and 6 cm; the angle threshold in the trace segment growth step is between 70° and 90°; the angle threshold in the trace segment connection step is between 50° and 70°, and the distance threshold should be at least 15 times the mean triangular mesh element size. The method is applied to the excavation face trace mapping of a drill-and-blast tunnel. The results show that the proposed discontinuity trace mapping method is fast and effective and could be used as a supplement to traditional direct measurement of discontinuity traces.

  14. Automated tracking and quantification of angiogenic vessel formation in 3D microfluidic devices.

    Wang, Mengmeng; Ong, Lee-Ling Sharon; Dauwels, Justin; Asada, H Harry

    2017-01-01

    Angiogenesis, the growth of new blood vessels from pre-existing vessels, is a critical step in cancer invasion. Better understanding of the angiogenic mechanisms is required to develop effective antiangiogenic therapies for cancer treatment. We culture angiogenic vessels in 3D microfluidic devices under different Sphingosin-1-phosphate (S1P) conditions and develop an automated vessel formation tracking system (AVFTS) to track the angiogenic vessel formation and extract quantitative vessel information from the experimental time-lapse phase contrast images. The proposed AVFTS first preprocesses the experimental images, then applies a distance transform and an augmented fast marching method in skeletonization, and finally implements the Hungarian method in branch tracking. When applying the AVFTS to our experimental data, we achieve 97.3% precision and 93.9% recall by comparing with the ground truth obtained from manual tracking by visual inspection. This system enables biologists to quantitatively compare the influence of different growth factors. Specifically, we conclude that the positive S1P gradient increases cell migration and vessel elongation, leading to a higher probability for branching to occur. The AVFTS is also applicable to distinguish tip and stalk cells by considering the relative cell locations in a branch. Moreover, we generate a novel type of cell lineage plot, which not only provides cell migration and proliferation histories but also demonstrates cell phenotypic changes and branch information.

  15. Fully 3-D list-mode positron emission tomography image reconstruction on a multi-GPU cluster

    Cui, Jingyu [Stanford Univ., CA (United States). Dept. of Electrical Engineering; Prevrhal, Sven; Shao, Lingxiong [Philips Healthcare, San Jose, CA (United States); Pratx, Guillem [Stanford Univ., CA (United States). Dept. of Radiation Oncology; Levin, Craig S. [Stanford Univ., CA (United States). Dept. of Radiology, Electrical Engineering, and Physics; Stanford Univ., CA (United States). Molecular Imaging Program at Stanford (MIPS); Stanford Univ., CA (United States). School of Medicine

    2011-07-01

    List-mode processing is an efficient way of dealing with the sparse nature of PET data sets, and is the processing method of choice for time-of-flight (ToF) PET. We present a novel method of computing line projection operations required for list-mode ordered subsets expectation maximization (OSEM) for fully 3-D PET image reconstruction on a graphics processing unit (GPU) using the compute unified device architecture (CUDA) framework. Our method overcomes challenges such as compute thread divergence, and exploits GPU capabilities such as shared memory and atomic operations. When applied to line projection operations for list-mode time-of-flight PET, this new GPU-CUDA reformulation is 188X faster than a single-threaded reference CPU implementation. When embedded in a multi-process environment on a GPU-equipped small cluster, a speedup of 4X was observed over the same configuration but without GPU support. Image quality is preserved with root mean squared (RMS) deviation of 0.05% between CPU and GPU-generated images, which has negligible effect in typical clinical applications. (orig.)

  16. Fully 3D tomographic reconstruction by Monte Carlo simulation of the system matrix in preclinical PET with iodine 124

    Moreau, Matthieu

    2014-01-01

    Immuno-PET imaging can be used to assess the pharmacokinetic in radioimmunotherapy. When using iodine-124, PET quantitative imaging is limited by physics-based degrading factors within the detection system and the object, such as the long positron range in water and the complex spectrum of gamma photons. The objective of this thesis was to develop a fully 3D tomographic reconstruction method (S(MC)2PET) using Monte Carlo simulations for estimating the system matrix, in the context of preclinical imaging with iodine-124. The Monte Carlo simulation platform GATE was used for that respect. Several complexities of system matrices were calculated, with at least a model of the PET system response function. Physics processes in the object was either neglected or taken into account using a precise or a simplified object description. The impact of modelling refinement and statistical variance related to the system matrix elements was evaluated on final reconstructed images. These studies showed that a high level of complexity did not always improve qualitative and quantitative results, owing to the high-variance of the associated system matrices. (author)

  17. Automated extraction and analysis of rock discontinuity characteristics from 3D point clouds

    Bianchetti, Matteo; Villa, Alberto; Agliardi, Federico; Crosta, Giovanni B.

    2016-04-01

    A reliable characterization of fractured rock masses requires an exhaustive geometrical description of discontinuities, including orientation, spacing, and size. These are required to describe discontinuum rock mass structure, perform Discrete Fracture Network and DEM modelling, or provide input for rock mass classification or equivalent continuum estimate of rock mass properties. Although several advanced methodologies have been developed in the last decades, a complete characterization of discontinuity geometry in practice is still challenging, due to scale-dependent variability of fracture patterns and difficult accessibility to large outcrops. Recent advances in remote survey techniques, such as terrestrial laser scanning and digital photogrammetry, allow a fast and accurate acquisition of dense 3D point clouds, which promoted the development of several semi-automatic approaches to extract discontinuity features. Nevertheless, these often need user supervision on algorithm parameters which can be difficult to assess. To overcome this problem, we developed an original Matlab tool, allowing fast, fully automatic extraction and analysis of discontinuity features with no requirements on point cloud accuracy, density and homogeneity. The tool consists of a set of algorithms which: (i) process raw 3D point clouds, (ii) automatically characterize discontinuity sets, (iii) identify individual discontinuity surfaces, and (iv) analyse their spacing and persistence. The tool operates in either a supervised or unsupervised mode, starting from an automatic preliminary exploration data analysis. The identification and geometrical characterization of discontinuity features is divided in steps. First, coplanar surfaces are identified in the whole point cloud using K-Nearest Neighbor and Principal Component Analysis algorithms optimized on point cloud accuracy and specified typical facet size. Then, discontinuity set orientation is calculated using Kernel Density Estimation and

  18. Noise and signal properties in PSF-based fully 3D PET image reconstruction: an experimental evaluation

    Tong, S; Alessio, A M; Kinahan, P E

    2010-01-01

    The addition of accurate system modeling in PET image reconstruction results in images with distinct noise texture and characteristics. In particular, the incorporation of point spread functions (PSF) into the system model has been shown to visually reduce image noise, but the noise properties have not been thoroughly studied. This work offers a systematic evaluation of noise and signal properties in different combinations of reconstruction methods and parameters. We evaluate two fully 3D PET reconstruction algorithms: (1) OSEM with exact scanner line of response modeled (OSEM+LOR), (2) OSEM with line of response and a measured point spread function incorporated (OSEM+LOR+PSF), in combination with the effects of four post-reconstruction filtering parameters and 1-10 iterations, representing a range of clinically acceptable settings. We used a modified NEMA image quality (IQ) phantom, which was filled with 68 Ge and consisted of six hot spheres of different sizes with a target/background ratio of 4:1. The phantom was scanned 50 times in 3D mode on a clinical system to provide independent noise realizations. Data were reconstructed with OSEM+LOR and OSEM+LOR+PSF using different reconstruction parameters, and our implementations of the algorithms match the vendor's product algorithms. With access to multiple realizations, background noise characteristics were quantified with four metrics. Image roughness and the standard deviation image measured the pixel-to-pixel variation; background variability and ensemble noise quantified the region-to-region variation. Image roughness is the image noise perceived when viewing an individual image. At matched iterations, the addition of PSF leads to images with less noise defined as image roughness (reduced by 35% for unfiltered data) and as the standard deviation image, while it has no effect on background variability or ensemble noise. In terms of signal to noise performance, PSF-based reconstruction has a 7% improvement in

  19. Fully automated measurement of anisotropy of magnetic susceptibility using 3D rotator

    Studýnka, J.; Chadima, Martin; Suza, P.

    2014-01-01

    Roč. 629, 26 August (2014), s. 6-13 ISSN 0040-1951 Institutional support: RVO:67985831 Keywords : AMS * Kappabridge * susceptibility tensor Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 2.872, year: 2014

  20. The digital code driven autonomous synthesis of ibuprofen automated in a 3D-printer-based robot.

    Kitson, Philip J; Glatzel, Stefan; Cronin, Leroy

    2016-01-01

    An automated synthesis robot was constructed by modifying an open source 3D printing platform. The resulting automated system was used to 3D print reaction vessels (reactionware) of differing internal volumes using polypropylene feedstock via a fused deposition modeling 3D printing approach and subsequently make use of these fabricated vessels to synthesize the nonsteroidal anti-inflammatory drug ibuprofen via a consecutive one-pot three-step approach. The synthesis of ibuprofen could be achieved on different scales simply by adjusting the parameters in the robot control software. The software for controlling the synthesis robot was written in the python programming language and hard-coded for the synthesis of ibuprofen by the method described, opening possibilities for the sharing of validated synthetic 'programs' which can run on similar low cost, user-constructed robotic platforms towards an 'open-source' regime in the area of chemical synthesis.

  1. The digital code driven autonomous synthesis of ibuprofen automated in a 3D-printer-based robot

    Philip J. Kitson

    2016-12-01

    Full Text Available An automated synthesis robot was constructed by modifying an open source 3D printing platform. The resulting automated system was used to 3D print reaction vessels (reactionware of differing internal volumes using polypropylene feedstock via a fused deposition modeling 3D printing approach and subsequently make use of these fabricated vessels to synthesize the nonsteroidal anti-inflammatory drug ibuprofen via a consecutive one-pot three-step approach. The synthesis of ibuprofen could be achieved on different scales simply by adjusting the parameters in the robot control software. The software for controlling the synthesis robot was written in the python programming language and hard-coded for the synthesis of ibuprofen by the method described, opening possibilities for the sharing of validated synthetic ‘programs’ which can run on similar low cost, user-constructed robotic platforms towards an ‘open-source’ regime in the area of chemical synthesis.

  2. Improving automated multiple sclerosis lesion segmentation with a cascaded 3D convolutional neural network approach.

    Valverde, Sergi; Cabezas, Mariano; Roura, Eloy; González-Villà, Sandra; Pareto, Deborah; Vilanova, Joan C; Ramió-Torrentà, Lluís; Rovira, Àlex; Oliver, Arnau; Lladó, Xavier

    2017-07-15

    In this paper, we present a novel automated method for White Matter (WM) lesion segmentation of Multiple Sclerosis (MS) patient images. Our approach is based on a cascade of two 3D patch-wise convolutional neural networks (CNN). The first network is trained to be more sensitive revealing possible candidate lesion voxels while the second network is trained to reduce the number of misclassified voxels coming from the first network. This cascaded CNN architecture tends to learn well from a small (n≤35) set of labeled data of the same MRI contrast, which can be very interesting in practice, given the difficulty to obtain manual label annotations and the large amount of available unlabeled Magnetic Resonance Imaging (MRI) data. We evaluate the accuracy of the proposed method on the public MS lesion segmentation challenge MICCAI2008 dataset, comparing it with respect to other state-of-the-art MS lesion segmentation tools. Furthermore, the proposed method is also evaluated on two private MS clinical datasets, where the performance of our method is also compared with different recent public available state-of-the-art MS lesion segmentation methods. At the time of writing this paper, our method is the best ranked approach on the MICCAI2008 challenge, outperforming the rest of 60 participant methods when using all the available input modalities (T1-w, T2-w and FLAIR), while still in the top-rank (3rd position) when using only T1-w and FLAIR modalities. On clinical MS data, our approach exhibits a significant increase in the accuracy segmenting of WM lesions when compared with the rest of evaluated methods, highly correlating (r≥0.97) also with the expected lesion volume. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Fully automated bone mineral density assessment from low-dose chest CT

    Liu, Shuang; Gonzalez, Jessica; Zulueta, Javier; de-Torres, Juan P.; Yankelevitz, David F.; Henschke, Claudia I.; Reeves, Anthony P.

    2018-02-01

    A fully automated system is presented for bone mineral density (BMD) assessment from low-dose chest CT (LDCT). BMD assessment is central in the diagnosis and follow-up therapy monitoring of osteoporosis, which is characterized by low bone density and is estimated to affect 12.3 million US population aged 50 years or older, creating tremendous social and economic burdens. BMD assessment from DXA scans (BMDDXA) is currently the most widely used and gold standard technique for the diagnosis of osteoporosis and bone fracture risk estimation. With the recent large-scale implementation of annual lung cancer screening using LDCT, great potential emerges for the concurrent opportunistic osteoporosis screening. In the presented BMDCT assessment system, each vertebral body is first segmented and labeled with its anatomical name. Various 3D region of interest (ROI) inside the vertebral body are then explored for BMDCT measurements at different vertebral levels. The system was validated using 76 pairs of DXA and LDCT scans of the same subject. Average BMDDXA of L1-L4 was used as the reference standard. Statistically significant (p-value correlation is obtained between BMDDXA and BMDCT at all vertebral levels (T1 - L2). A Pearson correlation of 0.857 was achieved between BMDDXA and average BMDCT of T9-T11 by using a 3D ROI taking into account of both trabecular and cortical bone tissue. These encouraging results demonstrate the feasibility of fully automated quantitative BMD assessment and the potential of opportunistic osteoporosis screening with concurrent lung cancer screening using LDCT.

  4. An automated design and fabrication pipeline for improving the strength of 3D printed artifacts under tensile loading

    Al, Can Mert; Yaman, Ulas

    2018-05-01

    In the scope of this study, an alternative automated method to the conventional design and fabrication pipeline of 3D printers is developed by using an integrated CAD/CAE/CAM approach. It increases the load carrying capacity of the parts by constructing heterogeneous infill structures. Traditional CAM software of Additive Manufacturing machinery starts with a design model in STL file format which only includes data about the outer boundary in the triangular mesh form. Depending on the given infill percentage, the algorithm running behind constructs the interior of the artifact by using homogeneous infill structures. As opposed to the current CAM software, the proposed method provides a way to construct heterogeneous infill structures with respect to the Von Misses stress field results obtained from a finite element analysis. Throughout the work, Rhinoceros3D is used for the design of the parts along with Grasshopper3D, an algorithmic design tool for Rhinoceros3D. In addition, finite element analyses are performed using Karamba3D, a plug-in for Grasshopper3D. According to the results of the tensile tests, the method offers an improvement of load carrying capacity about 50% compared to traditional slicing algorithms of 3D printing.

  5. Step-by-step guide to building an inexpensive 3D printed motorized positioning stage for automated high-content screening microscopy.

    Schneidereit, Dominik; Kraus, Larissa; Meier, Jochen C; Friedrich, Oliver; Gilbert, Daniel F

    2017-06-15

    High-content screening microscopy relies on automation infrastructure that is typically proprietary, non-customizable, costly and requires a high level of skill to use and maintain. The increasing availability of rapid prototyping technology makes it possible to quickly engineer alternatives to conventional automation infrastructure that are low-cost and user-friendly. Here, we describe a 3D printed inexpensive open source and scalable motorized positioning stage for automated high-content screening microscopy and provide detailed step-by-step instructions to re-building the device, including a comprehensive parts list, 3D design files in STEP (Standard for the Exchange of Product model data) and STL (Standard Tessellation Language) format, electronic circuits and wiring diagrams as well as software code. System assembly including 3D printing requires approx. 30h. The fully assembled device is light-weight (1.1kg), small (33×20×8cm) and extremely low-cost (approx. EUR 250). We describe positioning characteristics of the stage, including spatial resolution, accuracy and repeatability, compare imaging data generated with our device to data obtained using a commercially available microplate reader, demonstrate its suitability to high-content microscopy in 96-well high-throughput screening format and validate its applicability to automated functional Cl - - and Ca 2+ -imaging with recombinant HEK293 cells as a model system. A time-lapse video of the stage during operation and as part of a custom assembled screening robot can be found at https://vimeo.com/158813199. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  6. Development of a Fully-Automated Monte Carlo Burnup Code Monteburns

    Poston, D.I.; Trellue, H.R.

    1999-01-01

    Several computer codes have been developed to perform nuclear burnup calculations over the past few decades. In addition, because of advances in computer technology, it recently has become more desirable to use Monte Carlo techniques for such problems. Monte Carlo techniques generally offer two distinct advantages over discrete ordinate methods: (1) the use of continuous energy cross sections and (2) the ability to model detailed, complex, three-dimensional (3-D) geometries. These advantages allow more accurate burnup results to be obtained, provided that the user possesses the required computing power (which is required for discrete ordinate methods as well). Several linkage codes have been written that combine a Monte Carlo N-particle transport code (such as MCNP TM ) with a radioactive decay and burnup code. This paper describes one such code that was written at Los Alamos National Laboratory: monteburns. Monteburns links MCNP with the isotope generation and depletion code ORIGEN2. The basis for the development of monteburns was the need for a fully automated code that could perform accurate burnup (and other) calculations for any 3-D system (accelerator-driven or a full reactor core). Before the initial development of monteburns, a list of desired attributes was made and is given below. o The code should be fully automated (that is, after the input is set up, no further user interaction is required). . The code should allow for the irradiation of several materials concurrently (each material is evaluated collectively in MCNP and burned separately in 0RIGEN2). o The code should allow the transfer of materials (shuffling) between regions in MCNP. . The code should allow any materials to be added or removed before, during, or after each step in an automated fashion. . The code should not require the user to provide input for 0RIGEN2 and should have minimal MCNP input file requirements (other than a working MCNP deck). . The code should be relatively easy to use

  7. Fully automated data acquisition, processing, and display in equilibrium radioventriculography

    Bourguignon, M.H.; Douglass, K.H.; Links, J.M.; Wagner, H.N. Jr.; Johns Hopkins Medical Institutions, Baltimore, MD

    1981-01-01

    A fully automated data acquisition, processing, and display procedure was developed for equilibrium radioventriculography. After a standardized acquisition, the study is automatically analyzed to yield both right and left ventricular time-activity curves. The program first creates a series of edge-enhanced images (difference between squared images and scaled original images). A marker point within each ventricle is then identified as that pixel with maximum counts to the patient's right and left of the count center of gravity of a stroke volume image. Regions of interest are selected on each frame as the first contour of local maxima of the two-dimensional second derivative (pseudo-Laplacian) which encloses the appropriate marker point, using a method developed by Goris. After shifting the left ventricular end-systolic region of interest four pixels to the patient's left, a background region of interest is generated as the crescent-shaped area of the shifted region of interest not intersected by the end systolic region. The average counts/pixel in this background region in the end systolic frame of the original study are subtracted from each pixel in all frames of the gated study. Right and left ventricular time-activity curves are then obtained by applying each region of interest to its corresponding background-subtracted frame, and the ejection fraction, end diastolic, end systolic, and stroke counts determined for both ventricles. In fourteen consecutive patients, in addition to the automatic ejection fractions, manually drawn regions of interest were used to obtain ejection fractions for both ventricles. The manual regions of interest were drawn twice, and the average obtained. (orig./TR)

  8. Fully automated chest wall line segmentation in breast MRI by using context information

    Wu, Shandong; Weinstein, Susan P.; Conant, Emily F.; Localio, A. Russell; Schnall, Mitchell D.; Kontos, Despina

    2012-03-01

    Breast MRI has emerged as an effective modality for the clinical management of breast cancer. Evidence suggests that computer-aided applications can further improve the diagnostic accuracy of breast MRI. A critical and challenging first step for automated breast MRI analysis, is to separate the breast as an organ from the chest wall. Manual segmentation or user-assisted interactive tools are inefficient, tedious, and error-prone, which is prohibitively impractical for processing large amounts of data from clinical trials. To address this challenge, we developed a fully automated and robust computerized segmentation method that intensively utilizes context information of breast MR imaging and the breast tissue's morphological characteristics to accurately delineate the breast and chest wall boundary. A critical component is the joint application of anisotropic diffusion and bilateral image filtering to enhance the edge that corresponds to the chest wall line (CWL) and to reduce the effect of adjacent non-CWL tissues. A CWL voting algorithm is proposed based on CWL candidates yielded from multiple sequential MRI slices, in which a CWL representative is generated and used through a dynamic time warping (DTW) algorithm to filter out inferior candidates, leaving the optimal one. Our method is validated by a representative dataset of 20 3D unilateral breast MRI scans that span the full range of the American College of Radiology (ACR) Breast Imaging Reporting and Data System (BI-RADS) fibroglandular density categorization. A promising performance (average overlay percentage of 89.33%) is observed when the automated segmentation is compared to manually segmented ground truth obtained by an experienced breast imaging radiologist. The automated method runs time-efficiently at ~3 minutes for each breast MR image set (28 slices).

  9. Current automated 3D cell detection methods are not a suitable replacement for manual stereologic cell counting

    Christoph eSchmitz

    2014-05-01

    Full Text Available Stereologic cell counting has had a major impact on the field of neuroscience. A major bottleneck in stereologic cell counting is that the user must manually decide whether or not each cell is counted according to three-dimensional (3D stereologic counting rules by visual inspection within hundreds of microscopic fields-of-view per investigated brain or brain region. Reliance on visual inspection forces stereologic cell counting to be very labor-intensive and time-consuming, and is the main reason why biased, non-stereologic two-dimensional (2D cell counting approaches have remained in widespread use. We present an evaluation of the performance of modern automated cell detection and segmentation algorithms as a potential alternative to the manual approach in stereologic cell counting. The image data used in this study were 3D microscopic images of thick brain tissue sections prepared with a variety of commonly used nuclear and cytoplasmic stains. The evaluation compared the numbers and locations of cells identified unambiguously and counted exhaustively by an expert observer with those found by three automated 3D cell detection algorithms: nuclei segmentation from the FARSIGHT toolkit, nuclei segmentation by 3D multiple level set methods, and the 3D object counter plug-in for ImageJ. Of these methods, FARSIGHT performed best, with true-positive detection rates between 38–99% and false-positive rates from 3.6–82%. The results demonstrate that the current automated methods suffer from lower detection rates and higher false-positive rates than are acceptable for obtaining valid estimates of cell numbers. Thus, at present, stereologic cell counting with manual decision for object inclusion according to unbiased stereologic counting rules remains the only adequate method for unbiased cell quantification in histologic tissue sections.

  10. Practical system for recording spatially lifelike 5.1 surround sound and 3D fully periphonic reproduction

    Miller, Robert E. (Robin)

    2005-04-01

    In acoustic spaces that are played as extensions of musical instruments, tonality is a major contributor to the experience of reality. Tonality is described as a process of integration in our consciousness over the reverberation time of the room of many sonic arrivals in three dimensions, each directionally coded in a learned response by the listeners unique head-related transfer function (HRTF). Preserving this complex 3D directionality is key to lifelike reproduction of a recording. Conventional techniques such as stereo or 5.1-channel surround sound position the listener at the apex of a triangle or the center of a circle, not the center of the sphere of lifelike hearing. A periphonic reproduction system for music and movie entertainment, Virtual Reality, and Training Simulation termed PerAmbio 3D/2D (Pat. pending) is described in theory and subjective tests that capture the 3D sound field with a microphone array and transform the periphonic signals into ordinary 6-channel media for either decoderless 2D replay on 5.1 systems, or lossless 3D replay with decoder and five additional speakers. PerAmbio 3D/2D is described as a practical approach to preserving the spatial perception of reality, where the listening room and speakers disappear, leaving the acoustical impression of the original venue.

  11. Participation through Automation: Fully Automated Critical PeakPricing in Commercial Buildings

    Piette, Mary Ann; Watson, David S.; Motegi, Naoya; Kiliccote,Sila; Linkugel, Eric

    2006-06-20

    California electric utilities have been exploring the use of dynamic critical peak prices (CPP) and other demand response programs to help reduce peaks in customer electric loads. CPP is a tariff design to promote demand response. Levels of automation in DR can be defined as follows: Manual Demand Response involves a potentially labor-intensive approach such as manually turning off or changing comfort set points at each equipment switch or controller. Semi-Automated Demand Response involves a pre-programmed demand response strategy initiated by a person via centralized control system. Fully Automated Demand Response does not involve human intervention, but is initiated at a home, building, or facility through receipt of an external communications signal. The receipt of the external signal initiates pre-programmed demand response strategies. They refer to this as Auto-DR. This paper describes the development, testing, and results from automated CPP (Auto-CPP) as part of a utility project in California. The paper presents the project description and test methodology. This is followed by a discussion of Auto-DR strategies used in the field test buildings. They present a sample Auto-CPP load shape case study, and a selection of the Auto-CPP response data from September 29, 2005. If all twelve sites reached their maximum saving simultaneously, a total of approximately 2 MW of DR is available from these twelve sites that represent about two million ft{sup 2}. The average DR was about half that value, at about 1 MW. These savings translate to about 0.5 to 1.0 W/ft{sup 2} of demand reduction. They are continuing field demonstrations and economic evaluations to pursue increasing penetrations of automated DR that has demonstrated ability to provide a valuable DR resource for California.

  12. From SFM to 3d Print: Automated Workflow Addressed to Practitioner Aimed at the Conservation and Restauration

    Inzerillo, L.; Di Paola, F.

    2017-08-01

    In In the last years there has been an increasing use of digital techniques for conservation and restoration purposes. Among these, a very dominant rule is played by the use of digital photogrammetry packages (Agisoft Photoscan, 3D Zephir) which allow to obtain in few steps 3D textured models of real objects. Combined with digital documentation technologies digital fabrication technologies can be employed in a variety of ways to assist in heritage documentation, conservation and dissemination. This paper will give to practitioners an overview on the state of the art available technologies and a feasible workflow for optimizing point cloud and polygon mesh datasets for the purpose of fabrication using 3D printing. The goal is to give an important contribute to confer an automation aspect at the whole processing. We tried to individuate a workflow that should be applicable to several types of cases apart from small precautions. In our experimentation we used a DELTA WASP 2040 printer with PLA easyfil.

  13. An international crowdsourcing study into people's statements on fully automated driving

    Bazilinskyy, P.; Kyriakidis, M.; de Winter, J.C.F.; Ahram, Tareq; Karwowski, Waldemar; Schmorrow, Dylan

    2015-01-01

    Fully automated driving can potentially provide enormous benefits to society. However, it has been unclear whether people will appreciate such far-reaching technology. This study investigated anonymous textual comments regarding fully automated driving, based on data extracted from three online

  14. BranchAnalysis2D/3D automates morphometry analyses of branching structures.

    Srinivasan, Aditya; Muñoz-Estrada, Jesús; Bourgeois, Justin R; Nalwalk, Julia W; Pumiglia, Kevin M; Sheen, Volney L; Ferland, Russell J

    2018-01-15

    Morphometric analyses of biological features have become increasingly common in recent years with such analyses being subject to a large degree of observer bias, variability, and time consumption. While commercial software packages exist to perform these analyses, they are expensive, require extensive user training, and are usually dependent on the observer tracing the morphology. To address these issues, we have developed a broadly applicable, no-cost ImageJ plugin we call 'BranchAnalysis2D/3D', to perform morphometric analyses of structures with branching morphologies, such as neuronal dendritic spines, vascular morphology, and primary cilia. Our BranchAnalysis2D/3D algorithm allows for rapid quantification of the length and thickness of branching morphologies, independent of user tracing, in both 2D and 3D data sets. We validated the performance of BranchAnalysis2D/3D against pre-existing software packages using trained human observers and images from brain and retina. We found that the BranchAnalysis2D/3D algorithm outputs results similar to available software (i.e., Metamorph, AngioTool, Neurolucida), while allowing faster analysis times and unbiased quantification. BranchAnalysis2D/3D allows inexperienced observers to output results like a trained observer but more efficiently, thereby increasing the consistency, speed, and reliability of morphometric analyses. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Intention to use a fully automated car: attitudes and a priori acceptability

    PAYRE, William; CESTAC, Julien; DELHOMME, Patricia

    2014-01-01

    If previous research studied acceptability of partially or highly automated driving, few of them focused on fully automated driving (FAD), including the ability to master longitudinal control, lateral control and maneuvers. The present study analyzes a priori acceptability, attitudes, personality traits and intention to use a fully automated vehicle. 421 French drivers (153 males, M= 40.2 years, age range 19-73) answered an online questionnaire. 68.1% of the sample a priori accepted FAD. P...

  16. Toward Fully Automated Multicriterial Plan Generation: A Prospective Clinical Study

    Voet, Peter W.J.; Dirkx, Maarten L.P.; Breedveld, Sebastiaan; Fransen, Dennie; Levendag, Peter C.; Heijmen, Ben J.M.

    2013-01-01

    Purpose: To prospectively compare plans generated with iCycle, an in-house-developed algorithm for fully automated multicriterial intensity modulated radiation therapy (IMRT) beam profile and beam orientation optimization, with plans manually generated by dosimetrists using the clinical treatment planning system. Methods and Materials: For 20 randomly selected head-and-neck cancer patients with various tumor locations (of whom 13 received sequential boost treatments), we offered the treating physician the choice between an automatically generated iCycle plan and a manually optimized plan using standard clinical procedures. Although iCycle used a fixed “wish list” with hard constraints and prioritized objectives, the dosimetrists manually selected the beam configuration and fine tuned the constraints and objectives for each IMRT plan. Dosimetrists were not informed in advance whether a competing iCycle plan was made. The 2 plans were simultaneously presented to the physician, who then selected the plan to be used for treatment. For the patient group, differences in planning target volume coverage and sparing of critical tissues were quantified. Results: In 32 of 33 plan comparisons, the physician selected the iCycle plan for treatment. This highly consistent preference for the automatically generated plans was mainly caused by the improved sparing for the large majority of critical structures. With iCycle, the normal tissue complication probabilities for the parotid and submandibular glands were reduced by 2.4% ± 4.9% (maximum, 18.5%, P=.001) and 6.5% ± 8.3% (maximum, 27%, P=.005), respectively. The reduction in the mean oral cavity dose was 2.8 ± 2.8 Gy (maximum, 8.1 Gy, P=.005). For the swallowing muscles, the esophagus and larynx, the mean dose reduction was 3.3 ± 1.1 Gy (maximum, 9.2 Gy, P<.001). For 15 of the 20 patients, target coverage was also improved. Conclusions: In 97% of cases, automatically generated plans were selected for treatment because of

  17. Automated mammographic breast density estimation using a fully convolutional network.

    Lee, Juhun; Nishikawa, Robert M

    2018-03-01

    The purpose of this study was to develop a fully automated algorithm for mammographic breast density estimation using deep learning. Our algorithm used a fully convolutional network, which is a deep learning framework for image segmentation, to segment both the breast and the dense fibroglandular areas on mammographic images. Using the segmented breast and dense areas, our algorithm computed the breast percent density (PD), which is the faction of dense area in a breast. Our dataset included full-field digital screening mammograms of 604 women, which included 1208 mediolateral oblique (MLO) and 1208 craniocaudal (CC) views. We allocated 455, 58, and 91 of 604 women and their exams into training, testing, and validation datasets, respectively. We established ground truth for the breast and the dense fibroglandular areas via manual segmentation and segmentation using a simple thresholding based on BI-RADS density assessments by radiologists, respectively. Using the mammograms and ground truth, we fine-tuned a pretrained deep learning network to train the network to segment both the breast and the fibroglandular areas. Using the validation dataset, we evaluated the performance of the proposed algorithm against radiologists' BI-RADS density assessments. Specifically, we conducted a correlation analysis between a BI-RADS density assessment of a given breast and its corresponding PD estimate by the proposed algorithm. In addition, we evaluated our algorithm in terms of its ability to classify the BI-RADS density using PD estimates, and its ability to provide consistent PD estimates for the left and the right breast and the MLO and CC views of the same women. To show the effectiveness of our algorithm, we compared the performance of our algorithm against a state of the art algorithm, laboratory for individualized breast radiodensity assessment (LIBRA). The PD estimated by our algorithm correlated well with BI-RADS density ratings by radiologists. Pearson's rho values of

  18. Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

    Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

    2013-01-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

  19. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    Kamfai Chan

    Full Text Available Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs. Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers.

  20. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  1. A fully defined and scalable 3D culture system for human pluripotent stem cell expansion and differentiation

    Lei, Yuguo; Schaffer, David V.

    2013-12-01

    Human pluripotent stem cells (hPSCs), including human embryonic stem cells and induced pluripotent stem cells, are promising for numerous biomedical applications, such as cell replacement therapies, tissue and whole-organ engineering, and high-throughput pharmacology and toxicology screening. Each of these applications requires large numbers of cells of high quality; however, the scalable expansion and differentiation of hPSCs, especially for clinical utilization, remains a challenge. We report a simple, defined, efficient, scalable, and good manufacturing practice-compatible 3D culture system for hPSC expansion and differentiation. It employs a thermoresponsive hydrogel that combines easy manipulation and completely defined conditions, free of any human- or animal-derived factors, and entailing only recombinant protein factors. Under an optimized protocol, the 3D system enables long-term, serial expansion of multiple hPSCs lines with a high expansion rate (∼20-fold per 5-d passage, for a 1072-fold expansion over 280 d), yield (∼2.0 × 107 cells per mL of hydrogel), and purity (∼95% Oct4+), even with single-cell inoculation, all of which offer considerable advantages relative to current approaches. Moreover, the system enabled 3D directed differentiation of hPSCs into multiple lineages, including dopaminergic neuron progenitors with a yield of ∼8 × 107 dopaminergic progenitors per mL of hydrogel and ∼80-fold expansion by the end of a 15-d derivation. This versatile system may be useful at numerous scales, from basic biological investigation to clinical development.

  2. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    Badger, J.; Hendle, J.; Burley, S. K.; Kissinger, C. R.

    2005-01-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session

  3. Deposit3D: a tool for automating structure depositions to the Protein Data Bank

    Badger, J., E-mail: jbadger@active-sight.com; Hendle, J.; Burley, S. K.; Kissinger, C. R. [SGX Inc., 10505 Roselle Street, San Diego, CA 92121 (United States)

    2005-09-01

    This paper describes a Python script that may be used to gather all required structure-annotation information into an mmCIF file for upload through the RCSB PDB ADIT structure-deposition interface. Almost all successful protein structure-determination projects in the public sector culminate in a structure deposition to the Protein Data Bank (PDB). In order to expedite the deposition proces, Deposit3D has been developed. This command-line script calculates or gathers all the required structure-deposition information and outputs this data into a mmCIF file for subsequent upload through the RCSB PDB ADIT interface. Deposit3D might be particularly useful for structural genomics pipeline projects because it allows workers involved with various stages of a structure-determination project to pool their different categories of annotation information before starting a deposition session.

  4. A Fully Developed Flow Thermofluid Model for Topology Optimization of 3D-Printed Air-Cooled Heat Exchangers

    Haertel, Jan Hendrik Klaas; Nellis, Gregory F.

    2017-01-01

    In this work, density-based topology optimization is applied to the design of the air-side surface of dry-cooled power plant condensers. A topology optimization model assuming a steady-state, thermally and fluid dynamically fully developed internal flow is developed and used for this application....

  5. An accelerated, fully-coupled, parallel 3D hybrid finite-volume fluid–structure interaction scheme

    Malan, AG

    2012-09-01

    Full Text Available -elemental strain procedure is employed for the solid in the interest of accuracy. For the incompressible fluid, a split-step algorithm is presented which allows the entire fluid-solid system to be solved in a fully-implicit yet matrix-free manner. The algorithm...

  6. Automated 3D quantitative assessment and measurement of alpha angles from the femoral head-neck junction using MR imaging

    Xia, Ying; Chandra, Shekhar S; Crozier, Stuart; Fripp, Jurgen; Walker, Duncan; Engstrom, Craig

    2015-01-01

    To develop an automated approach for 3D quantitative assessment and measurement of alpha angles from the femoral head-neck (FHN) junction using bone models derived from magnetic resonance (MR) images of the hip joint.Bilateral MR images of the hip joints were acquired from 30 male volunteers (healthy active individuals and high-performance athletes, aged 18–49 years) using a water-excited 3D dual echo steady state (DESS) sequence. In a subset of these subjects (18 water-polo players), additional True Fast Imaging with Steady-state Precession (TrueFISP) images were acquired from the right hip joint. For both MR image sets, an active shape model based algorithm was used to generate automated 3D bone reconstructions of the proximal femur. Subsequently, a local coordinate system of the femur was constructed to compute a 2D shape map to project femoral head sphericity for calculation of alpha angles around the FHN junction. To evaluate automated alpha angle measures, manual analyses were performed on anterosuperior and anterior radial MR slices from the FHN junction that were automatically reformatted using the constructed coordinate system.High intra- and inter-rater reliability (intra-class correlation coefficients  >  0.95) was found for manual alpha angle measurements from the auto-extracted anterosuperior and anterior radial slices. Strong correlations were observed between manual and automatic measures of alpha angles for anterosuperior (r  =  0.84) and anterior (r  =  0.92) FHN positions. For matched DESS and TrueFISP images, there were no significant differences between automated alpha angle measures obtained from the upper anterior quadrant of the FHN junction (two-way repeated measures ANOVA, F  <  0.01, p  =  0.98).Our automatic 3D method analysed MR images of the hip joints to generate alpha angle measures around the FHN junction circumference with very good reliability and reproducibility. This work has the

  7. Generation of orientation tools for automated zebrafish screening assays using desktop 3D printing

    Wittbrodt, Jonas N.; Liebel, Urban; Gehrig, Jochen

    2014-01-01

    Background The zebrafish has been established as the main vertebrate model system for whole organism screening applications. However, the lack of consistent positioning of zebrafish embryos within wells of microtiter plates remains an obstacle for the comparative analysis of images acquired in automated screening assays. While technical solutions to the orientation problem exist, dissemination is often hindered by the lack of simple and inexpensive ways of distributing and duplicating tools. ...

  8. Automated detection system for pulmonary emphysema on 3D chest CT images

    Hara, Takeshi; Yamamoto, Akira; Zhou, Xiangrong; Iwano, Shingo; Itoh, Shigeki; Fujita, Hiroshi; Ishigaki, Takeo

    2004-05-01

    An automatic extraction of pulmonary emphysema area on 3-D chest CT images was performed using an adaptive thresholding technique. We proposed a method to estimate the ratio of the emphysema area to the whole lung volume. We employed 32 cases (15 normal and 17 abnormal) which had been already diagnosed by radiologists prior to the study. The ratio in all the normal cases was less than 0.02, and in abnormal cases, it ranged from 0.01 to 0.26. The effectiveness of our approach was confirmed through the results of the present study.

  9. Automation of Hessian-Based Tubularity Measure Response Function in 3D Biomedical Images

    Dzyubak, Oleksandr P.; Ritman, Erik L.

    2011-01-01

    The blood vessels and nerve trees consist of tubular objects interconnected into a complex tree- or web-like structure that has a range of structural scale 5 μm diameter capillaries to 3 cm aorta. This large-scale range presents two major problems; one is just making the measurements, and the other is the exponential increase of component numbers with decreasing scale. With the remarkable increase in the volume imaged by, and resolution of, modern day 3D imagers, it is almost impossible to ma...

  10. Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed MR images: proof-of-concept for subsecond position tracking.

    Thörmer, Gregor; Garnov, Nikita; Moche, Michael; Haase, Jürgen; Kahn, Thomas; Busse, Harald

    2012-04-01

    To determine whether a greatly reduced spatial resolution of fully reconstructed projection MR images can be used for the simultaneous 3D localization of multiple MR-visible markers and to assess the feasibility of a subsecond position tracking for clinical purposes. Miniature, inductively coupled RF coils were imaged in three orthogonal planes with a balanced steady-state free precession (SSFP) sequence and automatically localized using a two-dimensional template fitting and a subsequent three-dimensional (3D) matching of the coordinates. Precision, accuracy, speed and robustness of 3D localization were assessed for decreasing in-plane resolutions (0.6-4.7 mm). The feasibility of marker tracking was evaluated at the lowest resolution by following a robotically driven needle on a complex 3D trajectory. Average 3D precision and accuracy, sensitivity and specificity of localization ranged between 0.1 and 0.4 mm, 0.5 and 1.0 mm, 100% and 95%, and 100% and 96%, respectively. At the lowest resolution, imaging and localization took ≈350 ms and provided an accuracy of ≈1.0 mm. In the tracking experiment, the needle was clearly depicted on the oblique scan planes defined by the markers. Image-based marker localization at a greatly reduced spatial resolution is considered a feasible approach to monitor reference points or rigid instruments at subsecond update rates. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Automated pavement horizontal curve measurement methods based on inertial measurement unit and 3D profiling data

    Wenting Luo

    2016-04-01

    Full Text Available Pavement horizontal curve is designed to serve as a transition between straight segments, and its presence may cause a series of driving-related safety issues to motorists and drivers. As is recognized that traditional methods for curve geometry investigation are time consuming, labor intensive, and inaccurate, this study attempts to develop a method that can automatically conduct horizontal curve identification and measurement at network level. The digital highway data vehicle (DHDV was utilized for data collection, in which three Euler angles, driving speed, and acceleration of survey vehicle were measured with an inertial measurement unit (IMU. The 3D profiling data used for cross slope calibration was obtained with PaveVision3D Ultra technology at 1 mm resolution. In this study, the curve identification was based on the variation of heading angle, and the curve radius was calculated with kinematic method, geometry method, and lateral acceleration method. In order to verify the accuracy of the three methods, the analysis of variance (ANOVA test was applied by using the control variable of curve radius measured by field test. Based on the measured curve radius, a curve safety analysis model was used to predict the crash rates and safe driving speeds at horizontal curves. Finally, a case study on 4.35 km road segment demonstrated that the proposed method could efficiently conduct network level analysis.

  12. A fully MEMS-compatible process for 3D high aspect ratio micro coils obtained with an automatic wire bonder

    Kratt, K; Badilita, V; Burger, T; Wallrabe, U; Korvink, J G

    2010-01-01

    We report the fabrication of 3D micro coils made with an automatic wire bonder. Using standard MEMS processes such as spin coating and UV lithography on silicon and Pyrex® wafers results in high aspect ratio SU-8 posts with diameters down to 100 µm that serve as mechanical stabilization yokes for the coils. The wire bonder is employed to wind 25 µm insulated gold wire around the posts in an arbitrary (e.g. solenoidal) path, yielding arrays of micro coils. Each micro coil is bonded directly on-chip, so that loose wire ends are avoided and, compared to other winding methods, coil re-soldering is unnecessary. The manufacturing time for a single coil is about 200 ms, and although the process is serial, it is batch fabrication compatible due to the high throughput of the machine. Despite the speed of manufacture we obtain high manufacturing precision and reliability. The micro air-core solenoids show an RF quality factor of over 50 when tested at 400 MHz. We present a flexible coil making method where the number of windings is only limited by the post height. The coil diameter is restricted by limits defined by lithography and the mechanical strength of the posts. Based on this technique we present coils ranging from 100 µm diameter and 1 winding up to 1000 µm diameter and 20 windings

  13. Image-based point spread function implementation in a fully 3D OSEM reconstruction algorithm for PET.

    Rapisarda, E; Bettinardi, V; Thielemans, K; Gilardi, M C

    2010-07-21

    The interest in positron emission tomography (PET) and particularly in hybrid integrated PET/CT systems has significantly increased in the last few years due to the improved quality of the obtained images. Nevertheless, one of the most important limits of the PET imaging technique is still its poor spatial resolution due to several physical factors originating both at the emission (e.g. positron range, photon non-collinearity) and at detection levels (e.g. scatter inside the scintillating crystals, finite dimensions of the crystals and depth of interaction). To improve the spatial resolution of the images, a possible way consists of measuring the point spread function (PSF) of the system and then accounting for it inside the reconstruction algorithm. In this work, the system response of the GE Discovery STE operating in 3D mode has been characterized by acquiring (22)Na point sources in different positions of the scanner field of view. An image-based model of the PSF was then obtained by fitting asymmetric two-dimensional Gaussians on the (22)Na images reconstructed with small pixel sizes. The PSF was then incorporated, at the image level, in a three-dimensional ordered subset maximum likelihood expectation maximization (OS-MLEM) reconstruction algorithm. A qualitative and quantitative validation of the algorithm accounting for the PSF has been performed on phantom and clinical data, showing improved spatial resolution, higher contrast and lower noise compared with the corresponding images obtained using the standard OS-MLEM algorithm.

  14. The effect of metallicity on the atmospheres of exoplanets with fully coupled 3D hydrodynamics, equilibrium chemistry, and radiative transfer

    Drummond, B.; Mayne, N. J.; Baraffe, I.; Tremblin, P.; Manners, J.; Amundsen, D. S.; Goyal, J.; Acreman, D.

    2018-05-01

    In this work, we have performed a series of simulations of the atmosphere of GJ 1214b assuming different metallicities using the Met Office Unified Model (UM). The UM is a general circulation model (GCM) that solves the deep, non-hydrostatic equations of motion and uses a flexible and accurate radiative transfer scheme, based on the two-stream and correlated-k approximations, to calculate the heating rates. In this work we consistently couple a well-tested Gibbs energy minimisation scheme to solve for the chemical equilibrium abundances locally in each grid cell for a general set of elemental abundances, further improving the flexibility and accuracy of the model. As the metallicity of the atmosphere is increased we find significant changes in the dynamical and thermal structure, with subsequent implications for the simulated phase curve. The trends that we find are qualitatively consistent with previous works, though with quantitative differences. We investigate in detail the effect of increasing the metallicity by splitting the mechanism into constituents, involving the mean molecular weight, the heat capacity and the opacities. We find the opacity effect to be the dominant mechanism in altering the circulation and thermal structure. This result highlights the importance of accurately computing the opacities and radiative transfer in 3D GCMs.

  15. Dynamic CT myocardial perfusion imaging: performance of 3D semi-automated evaluation software

    Ebersberger, Ullrich [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); Heart Center Munich-Bogenhausen, Department of Cardiology and Intensive Care Medicine, Munich (Germany); Marcus, Roy P.; Nikolaou, Konstantin; Bamberg, Fabian [University of Munich, Institute of Clinical Radiology, Munich (Germany); Schoepf, U.J.; Gray, J.C.; McQuiston, Andrew D. [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); Lo, Gladys G. [Hong Kong Sanatorium and Hospital, Department of Diagnostic and Interventional Radiology, Hong Kong (China); Wang, Yining [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Department of Radiology, Beijing (China); Blanke, Philipp [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); University Hospital Freiburg, Department of Diagnostic Radiology, Freiburg (Germany); Geyer, Lucas L. [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); University of Munich, Institute of Clinical Radiology, Munich (Germany); Cho, Young Jun [Medical University of South Carolina, Heart and Vascular Center, Charleston, SC (United States); Konyang University College of Medicine, Department of Radiology, Daejeon (Korea, Republic of); Scheuering, Michael; Canstein, Christian [Siemens Healthcare, CT Division, Forchheim (Germany); Hoffmann, Ellen [Heart Center Munich-Bogenhausen, Department of Cardiology and Intensive Care Medicine, Munich (Germany)

    2014-01-15

    To evaluate the performance of three-dimensional semi-automated evaluation software for the assessment of myocardial blood flow (MBF) and blood volume (MBV) at dynamic myocardial perfusion computed tomography (CT). Volume-based software relying on marginal space learning and probabilistic boosting tree-based contour fitting was applied to CT myocardial perfusion imaging data of 37 subjects. In addition, all image data were analysed manually and both approaches were compared with SPECT findings. Study endpoints included time of analysis and conventional measures of diagnostic accuracy. Of 592 analysable segments, 42 showed perfusion defects on SPECT. Average analysis times for the manual and software-based approaches were 49.1 ± 11.2 and 16.5 ± 3.7 min respectively (P < 0.01). There was strong agreement between the two measures of interest (MBF, ICC = 0.91, and MBV, ICC = 0.88, both P < 0.01) and no significant difference in MBF/MBV with respect to diagnostic accuracy between the two approaches for both MBF and MBV for manual versus software-based approach; respectively; all comparisons P > 0.05. Three-dimensional semi-automated evaluation of dynamic myocardial perfusion CT data provides similar measures and diagnostic accuracy to manual evaluation, albeit with substantially reduced analysis times. This capability may aid the integration of this test into clinical workflows. (orig.)

  16. Automated Computational Processing of 3-D MR Images of Mouse Brain for Phenotyping of Living Animals.

    Medina, Christopher S; Manifold-Wheeler, Brett; Gonzales, Aaron; Bearer, Elaine L

    2017-07-05

    Magnetic resonance (MR) imaging provides a method to obtain anatomical information from the brain in vivo that is not typically available by optical imaging because of this organ's opacity. MR is nondestructive and obtains deep tissue contrast with 100-µm 3 voxel resolution or better. Manganese-enhanced MRI (MEMRI) may be used to observe axonal transport and localized neural activity in the living rodent and avian brain. Such enhancement enables researchers to investigate differences in functional circuitry or neuronal activity in images of brains of different animals. Moreover, once MR images of a number of animals are aligned into a single matrix, statistical analysis can be done comparing MR intensities between different multi-animal cohorts comprising individuals from different mouse strains or different transgenic animals, or at different time points after an experimental manipulation. Although preprocessing steps for such comparisons (including skull stripping and alignment) are automated for human imaging, no such automated processing has previously been readily available for mouse or other widely used experimental animals, and most investigators use in-house custom processing. This protocol describes a stepwise method to perform such preprocessing for mouse. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  17. EPE analysis of sub-N10 BEoL flow with and without fully self-aligned via using Coventor SEMulator3D

    Franke, Joern-Holger; Gallagher, Matt; Murdoch, Gayle; Halder, Sandip; Juncker, Aurelie; Clark, William

    2017-03-01

    During the last few decades, the semiconductor industry has been able to scale device performance up while driving costs down. What started off as simple geometrical scaling, driven mostly by advances in lithography, has recently been accompanied by advances in processing techniques and in device architectures. The trend to combine efforts using process technology and lithography is expected to intensify, as further scaling becomes ever more difficult. One promising component of future nodes are "scaling boosters", i.e. processing techniques that enable further scaling. An indispensable component in developing these ever more complex processing techniques is semiconductor process modeling software. Visualization of complex 3D structures in SEMulator3D, along with budget analysis on film thicknesses, CD and etch budgets, allow process integrators to compare flows before any physical wafers are run. Hundreds of "virtual" wafers allow comparison of different processing approaches, along with EUV or DUV patterning options for defined layers and different overlay schemes. This "virtual fabrication" technology produces massively parallel process variation studies that would be highly time-consuming or expensive in experiment. Here, we focus on one particular scaling booster, the fully self-aligned via (FSAV). We compare metal-via-metal (mevia-me) chains with self-aligned and fully-self-aligned via's using a calibrated model for imec's N7 BEoL flow. To model overall variability, 3D Monte Carlo modeling of as many variability sources as possible is critical. We use Coventor SEMulator3D to extract minimum me-me distances and contact areas and show how fully self-aligned vias allow a better me-via distance control and tighter via-me contact area variability compared with the standard self-aligned via (SAV) approach.

  18. Automated Coarse Registration of Point Clouds in 3d Urban Scenes Using Voxel Based Plane Constraint

    Xu, Y.; Boerner, R.; Yao, W.; Hoegner, L.; Stilla, U.

    2017-09-01

    For obtaining a full coverage of 3D scans in a large-scale urban area, the registration between point clouds acquired via terrestrial laser scanning (TLS) is normally mandatory. However, due to the complex urban environment, the automatic registration of different scans is still a challenging problem. In this work, we propose an automatic marker free method for fast and coarse registration between point clouds using the geometric constrains of planar patches under a voxel structure. Our proposed method consists of four major steps: the voxelization of the point cloud, the approximation of planar patches, the matching of corresponding patches, and the estimation of transformation parameters. In the voxelization step, the point cloud of each scan is organized with a 3D voxel structure, by which the entire point cloud is partitioned into small individual patches. In the following step, we represent points of each voxel with the approximated plane function, and select those patches resembling planar surfaces. Afterwards, for matching the corresponding patches, a RANSAC-based strategy is applied. Among all the planar patches of a scan, we randomly select a planar patches set of three planar surfaces, in order to build a coordinate frame via their normal vectors and their intersection points. The transformation parameters between scans are calculated from these two coordinate frames. The planar patches set with its transformation parameters owning the largest number of coplanar patches are identified as the optimal candidate set for estimating the correct transformation parameters. The experimental results using TLS datasets of different scenes reveal that our proposed method can be both effective and efficient for the coarse registration task. Especially, for the fast orientation between scans, our proposed method can achieve a registration error of less than around 2 degrees using the testing datasets, and much more efficient than the classical baseline methods.

  19. Automated 3D quantitative assessment and measurement of alpha angles from the femoral head-neck junction using MR imaging

    Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S.; Walker, Duncan; Crozier, Stuart; Engstrom, Craig

    2015-10-01

    To develop an automated approach for 3D quantitative assessment and measurement of alpha angles from the femoral head-neck (FHN) junction using bone models derived from magnetic resonance (MR) images of the hip joint. Bilateral MR images of the hip joints were acquired from 30 male volunteers (healthy active individuals and high-performance athletes, aged 18-49 years) using a water-excited 3D dual echo steady state (DESS) sequence. In a subset of these subjects (18 water-polo players), additional True Fast Imaging with Steady-state Precession (TrueFISP) images were acquired from the right hip joint. For both MR image sets, an active shape model based algorithm was used to generate automated 3D bone reconstructions of the proximal femur. Subsequently, a local coordinate system of the femur was constructed to compute a 2D shape map to project femoral head sphericity for calculation of alpha angles around the FHN junction. To evaluate automated alpha angle measures, manual analyses were performed on anterosuperior and anterior radial MR slices from the FHN junction that were automatically reformatted using the constructed coordinate system. High intra- and inter-rater reliability (intra-class correlation coefficients  >  0.95) was found for manual alpha angle measurements from the auto-extracted anterosuperior and anterior radial slices. Strong correlations were observed between manual and automatic measures of alpha angles for anterosuperior (r  =  0.84) and anterior (r  =  0.92) FHN positions. For matched DESS and TrueFISP images, there were no significant differences between automated alpha angle measures obtained from the upper anterior quadrant of the FHN junction (two-way repeated measures ANOVA, F  hip joints to generate alpha angle measures around the FHN junction circumference with very good reliability and reproducibility. This work has the potential to improve analyses of cam-type lesions of the FHN junction for large

  20. The Bubble Box: Towards an Automated Visual Sensor for 3D Analysis and Characterization of Marine Gas Release Sites

    Anne Jordt

    2015-12-01

    Full Text Available Several acoustic and optical techniques have been used for characterizing natural and anthropogenic gas leaks (carbon dioxide, methane from the ocean floor. Here, single-camera based methods for bubble stream observation have become an important tool, as they help estimating flux and bubble sizes under certain assumptions. However, they record only a projection of a bubble into the camera and therefore cannot capture the full 3D shape, which is particularly important for larger, non-spherical bubbles. The unknown distance of the bubble to the camera (making it appear larger or smaller than expected as well as refraction at the camera interface introduce extra uncertainties. In this article, we introduce our wide baseline stereo-camera deep-sea sensor bubble box that overcomes these limitations, as it observes bubbles from two orthogonal directions using calibrated cameras. Besides the setup and the hardware of the system, we discuss appropriate calibration and the different automated processing steps deblurring, detection, tracking, and 3D fitting that are crucial to arrive at a 3D ellipsoidal shape and rise speed of each bubble. The obtained values for single bubbles can be aggregated into statistical bubble size distributions or fluxes for extrapolation based on diffusion and dissolution models and large scale acoustic surveys. We demonstrate and evaluate the wide baseline stereo measurement model using a controlled test setup with ground truth information.

  1. FROM SFM TO 3D PRINT: AUTOMATED WORKFLOW ADDRESSED TO PRACTITIONER AIMED AT THE CONSERVATION AND RESTAURATION

    L. Inzerillo

    2017-08-01

    Full Text Available In In the last years there has been an increasing use of digital techniques for conservation and restoration purposes. Among these, a very dominant rule is played by the use of digital photogrammetry packages (Agisoft Photoscan, 3D Zephir which allow to obtain in few steps 3D textured models of real objects. Combined with digital documentation technologies digital fabrication technologies can be employed in a variety of ways to assist in heritage documentation, conservation and dissemination. This paper will give to practitioners an overview on the state of the art available technologies and a feasible workflow for optimizing point cloud and polygon mesh datasets for the purpose of fabrication using 3D printing. The goal is to give an important contribute to confer an automation aspect at the whole processing. We tried to individuate a workflow that should be applicable to several types of cases apart from small precautions. In our experimentation we used a DELTA WASP 2040 printer with PLA easyfil.

  2. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  3. Evaluation of an automated breast 3D-ultrasound system by comparing it with hand-held ultrasound (HHUS) and mammography.

    Golatta, Michael; Baggs, Christina; Schweitzer-Martin, Mirjam; Domschke, Christoph; Schott, Sarah; Harcos, Aba; Scharf, Alexander; Junkermann, Hans; Rauch, Geraldine; Rom, Joachim; Sohn, Christof; Heil, Joerg

    2015-04-01

    Automated three-dimensional (3D) breast ultrasound (US) systems are meant to overcome the shortcomings of hand-held ultrasound (HHUS). The aim of this study is to analyze and compare clinical performance of an automated 3D-US system by comparing it with HHUS, mammography and the clinical gold standard (defined as the combination of HHUS, mammography and-if indicated-histology). Nine hundred and eighty three patients (=1,966 breasts) were enrolled in this monocentric, explorative and prospective cohort study. All examinations were analyzed blinded to the patients´ history and to the results of the routine imaging. The agreement of automated 3D-US with HHUS, mammography and the gold standard was assessed with kappa statistics. Sensitivity, specificity and positive and negative predictive value were calculated to assess the test performance. Blinded to the results of the gold standard the agreement between automated 3D-US and HHUS or mammography was fair, given by a Kappa coefficient of 0.31 (95% CI [0.26;0.36], p automated 3D-US the sensitivity improved to 84% (NPV = 99%, specificity = 85%). The results of this study let us suggest, that automated 3D-US might be a helpful new tool in breast imaging, especially in screening.

  4. General imaging of advanced 3D mask objects based on the fully-vectorial extended Nijboer-Zernike (ENZ) theory

    van Haver, Sven; Janssen, Olaf T. A.; Braat, Joseph J. M.; Janssen, Augustus J. E. M.; Urbach, H. Paul; Pereira, Silvania F.

    2008-03-01

    In this paper we introduce a new mask imaging algorithm that is based on the source point integration method (or Abbe method). The method presented here distinguishes itself from existing methods by exploiting the through-focus imaging feature of the Extended Nijboer-Zernike (ENZ) theory of diffraction. An introduction to ENZ-theory and its application in general imaging is provided after which we describe the mask imaging scheme that can be derived from it. The remainder of the paper is devoted to illustrating the advantages of the new method over existing methods (Hopkins-based). To this extent several simulation results are included that illustrate advantages arising from: the accurate incorporation of isolated structures, the rigorous treatment of the object (mask topography) and the fully vectorial through-focus image formation of the ENZ-based algorithm.

  5. Automated voxelization of 3D atom probe data through kernel density estimation

    Srinivasan, Srikant; Kaluskar, Kaustubh; Dumpala, Santoshrupa; Broderick, Scott; Rajan, Krishna

    2015-01-01

    Identifying nanoscale chemical features from atom probe tomography (APT) data routinely involves adjustment of voxel size as an input parameter, through visual supervision, making the final outcome user dependent, reliant on heuristic knowledge and potentially prone to error. This work utilizes Kernel density estimators to select an optimal voxel size in an unsupervised manner to perform feature selection, in particular targeting resolution of interfacial features and chemistries. The capability of this approach is demonstrated through analysis of the γ / γ’ interface in a Ni–Al–Cr superalloy. - Highlights: • Develop approach for standardizing aspects of atom probe reconstruction. • Use Kernel density estimators to select optimal voxel sizes in an unsupervised manner. • Perform interfacial analysis of Ni–Al–Cr superalloy, using new automated approach. • Optimize voxel size to preserve the feature of interest and minimizing loss / noise.

  6. Automated fault extraction and classification using 3-D seismic data for the Ekofisk field development

    Signer, C.; Nickel, M.; Randen, T.; Saeter, T.; Soenneland, H.H.

    1998-12-31

    Mapping of fractures is important for the prediction of fluid flow in many reservoir types. The fluid flow depends mainly on the efficiency of the reservoir seals. Improved spatial mapping of the open and closed fracture systems will allow a better prediction of the fluid flow pattern. The primary objectives of this paper is to present fracture characterization at the reservoir scale combined with seismic facies mapping. The complexity of the giant Ekofisk field on the Norwegian continental shelf provides an ideal framework for testing the validity and the applicability of an automated seismic fault and fracture detection and mapping tool. The mapping of the faults can be based on seismic attribute grids, which means that attribute-responses related to faults are extracted along key horizons which were interpreted in the reservoir interval. 3 refs., 3 figs.

  7. Fully automated processing of fMRI data in SPM: from MRI scanner to PACS.

    Maldjian, Joseph A; Baer, Aaron H; Kraft, Robert A; Laurienti, Paul J; Burdette, Jonathan H

    2009-01-01

    Here we describe the Wake Forest University Pipeline, a fully automated method for the processing of fMRI data using SPM. The method includes fully automated data transfer and archiving from the point of acquisition, real-time batch script generation, distributed grid processing, interface to SPM in MATLAB, error recovery and data provenance, DICOM conversion and PACS insertion. It has been used for automated processing of fMRI experiments, as well as for the clinical implementation of fMRI and spin-tag perfusion imaging. The pipeline requires no manual intervention, and can be extended to any studies requiring offline processing.

  8. A Framework for Fully Automated Performance Testing for Smart Buildings

    Markoska, Elena; Johansen, Aslak; Lazarova-Molnar, Sanja

    2018-01-01

    , setup of performance tests has been manual and labor-intensive and has required intimate knowledge of buildings’ complexity and systems. The emergence of the concept of smart buildings has provided an opportunity to overcome this restriction. In this paper, we propose a framework for automated......A significant proportion of energy consumption by buildings worldwide, estimated to ca. 40%, has yielded a high importance to studying buildings’ performance. Performance testing is a mean by which buildings can be continuously commissioned to ensure that they operate as designed. Historically...... performance testing of smart buildings that utilizes metadata models. The approach features automatic detection of applicable performance tests using metadata queries and their corresponding instantiation, as well as continuous commissioning based on metadata. The presented approach has been implemented...

  9. AN AUTOMATED METHOD FOR 3D ROOF OUTLINE GENERATION AND REGULARIZATION IN AIRBONE LASER SCANNER DATA

    S. N. Perera

    2012-07-01

    Full Text Available In this paper, an automatic approach for the generation and regularization of 3D roof boundaries in Airborne Laser scanner data is presented. The workflow is commenced by segmentation of the point clouds. A classification step and a rule based roof extraction step are followed the planar segmentation. Refinement on roof extraction is performed in order to minimize the effect due to urban vegetation. Boundary points of the connected roof planes are extracted and fitted series of straight line segments. Each line is then regularized with respect to the dominant building orientation. We introduce the usage of cycle graphs for the best use of topological information. Ridge-lines and step-edges are basically extracted to recognise correct topological relationships among the roof faces. Inner roof corners are geometrically fitted based on the closed cycle graphs. Outer boundary is reconstructed using the same concept but with the outer most cycle graph. In here, union of the sub cycles is taken. Intermediate line segments (outer bounds are intersected to reconstruct the roof eave lines. Two test areas with two different point densities are tested with the developed approach. Performance analysis of the test results is provided to demonstrate the applicability of the method.

  10. Acquisition and automated 3-D segmentation of respiratory/cardiac-gated PET transmission images

    Reutter, B.W.; Klein, G.J.; Brennan, K.M.; Huesman, R.H.

    1996-01-01

    To evaluate the impact of respiratory motion on attenuation correction of cardiac PET data, we acquired and automatically segmented gated transmission data for a dog breathing on its own under gas anesthesia. Data were acquired for 20 min on a CTI/Siemens ECAT EXACT HR (47-slice) scanner configured for 12 gates in a static study, Two respiratory gates were obtained using data from a pneumatic bellows placed around the dog's chest, in conjunction with 6 cardiac gates from standard EKG gating. Both signals were directed to a LabVIEW-controlled Macintosh, which translated them into one of 12 gate addresses. The respiratory gating threshold was placed near end-expiration to acquire 6 cardiac-gated datasets at end-expiration and 6 cardiac-gated datasets during breaths. Breaths occurred about once every 10 sec and lasted about 1-1.5 sec. For each respiratory gate, data were summed over cardiac gates and torso and lung surfaces were segmented automatically using a differential 3-D edge detection algorithm. Three-dimensional visualizations showed that lung surfaces adjacent to the heart translated 9 mm inferiorly during breaths. Our results suggest that respiration-compensated attenuation correction is feasible with a modest amount of gated transmission data and is necessary for accurate quantitation of high-resolution gated cardiac PET data

  11. A machine learning pipeline for automated registration and classification of 3D lidar data

    Rajagopal, Abhejit; Chellappan, Karthik; Chandrasekaran, Shivkumar; Brown, Andrew P.

    2017-05-01

    Despite the large availability of geospatial data, registration and exploitation of these datasets remains a persis- tent challenge in geoinformatics. Popular signal processing and machine learning algorithms, such as non-linear SVMs and neural networks, rely on well-formatted input models as well as reliable output labels, which are not always immediately available. In this paper we outline a pipeline for gathering, registering, and classifying initially unlabeled wide-area geospatial data. As an illustrative example, we demonstrate the training and test- ing of a convolutional neural network to recognize 3D models in the OGRIP 2007 LiDAR dataset using fuzzy labels derived from OpenStreetMap as well as other datasets available on OpenTopography.org. When auxiliary label information is required, various text and natural language processing filters are used to extract and cluster keywords useful for identifying potential target classes. A subset of these keywords are subsequently used to form multi-class labels, with no assumption of independence. Finally, we employ class-dependent geometry extraction routines to identify candidates from both training and testing datasets. Our regression networks are able to identify the presence of 6 structural classes, including roads, walls, and buildings, in volumes as big as 8000 m3 in as little as 1.2 seconds on a commodity 4-core Intel CPU. The presented framework is neither dataset nor sensor-modality limited due to the registration process, and is capable of multi-sensor data-fusion.

  12. A quality assurance framework for the fully automated and objective evaluation of image quality in cone-beam computed tomography

    Steiding, Christian; Kolditz, Daniel; Kalender, Willi A.

    2014-01-01

    Purpose: Thousands of cone-beam computed tomography (CBCT) scanners for vascular, maxillofacial, neurological, and body imaging are in clinical use today, but there is no consensus on uniform acceptance and constancy testing for image quality (IQ) and dose yet. The authors developed a quality assurance (QA) framework for fully automated and time-efficient performance evaluation of these systems. In addition, the dependence of objective Fourier-based IQ metrics on direction and position in 3D volumes was investigated for CBCT. Methods: The authors designed a dedicated QA phantom 10 cm in length consisting of five compartments, each with a diameter of 10 cm, and an optional extension ring 16 cm in diameter. A homogeneous section of water-equivalent material allows measuring CT value accuracy, image noise and uniformity, and multidimensional global and local noise power spectra (NPS). For the quantitative determination of 3D high-contrast spatial resolution, the modulation transfer function (MTF) of centrally and peripherally positioned aluminum spheres was computed from edge profiles. Additional in-plane and axial resolution patterns were used to assess resolution qualitatively. The characterization of low-contrast detectability as well as CT value linearity and artifact behavior was tested by utilizing sections with soft-tissue-equivalent and metallic inserts. For an automated QA procedure, a phantom detection algorithm was implemented. All tests used in the dedicated QA program were initially verified in simulation studies and experimentally confirmed on a clinical dental CBCT system. Results: The automated IQ evaluation of volume data sets of the dental CBCT system was achieved with the proposed phantom requiring only one scan for the determination of all desired parameters. Typically, less than 5 min were needed for phantom set-up, scanning, and data analysis. Quantitative evaluation of system performance over time by comparison to previous examinations was also

  13. A quality assurance framework for the fully automated and objective evaluation of image quality in cone-beam computed tomography.

    Steiding, Christian; Kolditz, Daniel; Kalender, Willi A

    2014-03-01

    Thousands of cone-beam computed tomography (CBCT) scanners for vascular, maxillofacial, neurological, and body imaging are in clinical use today, but there is no consensus on uniform acceptance and constancy testing for image quality (IQ) and dose yet. The authors developed a quality assurance (QA) framework for fully automated and time-efficient performance evaluation of these systems. In addition, the dependence of objective Fourier-based IQ metrics on direction and position in 3D volumes was investigated for CBCT. The authors designed a dedicated QA phantom 10 cm in length consisting of five compartments, each with a diameter of 10 cm, and an optional extension ring 16 cm in diameter. A homogeneous section of water-equivalent material allows measuring CT value accuracy, image noise and uniformity, and multidimensional global and local noise power spectra (NPS). For the quantitative determination of 3D high-contrast spatial resolution, the modulation transfer function (MTF) of centrally and peripherally positioned aluminum spheres was computed from edge profiles. Additional in-plane and axial resolution patterns were used to assess resolution qualitatively. The characterization of low-contrast detectability as well as CT value linearity and artifact behavior was tested by utilizing sections with soft-tissue-equivalent and metallic inserts. For an automated QA procedure, a phantom detection algorithm was implemented. All tests used in the dedicated QA program were initially verified in simulation studies and experimentally confirmed on a clinical dental CBCT system. The automated IQ evaluation of volume data sets of the dental CBCT system was achieved with the proposed phantom requiring only one scan for the determination of all desired parameters. Typically, less than 5 min were needed for phantom set-up, scanning, and data analysis. Quantitative evaluation of system performance over time by comparison to previous examinations was also verified. The maximum

  14. A fully automated algorithm of baseline correction based on wavelet feature points and segment interpolation

    Qian, Fang; Wu, Yihui; Hao, Peng

    2017-11-01

    Baseline correction is a very important part of pre-processing. Baseline in the spectrum signal can induce uneven amplitude shifts across different wavenumbers and lead to bad results. Therefore, these amplitude shifts should be compensated before further analysis. Many algorithms are used to remove baseline, however fully automated baseline correction is convenient in practical application. A fully automated algorithm based on wavelet feature points and segment interpolation (AWFPSI) is proposed. This algorithm finds feature points through continuous wavelet transformation and estimates baseline through segment interpolation. AWFPSI is compared with three commonly introduced fully automated and semi-automated algorithms, using simulated spectrum signal, visible spectrum signal and Raman spectrum signal. The results show that AWFPSI gives better accuracy and has the advantage of easy use.

  15. Automated materials discrimination using 3D dual energy X ray images

    Wang, Ta Wee

    2002-01-01

    The ability of a human observer to identify an explosive device concealed in complex arrangements of objects routinely encountered in the 2D x-ray screening of passenger baggage at airports is often problematic. Standard dual-energy x-ray techniques enable colour encoding of the resultant images in terms of organic, inorganic and metal substances. This transmission imaging technique produces colour information computed from a high-energy x-ray signal and a low energy x-ray signal (80keV eff ≤ 13) to be automatically discriminated from many layers of overlapping substances. This is achieved by applying a basis materials subtraction technique to the data provided by a wavelet image segmentation algorithm. This imaging technique is reliant upon the image data for the masking substances to be discriminated independently of the target material. Further work investigated the extraction of depth data from stereoscopic images to estimate the mass density of the target material. A binocular stereoscopic dual-energy x-ray machine previously developed by the Vision Systems Group at The Nottingham Trent University in collaboration with The Home Office Science and Technology Group provided the image data for the empirical investigation. This machine utilises a novel linear castellated dual-energy x-ray detector recently developed by the Vision Systems Group. This detector array employs half the number of scintillator-photodiode sensors in comparison to a conventional linear dual-energy sensor. The castellated sensor required the development of an image enhancement algorithm to remove the spatial interlace effect in the resultant images prior to the calibration of the system for materials discrimination. To automate the basis materials subtraction technique a wavelet image segmentation and classification algorithm was developed. This enabled overlapping image structures in the x-rayed baggage to be partitioned. A series of experiments was conducted to investigate the

  16. Automated torso organ segmentation from 3D CT images using structured perceptron and dual decomposition

    Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Mori, Kensaku

    2015-03-01

    This paper presents a method for torso organ segmentation from abdominal CT images using structured perceptron and dual decomposition. A lot of methods have been proposed to enable automated extraction of organ regions from volumetric medical images. However, it is necessary to adjust empirical parameters of them to obtain precise organ regions. This paper proposes an organ segmentation method using structured output learning. Our method utilizes a graphical model and binary features which represent the relationship between voxel intensities and organ labels. Also we optimize the weights of the graphical model by structured perceptron and estimate the best organ label for a given image by dynamic programming and dual decomposition. The experimental result revealed that the proposed method can extract organ regions automatically using structured output learning. The error of organ label estimation was 4.4%. The DICE coefficients of left lung, right lung, heart, liver, spleen, pancreas, left kidney, right kidney, and gallbladder were 0.91, 0.95, 0.77, 0.81, 0.74, 0.08, 0.83, 0.84, and 0.03, respectively.

  17. Automated segmentation of blood-flow regions in large thoracic arteries using 3D-cine PC-MRI measurements.

    van Pelt, Roy; Nguyen, Huy; ter Haar Romeny, Bart; Vilanova, Anna

    2012-03-01

    Quantitative analysis of vascular blood flow, acquired by phase-contrast MRI, requires accurate segmentation of the vessel lumen. In clinical practice, 2D-cine velocity-encoded slices are inspected, and the lumen is segmented manually. However, segmentation of time-resolved volumetric blood-flow measurements is a tedious and time-consuming task requiring automation. Automated segmentation of large thoracic arteries, based solely on the 3D-cine phase-contrast MRI (PC-MRI) blood-flow data, was done. An active surface model, which is fast and topologically stable, was used. The active surface model requires an initial surface, approximating the desired segmentation. A method to generate this surface was developed based on a voxel-wise temporal maximum of blood-flow velocities. The active surface model balances forces, based on the surface structure and image features derived from the blood-flow data. The segmentation results were validated using volunteer studies, including time-resolved 3D and 2D blood-flow data. The segmented surface was intersected with a velocity-encoded PC-MRI slice, resulting in a cross-sectional contour of the lumen. These cross-sections were compared to reference contours that were manually delineated on high-resolution 2D-cine slices. The automated approach closely approximates the manual blood-flow segmentations, with error distances on the order of the voxel size. The initial surface provides a close approximation of the desired luminal geometry. This improves the convergence time of the active surface and facilitates parametrization. An active surface approach for vessel lumen segmentation was developed, suitable for quantitative analysis of 3D-cine PC-MRI blood-flow data. As opposed to prior thresholding and level-set approaches, the active surface model is topologically stable. A method to generate an initial approximate surface was developed, and various features that influence the segmentation model were evaluated. The active surface

  18. Improving reticle defect disposition via fully automated lithography simulation

    Mann, Raunak; Goodman, Eliot; Lao, Keith; Ha, Steven; Vacca, Anthony; Fiekowsky, Peter; Fiekowsky, Dan

    2016-03-01

    Most advanced wafer fabs have embraced complex pattern decoration, which creates numerous challenges during in-fab reticle qualification. These optical proximity correction (OPC) techniques create assist features that tend to be very close in size and shape to the main patterns as seen in Figure 1. A small defect on an assist feature will most likely have little or no impact on the fidelity of the wafer image, whereas the same defect on a main feature could significantly decrease device functionality. In order to properly disposition these defects, reticle inspection technicians need an efficient method that automatically separates main from assist features and predicts the resulting defect impact on the wafer image. Analysis System (ADAS) defect simulation system[1]. Up until now, using ADAS simulation was limited to engineers due to the complexity of the settings that need to be manually entered in order to create an accurate result. A single error in entering one of these values can cause erroneous results, therefore full automation is necessary. In this study, we propose a new method where all needed simulation parameters are automatically loaded into ADAS. This is accomplished in two parts. First we have created a scanner parameter database that is automatically identified from mask product and level names. Second, we automatically determine the appropriate simulation printability threshold by using a new reference image (provided by the inspection tool) that contains a known measured value of the reticle critical dimension (CD). This new method automatically loads the correct scanner conditions, sets the appropriate simulation threshold, and automatically measures the percentage of CD change caused by the defect. This streamlines qualification and reduces the number of reticles being put on hold, waiting for engineer review. We also present data showing the consistency and reliability of the new method, along with the impact on the efficiency of in

  19. Current advances and strategies towards fully automated sample preparation for regulated LC-MS/MS bioanalysis.

    Zheng, Naiyu; Jiang, Hao; Zeng, Jianing

    2014-09-01

    Robotic liquid handlers (RLHs) have been widely used in automated sample preparation for liquid chromatography-tandem mass spectrometry (LC-MS/MS) bioanalysis. Automated sample preparation for regulated bioanalysis offers significantly higher assay efficiency, better data quality and potential bioanalytical cost-savings. For RLHs that are used for regulated bioanalysis, there are additional requirements, including 21 CFR Part 11 compliance, software validation, system qualification, calibration verification and proper maintenance. This article reviews recent advances in automated sample preparation for regulated bioanalysis in the last 5 years. Specifically, it covers the following aspects: regulated bioanalysis requirements, recent advances in automation hardware and software development, sample extraction workflow simplification, strategies towards fully automated sample extraction, and best practices in automated sample preparation for regulated bioanalysis.

  20. Initial results of the FUSION-X-US prototype combining 3D automated breast ultrasound and digital breast tomosynthesis.

    Schaefgen, Benedikt; Heil, Joerg; Barr, Richard G; Radicke, Marcus; Harcos, Aba; Gomez, Christina; Stieber, Anne; Hennigs, André; von Au, Alexandra; Spratte, Julia; Rauch, Geraldine; Rom, Joachim; Schütz, Florian; Sohn, Christof; Golatta, Michael

    2018-06-01

    To determine the feasibility of a prototype device combining 3D-automated breast ultrasound (ABVS) and digital breast tomosynthesis in a single device to detect and characterize breast lesions. In this prospective feasibility study, the FUSION-X-US prototype was used to perform digital breast tomosynthesis and ABVS in 23 patients with an indication for tomosynthesis based on current guidelines after clinical examination and standard imaging. The ABVS and tomosynthesis images of the prototype were interpreted separately by two blinded experts. The study compares the detection and BI-RADS® scores of breast lesions using only the tomosynthesis and ABVS data from the FUSION-X-US prototype to the results of the complete diagnostic workup. Image acquisition and processing by the prototype was fast and accurate, with some limitations in ultrasound coverage and image quality. In the diagnostic workup, 29 solid lesions (23 benign, including three cases with microcalcifications, and six malignant lesions) were identified. Using the prototype, all malignant lesions were detected and classified as malignant or suspicious by both investigators. Solid breast lesions can be localized accurately and fast by the Fusion-X-US system. Technical improvements of the ultrasound image quality and ultrasound coverage are needed to further study this new device. The prototype combines tomosynthesis and automated 3D-ultrasound (ABVS) in one device. It allows accurate detection of malignant lesions, directly correlating tomosynthesis and ABVS data. The diagnostic evaluation of the prototype-acquired data was interpreter-independent. The prototype provides a time-efficient and technically reliable diagnostic procedure. The combination of tomosynthesis and ABVS is a promising diagnostic approach.

  1. A Fully Automated Classification for Mapping the Annual Cropland Extent

    Waldner, F.; Defourny, P.

    2015-12-01

    Mapping the global cropland extent is of paramount importance for food security. Indeed, accurate and reliable information on cropland and the location of major crop types is required to make future policy, investment, and logistical decisions, as well as production monitoring. Timely cropland information directly feed early warning systems such as GIEWS and, FEWS NET. In Africa, and particularly in the arid and semi-arid region, food security is center of debate (at least 10% of the population remains undernourished) and accurate cropland estimation is a challenge. Space borne Earth Observation provides opportunities for global cropland monitoring in a spatially explicit, economic, efficient, and objective fashion. In the both agriculture monitoring and climate modelling, cropland maps serve as mask to isolate agricultural land for (i) time-series analysis for crop condition monitoring and (ii) to investigate how the cropland is respond to climatic evolution. A large diversity of mapping strategies ranging from the local to the global scale and associated with various degrees of accuracy can be found in the literature. At the global scale, despite efforts, cropland is generally one of classes with the poorest accuracy which make difficult the use for agricultural. This research aims at improving the cropland delineation from the local scale to the regional and global scales as well as allowing near real time updates. To that aim, five temporal features were designed to target the key- characteristics of crop spectral-temporal behavior. To ensure a high degree of automation, training data is extracted from available baseline land cover maps. The method delivers cropland maps with a high accuracy over contrasted agro-systems in Ukraine, Argentina, China and Belgium. The accuracy reached are comparable to those obtained with classifiers trained with in-situ data. Besides, it was found that the cropland class is associated with a low uncertainty. The temporal features

  2. Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs.

    Mishchenko, Yuriy

    2009-01-30

    We describe an approach for automation of the process of reconstruction of neural tissue from serial section transmission electron micrographs. Such reconstructions require 3D segmentation of individual neuronal processes (axons and dendrites) performed in densely packed neuropil. We first detect neuronal cell profiles in each image in a stack of serial micrographs with multi-scale ridge detector. Short breaks in detected boundaries are interpolated using anisotropic contour completion formulated in fuzzy-logic framework. Detected profiles from adjacent sections are linked together based on cues such as shape similarity and image texture. Thus obtained 3D segmentation is validated by human operators in computer-guided proofreading process. Our approach makes possible reconstructions of neural tissue at final rate of about 5 microm3/manh, as determined primarily by the speed of proofreading. To date we have applied this approach to reconstruct few blocks of neural tissue from different regions of rat brain totaling over 1000microm3, and used these to evaluate reconstruction speed, quality, error rates, and presence of ambiguous locations in neuropil ssTEM imaging data.

  3. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Siamak Ravanbakhsh

    Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

  4. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-01-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF 6 .

  5. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

    2011-09-01

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

  6. Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

    Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N. [Voss Scientific, LLC, Albuquerque, New Mexico 87108 (United States); Rambo, P. K.; Atherton, B. W. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States)

    2011-09-15

    Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF{sub 6}.

  7. Global left ventricular function in cardiac CT. Evaluation of an automated 3D region-growing segmentation algorithm

    Muehlenbruch, Georg; Das, Marco; Hohl, Christian; Wildberger, Joachim E.; Guenther, Rolf W.; Mahnken, Andreas H.; Rinck, Daniel; Flohr, Thomas G.; Koos, Ralf; Knackstedt, Christian

    2006-01-01

    The purpose was to evaluate a new semi-automated 3D region-growing segmentation algorithm for functional analysis of the left ventricle in multislice CT (MSCT) of the heart. Twenty patients underwent contrast-enhanced MSCT of the heart (collimation 16 x 0.75 mm; 120 kV; 550 mAseff). Multiphase image reconstructions with 1-mm axial slices and 8-mm short-axis slices were performed. Left ventricular volume measurements (end-diastolic volume, end-systolic volume, ejection fraction and stroke volume) from manually drawn endocardial contours in the short axis slices were compared to semi-automated region-growing segmentation of the left ventricle from the 1-mm axial slices. The post-processing-time for both methods was recorded. Applying the new region-growing algorithm in 13/20 patients (65%), proper segmentation of the left ventricle was feasible. In these patients, the signal-to-noise ratio was higher than in the remaining patients (3.2±1.0 vs. 2.6±0.6). Volume measurements of both segmentation algorithms showed an excellent correlation (all P≤0.0001); the limits of agreement for the ejection fraction were 2.3±8.3 ml. In the patients with proper segmentation the mean post-processing time using the region-growing algorithm was diminished by 44.2%. On the basis of a good contrast-enhanced data set, a left ventricular volume analysis using the new semi-automated region-growing segmentation algorithm is technically feasible, accurate and more time-effective. (orig.)

  8. Fully automated data collection and processing system on macromolecular crystallography beamlines at the PF

    Yamada, Yusuke; Hiraki, Masahiko; Matsugaki, Naohiro; Chavas, Leonard M.G.; Igarashi, Noriyuki; Wakatsuki, Soichi

    2012-01-01

    Fully automated data collection and processing system has been developed on macromolecular crystallography beamlines at the Photon Factory. In this system, the sample exchange, centering and data collection are sequentially performed for all samples stored in the sample exchange system at a beamline without any manual operations. Data processing of collected data sets is also performed automatically. These results are stored into the database system, and users can monitor the progress and results of automated experiment via a Web browser. (author)

  9. Development of a fully automated online mixing system for SAXS protein structure analysis

    Nielsen, Søren Skou; Arleth, Lise

    2010-01-01

    This thesis presents the development of an automated high-throughput mixing and exposure system for Small-Angle Scattering analysis on a synchrotron using polymer microfluidics. Software and hardware for both automated mixing, exposure control on a beamline and automated data reduction...... and preliminary analysis is presented. Three mixing systems that have been the corner stones of the development process are presented including a fully functioning high-throughput microfluidic system that is able to produce and expose 36 mixed samples per hour using 30 μL of sample volume. The system is tested...

  10. A fully automated microfluidic femtosecond laser axotomy platform for nerve regeneration studies in C. elegans.

    Gokce, Sertan Kutal; Guo, Samuel X; Ghorashian, Navid; Everett, W Neil; Jarrell, Travis; Kottek, Aubri; Bovik, Alan C; Ben-Yakar, Adela

    2014-01-01

    Femtosecond laser nanosurgery has been widely accepted as an axonal injury model, enabling nerve regeneration studies in the small model organism, Caenorhabditis elegans. To overcome the time limitations of manual worm handling techniques, automation and new immobilization technologies must be adopted to improve throughput in these studies. While new microfluidic immobilization techniques have been developed that promise to reduce the time required for axotomies, there is a need for automated procedures to minimize the required amount of human intervention and accelerate the axotomy processes crucial for high-throughput. Here, we report a fully automated microfluidic platform for performing laser axotomies of fluorescently tagged neurons in living Caenorhabditis elegans. The presented automation process reduces the time required to perform axotomies within individual worms to ∼17 s/worm, at least one order of magnitude faster than manual approaches. The full automation is achieved with a unique chip design and an operation sequence that is fully computer controlled and synchronized with efficient and accurate image processing algorithms. The microfluidic device includes a T-shaped architecture and three-dimensional microfluidic interconnects to serially transport, position, and immobilize worms. The image processing algorithms can identify and precisely position axons targeted for ablation. There were no statistically significant differences observed in reconnection probabilities between axotomies carried out with the automated system and those performed manually with anesthetics. The overall success rate of automated axotomies was 67.4±3.2% of the cases (236/350) at an average processing rate of 17.0±2.4 s. This fully automated platform establishes a promising methodology for prospective genome-wide screening of nerve regeneration in C. elegans in a truly high-throughput manner.

  11. PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

    Lee, Woonghee; Stark, Jaime L; Markley, John L

    2014-11-01

    Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727-1728. doi: 10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets ((13)C- and/or (15)N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625-626. doi: 10.1038/nmeth0909-625 , 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1-2 days.

  12. Modeling of Hydraulic Fracture Propagation at the kISMET Site Using a Fully Coupled 3D Network-Flow and Quasi- Static Discrete Element Model

    Zhou, Jing [Idaho National Lab. (INL), Idaho Falls, ID (United States); Huang, Hai [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mattson, Earl [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wang, Herb F. [Univ. of Wisconsin, Madison, WI (United States); Haimson, Bezalel C. [Univ. of Wisconsin, Madison, WI (United States); Doe, Thomas W. [Golder Associates Inc., Redmond, VA (United States); Oldenburg, Curtis M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Dobson, Patrick F. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2017-02-01

    Aimed at supporting the design of hydraulic fracturing experiments at the kISMET site, ~1500 m below ground in a deep mine, we performed pre-experimental hydraulic fracturing simulations in order to estimate the breakdown pressure, propagation pressure, fracture geometry, and the magnitude of induced seismicity using a newly developed fully coupled three-dimensional (3D) network flow and quasi-static discrete element model (DEM). The quasi-static DEM model, which is constructed by Delaunay tessellation of the rock volume, considers rock fabric heterogeneities by using the “disordered” DEM mesh and adding random perturbations to the stiffness and tensile/shear strengths of individual DEM elements and the elastic beams between them. A conjugate 3D flow network based on the DEM lattice is constructed to calculate the fluid flow in both the fracture and porous matrix. One distinctive advantage of the model is that fracturing is naturally described by the breakage of elastic beams between DEM elements. It is also extremely convenient to introduce mechanical anisotropy into the model by simply assigning orientation-dependent tensile/shear strengths to the elastic beams. In this paper, the 3D hydraulic fracturing model was verified against the analytic solution for a penny-shaped crack model. We applied the model to simulate fracture propagation from a vertical open borehole based on initial estimates of rock mechanical properties and in-situ stress conditions. The breakdown pressure and propagation pressure are directly obtained from the simulation. In addition, the released elastic strain energies of individual fracturing events were calculated and used as a conservative estimate for the magnitudes of the potential induced seismic activities associated with fracturing. The comparisons between model predictions and experimental results are still ongoing.

  13. Fully automated joint space width measurement and digital X-ray radiogrammetry in early RA

    Platten, Michael; Kisten, Yogan; Kälvesten, Johan; Arnaud, Laurent; Forslind, Kristina; van Vollenhoven, Ronald

    2017-01-01

    To study fully automated digital joint space width (JSW) and bone mineral density (BMD) in relation to a conventional radiographic scoring method in early rheumatoid arthritis (eRA). Radiographs scored by the modified Sharp van der Heijde score (SHS) in patients with eRA were acquired from the

  14. Deep multi-scale location-aware 3D convolutional neural networks for automated detection of lacunes of presumed vascular origin

    Mohsen Ghafoorian

    2017-01-01

    In this paper, we propose an automated two-stage method using deep convolutional neural networks (CNN. We show that this method has good performance and can considerably benefit readers. We first use a fully convolutional neural network to detect initial candidates. In the second step, we employ a 3D CNN as a false positive reduction tool. As the location information is important to the analysis of candidate structures, we further equip the network with contextual information using multi-scale analysis and integration of explicit location features. We trained, validated and tested our networks on a large dataset of 1075 cases obtained from two different studies. Subsequently, we conducted an observer study with four trained observers and compared our method with them using a free-response operating characteristic analysis. Shown on a test set of 111 cases, the resulting CAD system exhibits performance similar to the trained human observers and achieves a sensitivity of 0.974 with 0.13 false positives per slice. A feasibility study also showed that a trained human observer would considerably benefit once aided by the CAD system.

  15. The future of fully automated vehicles : opportunities for vehicle- and ride-sharing, with cost and emissions savings.

    2014-08-01

    Fully automated or autonomous vehicles (AVs) hold great promise for the future of transportation. By 2020 : Google, auto manufacturers and other technology providers intend to introduce self-driving cars to the public with : either limited or fully a...

  16. A fully automated fast analysis system for capillary gas chromatography. Part 1. Automation of system control

    Snijders, H.M.J.; Rijks, J.P.E.M.; Bombeeck, A.J.; Rijks, J.A.; Sandra, P.; Lee, M.L.

    1992-01-01

    This paper is dealing with the design, the automation and evaluation of a high speed capillary gas chromatographic system. A combination of software and hardware was developed for a new cold trap/reinjection device that allows selective solvent eliminating and on column sample enrichment and an

  17. Comparison Between Laser Scanning and Automated 3d Modelling Techniques to Reconstruct Complex and Extensive Cultural Heritage Areas

    Fassi, F.; Fregonese, L.; Ackermann, S.; De Troia, V.

    2013-02-01

    In Cultural Heritage field, the necessity to survey objects in a fast manner, with the ability to repeat the measurements several times for deformation or degradation monitoring purposes, is increasing. In this paper, two significant cases, an architectonical one and an archaeological one, are presented. Due to different reasons and emergency situations, the finding of the optimal solution to enable quick and well-timed survey for a complete digital reconstruction of the object is required. In both cases, two survey methods have been tested and used: a laser scanning approach that allows to obtain high-resolution and complete scans within a short time and a photogrammetric one that allows the three-dimensional reconstruction of the object from images. In the last months, several methodologies, including free or low cost techniques, have arisen. These kinds of software allow the fully automatically three-dimensional reconstruction of objects from images, giving back a dense point cloud and, in some case, a surfaced mesh model. In this paper some comparisons between the two methodologies above mentioned are presented, using the example of some real cases of study. The surveys have been performed by employing both photogrammetry and laser scanner techniques. The methodological operational choices, depending on the required goal, the difficulties encountered during the survey with these methods, the execution time (that is the key parameter), and finally the obtained results, are fully described and examinated. On the final 3D model, an analytical comparison has been made, to analyse the differences, the tolerances, the possibility of accuracy improvement and the future developments.

  18. Fully automated segmentation of callus by micro-CT compared to biomechanics.

    Bissinger, Oliver; Götz, Carolin; Wolff, Klaus-Dietrich; Hapfelmeier, Alexander; Prodinger, Peter Michael; Tischer, Thomas

    2017-07-11

    A high percentage of closed femur fractures have slight comminution. Using micro-CT (μCT), multiple fragment segmentation is much more difficult than segmentation of unfractured or osteotomied bone. Manual or semi-automated segmentation has been performed to date. However, such segmentation is extremely laborious, time-consuming and error-prone. Our aim was to therefore apply a fully automated segmentation algorithm to determine μCT parameters and examine their association with biomechanics. The femura of 64 rats taken after randomised inhibitory or neutral medication, in terms of the effect on fracture healing, and controls were closed fractured after a Kirschner wire was inserted. After 21 days, μCT and biomechanical parameters were determined by a fully automated method and correlated (Pearson's correlation). The fully automated segmentation algorithm automatically detected bone and simultaneously separated cortical bone from callus without requiring ROI selection for each single bony structure. We found an association of structural callus parameters obtained by μCT to the biomechanical properties. However, results were only explicable by additionally considering the callus location. A large number of slightly comminuted fractures in combination with therapies that influence the callus qualitatively and/or quantitatively considerably affects the association between μCT and biomechanics. In the future, contrast-enhanced μCT imaging of the callus cartilage might provide more information to improve the non-destructive and non-invasive prediction of callus mechanical properties. As studies evaluating such important drugs increase, fully automated segmentation appears to be clinically important.

  19. Fully automated reconstruction of three-dimensional vascular tree structures from two orthogonal views using computational algorithms and productionrules

    Liu, Iching; Sun, Ying

    1992-10-01

    A system for reconstructing 3-D vascular structure from two orthogonally projected images is presented. The formidable problem of matching segments between two views is solved using knowledge of the epipolar constraint and the similarity of segment geometry and connectivity. The knowledge is represented in a rule-based system, which also controls the operation of several computational algorithms for tracking segments in each image, representing 2-D segments with directed graphs, and reconstructing 3-D segments from matching 2-D segment pairs. Uncertain reasoning governs the interaction between segmentation and matching; it also provides a framework for resolving the matching ambiguities in an iterative way. The system was implemented in the C language and the C Language Integrated Production System (CLIPS) expert system shell. Using video images of a tree model, the standard deviation of reconstructed centerlines was estimated to be 0.8 mm (1.7 mm) when the view direction was parallel (perpendicular) to the epipolar plane. Feasibility of clinical use was shown using x-ray angiograms of a human chest phantom. The correspondence of vessel segments between two views was accurate. Computational time for the entire reconstruction process was under 30 s on a workstation. A fully automated system for two-view reconstruction that does not require the a priori knowledge of vascular anatomy is demonstrated.

  20. A novel method to determine simultaneously methane production during in vitro gas production using fully automated equipment

    Pellikaan, W.F.; Hendriks, W.H.; Uwimanaa, G.; Bongers, L.J.G.M.; Becker, P.M.; Cone, J.W.

    2011-01-01

    An adaptation of fully automated gas production equipment was tested for its ability to simultaneously measure methane and total gas. The simultaneous measurement of gas production and gas composition was not possible using fully automated equipment, as the bottles should be kept closed during the

  1. A Fully Automated Method to Detect and Segment a Manufactured Object in an Underwater Color Image

    Barat, Christian; Phlypo, Ronald

    2010-12-01

    We propose a fully automated active contours-based method for the detection and the segmentation of a moored manufactured object in an underwater image. Detection of objects in underwater images is difficult due to the variable lighting conditions and shadows on the object. The proposed technique is based on the information contained in the color maps and uses the visual attention method, combined with a statistical approach for the detection and an active contour for the segmentation of the object to overcome the above problems. In the classical active contour method the region descriptor is fixed and the convergence of the method depends on the initialization. With our approach, this dependence is overcome with an initialization using the visual attention results and a criterion to select the best region descriptor. This approach improves the convergence and the processing time while providing the advantages of a fully automated method.

  2. Development of Fully Automated Low-Cost Immunoassay System for Research Applications.

    Wang, Guochun; Das, Champak; Ledden, Bradley; Sun, Qian; Nguyen, Chien

    2017-10-01

    Enzyme-linked immunosorbent assay (ELISA) automation for routine operation in a small research environment would be very attractive. A portable fully automated low-cost immunoassay system was designed, developed, and evaluated with several protein analytes. It features disposable capillary columns as the reaction sites and uses real-time calibration for improved accuracy. It reduces the overall assay time to less than 75 min with the ability of easy adaptation of new testing targets. The running cost is extremely low due to the nature of automation, as well as reduced material requirements. Details about system configuration, components selection, disposable fabrication, system assembly, and operation are reported. The performance of the system was initially established with a rabbit immunoglobulin G (IgG) assay, and an example of assay adaptation with an interleukin 6 (IL6) assay is shown. This system is ideal for research use, but could work for broader testing applications with further optimization.

  3. How a Fully Automated eHealth Program Simulates Three Therapeutic Processes: A Case Study.

    Holter, Marianne T S; Johansen, Ayna; Brendryen, Håvar

    2016-06-28

    eHealth programs may be better understood by breaking down the components of one particular program and discussing its potential for interactivity and tailoring in regard to concepts from face-to-face counseling. In the search for the efficacious elements within eHealth programs, it is important to understand how a program using lapse management may simultaneously support working alliance, internalization of motivation, and behavior maintenance. These processes have been applied to fully automated eHealth programs individually. However, given their significance in face-to-face counseling, it may be important to simulate the processes simultaneously in interactive, tailored programs. We propose a theoretical model for how fully automated behavior change eHealth programs may be more effective by simulating a therapist's support of a working alliance, internalization of motivation, and managing lapses. We show how the model is derived from theory and its application to Endre, a fully automated smoking cessation program that engages the user in several "counseling sessions" about quitting. A descriptive case study based on tools from the intervention mapping protocol shows how each therapeutic process is simulated. The program supports the user's working alliance through alliance factors, the nonembodied relational agent Endre and computerized motivational interviewing. Computerized motivational interviewing also supports internalized motivation to quit, whereas a lapse management component responds to lapses. The description operationalizes working alliance, internalization of motivation, and managing lapses, in terms of eHealth support of smoking cessation. A program may simulate working alliance, internalization of motivation, and lapse management through interactivity and individual tailoring, potentially making fully automated eHealth behavior change programs more effective.

  4. Fully automated system for Pu measurement by gamma spectrometry of alpha contaminated solid wastes

    Cresti, P.

    1986-01-01

    A description is given of a fully automated system developed at Comb/Mepis Laboratories which is based on the detection of specific gamma signatures of Pu isotopes for monitoring Pu content in 15-25 l containers of low density (0.1 g/cm 3 ) wastes. The methodological approach is discussed; based on experimental data, an evaluation of the achievable performances (detection limit, precision, accuracy, etc.) is also given

  5. Performance of a fully automated scatterometer for BRDF and BTDF measurements at visible and infrared wavelengths

    Anderson, S.; Shepard, D.F.; Pompea, S.M.; Castonguay, R.

    1989-01-01

    The general performance of a fully automated scatterometer shows that the instrument can make rapid, accurate BRDF (bidirectional reflectance distribution function) and BTDF (bidirectional transmittance distribution function) measurements of optical surfaces over a range of approximately ten orders of magnitude in BRDF. These measurements can be made for most surfaces even with the detector at the specular angle, because of beam-attenuation techniques. He-Ne and CO2 lasers are used as sources in conjunction with a reference detector and chopper

  6. A 3D, fully Eulerian, VOF-based solver to study the interaction between two fluids and moving rigid bodies using the fictitious domain method

    Pathak, Ashish; Raessi, Mehdi

    2016-04-01

    We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.

  7. A fully consistent and conservative vertically adaptive coordinate system for SLIM 3D v0.4 with an application to the thermocline oscillations of Lake Tanganyika

    Delandmeter, Philippe; Lambrechts, Jonathan; Legat, Vincent; Vallaeys, Valentin; Naithani, Jaya; Thiery, Wim; Remacle, Jean-François; Deleersnijder, Eric

    2018-03-01

    The discontinuous Galerkin (DG) finite element method is well suited for the modelling, with a relatively small number of elements, of three-dimensional flows exhibiting strong velocity or density gradients. Its performance can be highly enhanced by having recourse to r-adaptivity. Here, a vertical adaptive mesh method is developed for DG finite elements. This method, originally designed for finite difference schemes, is based on the vertical diffusion of the mesh nodes, with the diffusivity controlled by the density jumps at the mesh element interfaces. The mesh vertical movement is determined by means of a conservative arbitrary Lagrangian-Eulerian (ALE) formulation. Though conservativity is naturally achieved, tracer consistency is obtained by a suitable construction of the mesh vertical velocity field, which is defined in such a way that it is fully compatible with the tracer and continuity equations at a discrete level. The vertically adaptive mesh approach is implemented in the three-dimensional version of the geophysical and environmental flow Second-generation Louvain-la-Neuve Ice-ocean Model (SLIM 3D; www.climate.be/slim). Idealised benchmarks, aimed at simulating the oscillations of a sharp thermocline, are dealt with. Then, the relevance of the vertical adaptivity technique is assessed by simulating thermocline oscillations of Lake Tanganyika. The results are compared to measured vertical profiles of temperature, showing similar stratification and outcropping events.

  8. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon’s ray-tracer, we propose another more simplified geometrical projector based on the Bresenham’s ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model. (paper)

  9. Fully Automated Volumetric Modulated Arc Therapy Plan Generation for Prostate Cancer Patients

    Voet, Peter W.J.; Dirkx, Maarten L.P.; Breedveld, Sebastiaan; Al-Mamgani, Abrahim; Incrocci, Luca; Heijmen, Ben J.M.

    2014-01-01

    Purpose: To develop and evaluate fully automated volumetric modulated arc therapy (VMAT) treatment planning for prostate cancer patients, avoiding manual trial-and-error tweaking of plan parameters by dosimetrists. Methods and Materials: A system was developed for fully automated generation of VMAT plans with our commercial clinical treatment planning system (TPS), linked to the in-house developed Erasmus-iCycle multicriterial optimizer for preoptimization. For 30 randomly selected patients, automatically generated VMAT plans (VMAT auto ) were compared with VMAT plans generated manually by 1 expert dosimetrist in the absence of time pressure (VMAT man ). For all treatment plans, planning target volume (PTV) coverage and sparing of organs-at-risk were quantified. Results: All generated plans were clinically acceptable and had similar PTV coverage (V 95%  > 99%). For VMAT auto and VMAT man plans, the organ-at-risk sparing was similar as well, although only the former plans were generated without any planning workload. Conclusions: Fully automated generation of high-quality VMAT plans for prostate cancer patients is feasible and has recently been implemented in our clinic

  10. Automation and Preclinical Evaluation of a Dedicated Emission Mammotomography System for Fully 3-D Molecular Breast Imaging

    Cutler, Spencer J

    2007-01-01

    .... A retrospective study of 103 clinical MRI uncompressed breast scans was conducted to create surface renderings of the uncompressed breasts and analyze how to adapt existing acquisition orbits for varying breast shapes...

  11. Comparison of semi-automated center-dot and fully automated endothelial cell analyses from specular microscopy images.

    Maruoka, Sachiko; Nakakura, Shunsuke; Matsuo, Naoko; Yoshitomi, Kayo; Katakami, Chikako; Tabuchi, Hitoshi; Chikama, Taiichiro; Kiuchi, Yoshiaki

    2017-10-30

    To evaluate two specular microscopy analysis methods across different endothelial cell densities (ECDs). Endothelial images of one eye from each of 45 patients were taken by using three different specular microscopes (three replicates each). To determine the consistency of the center-dot method, we compared SP-6000 and SP-2000P images. CME-530 and SP-6000 images were compared to assess the consistency of the fully automated method. The SP-6000 images from the two methods were compared. Intraclass correlation coefficients (ICCs) for the three measurements were calculated, and parametric multiple comparisons tests and Bland-Altman analysis were performed. The ECD mean value was 2425 ± 883 (range 516-3707) cells/mm 2 . ICC values were > 0.9 for all three microscopes for ECD, but the coefficients of variation (CVs) were 0.3-0.6. For ECD measurements, Bland-Altman analysis revealed that the mean difference was 42 cells/mm 2 between the SP-2000P and SP-6000 for the center-dot method; 57 cells/mm 2 between the SP-6000 measurements from both methods; and -5 cells/mm 2 between the SP-6000 and CME-530 for the fully automated method (95% limits of agreement: - 201 to 284 cell/mm 2 , - 410 to 522 cells/mm 2 , and - 327 to 318 cells/mm 2 , respectively). For CV measurements, the mean differences were - 3, - 12, and 13% (95% limits of agreement - 18 to 11, - 26 to 2, and - 5 to 32%, respectively). Despite using three replicate measurements, the precision of the center-dot method with the SP-2000P and SP-6000 software was only ± 10% for ECD data and was even worse for the fully automated method. Japan Clinical Trials Register ( http://www.umin.ac.jp/ctr/index/htm9 ) number UMIN 000015236.

  12. A Fully Automated High-Throughput Flow Cytometry Screening System Enabling Phenotypic Drug Discovery.

    Joslin, John; Gilligan, James; Anderson, Paul; Garcia, Catherine; Sharif, Orzala; Hampton, Janice; Cohen, Steven; King, Miranda; Zhou, Bin; Jiang, Shumei; Trussell, Christopher; Dunn, Robert; Fathman, John W; Snead, Jennifer L; Boitano, Anthony E; Nguyen, Tommy; Conner, Michael; Cooke, Mike; Harris, Jennifer; Ainscow, Ed; Zhou, Yingyao; Shaw, Chris; Sipes, Dan; Mainquist, James; Lesley, Scott

    2018-05-01

    The goal of high-throughput screening is to enable screening of compound libraries in an automated manner to identify quality starting points for optimization. This often involves screening a large diversity of compounds in an assay that preserves a connection to the disease pathology. Phenotypic screening is a powerful tool for drug identification, in that assays can be run without prior understanding of the target and with primary cells that closely mimic the therapeutic setting. Advanced automation and high-content imaging have enabled many complex assays, but these are still relatively slow and low throughput. To address this limitation, we have developed an automated workflow that is dedicated to processing complex phenotypic assays for flow cytometry. The system can achieve a throughput of 50,000 wells per day, resulting in a fully automated platform that enables robust phenotypic drug discovery. Over the past 5 years, this screening system has been used for a variety of drug discovery programs, across many disease areas, with many molecules advancing quickly into preclinical development and into the clinic. This report will highlight a diversity of approaches that automated flow cytometry has enabled for phenotypic drug discovery.

  13. Assessment of the structural integrity of a prototypical instrumented IFMIF high flux test module rig by fully 3D X-ray microtomography

    Tiseanu, Ion [National Institute for Laser, Plasma and Radiation Physics, Plasma Physics and Nuclear Fusion Laboratory NILPRP, P.O. Box MG-36, R-77125 Bucharest-Magurele (Romania)], E-mail: tiseanu@infim.ro; Simon, Martin [Hans Waelischmiller GmbH (HWM), Schiessstattweg 16, D-88677 Markdorf (Germany); Craciunescu, Teddy; Mandache, Bogdan N. [National Institute for Laser, Plasma and Radiation Physics, Plasma Physics and Nuclear Fusion Laboratory NILPRP, P.O. Box MG-36, R-77125 Bucharest-Magurele (Romania); Heinzel, Volker; Stratmanns, Erwin; Simakov, Stanislaw P.; Leichtle, Dieter [Forschungszentrum Karlsruhe (FZK), Institut fuer Reaktorsicherheit IRS, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)

    2007-10-15

    An inspection procedure to assess the mechanical integrity of the International Fusion Materials Irradiation Facility (IFMIF) capsules and rigs during the irradiation campaign is necessary. Due to its penetration ability and contrast mechanism, the X-ray microtomography is the only known tool that could meet these requirements. In the high flux test module (HFTM) of IFMIF miniaturized specimens are densely packed in capsules. The capsules, which wear electric heaters and thermocouples, are housed in rigs. To assure a well-defined thermal contact the heater wires have to be attached to the capsules by brazing them into grooves. The examination of the quality of the braze material layer is of crucial interest in order to assure the best heat coupling of the heater wires to the capsule. A high density of the heaters is necessary to maintain the required temperature and, in addition NaK filling of narrow channels is employed for improving the 3D-heat transfer between the irradiation specimens and the capsule wall. Fully 3D tomographic inspections of a prototypical HFTM instrumented capsule, developed and manufactured at FZK, were conducted. In order to identify the optimum irradiation parameters and scanning configuration we carried out a comparative NDT analysis on two microtomography facilities: a compact, high magnification installation at NILPRP and a high-end industrial tomography facility with higher X-ray energy and intensity at HWM. At optimum inspection parameters of a directional microfocus X-ray source (U = 220 kV and I = 300 {mu}A) the geometry resolution was about 30 microns for characteristic dimension of the sample of 50 mm. Voids of 30 microns diameter and cracks of about 20 microns width can be detected. The absolute error of geometrical measurements is sufficient for the assessment of the structural integrity of the irradiation capsule and for the geometry description within the thermal-hydraulic modeling. The space resolution and the overall

  14. Assessment of the structural integrity of a prototypical instrumented IFMIF high flux test module rig by fully 3D X-ray microtomography

    Tiseanu, Ion; Simon, Martin; Craciunescu, Teddy; Mandache, Bogdan N.; Heinzel, Volker; Stratmanns, Erwin; Simakov, Stanislaw P.; Leichtle, Dieter

    2007-01-01

    An inspection procedure to assess the mechanical integrity of the International Fusion Materials Irradiation Facility (IFMIF) capsules and rigs during the irradiation campaign is necessary. Due to its penetration ability and contrast mechanism, the X-ray microtomography is the only known tool that could meet these requirements. In the high flux test module (HFTM) of IFMIF miniaturized specimens are densely packed in capsules. The capsules, which wear electric heaters and thermocouples, are housed in rigs. To assure a well-defined thermal contact the heater wires have to be attached to the capsules by brazing them into grooves. The examination of the quality of the braze material layer is of crucial interest in order to assure the best heat coupling of the heater wires to the capsule. A high density of the heaters is necessary to maintain the required temperature and, in addition NaK filling of narrow channels is employed for improving the 3D-heat transfer between the irradiation specimens and the capsule wall. Fully 3D tomographic inspections of a prototypical HFTM instrumented capsule, developed and manufactured at FZK, were conducted. In order to identify the optimum irradiation parameters and scanning configuration we carried out a comparative NDT analysis on two microtomography facilities: a compact, high magnification installation at NILPRP and a high-end industrial tomography facility with higher X-ray energy and intensity at HWM. At optimum inspection parameters of a directional microfocus X-ray source (U = 220 kV and I = 300 μA) the geometry resolution was about 30 microns for characteristic dimension of the sample of 50 mm. Voids of 30 microns diameter and cracks of about 20 microns width can be detected. The absolute error of geometrical measurements is sufficient for the assessment of the structural integrity of the irradiation capsule and for the geometry description within the thermal-hydraulic modeling. The space resolution and the overall

  15. Assessment of the Structural Integrity of a Prototypical Instrumented IFMIF High Flux Test Module Rig by Fully 3D X-Ray Microtomography

    Tiseanu, I.; Craciunescu, T.; Mandache, B.N.; Simon, M.; Heinzel, V.; Stratmanns, E.; Simakov, S.P.; Leichtle, D.

    2006-01-01

    An inspection procedure to asses the mechanical integrity of IFMIF (International Fusion Materials Irradiation Facility) capsules and rigs during the irradiation campaign is necessary. Due to its penetration ability and contrast mechanism, the X-ray micro-tomography is the only known tool that could meet these requirements. In the High Flux Test Module (HFTM) of IFMIF miniaturized specimens are densely packed in capsules. The capsules which wear electric heaters and thermocouples are housed in rigs. To assure a well defined thermal contact the heater wires have to be attached to the capsules by brazing them into grooves. The examination of the quality of the braze material layer is of crucial interest in order to assure the best heat coupling of the heater wires to the capsule. A high density of the heaters is necessary to maintain the required temperature and, in addition NaK filling of narrow channels is employed for improving the 3D-heat transfer between the irradiation specimens and the capsule wall. Fully 3D tomographic inspections of a prototypical HFTM instrumented capsule, developed and manufactures at FZK, were conducted. In order to identify the optimum irradiation parameters and scanning configuration we carried out a comparative NDT analysis on two micro-tomography facilities, our compact, high magnification installation at NILPRP and two high-end industrial tomography facilities with higher X-ray energy and intensity at HWM. At optimum inspection parameters of a microfocus X-ray source (U=220 kV and I=300 μA) the geometry resolution was about 30-50 microns for characteristic dimension of the sample of 50 mm. Voids of 30 microns diameter and cracks of about 20 microns width can be detected. The absolute error of geometrical measurements should be sufficient for the assessment of the structural integrity of the irradiation capsule and for the geometry description within the thermal-hydraulic modeling. Space resolution could be further improved if one

  16. Deep multi-scale location-aware 3D convolutional neural networks for automated detection of lacunes of presumed vascular origin.

    Ghafoorian, Mohsen; Karssemeijer, Nico; Heskes, Tom; Bergkamp, Mayra; Wissink, Joost; Obels, Jiri; Keizer, Karlijn; de Leeuw, Frank-Erik; Ginneken, Bram van; Marchiori, Elena; Platel, Bram

    2017-01-01

    Lacunes of presumed vascular origin (lacunes) are associated with an increased risk of stroke, gait impairment, and dementia and are a primary imaging feature of the small vessel disease. Quantification of lacunes may be of great importance to elucidate the mechanisms behind neuro-degenerative disorders and is recommended as part of study standards for small vessel disease research. However, due to the different appearance of lacunes in various brain regions and the existence of other similar-looking structures, such as perivascular spaces, manual annotation is a difficult, elaborative and subjective task, which can potentially be greatly improved by reliable and consistent computer-aided detection (CAD) routines. In this paper, we propose an automated two-stage method using deep convolutional neural networks (CNN). We show that this method has good performance and can considerably benefit readers. We first use a fully convolutional neural network to detect initial candidates. In the second step, we employ a 3D CNN as a false positive reduction tool. As the location information is important to the analysis of candidate structures, we further equip the network with contextual information using multi-scale analysis and integration of explicit location features. We trained, validated and tested our networks on a large dataset of 1075 cases obtained from two different studies. Subsequently, we conducted an observer study with four trained observers and compared our method with them using a free-response operating characteristic analysis. Shown on a test set of 111 cases, the resulting CAD system exhibits performance similar to the trained human observers and achieves a sensitivity of 0.974 with 0.13 false positives per slice. A feasibility study also showed that a trained human observer would considerably benefit once aided by the CAD system.

  17. A fully automated Drosophila olfactory classical conditioning and testing system for behavioral learning and memory assessment.

    Jiang, Hui; Hanna, Eriny; Gatto, Cheryl L; Page, Terry L; Bhuva, Bharat; Broadie, Kendal

    2016-03-01

    Aversive olfactory classical conditioning has been the standard method to assess Drosophila learning and memory behavior for decades, yet training and testing are conducted manually under exceedingly labor-intensive conditions. To overcome this severe limitation, a fully automated, inexpensive system has been developed, which allows accurate and efficient Pavlovian associative learning/memory analyses for high-throughput pharmacological and genetic studies. The automated system employs a linear actuator coupled to an odorant T-maze with airflow-mediated transfer of animals between training and testing stages. Odorant, airflow and electrical shock delivery are automatically administered and monitored during training trials. Control software allows operator-input variables to define parameters of Drosophila learning, short-term memory and long-term memory assays. The approach allows accurate learning/memory determinations with operational fail-safes. Automated learning indices (immediately post-training) and memory indices (after 24h) are comparable to traditional manual experiments, while minimizing experimenter involvement. The automated system provides vast improvements over labor-intensive manual approaches with no experimenter involvement required during either training or testing phases. It provides quality control tracking of airflow rates, odorant delivery and electrical shock treatments, and an expanded platform for high-throughput studies of combinational drug tests and genetic screens. The design uses inexpensive hardware and software for a total cost of ∼$500US, making it affordable to a wide range of investigators. This study demonstrates the design, construction and testing of a fully automated Drosophila olfactory classical association apparatus to provide low-labor, high-fidelity, quality-monitored, high-throughput and inexpensive learning and memory behavioral assays. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. A fully automatic, threshold-based segmentation method for the estimation of the Metabolic Tumor Volume from PET images: validation on 3D printed anthropomorphic oncological lesions

    Gallivanone, F.; Interlenghi, M.; Canervari, C.; Castiglioni, I.

    2016-01-01

    18F-Fluorodeoxyglucose (18F-FDG) Positron Emission Tomography (PET) is a standard functional diagnostic technique to in vivo image cancer. Different quantitative paramters can be extracted from PET images and used as in vivo cancer biomarkers. Between PET biomarkers Metabolic Tumor Volume (MTV) has gained an important role in particular considering the development of patient-personalized radiotherapy treatment for non-homogeneous dose delivery. Different imaging processing methods have been developed to define MTV. The different proposed PET segmentation strategies were validated in ideal condition (e.g. in spherical objects with uniform radioactivity concentration), while the majority of cancer lesions doesn't fulfill these requirements. In this context, this work has a twofold objective: 1) to implement and optimize a fully automatic, threshold-based segmentation method for the estimation of MTV, feasible in clinical practice 2) to develop a strategy to obtain anthropomorphic phantoms, including non-spherical and non-uniform objects, miming realistic oncological patient conditions. The developed PET segmentation algorithm combines an automatic threshold-based algorithm for the definition of MTV and a k-means clustering algorithm for the estimation of the background. The method is based on parameters always available in clinical studies and was calibrated using NEMA IQ Phantom. Validation of the method was performed both in ideal (e.g. in spherical objects with uniform radioactivity concentration) and non-ideal (e.g. in non-spherical objects with a non-uniform radioactivity concentration) conditions. The strategy to obtain a phantom with synthetic realistic lesions (e.g. with irregular shape and a non-homogeneous uptake) consisted into the combined use of standard anthropomorphic phantoms commercially and irregular molds generated using 3D printer technology and filled with a radioactive chromatic alginate. The proposed segmentation algorithm was feasible in a

  19. Study on the stress changes due to the regional groundwater exploitation based on a 3-D fully coupled poroelastic model: An example of the North China Plain

    Cheng, H.; Zhang, H.; Pang, Y. J.; Shi, Y.

    2017-12-01

    With the quick urban development, over-exploitation of groundwater resources becomes more and more intense, which leads to not only widespread groundwater depression cones but also a series of harsh environmental and geological hazards. Among which, the most intuitive phenomenon is the ground subsidence in loose sediments. However, another direct consequence triggered by the groundwater depletion is the substantial crustal deformation and potential modulation of crustal stress underneath the groundwater over-pumping zones. In our previous 3-D viscoelastic finite element model, we found that continuous over-exploitation of groundwater resources in North China Plain during the past 60 years give rise to crustal-scale uplift reaching 4.9cm, with the Coulomb failure stress decreasing by up to 12 kPa, which may inhibit the nucleation of possible big earthquake events. Furthermore, according to the effective pressure principle and lab experiments, the pore pressure may also have changed due to the reduced water level. In order to quantitatively analyze the stress changes due to the regional groundwater exploitation in North China Plain, a three-dimensional fully coupled poroelastic finite element model is developed in this study. The high resolution topography, grounwater level fluctuation, fault parameters and etc, are taken into consideration. Further, the changes of Coulomb Failure Stress, in correspondence to elastic stress and pore pressure changes induced by fluid diffusion are calculated. Meanwhile, the elastic strain energy accumulation in region due to the regional groundwater exploitation is obtained. Finally, we try to analyze the seismic risk of major faults within North China Plain to further discuss the regional seismic activities.

  20. Towards 3D crystal orientation reconstruction using automated crystal orientation mapping transmission electron microscopy (ACOM-TEM).

    Kobler, Aaron; Kübel, Christian

    2018-01-01

    To relate the internal structure of a volume (crystallite and phase boundaries) to properties (electrical, magnetic, mechanical, thermal), a full 3D reconstruction in combination with in situ testing is desirable. In situ testing allows the crystallographic changes in a material to be followed by tracking and comparing the individual crystals and phases. Standard transmission electron microscopy (TEM) delivers a projection image through the 3D volume of an electron-transparent TEM sample lamella. Only with the help of a dedicated TEM tomography sample holder is an accurate 3D reconstruction of the TEM lamella currently possible. 2D crystal orientation mapping has become a standard method for crystal orientation and phase determination while 3D crystal orientation mapping have been reported only a few times. The combination of in situ testing with 3D crystal orientation mapping remains a challenge in terms of stability and accuracy. Here, we outline a method to 3D reconstruct the crystal orientation from a superimposed diffraction pattern of overlapping crystals without sample tilt. Avoiding the typically required tilt series for 3D reconstruction enables not only faster in situ tests but also opens the possibility for more stable and more accurate in situ mechanical testing. The approach laid out here should serve as an inspiration for further research and does not make a claim to be complete.

  1. Fully Automated Trimethylsilyl (TMS Derivatisation Protocol for Metabolite Profiling by GC-MS

    Erica Zarate

    2016-12-01

    Full Text Available Gas Chromatography-Mass Spectrometry (GC-MS has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches. Here, we present a fully automated TMS derivatisation protocol using robotic autosamplers and we also evaluate a commercial software, Maestro available from Gerstel GmbH. Because of automation, there was no waiting time of derivatised samples on the autosamplers, thus reducing degradation of unstable metabolites. Moreover, this method allowed us to overlap samples and improved throughputs. We compared data obtained from both manual and automated TMS methods performed on three different matrices, including standard mix, wine, and plasma samples. The automated TMS method showed better reproducibility and higher peak intensity for most of the identified metabolites than the manual derivatisation method. We also validated the automated method using 114 quality control plasma samples. Additionally, we showed that this online method was highly reproducible for most of the metabolites detected and identified (RSD < 20 and specifically achieved excellent results for sugars, sugar alcohols, and some organic acids. To the very best of our knowledge, this is the first time that the automated TMS method has been applied to analyse a large number of complex plasma samples. Furthermore, we found that this method was highly applicable for routine metabolite profiling (both targeted and untargeted in any metabolomics laboratory.

  2. A fully automated system for ultrasonic power measurement and simulation accordingly to IEC 61161:2006

    Costa-Felix, Rodrigo P B; Alvarenga, Andre V; Hekkenberg, Rob

    2011-01-01

    The ultrasonic power measurement, worldwide accepted, standard is the IEC 61161, presently in its 2nd edition (2006), but under review. To fulfil its requirements, considering that a radiation force balance is to be used as ultrasonic power detector, a large amount of raw data (mass measurement) shall be collected as function of time to perform all necessary calculations and corrections. Uncertainty determination demands calculation effort of raw and processed data. Although it is possible to be undertaken in an old-fashion way, using spread sheets and manual data collection, automation software are often used in metrology to provide a virtually error free environment concerning data acquisition and repetitive calculations and corrections. Considering that, a fully automate ultrasonic power measurement system was developed and comprehensively tested. A 0,1 mg of precision balance model CP224S (Sartorius, Germany) was used as measuring device and a calibrated continuous wave ultrasound check source (Precision Acoustics, UK) was the device under test. A 150 ml container filled with degassed water and containing an absorbing target at the bottom was placed on the balance pan. Besides the feature of automation software, a routine of power measurement simulation was implemented. It was idealized as a teaching tool of how ultrasonic power emission behaviour is with a radiation force balance equipped with an absorbing target. Automation software was considered as an effective tool for speeding up ultrasonic power measurement, while allowing accurate calculation and attractive graphical partial and final results.

  3. Fully Automated Driving: Impact of Trust and Practice on Manual Control Recovery.

    Payre, William; Cestac, Julien; Delhomme, Patricia

    2016-03-01

    An experiment was performed in a driving simulator to investigate the impacts of practice, trust, and interaction on manual control recovery (MCR) when employing fully automated driving (FAD). To increase the use of partially or highly automated driving efficiency and to improve safety, some studies have addressed trust in driving automation and training, but few studies have focused on FAD. FAD is an autonomous system that has full control of a vehicle without any need for intervention by the driver. A total of 69 drivers with a valid license practiced with FAD. They were distributed evenly across two conditions: simple practice and elaborate practice. When examining emergency MCR, a correlation was found between trust and reaction time in the simple practice group (i.e., higher trust meant a longer reaction time), but not in the elaborate practice group. This result indicated that to mitigate the negative impact of overtrust on reaction time, more appropriate practice may be needed. Drivers should be trained in how the automated device works so as to improve MCR performance in case of an emergency. The practice format used in this study could be used for the first interaction with an FAD car when acquiring such a vehicle. © 2015, Human Factors and Ergonomics Society.

  4. Performance of a fully automated program for measurement of left ventricular ejection fraction

    Douglass, K.H.; Tibbits, P.; Kasecamp, W.; Han, S.T.; Koller, D.; Links, J.M.; Wagner, H.H. Jr.

    1982-01-01

    A fully automated program developed by us for measurement of left ventricular ejection fraction from equilibrium gated blood studies was evaluated in 130 additional patients. Both of 6-min (130 studies) and 2-min (142 studies in 31 patients) gated blood pool studies were acquired and processed. The program successfully generated ejection fractions in 86% of the studies. These automatically generated ejection fractions were compared with ejection fractions derived from manually drawn regions the interest. When studies were acquired for 6-min with the patient at rest, the correlation between automated and manual ejection fractions was 0.92. When studies were acquired for 2-min, both at rest and during bicycle exercise, the correlation was 0.81. In 25 studies from patients who also underwent contrast ventriculography, the program successfully generated regions of interest in 22 (88%). The correlation between the ejection fraction determined by contrast ventriculography and the automatically generated radionuclide ejection fraction was 0.79. (orig.)

  5. Fully automated gamma spectrometry gauge observing possible radioactive contamination of melting-shop samples

    Kroos, J.; Westkaemper, G.; Stein, J.

    1999-01-01

    At Salzgitter AG, several monitoring systems have been installed to check the scrap transport by rail and by car. At the moment, the scrap transport by ship is reloaded onto wagons for monitoring afterwards. In the future, a detection system will be mounted onto a crane for a direct check on scrap upon the departure of ship. Furthermore, at Salzgitter AG Central Chemical Laboratory, a fully automated gamma spectrometry gauge is installed in order to observe a possible radioactive contamination of the products. The gamma spectrometer is integrated into the automated OE spectrometry line for testing melting shop samples after performing the OE spectrometry. With this technique the specific activity of selected nuclides and dose rate will be determined. The activity observation is part of the release procedure. The corresponding measurement data are stored in a database for quality management reasons. (author)

  6. TreeRipper web application: towards a fully automated optical tree recognition software

    Hughes Joseph

    2011-05-01

    Full Text Available Abstract Background Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. Results TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/. The program accepts a range of input image formats (PNG, JPG/JPEG or GIF. The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.

  7. Fully automated joint space width measurement and digital X-ray radiogrammetry in early RA.

    Platten, Michael; Kisten, Yogan; Kälvesten, Johan; Arnaud, Laurent; Forslind, Kristina; van Vollenhoven, Ronald

    2017-01-01

    To study fully automated digital joint space width (JSW) and bone mineral density (BMD) in relation to a conventional radiographic scoring method in early rheumatoid arthritis (eRA). Radiographs scored by the modified Sharp van der Heijde score (SHS) in patients with eRA were acquired from the SWEdish FarmacOTherapy study. Fully automated JSW measurements of bilateral metacarpals 2, 3 and 4 were compared with the joint space narrowing (JSN) score in SHS. Multilevel mixed model statistics were applied to calculate the significance of the association between ΔJSW and ΔBMD over 1 year, and the JSW differences between damaged and undamaged joints as evaluated by the JSN. Based on 576 joints of 96 patients with eRA, a significant reduction from baseline to 1 year was observed in the JSW from 1.69 (±0.19) mm to 1.66 (±0.19) mm (p0) joints: 1.68 mm (95% CI 1.70 to 1.67) vs 1.54 mm (95% CI 1.63 to 1.46). Similarly the unadjusted multilevel model showed significant differences in JSW between undamaged (1.68 mm (95% CI 1.72 to 1.64)) and damaged joints (1.63 mm (95% CI 1.68 to 1.58)) (p=0.0048). This difference remained significant in the adjusted model: 1.66 mm (95% CI 1.70 to 1.61) vs 1.62 mm (95% CI 1.68 to 1.56) (p=0.042). To measure the JSW with this fully automated digital tool may be useful as a quick and observer-independent application for evaluating cartilage damage in eRA. NCT00764725.

  8. MVO Automation Platform: Addressing Unmet Needs in Clinical Laboratories with Microcontrollers, 3D Printing, and Open-Source Hardware/Software.

    Iglehart, Brian

    2018-05-01

    Laboratory automation improves test reproducibility, which is vital to patient care in clinical laboratories. Many small and specialty laboratories are excluded from the benefits of automation due to low sample number, cost, space, and/or lack of automation expertise. The Minimum Viable Option (MVO) automation platform was developed to address these hurdles and fulfill an unmet need. Consumer 3D printing enabled rapid iterative prototyping to allow for a variety of instrumentation and assay setups and procedures. Three MVO versions have been produced. MVOv1.1 successfully performed part of a clinical assay, and results were comparable to those of commercial automation. Raspberry Pi 3 Model B (RPI3) single-board computers with Sense Hardware Attached on Top (HAT) and Raspberry Pi Camera Module V2 hardware were remotely accessed and evaluated for their suitability to qualify the latest MVOv1.2 platform. Sense HAT temperature, barometric pressure, and relative humidity sensors were stable in climate-controlled environments and are useful in identifying appropriate laboratory spaces for automation placement. The RPI3 with camera plus digital dial indicator logged axis travel experiments. RPI3 with camera and Sense HAT as a light source showed promise when used for photometric dispensing tests. Individual well standard curves were necessary for well-to-well light and path length compensations.

  9. Development of a fully automated software system for rapid analysis/processing of the falling weight deflectometer data.

    2009-02-01

    The Office of Special Investigations at Iowa Department of Transportation (DOT) collects FWD data on regular basis to evaluate pavement structural conditions. The primary objective of this study was to develop a fully-automated software system for ra...

  10. Detection of virus-specific intrathecally synthesised immunoglobulin G with a fully automated enzyme immunoassay system

    Weissbrich Benedikt

    2007-05-01

    Full Text Available Abstract Background The determination of virus-specific immunoglobulin G (IgG antibodies in cerebrospinal fluid (CSF is useful for the diagnosis of virus associated diseases of the central nervous system (CNS and for the detection of a polyspecific intrathecal immune response in patients with multiple sclerosis. Quantification of virus-specific IgG in the CSF is frequently performed by calculation of a virus-specific antibody index (AI. Determination of the AI is a demanding and labour-intensive technique and therefore automation is desirable. We evaluated the precision and the diagnostic value of a fully automated enzyme immunoassay for the detection of virus-specific IgG in serum and CSF using the analyser BEP2000 (Dade Behring. Methods The AI for measles, rubella, varicella-zoster, and herpes simplex virus IgG was determined from pairs of serum and CSF samples of patients with viral CNS infections, multiple sclerosis and of control patients. CSF and serum samples were tested simultaneously with reference to a standard curve. Starting dilutions were 1:6 and 1:36 for CSF and 1:1386 and 1:8316 for serum samples. Results The interassay coefficient of variation was below 10% for all parameters tested. There was good agreement between AIs obtained with the BEP2000 and AIs derived from the semi-automated reference method. Conclusion Determination of virus-specific IgG in serum-CSF-pairs for calculation of AI has been successfully automated on the BEP2000. Current limitations of the assay layout imposed by the analyser software should be solved in future versions to offer more convenience in comparison to manual or semi-automated methods.

  11. Fully Automated Trimethylsilyl (TMS) Derivatisation Protocol for Metabolite Profiling by GC-MS.

    Zarate, Erica; Boyle, Veronica; Rupprecht, Udo; Green, Saras; Villas-Boas, Silas G; Baker, Philip; Pinu, Farhana R

    2016-12-29

    Gas Chromatography-Mass Spectrometry (GC-MS) has long been used for metabolite profiling of a wide range of biological samples. Many derivatisation protocols are already available and among these, trimethylsilyl (TMS) derivatisation is one of the most widely used in metabolomics. However, most TMS methods rely on off-line derivatisation prior to GC-MS analysis. In the case of manual off-line TMS derivatisation, the derivative created is unstable, so reduction in recoveries occurs over time. Thus, derivatisation is carried out in small batches. Here, we present a fully automated TMS derivatisation protocol using robotic autosamplers and we also evaluate a commercial software, Maestro available from Gerstel GmbH. Because of automation, there was no waiting time of derivatised samples on the autosamplers, thus reducing degradation of unstable metabolites. Moreover, this method allowed us to overlap samples and improved throughputs. We compared data obtained from both manual and automated TMS methods performed on three different matrices, including standard mix, wine, and plasma samples. The automated TMS method showed better reproducibility and higher peak intensity for most of the identified metabolites than the manual derivatisation method. We also validated the automated method using 114 quality control plasma samples. Additionally, we showed that this online method was highly reproducible for most of the metabolites detected and identified (RSD TMS method has been applied to analyse a large number of complex plasma samples. Furthermore, we found that this method was highly applicable for routine metabolite profiling (both targeted and untargeted) in any metabolomics laboratory.

  12. Validation of Fully Automated VMAT Plan Generation for Library-Based Plan-of-the-Day Cervical Cancer Radiotherapy

    Sharfo, Abdul Wahab M.; Breedveld, Sebastiaan; Voet, Peter W. J.; Heijkoop, Sabrina T.; Mens, Jan-Willem M.; Hoogeman, Mischa S.; Heijmen, Ben J. M.

    2016-01-01

    textabstractPurpose: To develop and validate fully automated generation of VMAT plan-libraries for plan-of-the-day adaptive radiotherapy in locally-advanced cervical cancer. Material and Methods: Our framework for fully automated treatment plan generation (Erasmus-iCycle) was adapted to create dual-arc VMAT treatment plan libraries for cervical cancer patients. For each of 34 patients, automatically generated VMAT plans (autoVMAT) were compared to manually generated, clinically delivered 9-be...

  13. Prediction of spontaneous ureteral stone passage: Automated 3D-measurements perform equal to radiologists, and linear measurements equal to volumetric.

    Jendeberg, Johan; Geijer, Håkan; Alshamari, Muhammed; Lidén, Mats

    2018-01-24

    To compare the ability of different size estimates to predict spontaneous passage of ureteral stones using a 3D-segmentation and to investigate the impact of manual measurement variability on the prediction of stone passage. We retrospectively included 391 consecutive patients with ureteral stones on non-contrast-enhanced CT (NECT). Three-dimensional segmentation size estimates were compared to the mean of three radiologists' measurements. Receiver-operating characteristic (ROC) analysis was performed for the prediction of spontaneous passage for each estimate. The difference in predicted passage probability between the manual estimates in upper and lower stones was compared. The area under the ROC curve (AUC) for the measurements ranged from 0.88 to 0.90. Between the automated 3D algorithm and the manual measurements the 95% limits of agreement were 0.2 ± 1.4 mm for the width. The manual bone window measurements resulted in a > 20 percentage point (ppt) difference between the readers in the predicted passage probability in 44% of the upper and 6% of the lower ureteral stones. All automated 3D algorithm size estimates independently predicted the spontaneous stone passage with similar high accuracy as the mean of three readers' manual linear measurements. Manual size estimation of upper stones showed large inter-reader variations for spontaneous passage prediction. • An automated 3D technique predicts spontaneous stone passage with high accuracy. • Linear, areal and volumetric measurements performed similarly in predicting stone passage. • Reader variability has a large impact on the predicted prognosis for stone passage.

  14. DG-AMMOS: a new tool to generate 3d conformation of small molecules using distance geometry and automated molecular mechanics optimization for in silico screening.

    Lagorce, David; Pencheva, Tania; Villoutreix, Bruno O; Miteva, Maria A

    2009-11-13

    Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

  15. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    Villoutreix Bruno O

    2009-11-01

    Full Text Available Abstract Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

  16. Fully automated segmentation of left ventricle using dual dynamic programming in cardiac cine MR images

    Jiang, Luan; Ling, Shan; Li, Qiang

    2016-03-01

    Cardiovascular diseases are becoming a leading cause of death all over the world. The cardiac function could be evaluated by global and regional parameters of left ventricle (LV) of the heart. The purpose of this study is to develop and evaluate a fully automated scheme for segmentation of LV in short axis cardiac cine MR images. Our fully automated method consists of three major steps, i.e., LV localization, LV segmentation at end-diastolic phase, and LV segmentation propagation to the other phases. First, the maximum intensity projection image along the time phases of the midventricular slice, located at the center of the image, was calculated to locate the region of interest of LV. Based on the mean intensity of the roughly segmented blood pool in the midventricular slice at each phase, end-diastolic (ED) and end-systolic (ES) phases were determined. Second, the endocardial and epicardial boundaries of LV of each slice at ED phase were synchronously delineated by use of a dual dynamic programming technique. The external costs of the endocardial and epicardial boundaries were defined with the gradient values obtained from the original and enhanced images, respectively. Finally, with the advantages of the continuity of the boundaries of LV across adjacent phases, we propagated the LV segmentation from the ED phase to the other phases by use of dual dynamic programming technique. The preliminary results on 9 clinical cardiac cine MR cases show that the proposed method can obtain accurate segmentation of LV based on subjective evaluation.

  17. Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.

    Zhang, Zhongqi; Zhang, Aming; Xiao, Gang

    2012-06-05

    Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.

  18. Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes

    Hiraki, Masahiko; Watanabe, Shokei; Chavas, Leonard M. G.; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Wakatsuki, Soichi; Fujihashi, Masahiro; Miki, Kunio; Baba, Seiki; Ueno, Go; Yamamoto, Masaki; Suzuki, Mamoru; Nakagawa, Atsushi; Watanabe, Nobuhisa; Tanaka, Isao

    2010-06-01

    To remotely control and automatically collect data in high-throughput X-ray data collection experiments, the Structural Biology Research Center at the Photon Factory (PF) developed and installed sample exchange robots PAM (PF Automated Mounting system) at PF macromolecular crystallography beamlines; BL-5A, BL-17A, AR-NW12A and AR-NE3A. We developed and installed software that manages the flow of the automated X-ray experiments; sample exchanges, loop-centering and X-ray diffraction data collection. The fully automated data collection function has been available since February 2009. To identify sample cassettes, PAM employs a two-dimensional bar code reader. New beamlines, BL-1A at the Photon Factory and BL32XU at SPring-8, are currently under construction as part of Targeted Proteins Research Program (TPRP) by the Ministry of Education, Culture, Sports, Science and Technology of Japan. However, different robots, PAM and SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), will be installed at BL-1A and BL32XU, respectively. For the convenience of the users of both facilities, pins and cassettes for PAM and SPACE are developed as part of the TPRP.

  19. A new fully automated FTIR system for total column measurements of greenhouse gases

    M. C. Geibel

    2010-10-01

    Full Text Available This article introduces a new fully automated FTIR system that is part of the Total Carbon Column Observing Network (TCCON. It will provide continuous ground-based measurements of column-averaged volume mixing ratio for CO2, CH4 and several other greenhouse gases in the tropics.

    Housed in a 20-foot shipping container it was developed as a transportable system that could be deployed almost anywhere in the world. We describe the automation concept which relies on three autonomous subsystems and their interaction. Crucial components like a sturdy and reliable solar tracker dome are described in detail. The automation software employs a new approach relying on multiple processes, database logging and web-based remote control.

    First results of total column measurements at Jena, Germany show that the instrument works well and can provide parts of the diurnal as well as seasonal cycle for CO2. Instrument line shape measurements with an HCl cell suggest that the instrument stays well-aligned over several months.

    After a short test campaign for side by side intercomaprison with an existing TCCON instrument in Australia, the system will be transported to its final destination Ascension Island.

  20. A new fully automated FTIR system for total column measurements of greenhouse gases

    Geibel, M. C.; Gerbig, C.; Feist, D. G.

    2010-10-01

    This article introduces a new fully automated FTIR system that is part of the Total Carbon Column Observing Network (TCCON). It will provide continuous ground-based measurements of column-averaged volume mixing ratio for CO2, CH4 and several other greenhouse gases in the tropics. Housed in a 20-foot shipping container it was developed as a transportable system that could be deployed almost anywhere in the world. We describe the automation concept which relies on three autonomous subsystems and their interaction. Crucial components like a sturdy and reliable solar tracker dome are described in detail. The automation software employs a new approach relying on multiple processes, database logging and web-based remote control. First results of total column measurements at Jena, Germany show that the instrument works well and can provide parts of the diurnal as well as seasonal cycle for CO2. Instrument line shape measurements with an HCl cell suggest that the instrument stays well-aligned over several months. After a short test campaign for side by side intercomaprison with an existing TCCON instrument in Australia, the system will be transported to its final destination Ascension Island.

  1. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    B. Antony (Bhavna); M.D. Abràmoff (Michael); L. Tang (Li); W.D. Ramdas (Wishal); J.R. Vingerling (Hans); N.M. Jansonius (Nomdo); K. Lee (Kyungmoo); Y.H. Kwon (Young); M. Sonka (Milan); M.K. Garvin (Mona)

    2011-01-01

    textabstractThe 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate

  2. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    Antony, Bhavna; Abramoff, Michael D.; Tang, Li; Ramdas, Wishal D.; Vingerling, Johannes R.; Jansonius, Nomdo M.; Lee, Kyungmoo; Kwon, Young H.; Sonka, Milan; Garvin, Mona K.

    2011-01-01

    The 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate and correct

  3. A linear programming approach to reconstructing subcellular structures from confocal images for automated generation of representative 3D cellular models.

    Wood, Scott T; Dean, Brian C; Dean, Delphine

    2013-04-01

    This paper presents a novel computer vision algorithm to analyze 3D stacks of confocal images of fluorescently stained single cells. The goal of the algorithm is to create representative in silico model structures that can be imported into finite element analysis software for mechanical characterization. Segmentation of cell and nucleus boundaries is accomplished via standard thresholding methods. Using novel linear programming methods, a representative actin stress fiber network is generated by computing a linear superposition of fibers having minimum discrepancy compared with an experimental 3D confocal image. Qualitative validation is performed through analysis of seven 3D confocal image stacks of adherent vascular smooth muscle cells (VSMCs) grown in 2D culture. The presented method is able to automatically generate 3D geometries of the cell's boundary, nucleus, and representative F-actin network based on standard cell microscopy data. These geometries can be used for direct importation and implementation in structural finite element models for analysis of the mechanics of a single cell to potentially speed discoveries in the fields of regenerative medicine, mechanobiology, and drug discovery. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. UBO Detector - A cluster-based, fully automated pipeline for extracting white matter hyperintensities.

    Jiang, Jiyang; Liu, Tao; Zhu, Wanlin; Koncz, Rebecca; Liu, Hao; Lee, Teresa; Sachdev, Perminder S; Wen, Wei

    2018-07-01

    We present 'UBO Detector', a cluster-based, fully automated pipeline for extracting and calculating variables for regions of white matter hyperintensities (WMH) (available for download at https://cheba.unsw.edu.au/group/neuroimaging-pipeline). It takes T1-weighted and fluid attenuated inversion recovery (FLAIR) scans as input, and SPM12 and FSL functions are utilised for pre-processing. The candidate clusters are then generated by FMRIB's Automated Segmentation Tool (FAST). A supervised machine learning algorithm, k-nearest neighbor (k-NN), is applied to determine whether the candidate clusters are WMH or non-WMH. UBO Detector generates both image and text (volumes and the number of WMH clusters) outputs for whole brain, periventricular, deep, and lobar WMH, as well as WMH in arterial territories. The computation time for each brain is approximately 15 min. We validated the performance of UBO Detector by showing a) high segmentation (similarity index (SI) = 0.848) and volumetric (intraclass correlation coefficient (ICC) = 0.985) agreement between the UBO Detector-derived and manually traced WMH; b) highly correlated (r 2  > 0.9) and a steady increase of WMH volumes over time; and c) significant associations of periventricular (t = 22.591, p deep (t = 14.523, p < 0.001) WMH volumes generated by UBO Detector with Fazekas rating scores. With parallel computing enabled in UBO Detector, the processing can take advantage of multi-core CPU's that are commonly available on workstations. In conclusion, UBO Detector is a reliable, efficient and fully automated WMH segmentation pipeline. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Feasibility of Commercially Available, Fully Automated Hepatic CT Volumetry for Assessing Both Total and Territorial Liver Volumes in Liver Transplantation

    Shin, Cheong Il; Kim, Se Hyung; Rhim, Jung Hyo; Yi, Nam Joon; Suh, Kyung Suk; Lee, Jeong Min; Han, Joon Koo; Choi, Byung Ihn [Seoul National University Hospital, Seoul (Korea, Republic of)

    2013-02-15

    To assess the feasibility of commercially-available, fully automated hepatic CT volumetry for measuring both total and territorial liver volumes by comparing with interactive manual volumetry and measured ex-vivo liver volume. For the assessment of total and territorial liver volume, portal phase CT images of 77 recipients and 107 donors who donated right hemiliver were used. Liver volume was measured using both the fully automated and interactive manual methods with Advanced Liver Analysis software. The quality of the automated segmentation was graded on a 4-point scale. Grading was performed by two radiologists in consensus. For the cases with excellent-to-good quality, the accuracy of automated volumetry was compared with interactive manual volumetry and measured ex-vivo liver volume which was converted from weight using analysis of variance test and Pearson's or Spearman correlation test. Processing time for both automated and interactive manual methods was also compared. Excellent-to-good quality of automated segmentation for total liver and right hemiliver was achieved in 57.1% (44/77) and 17.8% (19/107), respectively. For both total and right hemiliver volumes, there were no significant differences among automated, manual, and ex-vivo volumes except between automate volume and manual volume of the total liver (p = 0.011). There were good correlations between automate volume and ex-vivo liver volume ({gamma}= 0.637 for total liver and {gamma}= 0.767 for right hemiliver). Both correlation coefficients were higher than those with manual method. Fully automated volumetry required significantly less time than interactive manual method (total liver: 48.6 sec vs. 53.2 sec, right hemiliver: 182 sec vs. 244.5 sec). Fully automated hepatic CT volumetry is feasible and time-efficient for total liver volume measurement. However, its usefulness for territorial liver volumetry needs to be improved.

  6. Feasibility of Commercially Available, Fully Automated Hepatic CT Volumetry for Assessing Both Total and Territorial Liver Volumes in Liver Transplantation

    Shin, Cheong Il; Kim, Se Hyung; Rhim, Jung Hyo; Yi, Nam Joon; Suh, Kyung Suk; Lee, Jeong Min; Han, Joon Koo; Choi, Byung Ihn

    2013-01-01

    To assess the feasibility of commercially-available, fully automated hepatic CT volumetry for measuring both total and territorial liver volumes by comparing with interactive manual volumetry and measured ex-vivo liver volume. For the assessment of total and territorial liver volume, portal phase CT images of 77 recipients and 107 donors who donated right hemiliver were used. Liver volume was measured using both the fully automated and interactive manual methods with Advanced Liver Analysis software. The quality of the automated segmentation was graded on a 4-point scale. Grading was performed by two radiologists in consensus. For the cases with excellent-to-good quality, the accuracy of automated volumetry was compared with interactive manual volumetry and measured ex-vivo liver volume which was converted from weight using analysis of variance test and Pearson's or Spearman correlation test. Processing time for both automated and interactive manual methods was also compared. Excellent-to-good quality of automated segmentation for total liver and right hemiliver was achieved in 57.1% (44/77) and 17.8% (19/107), respectively. For both total and right hemiliver volumes, there were no significant differences among automated, manual, and ex-vivo volumes except between automate volume and manual volume of the total liver (p = 0.011). There were good correlations between automate volume and ex-vivo liver volume (γ= 0.637 for total liver and γ= 0.767 for right hemiliver). Both correlation coefficients were higher than those with manual method. Fully automated volumetry required significantly less time than interactive manual method (total liver: 48.6 sec vs. 53.2 sec, right hemiliver: 182 sec vs. 244.5 sec). Fully automated hepatic CT volumetry is feasible and time-efficient for total liver volume measurement. However, its usefulness for territorial liver volumetry needs to be improved.

  7. Optic disc boundary segmentation from diffeomorphic demons registration of monocular fundus image sequences versus 3D visualization of stereo fundus image pairs for automated early stage glaucoma assessment

    Gatti, Vijay; Hill, Jason; Mitra, Sunanda; Nutter, Brian

    2014-03-01

    Despite the current availability in resource-rich regions of advanced technologies in scanning and 3-D imaging in current ophthalmology practice, world-wide screening tests for early detection and progression of glaucoma still consist of a variety of simple tools, including fundus image-based parameters such as CDR (cup to disc diameter ratio) and CAR (cup to disc area ratio), especially in resource -poor regions. Reliable automated computation of the relevant parameters from fundus image sequences requires robust non-rigid registration and segmentation techniques. Recent research work demonstrated that proper non-rigid registration of multi-view monocular fundus image sequences could result in acceptable segmentation of cup boundaries for automated computation of CAR and CDR. This research work introduces a composite diffeomorphic demons registration algorithm for segmentation of cup boundaries from a sequence of monocular images and compares the resulting CAR and CDR values with those computed manually by experts and from 3-D visualization of stereo pairs. Our preliminary results show that the automated computation of CDR and CAR from composite diffeomorphic segmentation of monocular image sequences yield values comparable with those from the other two techniques and thus may provide global healthcare with a cost-effective yet accurate tool for management of glaucoma in its early stage.

  8. Development of an automated 3D segmentation program for volume quantification of body fat distribution using CT

    Ohshima, Shunsuke; Yamamoto, Shuji; Yamaji, Taiki

    2008-01-01

    The objective of this study was to develop a computing tool for full-automatic segmentation of body fat distributions on volumetric CT images. We developed an algorithm to automatically identify the body perimeter and the inner contour that separates visceral fat from subcutaneous fat. Diaphragmatic surfaces can be extracted by model-based segmentation to match the bottom surface of the lung in CT images for determination of the upper limitation of the abdomen. The functions for quantitative evaluation of abdominal obesity or obesity-related metabolic syndrome were implemented with a prototype three-dimensional (3D) image processing workstation. The volumetric ratios of visceral fat to total fat and visceral fat to subcutaneous fat for each subject can be calculated. Additionally, color intensity mapping of subcutaneous areas and the visceral fat layer is quite obvious in understanding the risk of abdominal obesity with the 3D surface display. Preliminary results obtained have been useful in medical checkups and have contributed to improved efficiency in checking obesity throughout the whole range of the abdomen with 3D visualization and analysis. (author)

  9. Semi-automated tabulation of the 3D topology and morphology of branching networks using CT: application to the airway tree

    Sauret, V.; Bailey, A.G.

    1999-01-01

    Detailed information on biological branching networks (optical nerves, airways or blood vessels) is often required to improve the analysis of 3D medical imaging data. A semi-automated algorithm has been developed to obtain the full 3D topology and dimensions (direction cosine, length, diameter, branching and gravity angles) of branching networks using their CT images. It has been tested using CT images of a simple Perspex branching network and applied to the CT images of a human cast of the airway tree. The morphology and topology of the computer derived network were compared with the manually measured dimensions. Good agreement was found. The airways dimensions also compared well with previous values quoted in literature. This algorithm can provide complete data set analysis much more quickly than manual measurements. Its use is limited by the CT resolution which means that very small branches are not visible. New data are presented on the branching angles of the airway tree. (author)

  10. Microscope image based fully automated stomata detection and pore measurement method for grapevines

    Hiranya Jayakody

    2017-11-01

    Full Text Available Abstract Background Stomatal behavior in grapevines has been identified as a good indicator of the water stress level and overall health of the plant. Microscope images are often used to analyze stomatal behavior in plants. However, most of the current approaches involve manual measurement of stomatal features. The main aim of this research is to develop a fully automated stomata detection and pore measurement method for grapevines, taking microscope images as the input. The proposed approach, which employs machine learning and image processing techniques, can outperform available manual and semi-automatic methods used to identify and estimate stomatal morphological features. Results First, a cascade object detection learning algorithm is developed to correctly identify multiple stomata in a large microscopic image. Once the regions of interest which contain stomata are identified and extracted, a combination of image processing techniques are applied to estimate the pore dimensions of the stomata. The stomata detection approach was compared with an existing fully automated template matching technique and a semi-automatic maximum stable extremal regions approach, with the proposed method clearly surpassing the performance of the existing techniques with a precision of 91.68% and an F1-score of 0.85. Next, the morphological features of the detected stomata were measured. Contrary to existing approaches, the proposed image segmentation and skeletonization method allows us to estimate the pore dimensions even in cases where the stomatal pore boundary is only partially visible in the microscope image. A test conducted using 1267 images of stomata showed that the segmentation and skeletonization approach was able to correctly identify the stoma opening 86.27% of the time. Further comparisons made with manually traced stoma openings indicated that the proposed method is able to estimate stomata morphological features with accuracies of 89.03% for area

  11. Evaluation of right ventricular function by coronary computed tomography angiography using a novel automated 3D right ventricle volume segmentation approach: a validation study.

    Burghard, Philipp; Plank, Fabian; Beyer, Christoph; Müller, Silvana; Dörler, Jakob; Zaruba, Marc-Michael; Pölzl, Leo; Pölzl, Gerhard; Klauser, Andrea; Rauch, Stefan; Barbieri, Fabian; Langer, Christian-Ekkehardt; Schgoer, Wilfried; Williamson, Eric E; Feuchtner, Gudrun

    2018-06-04

    To evaluate right ventricle (RV) function by coronary computed tomography angiography (CTA) using a novel automated three-dimensional (3D) RV volume segmentation tool in comparison with clinical reference modalities. Twenty-six patients with severe end-stage heart failure [left ventricle (LV) ejection fraction (EF) right heart invasive catheterisation (IC). Automated 3D RV volume segmentation was successful in 26 (100%) patients. Read-out time was 3 min 33 s (range, 1 min 50s-4 min 33s). RV EF by CTA was stronger correlated with right atrial pressure (RAP) by IC (r = -0.595; p = 0.006) but weaker with TAPSE (r = 0.366, p = 0.94). When comparing TAPSE with RAP by IC (r = -0.317, p = 0.231), a weak-to-moderate non-significant inverse correlation was found. Interobserver correlation was high with r = 0.96 (p right atrium (RA) and right ventricle (RV) was 196.9 ± 75.3 and 217.5 ± 76.1 HU, respectively. Measurement of RV function by CTA using a novel 3D volumetric segmentation tool is fast and reliable by applying a dedicated biphasic injection protocol. The RV EF from CTA is a closer surrogate of RAP than TAPSE by TTE. • Evaluation of RV function by cardiac CTA by using a novel 3D volume segmentation tool is fast and reliable. • A biphasic contrast agent injection protocol ensures homogenous RV contrast attenuation. • Cardiac CT is a valuable alternative modality to CMR for the evaluation of RV function.

  12. AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

    Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

    2013-01-01

    New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

  13. Development and evaluation of fully automated demand response in large facilities

    Piette, Mary Ann; Sezgen, Osman; Watson, David S.; Motegi, Naoya; Shockman, Christine; ten Hope, Laurie

    2004-03-30

    This report describes the results of a research project to develop and evaluate the performance of new Automated Demand Response (Auto-DR) hardware and software technology in large facilities. Demand Response (DR) is a set of activities to reduce or shift electricity use to improve electric grid reliability, manage electricity costs, and ensure that customers receive signals that encourage load reduction during times when the electric grid is near its capacity. The two main drivers for widespread demand responsiveness are the prevention of future electricity crises and the reduction of electricity prices. Additional goals for price responsiveness include equity through cost of service pricing, and customer control of electricity usage and bills. The technology developed and evaluated in this report could be used to support numerous forms of DR programs and tariffs. For the purpose of this report, we have defined three levels of Demand Response automation. Manual Demand Response involves manually turning off lights or equipment; this can be a labor-intensive approach. Semi-Automated Response involves the use of building energy management control systems for load shedding, where a preprogrammed load shedding strategy is initiated by facilities staff. Fully-Automated Demand Response is initiated at a building or facility through receipt of an external communications signal--facility staff set up a pre-programmed load shedding strategy which is automatically initiated by the system without the need for human intervention. We have defined this approach to be Auto-DR. An important concept in Auto-DR is that a facility manager is able to ''opt out'' or ''override'' an individual DR event if it occurs at a time when the reduction in end-use services is not desirable. This project sought to improve the feasibility and nature of Auto-DR strategies in large facilities. The research focused on technology development, testing

  14. Semi-automated landmark-based 3D analysis reveals new morphometric characteristics in the trochlear dysplastic femur.

    Van Haver, Annemieke; De Roo, Karel; De Beule, Matthieu; Van Cauter, Sofie; Audenaert, Emmanuel; Claessens, Tom; Verdonk, Peter

    2014-11-01

    The authors hypothesise that the trochlear dysplastic distal femur is not only characterised by morphological changes to the trochlea. The purpose of this study is to describe the morphological characteristics of the trochlear dysplastic femur in and outside the trochlear region with a landmark-based 3D analysis. Arthro-CT scans of 20 trochlear dysplastic and 20 normal knees were used to generate 3D models including the cartilage. To rule out size differences, a set of landmarks were defined on the distal femur to isotropically scale the 3D models to a standard size. A predefined series of landmark-based reference planes were applied on the distal femur. With these landmarks and reference planes, a series of previously described characteristics associated with trochlear dysplasia as well as a series of morphometric characteristics were measured. For the previously described characteristics, the analysis replicated highly significant differences between trochlear dysplastic and normal knees. Furthermore, the analysis showed that, when knee size is taken into account, the cut-off values of the trochlear bump and depth would be 1 mm larger in the largest knees compared to the smallest knees. For the morphometric characteristics, the analysis revealed that the trochlear dysplastic femur is also characterised by a 10% smaller intercondylar notch, 6-8% larger posterior condyles (lateral-medial) in the anteroposterior direction and a 6% larger medial condyle in the proximodistal direction compared to a normal femur. This study shows that knee size is important in the application of absolute metric cut-off values and that the posterior femur also shows a significantly different morphology.

  15. Evaluation of left atrial function by multidetector computed tomography before left atrial radiofrequency-catheter ablation: Comparison of a manual and automated 3D volume segmentation method

    Wolf, Florian; Ourednicek, Petr; Loewe, Christian; Richter, Bernhard; Goessinger, Heinz David; Gwechenberger, Marianne; Plank, Christina; Schernthaner, Ruediger Egbert; Toepker, Michael; Lammer, Johannes; Feuchtner, Gudrun M.

    2010-01-01

    Introduction: The purpose of this study was to compare a manual and automated 3D volume segmentation tool for evaluation of left atrial (LA) function by 64-slice multidetector-CT (MDCT). Methods and materials: In 33 patients with paroxysmal atrial fibrillation a MDCT scan was performed before radiofrequency-catheter ablation. Atrial function (minimal volume (LAmin), maximal volume (LAmax), stroke volume (SV), ejection fraction (EF)) was evaluated by two readers using a manual and an automatic tool and measurement time was evaluated. Results: Automated LA volume segmentation failed in one patient due to low LA enhancement (103HU). Mean LAmax, LAmin, SV and EF were 127.7 ml, 93 ml, 34.7 ml, 27.1% by the automated, and 122.7 ml, 89.9 ml, 32.8 ml, 26.3% by the manual method with no significant difference (p > 0.05) and high Pearsons correlation coefficients (r = 0.94, r = 0.94, r = 0.82 and r = 0.85, p < 0.0001), respectively. The automated method was significantly faster (p < 0.001). Interobserver variability was low for both methods with Pearson's correlation coefficients between 0.98 and 0.99 (p < 0.0001). Conclusions: Evaluation of LA volume and function with 64-slice MDCT is feasible with a very low interobserver variability. The automatic method is as accurate as the manual method but significantly less time consuming permitting a routine use in clinical practice before RF-catheter ablation.

  16. Self-consistent hybrid functionals for solids: a fully-automated implementation

    Erba, A.

    2017-08-01

    A fully-automated algorithm for the determination of the system-specific optimal fraction of exact exchange in self-consistent hybrid functionals of the density-functional-theory is illustrated, as implemented into the public Crystal program. The exchange fraction of this new class of functionals is self-consistently updated proportionally to the inverse of the dielectric response of the system within an iterative procedure (Skone et al 2014 Phys. Rev. B 89, 195112). Each iteration of the present scheme, in turn, implies convergence of a self-consistent-field (SCF) and a coupled-perturbed-Hartree-Fock/Kohn-Sham (CPHF/KS) procedure. The present implementation, beside improving the user-friendliness of self-consistent hybrids, exploits the unperturbed and electric-field perturbed density matrices from previous iterations as guesses for subsequent SCF and CPHF/KS iterations, which is documented to reduce the overall computational cost of the whole process by a factor of 2.

  17. Fully automated laser ray tracing system to measure changes in the crystalline lens GRIN profile.

    Qiu, Chen; Maceo Heilman, Bianca; Kaipio, Jari; Donaldson, Paul; Vaghefi, Ehsan

    2017-11-01

    Measuring the lens gradient refractive index (GRIN) accurately and reliably has proven an extremely challenging technical problem. A fully automated laser ray tracing (LRT) system was built to address this issue. The LRT system captures images of multiple laser projections before and after traversing through an ex vivo lens. These LRT images, combined with accurate measurements of the lens geometry, are used to calculate the lens GRIN profile. Mathematically, this is an ill-conditioned problem; hence, it is essential to apply biologically relevant constraints to produce a feasible solution. The lens GRIN measurements were compared with previously published data. Our GRIN retrieval algorithm produces fast and accurate measurements of the lens GRIN profile. Experiments to study the optics of physiologically perturbed lenses are the future direction of this research.

  18. Fully automated left ventricular contour detection for gated radionuclide angiography, (1)

    Hosoba, Minoru; Wani, Hidenobu; Hiroe, Michiaki; Kusakabe, Kiyoko.

    1984-01-01

    A fully automated practical method has been developed to detect the left ventricular (LV) contour from gated pool images. Ejection fraction and volume curve can be computed accurately without operater variance. The characteristics of the method are summarized as follows: 1. Optimal design of the filter that works on Fourier domain, can be achieved to improve the signal to noise ratio. 2. New algorithm which use the cosine and sine transform images has been developed for the separating ventricle from atrium and defining center of LV. 3. Contrast enhancement by optimized square filter. 4. Radial profiles are generated from the center of LV and smoothed by fourth order Fourier series approximation. The crossing point with local threshold value searched from the center of the LV is defined as edge. 5. LV contour is obtained by conecting all the edge points defined on radial profiles by fitting them to Fourier function. (author)

  19. Clinical validation of fully automated computation of ejection fraction from gated equilibrium blood-pool scintigrams

    Reiber, J.H.C.; Lie, S.P.; Simoons, M.L.; Hoek, C.; Gerbrands, J.J.; Wijns, W.; Bakker, W.H.; Kooij, P.P.M.

    1983-01-01

    A fully automated procedure for the computation of left-ventricular ejection fraction (EF) from cardiac-gated Tc-99m blood-pool (GBP) scintigrams with fixed, dual, and variable ROI methods is described. By comparison with EF data from contrast ventriculography in 68 patients, the dual-ROI method (separate end-diastolic and end-systolic contours) was found to be the method of choice; processing time was 2 min. Success score of dual-ROI procedure was 92% as assessed from 100 GBP studies. Overall reproducibility of data acquisition and analysis was determined in 12 patients. Mean value and standard deviation of differences between repeat studies (average time interval 27 min) were 0.8% and 4.3% EF units, respectively, (r=0.98). The authors conclude that left-ventricular EF can be computed automatically from GBP scintigrams with minimal operator-interaction and good reproducibility; EFs are similar to those from contrast ventriculography

  20. A fully automated entanglement-based quantum cryptography system for telecom fiber networks

    Treiber, Alexander; Ferrini, Daniele; Huebel, Hannes; Zeilinger, Anton; Poppe, Andreas; Loruenser, Thomas; Querasser, Edwin; Matyus, Thomas; Hentschel, Michael

    2009-01-01

    We present in this paper a quantum key distribution (QKD) system based on polarization entanglement for use in telecom fibers. A QKD exchange up to 50 km was demonstrated in the laboratory with a secure key rate of 550 bits s -1 . The system is compact and portable with a fully automated start-up, and stabilization modules for polarization, synchronization and photon coupling allow hands-off operation. Stable and reliable key exchange in a deployed optical fiber of 16 km length was demonstrated. In this fiber network, we achieved over 2 weeks an automatic key generation with an average key rate of 2000 bits s -1 without manual intervention. During this period, the system had an average entanglement visibility of 93%, highlighting the technical level and stability achieved for entanglement-based quantum cryptography.

  1. The worldwide NORM production and a fully automated gamma-ray spectrometer for their characterization

    Xhixha, G.; Callegari, I.; Guastaldi, E.; De Bianchi, S.; Fiorentini, G.; Universita di Ferrara, Ferrara; Istituto Nazionale di Fisica Nucleare; Kaceli Xhixha, M.

    2013-01-01

    Materials containing radionuclides of natural origin and being subject to regulation because of their radioactivity are known as Naturally Occurring Radioactive Material (NORM). By following International Atomic Energy Agency, we include in NORM those materials with an activity concentration, which is modified by human made processes. We present a brief review of the main categories of non-nuclear industries together with the levels of activity concentration in feed raw materials, products and waste, including mechanisms of radioisotope enrichments. The global management of NORM shows a high level of complexity, mainly due to different degrees of radioactivity enhancement and the huge amount of worldwide waste production. The future tendency of guidelines concerning environmental protection will require both a systematic monitoring based on the ever-increasing sampling and high performance of gamma-ray spectroscopy. On the ground of these requirements a new low-background fully automated high-resolution gamma-ray spectrometer MCA R ad has been developed. The design of lead and cooper shielding allowed to reach a background reduction of two order of magnitude with respect to laboratory radioactivity. A severe lowering of manpower cost is obtained through a fully automation system, which enables up to 24 samples to be measured without any human attendance. Two coupled HPGe detectors increase the detection efficiency, performing accurate measurements on small sample volume (180 cm 3 ) with a reduction of sample transport cost of material. Details of the instrument calibration method are presented. MCA R ad system can measure in less than one hour a typical NORM sample enriched in U and Th with some hundreds of Bq kg -1 , with an overall uncertainty less than 5 %. Quality control of this method has been tested. Measurements of three certified reference materials RGK-1, RGU-2 and RGTh-1 containing concentrations of potassium, uranium and thorium comparable to NORM have

  2. Development of a phantom to test fully automated breast density software – A work in progress

    Waade, G.G.; Hofvind, S.; Thompson, J.D.; Highnam, R.; Hogg, P.

    2017-01-01

    Objectives: Mammographic density (MD) is an independent risk factor for breast cancer and may have a future role for stratified screening. Automated software can estimate MD but the relationship between breast thickness reduction and MD is not fully understood. Our aim is to develop a deformable breast phantom to assess automated density software and the impact of breast thickness reduction on MD. Methods: Several different configurations of poly vinyl alcohol (PVAL) phantoms were created. Three methods were used to estimate their density. Raw image data of mammographic images were processed using Volpara to estimate volumetric breast density (VBD%); Hounsfield units (HU) were measured on CT images; and physical density (g/cm 3 ) was calculated using a formula involving mass and volume. Phantom volume versus contact area and phantom volume versus phantom thickness was compared to values of real breasts. Results: Volpara recognized all deformable phantoms as female breasts. However, reducing the phantom thickness caused a change in phantom density and the phantoms were not able to tolerate same level of compression and thickness reduction experienced by female breasts during mammography. Conclusion: Our results are promising as all phantoms resulted in valid data for automated breast density measurement. Further work should be conducted on PVAL and other materials to produce deformable phantoms that mimic female breast structure and density with the ability of being compressed to the same level as female breasts. Advances in knowledge: We are the first group to have produced deformable phantoms that are recognized as breasts by Volpara software. - Highlights: • Several phantoms of different configurations were created. • Three methods to assess phantom density were implemented. • All phantoms were identified as breasts by the Volpara software. • Reducing phantom thickness caused a change in phantom density.

  3. A fully automated system for quantification of background parenchymal enhancement in breast DCE-MRI

    Ufuk Dalmiş, Mehmet; Gubern-Mérida, Albert; Borelli, Cristina; Vreemann, Suzan; Mann, Ritse M.; Karssemeijer, Nico

    2016-03-01

    Background parenchymal enhancement (BPE) observed in breast dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) has been identified as an important biomarker associated with risk for developing breast cancer. In this study, we present a fully automated framework for quantification of BPE. We initially segmented fibroglandular tissue (FGT) of the breasts using an improved version of an existing method. Subsequently, we computed BPEabs (volume of the enhancing tissue), BPErf (BPEabs divided by FGT volume) and BPErb (BPEabs divided by breast volume), using different relative enhancement threshold values between 1% and 100%. To evaluate and compare the previous and improved FGT segmentation methods, we used 20 breast DCE-MRI scans and we computed Dice similarity coefficient (DSC) values with respect to manual segmentations. For evaluation of the BPE quantification, we used a dataset of 95 breast DCE-MRI scans. Two radiologists, in individual reading sessions, visually analyzed the dataset and categorized each breast into minimal, mild, moderate and marked BPE. To measure the correlation between automated BPE values to the radiologists' assessments, we converted these values into ordinal categories and we used Spearman's rho as a measure of correlation. According to our results, the new segmentation method obtained an average DSC of 0.81 0.09, which was significantly higher (p<0.001) compared to the previous method (0.76 0.10). The highest correlation values between automated BPE categories and radiologists' assessments were obtained with the BPErf measurement (r=0.55, r=0.49, p<0.001 for both), while the correlation between the scores given by the two radiologists was 0.82 (p<0.001). The presented framework can be used to systematically investigate the correlation between BPE and risk in large screening cohorts.

  4. A fully automated cell segmentation and morphometric parameter system for quantifying corneal endothelial cell morphology.

    Al-Fahdawi, Shumoos; Qahwaji, Rami; Al-Waisy, Alaa S; Ipson, Stanley; Ferdousi, Maryam; Malik, Rayaz A; Brahma, Arun

    2018-07-01

    Corneal endothelial cell abnormalities may be associated with a number of corneal and systemic diseases. Damage to the endothelial cells can significantly affect corneal transparency by altering hydration of the corneal stroma, which can lead to irreversible endothelial cell pathology requiring corneal transplantation. To date, quantitative analysis of endothelial cell abnormalities has been manually performed by ophthalmologists using time consuming and highly subjective semi-automatic tools, which require an operator interaction. We developed and applied a fully-automated and real-time system, termed the Corneal Endothelium Analysis System (CEAS) for the segmentation and computation of endothelial cells in images of the human cornea obtained by in vivo corneal confocal microscopy. First, a Fast Fourier Transform (FFT) Band-pass filter is applied to reduce noise and enhance the image quality to make the cells more visible. Secondly, endothelial cell boundaries are detected using watershed transformations and Voronoi tessellations to accurately quantify the morphological parameters of the human corneal endothelial cells. The performance of the automated segmentation system was tested against manually traced ground-truth images based on a database consisting of 40 corneal confocal endothelial cell images in terms of segmentation accuracy and obtained clinical features. In addition, the robustness and efficiency of the proposed CEAS system were compared with manually obtained cell densities using a separate database of 40 images from controls (n = 11), obese subjects (n = 16) and patients with diabetes (n = 13). The Pearson correlation coefficient between automated and manual endothelial cell densities is 0.9 (p system, and the possibility of utilizing it in a real world clinical setting to enable rapid diagnosis and for patient follow-up, with an execution time of only 6 seconds per image. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Toxicity assessment of ionic liquids with Vibrio fischeri: an alternative fully automated methodology.

    Costa, Susana P F; Pinto, Paula C A G; Lapa, Rui A S; Saraiva, M Lúcia M F S

    2015-03-02

    A fully automated Vibrio fischeri methodology based on sequential injection analysis (SIA) has been developed. The methodology was based on the aspiration of 75 μL of bacteria and 50 μL of inhibitor followed by measurement of the luminescence of bacteria. The assays were conducted for contact times of 5, 15, and 30 min, by means of three mixing chambers that ensured adequate mixing conditions. The optimized methodology provided a precise control of the reaction conditions which is an asset for the analysis of a large number of samples. The developed methodology was applied to the evaluation of the impact of a set of ionic liquids (ILs) on V. fischeri and the results were compared with those provided by a conventional assay kit (Biotox(®)). The collected data evidenced the influence of different cation head groups and anion moieties on the toxicity of ILs. Generally, aromatic cations and fluorine-containing anions displayed higher impact on V. fischeri, evidenced by lower EC50. The proposed methodology was validated through statistical analysis which demonstrated a strong positive correlation (P>0.98) between assays. It is expected that the automated methodology can be tested for more classes of compounds and used as alternative to microplate based V. fischeri assay kits. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Photochemical-chemiluminometric determination of aldicarb in a fully automated multicommutation based flow-assembly

    Palomeque, M.; Garcia Bautista, J.A.; Catala Icardo, M.; Garcia Mateo, J.V.; Martinez Calatayud, J.

    2004-01-01

    A sensitive and fully automated method for determination of aldicarb in technical formulations (Temik) and mineral waters is proposed. The automation of the flow-assembly is based on the multicommutation approach, which uses a set of solenoid valves acting as independent switchers. The operating cycle for obtaining a typical analytical transient signal can be easily programmed by means of a home-made software running in the Windows environment. The manifold is provided with a photoreactor consisting of a 150 cm long x 0.8 mm i.d. piece of PTFE tubing coiled around a 20 W low-pressure mercury lamp. The determination of aldicarb is performed on the basis of the iron(III) catalytic mineralization of the pesticide by UV irradiation (150 s), and the chemiluminescent (CL) behavior of the photodegradated pesticide in presence of potassium permanganate and quinine sulphate as sensitizer. UV irradiation of aldicarb turns the very week chemiluminescent pesticide into a strongly chemiluminescent photoproduct. The method is linear over the range 2.2-100.0 μg l -1 of aldicarb; the limit of detection is 0.069 μg l -1 ; the reproducibility (as the R.S.D. of 20 peaks of a 24 μg l -1 solution) is 3.7% and the sample throughput is 17 h -1

  7. Fully automated synthesis system of 3'-deoxy-3'-[18F]fluorothymidine

    Oh, Seung Jun; Mosdzianowski, Christoph; Chi, Dae Yoon; Kim, Jung Young; Kang, Se Hun; Ryu, Jin Sook; Yeo, Jeong Seok; Moon, Dae Hyuk

    2004-01-01

    We developed a new fully automated method for the synthesis of 3'-deoxy-3'-[ 18 F]fluorothymidine ([ 18 F]FLT), by modifying a commercial FDG synthesizer and its disposable fluid pathway. Optimal labeling condition was that 40 mg of precursor in acetonitrile (2 mL) was heated at 150 degree sign C for 100 sec, followed by heating at 85 degree sign C for 450 sec and hydrolysis with 1 N HCl at 105 degree sign C for 300 sec. Using 3.7 GBq of [ 18 F]F - as starting activity, [ 18 F]FLT was obtained with a yield of 50.5±5.2% (n=28, decay corrected) within 60.0±5.4 min including HPLC purification. With 37.0 GBq, we obtained 48.7±5.6% (n=10). The [ 18 F]FLT showed the good stability for 6 h. This new automated synthesis procedure combines high and reproducible yields with the benefits of a disposable cassette system

  8. Fully automated muscle quality assessment by Gabor filtering of second harmonic generation images

    Paesen, Rik; Smolders, Sophie; Vega, José Manolo de Hoyos; Eijnde, Bert O.; Hansen, Dominique; Ameloot, Marcel

    2016-02-01

    Although structural changes on the sarcomere level of skeletal muscle are known to occur due to various pathologies, rigorous studies of the reduced sarcomere quality remain scarce. This can possibly be explained by the lack of an objective tool for analyzing and comparing sarcomere images across biological conditions. Recent developments in second harmonic generation (SHG) microscopy and increasing insight into the interpretation of sarcomere SHG intensity profiles have made SHG microscopy a valuable tool to study microstructural properties of sarcomeres. Typically, sarcomere integrity is analyzed by fitting a set of manually selected, one-dimensional SHG intensity profiles with a supramolecular SHG model. To circumvent this tedious manual selection step, we developed a fully automated image analysis procedure to map the sarcomere disorder for the entire image at once. The algorithm relies on a single-frequency wavelet-based Gabor approach and includes a newly developed normalization procedure allowing for unambiguous data interpretation. The method was validated by showing the correlation between the sarcomere disorder, quantified by the M-band size obtained from manually selected profiles, and the normalized Gabor value ranging from 0 to 1 for decreasing disorder. Finally, to elucidate the applicability of our newly developed protocol, Gabor analysis was used to study the effect of experimental autoimmune encephalomyelitis on the sarcomere regularity. We believe that the technique developed in this work holds great promise for high-throughput, unbiased, and automated image analysis to study sarcomere integrity by SHG microscopy.

  9. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. A fully automated FTIR system for remote sensing of greenhouse gases in the tropics

    Geibel, M. C.; Gerbig, C.; Feist, D. G.

    2010-07-01

    This article introduces a new fully automated FTIR system that is part of the Total Carbon Column Observing Network. It will provide continuous ground-based measurements of column-averaged volume mixing ratio for CO2, CH4 and several other greenhouse gases in the tropics. Housed in a 20-foot shipping container it was developed as a transportable system that could be deployed almost anywhere in the world. We describe the automation concept which relies on three autonomous subsystems and their interaction. Crucial components like a sturdy and reliable solar tracker dome are described in detail. First results of total column measurements at Jena, Germany show that the instrument works well and can provide diurnal as well as seasonal cycle for CO2. Instrument line shape measurements with an HCl cell suggest that the instrument stays well-aligned over several months. After a short test campaign for side by side intercomaprison with an existing TCCON instrument in Australia, the system will be transported to its final destination Ascension Island.

  11. The first fully functional 3D CMOS chip with Deep N-well active pixel sensors for the ILC vertex detector

    Traversi, G.; Gaioni, L.; Manazza, A.; Manghisoni, M.; Ratti, L.; Re, V.

    2013-01-01

    This work presents the characterization of Deep N-well (DNW) active pixel sensors fabricated in a vertically integrated technology. The DNW approach takes advantage of the triple well structure to lay out a sensor with relatively large charge collecting area (as compared to standard three transistor MAPS), while the readout is performed by a classical signal processing chain for capacitive detectors. This new 3D design relies upon stacking two homogeneous tiers fabricated in a 130 nm CMOS process where the top tier is thinned down to about 12μm to expose through silicon vias (TSV), therefore making connection to the buried circuits possible. This technology has been used to design a fine pitch 3D CMOS sensor with sparsification capabilities, in view of vertexing applications to the International Linear Collider (ILC) experiments. Results from the characterization of different kind of test structures, including single pixels, 3×3 and 8×8 matrices, are presented

  12. A multi-resolution approach for an automated fusion of different low-cost 3D sensors.

    Dupuis, Jan; Paulus, Stefan; Behmann, Jan; Plümer, Lutz; Kuhlmann, Heiner

    2014-04-24

    The 3D acquisition of object structures has become a common technique in many fields of work, e.g., industrial quality management, cultural heritage or crime scene documentation. The requirements on the measuring devices are versatile, because spacious scenes have to be imaged with a high level of detail for selected objects. Thus, the used measuring systems are expensive and require an experienced operator. With the rise of low-cost 3D imaging systems, their integration into the digital documentation process is possible. However, common low-cost sensors have the limitation of a trade-off between range and accuracy, providing either a low resolution of single objects or a limited imaging field. Therefore, the use of multiple sensors is desirable. We show the combined use of two low-cost sensors, the Microsoft Kinect and the David laserscanning system, to achieve low-resolved scans of the whole scene and a high level of detail for selected objects, respectively. Afterwards, the high-resolved David objects are automatically assigned to their corresponding Kinect object by the use of surface feature histograms and SVM-classification. The corresponding objects are fitted using an ICP-implementation to produce a multi-resolution map. The applicability is shown for a fictional crime scene and the reconstruction of a ballistic trajectory.

  13. Toward fully automated processing of dynamic susceptibility contrast perfusion MRI for acute ischemic cerebral stroke.

    Kim, Jinsuh; Leira, Enrique C; Callison, Richard C; Ludwig, Bryan; Moritani, Toshio; Magnotta, Vincent A; Madsen, Mark T

    2010-05-01

    We developed fully automated software for dynamic susceptibility contrast (DSC) MR perfusion-weighted imaging (PWI) to efficiently and reliably derive critical hemodynamic information for acute stroke treatment decisions. Brain MR PWI was performed in 80 consecutive patients with acute nonlacunar ischemic stroke within 24h after onset of symptom from January 2008 to August 2009. These studies were automatically processed to generate hemodynamic parameters that included cerebral blood flow and cerebral blood volume, and the mean transit time (MTT). To develop reliable software for PWI analysis, we used computationally robust algorithms including the piecewise continuous regression method to determine bolus arrival time (BAT), log-linear curve fitting, arrival time independent deconvolution method and sophisticated motion correction methods. An optimal arterial input function (AIF) search algorithm using a new artery-likelihood metric was also developed. Anatomical locations of the automatically determined AIF were reviewed and validated. The automatically computed BAT values were statistically compared with estimated BAT by a single observer. In addition, gamma-variate curve-fitting errors of AIF and inter-subject variability of AIFs were analyzed. Lastly, two observes independently assessed the quality and area of hypoperfusion mismatched with restricted diffusion area from motion corrected MTT maps and compared that with time-to-peak (TTP) maps using the standard approach. The AIF was identified within an arterial branch and enhanced areas of perfusion deficit were visualized in all evaluated cases. Total processing time was 10.9+/-2.5s (mean+/-s.d.) without motion correction and 267+/-80s (mean+/-s.d.) with motion correction on a standard personal computer. The MTT map produced with our software adequately estimated brain areas with perfusion deficit and was significantly less affected by random noise of the PWI when compared with the TTP map. Results of image

  14. FluidCam 1&2 - UAV-based Fluid Lensing Instruments for High-Resolution 3D Subaqueous Imaging and Automated Remote Biosphere Assessment of Reef Ecosystems

    Chirayath, V.; Instrella, R.

    2016-02-01

    We present NASA ESTO FluidCam 1 & 2, Visible and NIR Fluid-Lensing-enabled imaging payloads for Unmanned Aerial Vehicles (UAVs). Developed as part of a focused 2014 earth science technology grant, FluidCam 1&2 are Fluid-Lensing-based computational optical imagers designed for automated 3D mapping and remote sensing of underwater coastal targets from airborne platforms. Fluid Lensing has been used to map underwater reefs in 3D in American Samoa and Hamelin Pool, Australia from UAV platforms at sub-cm scale, which has proven a valuable tool in modern marine research for marine biosphere assessment and conservation. We share FluidCam 1&2 instrument validation and testing results as well as preliminary processed data from field campaigns. Petabyte-scale aerial survey efforts using Fluid Lensing to image at-risk reefs demonstrate broad applicability to large-scale automated species identification, morphology studies and reef ecosystem characterization for shallow marine environments and terrestrial biospheres, of crucial importance to improving bathymetry data for physical oceanographic models and understanding climate change's impact on coastal zones, global oxygen production, carbon sequestration.

  15. FULLY AUTOMATED GENERATION OF ACCURATE DIGITAL SURFACE MODELS WITH SUB-METER RESOLUTION FROM SATELLITE IMAGERY

    J. Wohlfeil

    2012-07-01

    Full Text Available Modern pixel-wise image matching algorithms like Semi-Global Matching (SGM are able to compute high resolution digital surface models from airborne and spaceborne stereo imagery. Although image matching itself can be performed automatically, there are prerequisites, like high geometric accuracy, which are essential for ensuring the high quality of resulting surface models. Especially for line cameras, these prerequisites currently require laborious manual interaction using standard tools, which is a growing problem due to continually increasing demand for such surface models. The tedious work includes partly or fully manual selection of tie- and/or ground control points for ensuring the required accuracy of the relative orientation of images for stereo matching. It also includes masking of large water areas that seriously reduce the quality of the results. Furthermore, a good estimate of the depth range is required, since accurate estimates can seriously reduce the processing time for stereo matching. In this paper an approach is presented that allows performing all these steps fully automated. It includes very robust and precise tie point selection, enabling the accurate calculation of the images’ relative orientation via bundle adjustment. It is also shown how water masking and elevation range estimation can be performed automatically on the base of freely available SRTM data. Extensive tests with a large number of different satellite images from QuickBird and WorldView are presented as proof of the robustness and reliability of the proposed method.

  16. Developing Automated Spectral Analysis Tools for Interstellar Features Extractionto Support Construction of the 3D ISM Map

    Puspitarini, L.; Lallement, R.; Monreal-Ibero, A.; Chen, H.-C.; Malasan, H. L.; Aprilia; Arifyanto, M. I.; Irfan, M.

    2018-04-01

    One of the ways to obtain a detailed 3D ISM map is by gathering interstellar (IS) absorption data toward widely distributed background target stars at known distances (line-of-sight/LOS data). The radial and angular evolution of the LOS measurements allow the inference of the ISM spatial distribution. For a better spatial resolution, one needs a large number of the LOS data. It requires building fast tools to measure IS absorption. One of the tools is a global analysis that fit two different diffuse interstellar bands (DIBs) simultaneously. We derived the equivalent width (EW) ratio of the two DIBs recorded in each spectrum of target stars. The ratio variability can be used to study IS environmental conditions or to detect DIB family.

  17. Automated real-time search and analysis algorithms for a non-contact 3D profiling system

    Haynes, Mark; Wu, Chih-Hang John; Beck, B. Terry; Peterman, Robert J.

    2013-04-01

    The purpose of this research is to develop a new means of identifying and extracting geometrical feature statistics from a non-contact precision-measurement 3D profilometer. Autonomous algorithms have been developed to search through large-scale Cartesian point clouds to identify and extract geometrical features. These algorithms are developed with the intent of providing real-time production quality control of cold-rolled steel wires. The steel wires in question are prestressing steel reinforcement wires for concrete members. The geometry of the wire is critical in the performance of the overall concrete structure. For this research a custom 3D non-contact profilometry system has been developed that utilizes laser displacement sensors for submicron resolution surface profiling. Optimizations in the control and sensory system allow for data points to be collected at up to an approximate 400,000 points per second. In order to achieve geometrical feature extraction and tolerancing with this large volume of data, the algorithms employed are optimized for parsing large data quantities. The methods used provide a unique means of maintaining high resolution data of the surface profiles while keeping algorithm running times within practical bounds for industrial application. By a combination of regional sampling, iterative search, spatial filtering, frequency filtering, spatial clustering, and template matching a robust feature identification method has been developed. These algorithms provide an autonomous means of verifying tolerances in geometrical features. The key method of identifying the features is through a combination of downhill simplex and geometrical feature templates. By performing downhill simplex through several procedural programming layers of different search and filtering techniques, very specific geometrical features can be identified within the point cloud and analyzed for proper tolerancing. Being able to perform this quality control in real time

  18. [18F]FMeNER-D2: Reliable fully-automated synthesis for visualization of the norepinephrine transporter

    Rami-Mark, Christina; Zhang, Ming-Rong; Mitterhauser, Markus; Lanzenberger, Rupert; Hacker, Marcus; Wadsak, Wolfgang

    2013-01-01

    Purpose: In neurodegenerative diseases and neuropsychiatric disorders dysregulation of the norepinephrine transporter (NET) has been reported. For visualization of NET availability and occupancy in the human brain PET imaging can be used. Therefore, selective NET-PET tracers with high affinity are required. Amongst these, [ 18 F]FMeNER-D2 is showing the best results so far. Furthermore, a reliable fully automated radiosynthesis is a prerequisite for successful application of PET-tracers. The aim of this work was the automation of [ 18 F]FMeNER-D2 radiolabelling for subsequent clinical use. The presented study comprises 25 automated large-scale syntheses, which were directly applied to healthy volunteers and adult patients suffering from attention deficit hyperactivity disorder (ADHD). Procedures: Synthesis of [ 18 F]FMeNER-D2 was automated within a Nuclear Interface Module. Starting from 20–30 GBq [ 18 F]fluoride, azeotropic drying, reaction with Br 2 CD 2 , distillation of 1-bromo-2-[ 18 F]fluoromethane-D2 ([ 18 F]BFM) and reaction of the pure [ 18 F]BFM with unprotected precursor NER were optimized and completely automated. HPLC purification and SPE procedure were completed, formulation and sterile filtration were achieved on-line and full quality control was performed. Results: Purified product was obtained in a fully automated synthesis in clinical scale allowing maximum radiation safety and routine production under GMP-like manner. So far, more than 25 fully automated syntheses were successfully performed, yielding 1.0–2.5 GBq of formulated [ 18 F]FMeNER-D2 with specific activities between 430 and 1707 GBq/μmol within 95 min total preparation time. Conclusions: A first fully automated [ 18 F]FMeNER-D2 synthesis was established, allowing routine production of this NET-PET tracer under maximum radiation safety and standardization

  19. [{sup 18}F]FMeNER-D2: Reliable fully-automated synthesis for visualization of the norepinephrine transporter

    Rami-Mark, Christina [Radiochemistry and Biomarker Development Unit, Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna (Austria); Department of Inorganic Chemistry, University of Vienna (Austria); Zhang, Ming-Rong [Molecular Imaging Center, National Institute of Radiological Sciences, Chiba (Japan); Mitterhauser, Markus [Radiochemistry and Biomarker Development Unit, Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna (Austria); Hospital Pharmacy of the General Hospital of Vienna (Austria); Lanzenberger, Rupert [Department of Psychiatry and Psychotherapy, Medical University of Vienna (Austria); Hacker, Marcus [Radiochemistry and Biomarker Development Unit, Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna (Austria); Wadsak, Wolfgang [Radiochemistry and Biomarker Development Unit, Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna (Austria); Department of Inorganic Chemistry, University of Vienna (Austria)

    2013-11-15

    Purpose: In neurodegenerative diseases and neuropsychiatric disorders dysregulation of the norepinephrine transporter (NET) has been reported. For visualization of NET availability and occupancy in the human brain PET imaging can be used. Therefore, selective NET-PET tracers with high affinity are required. Amongst these, [{sup 18}F]FMeNER-D2 is showing the best results so far. Furthermore, a reliable fully automated radiosynthesis is a prerequisite for successful application of PET-tracers. The aim of this work was the automation of [{sup 18}F]FMeNER-D2 radiolabelling for subsequent clinical use. The presented study comprises 25 automated large-scale syntheses, which were directly applied to healthy volunteers and adult patients suffering from attention deficit hyperactivity disorder (ADHD). Procedures: Synthesis of [{sup 18}F]FMeNER-D2 was automated within a Nuclear Interface Module. Starting from 20–30 GBq [{sup 18}F]fluoride, azeotropic drying, reaction with Br{sub 2}CD{sub 2}, distillation of 1-bromo-2-[{sup 18}F]fluoromethane-D2 ([{sup 18}F]BFM) and reaction of the pure [{sup 18}F]BFM with unprotected precursor NER were optimized and completely automated. HPLC purification and SPE procedure were completed, formulation and sterile filtration were achieved on-line and full quality control was performed. Results: Purified product was obtained in a fully automated synthesis in clinical scale allowing maximum radiation safety and routine production under GMP-like manner. So far, more than 25 fully automated syntheses were successfully performed, yielding 1.0–2.5 GBq of formulated [{sup 18}F]FMeNER-D2 with specific activities between 430 and 1707 GBq/μmol within 95 min total preparation time. Conclusions: A first fully automated [{sup 18}F]FMeNER-D2 synthesis was established, allowing routine production of this NET-PET tracer under maximum radiation safety and standardization.

  20. [18F]FMeNER-D2: reliable fully-automated synthesis for visualization of the norepinephrine transporter.

    Rami-Mark, Christina; Zhang, Ming-Rong; Mitterhauser, Markus; Lanzenberger, Rupert; Hacker, Marcus; Wadsak, Wolfgang

    2013-11-01

    In neurodegenerative diseases and neuropsychiatric disorders dysregulation of the norepinephrine transporter (NET) has been reported. For visualization of NET availability and occupancy in the human brain PET imaging can be used. Therefore, selective NET-PET tracers with high affinity are required. Amongst these, [(18)F]FMeNER-D2 is showing the best results so far. Furthermore, a reliable fully automated radiosynthesis is a prerequisite for successful application of PET-tracers. The aim of this work was the automation of [(18)F]FMeNER-D2 radiolabelling for subsequent clinical use. The presented study comprises 25 automated large-scale syntheses, which were directly applied to healthy volunteers and adult patients suffering from attention deficit hyperactivity disorder (ADHD). Synthesis of [(18)F]FMeNER-D2 was automated within a Nuclear Interface Module. Starting from 20-30 GBq [(18)F]fluoride, azeotropic drying, reaction with Br2CD2, distillation of 1-bromo-2-[(18)F]fluoromethane-D2 ([(18)F]BFM) and reaction of the pure [(18)F]BFM with unprotected precursor NER were optimized and completely automated. HPLC purification and SPE procedure were completed, formulation and sterile filtration were achieved on-line and full quality control was performed. Purified product was obtained in a fully automated synthesis in clinical scale allowing maximum radiation safety and routine production under GMP-like manner. So far, more than 25 fully automated syntheses were successfully performed, yielding 1.0-2.5 GBq of formulated [(18)F]FMeNER-D2 with specific activities between 430 and 1707 GBq/μmol within 95 min total preparation time. A first fully automated [(18)F]FMeNER-D2 synthesis was established, allowing routine production of this NET-PET tracer under maximum radiation safety and standardization. © 2013.

  1. Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome.

    Nick M Powell

    Full Text Available We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques-superior to single-atlas methods-together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry-advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings.

  2. Open-Source Assisted Laboratory Automation through Graphical User Interfaces and 3D Printers: Application to Equipment Hyphenation for Higher-Order Data Generation.

    Siano, Gabriel G; Montemurro, Milagros; Alcaráz, Mirta R; Goicoechea, Héctor C

    2017-10-17

    Higher-order data generation implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation are the key to obtaining higher-order data, the required simultaneous control of them demands funds for new hardware, software, and licenses, in addition to very skilled operators. In this work, we present Design of Inputs-Outputs with Sikuli (DIOS), a free and open-source code program that provides a general framework for the design of automated experimental procedures without prior knowledge of programming or electronics. Basically, instruments and devices are considered as nodes in a network, and every node is associated both with physical and virtual inputs and outputs. Virtual components, such as graphical user interfaces (GUIs) of equipment, are handled by means of image recognition tools provided by Sikuli scripting language, while handling of their physical counterparts is achieved using an adapted open-source three-dimensional (3D) printer. Two previously reported experiments of our research group, related to fluorescence matrices derived from kinetics and high-performance liquid chromatography, were adapted to be carried out in a more automated fashion. Satisfactory results, in terms of analytical performance, were obtained. Similarly, advantages derived from open-source tools assistance could be appreciated, mainly in terms of lesser intervention of operators and cost savings.

  3. Automated volume analysis of head and neck lesions on CT scans using 3D level set segmentation

    Street, Ethan; Hadjiiski, Lubomir; Sahiner, Berkman; Gujar, Sachin; Ibrahim, Mohannad; Mukherji, Suresh K.; Chan, Heang-Ping

    2007-01-01

    The authors have developed a semiautomatic system for segmentation of a diverse set of lesions in head and neck CT scans. The system takes as input an approximate bounding box, and uses a multistage level set to perform the final segmentation. A data set consisting of 69 lesions marked on 33 scans from 23 patients was used to evaluate the performance of the system. The contours from automatic segmentation were compared to both 2D and 3D gold standard contours manually drawn by three experienced radiologists. Three performance metric measures were used for the comparison. In addition, a radiologist provided quality ratings on a 1 to 10 scale for all of the automatic segmentations. For this pilot study, the authors observed that the differences between the automatic and gold standard contours were larger than the interobserver differences. However, the system performed comparably to the radiologists, achieving an average area intersection ratio of 85.4% compared to an average of 91.2% between two radiologists. The average absolute area error was 21.1% compared to 10.8%, and the average 2D distance was 1.38 mm compared to 0.84 mm between the radiologists. In addition, the quality rating data showed that, despite the very lax assumptions made on the lesion characteristics in designing the system, the automatic contours approximated many of the lesions very well

  4. In Situ 3D Segmentation of Individual Plant Leaves Using a RGB-D Camera for Agricultural Automation

    Chunlei Xia

    2015-08-01

    Full Text Available In this paper, we present a challenging task of 3D segmentation of individual plant leaves from occlusions in the complicated natural scene. Depth data of plant leaves is introduced to improve the robustness of plant leaf segmentation. The low cost RGB-D camera is utilized to capture depth and color image in fields. Mean shift clustering is applied to segment plant leaves in depth image. Plant leaves are extracted from the natural background by examining vegetation of the candidate segments produced by mean shift. Subsequently, individual leaves are segmented from occlusions by active contour models. Automatic initialization of the active contour models is implemented by calculating the center of divergence from the gradient vector field of depth image. The proposed segmentation scheme is tested through experiments under greenhouse conditions. The overall segmentation rate is 87.97% while segmentation rates for single and occluded leaves are 92.10% and 86.67%, respectively. Approximately half of the experimental results show segmentation rates of individual leaves higher than 90%. Nevertheless, the proposed method is able to segment individual leaves from heavy occlusions.

  5. Automated matching of corresponding seed images of three simulator radiographs to allow 3D triangulation of implanted seeds

    Altschuler, Martin D.; Kassaee, Alireza

    1997-02-01

    To match corresponding seed images in different radiographs so that the 3D seed locations can be triangulated automatically and without ambiguity requires (at least) three radiographs taken from different perspectives, and an algorithm that finds the proper permutations of the seed-image indices. Matching corresponding images in only two radiographs introduces inherent ambiguities which can be resolved only with the use of non-positional information obtained with intensive human effort. Matching images in three or more radiographs is an `NP (Non-determinant in Polynomial time)-complete' problem. Although the matching problem is fundamental, current methods for three-radiograph seed-image matching use `local' (seed-by-seed) methods that may lead to incorrect matchings. We describe a permutation-sampling method which not only gives good `global' (full permutation) matches for the NP-complete three-radiograph seed-matching problem, but also determines the reliability of the radiographic data themselves, namely, whether the patient moved in the interval between radiographic perspectives.

  6. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images

    Antony, Bhavna; Abràmoff, Michael D.; Tang, Li; Ramdas, Wishal D.; Vingerling, Johannes R.; Jansonius, Nomdo M.; Lee, Kyungmoo; Kwon, Young H.; Sonka, Milan; Garvin, Mona K.

    2011-01-01

    The 3-D spectral-domain optical coherence tomography (SD-OCT) images of the retina often do not reflect the true shape of the retina and are distorted differently along the x and y axes. In this paper, we propose a novel technique that uses thin-plate splines in two stages to estimate and correct the distinct axial artifacts in SD-OCT images. The method was quantitatively validated using nine pairs of OCT scans obtained with orthogonal fast-scanning axes, where a segmented surface was compared after both datasets had been corrected. The mean unsigned difference computed between the locations of this artifact-corrected surface after the single-spline and dual-spline correction was 23.36 ± 4.04 μm and 5.94 ± 1.09 μm, respectively, and showed a significant difference (p < 0.001 from two-tailed paired t-test). The method was also validated using depth maps constructed from stereo fundus photographs of the optic nerve head, which were compared to the flattened top surface from the OCT datasets. Significant differences (p < 0.001) were noted between the artifact-corrected datasets and the original datasets, where the mean unsigned differences computed over 30 optic-nerve-head-centered scans (in normalized units) were 0.134 ± 0.035 and 0.302 ± 0.134, respectively. PMID:21833377

  7. Fully automatic diagnostic system for early- and late-onset mild Alzheimer's disease using FDG PET and 3D-SSP

    Ishii, Kazunari; Kono, Atsushi K.; Sasaki, Hiroki; Miyamoto, Naokazu; Fukuda, Tetsuya; Sakamoto, Setsu; Mori, Etsuro

    2006-01-01

    The purpose of this study was to design a fully automatic computer-assisted diagnostic system for early- and late-onset mild Alzheimer's disease (AD). Glucose metabolic images were obtained from mild AD patients and normal controls using positron emission tomography (PET) and 18 F-fluorodeoxyglucose (FDG). Two groups of 20 mild AD patients with different ages of onset were examined. A fully automatic diagnostic system using the statistical brain mapping method was established from the early-onset (EO) and late-onset (LO) groups, with mean ages of 59.1 and 70.9 years and mean MMSE scores of 23.3 and 22.8, respectively. Aged-matched normal subjects were used as controls. We compared the diagnostic performance of visual inspection of conventional axial FDG PET images by experts and beginners with that of our fully automatic diagnostic system in another 15 EO and 15 LO AD patients (mean age 58.4 and 71.7, mean MMSE 23.6 and 23.1, respectively) and 30 age-matched normal controls. A receiver operating characteristic (ROC) analysis was performed to compare data. The diagnostic performance of the automatic diagnostic system was comparable with that of visual inspection by experts. The area under the ROC curve for the automatic diagnostic system was 0.967 for EO AD patients and 0.878 for LO AD patients. The mean area under the ROC curve for visual inspection by experts was 0.863 and 0.881 for the EO and LO AD patients, respectively. The mean area under the ROC curve for visual inspection by beginners was 0.828 and 0.717, respectively. The fully automatic diagnostic system for EO and LO AD was able to perform at a similar diagnostic level to visual inspection of conventional axial images by experts. (orig.)

  8. A Fully Automated Diabetes Prevention Program, Alive-PD: Program Design and Randomized Controlled Trial Protocol.

    Block, Gladys; Azar, Kristen Mj; Block, Torin J; Romanelli, Robert J; Carpenter, Heather; Hopkins, Donald; Palaniappan, Latha; Block, Clifford H

    2015-01-21

    In the United States, 86 million adults have pre-diabetes. Evidence-based interventions that are both cost effective and widely scalable are needed to prevent diabetes. Our goal was to develop a fully automated diabetes prevention program and determine its effectiveness in a randomized controlled trial. Subjects with verified pre-diabetes were recruited to participate in a trial of the effectiveness of Alive-PD, a newly developed, 1-year, fully automated behavior change program delivered by email and Web. The program involves weekly tailored goal-setting, team-based and individual challenges, gamification, and other opportunities for interaction. An accompanying mobile phone app supports goal-setting and activity planning. For the trial, participants were randomized by computer algorithm to start the program immediately or after a 6-month delay. The primary outcome measures are change in HbA1c and fasting glucose from baseline to 6 months. The secondary outcome measures are change in HbA1c, glucose, lipids, body mass index (BMI), weight, waist circumference, and blood pressure at 3, 6, 9, and 12 months. Randomization and delivery of the intervention are independent of clinic staff, who are blinded to treatment assignment. Outcomes will be evaluated for the intention-to-treat and per-protocol populations. A total of 340 subjects with pre-diabetes were randomized to the intervention (n=164) or delayed-entry control group (n=176). Baseline characteristics were as follows: mean age 55 (SD 8.9); mean BMI 31.1 (SD 4.3); male 68.5%; mean fasting glucose 109.9 (SD 8.4) mg/dL; and mean HbA1c 5.6 (SD 0.3)%. Data collection and analysis are in progress. We hypothesize that participants in the intervention group will achieve statistically significant reductions in fasting glucose and HbA1c as compared to the control group at 6 months post baseline. The randomized trial will provide rigorous evidence regarding the efficacy of this Web- and Internet-based program in reducing or

  9. Evaluation of left atrial function by multidetector computed tomography before left atrial radiofrequency-catheter ablation: Comparison of a manual and automated 3D volume segmentation method

    Wolf, Florian, E-mail: florian.wolf@meduniwien.ac.a [Department of Radiology, Medical University of Vienna, Vienna (Austria); Ourednicek, Petr [Philips Medical Systems, Prague (Czech Republic); Loewe, Christian [Department of Radiology, Medical University of Vienna, Vienna (Austria); Richter, Bernhard; Goessinger, Heinz David; Gwechenberger, Marianne [Department of Cardiology, Medical University of Vienna, Vienna (Austria); Plank, Christina; Schernthaner, Ruediger Egbert; Toepker, Michael; Lammer, Johannes [Department of Radiology, Medical University of Vienna, Vienna (Austria); Feuchtner, Gudrun M. [Department of Radiology, Innsbruck Medical University, Innsbruck (Austria); Institute of Diagnostic Radiology, University Hospital Zurich (Switzerland)

    2010-08-15

    Introduction: The purpose of this study was to compare a manual and automated 3D volume segmentation tool for evaluation of left atrial (LA) function by 64-slice multidetector-CT (MDCT). Methods and materials: In 33 patients with paroxysmal atrial fibrillation a MDCT scan was performed before radiofrequency-catheter ablation. Atrial function (minimal volume (LAmin), maximal volume (LAmax), stroke volume (SV), ejection fraction (EF)) was evaluated by two readers using a manual and an automatic tool and measurement time was evaluated. Results: Automated LA volume segmentation failed in one patient due to low LA enhancement (103HU). Mean LAmax, LAmin, SV and EF were 127.7 ml, 93 ml, 34.7 ml, 27.1% by the automated, and 122.7 ml, 89.9 ml, 32.8 ml, 26.3% by the manual method with no significant difference (p > 0.05) and high Pearsons correlation coefficients (r = 0.94, r = 0.94, r = 0.82 and r = 0.85, p < 0.0001), respectively. The automated method was significantly faster (p < 0.001). Interobserver variability was low for both methods with Pearson's correlation coefficients between 0.98 and 0.99 (p < 0.0001). Conclusions: Evaluation of LA volume and function with 64-slice MDCT is feasible with a very low interobserver variability. The automatic method is as accurate as the manual method but significantly less time consuming permitting a routine use in clinical practice before RF-catheter ablation.

  10. Analysis of xanthines in beverages using a fully automated SPE-SPC-DAD hyphenated system

    Medvedovici, A. [Bucarest Univ., Bucarest (Romania). Faculty of Chemistry, Dept. of Analytical Chemistry; David, F.; David, V.; Sandra, P. [Research Institute of Chromatography, Kortrijk (Belgium)

    2000-08-01

    Analysis of some xanthines (caffeine, theophylline and theobromine) in beverages has been achieved by a fully automated on-line Solid Phase Extraction - Supercritical Fluid Chromatography - Diode Array Detection (Spe - Sofc - Dad). Three adsorbents have been tested for the Spe procedure: octadecyl modified silicagel (ODS) and two types of styrene-divinylbenzen copolymer based materials, from which Porapack proved to be the most suitable adsorbent. Optimisation and correlation of both Spe and Sofc operational parameters are also discussed. By this technique, caffeine was determined in ice tea and Coca-Cola in a concentration of 0.15 ppm, theobromine - 1.5 ppb, and theophylline - 0.15 ppb. [Italian] Si e' realizzata l'analis di alcune xantine (caffeina, teofillina e teobromina) mediante un sistema, in linea, completamente automatizzato basato su Estrazione in Fase Solida - Cromatografia in Fase Supercritica - Rivelazione con Diode Array (Spe - Sfc - Dad). Per la procedura Spe sono stati valutati tre substrati: silice ottadecilica (ODS) e due tipi di materiali polimerici a base stirene-divinilbenzene, di cui, quello denominato PRP-1, e' risultato essere il piu' efficiente. Sono discusse sia l'ottimizzazione che la correlazione dei parametri operazionali per la Spe e la Sfc. Con questa tecnica sono state determinate, in te' ghiacciato e Coca-Cola, la caffeina, la teobromina e la teofillina alle concentrazini di 0.15, 1.5 e 0.15 ppm.

  11. Development of a fully automated adaptive unsharp masking technique in digital chest radiograph

    Abe, Katsumi; Katsuragawa, Shigehiko; Sasaki, Yasuo

    1991-01-01

    We are developing a fully automated adaptive unsharp masking technique with various parameters depending on regional image features of a digital chest radiograph. A chest radiograph includes various regions such as lung fields, retrocardiac area and spine in which their texture patterns and optical densities are extremely different. Therefore, it is necessary to enhance image contrast of each region by each optimum parameter. First, we investigated optimum weighting factors and mask sizes of unsharp masking technique in a digital chest radiograph. Then, a chest radiograph is automatically divided into three segments, one for the lung field, one for the retrocardiac area, and one for the spine, by using histogram analysis of pixel values. Finally, high frequency components of the lung field and retrocardiac area are selectively enhanced with a small mask size and mild weighting factors which are previously determined as optimum parameters. In addition, low frequency components of the spine are enhanced with a large mask size and adequate weighting factors. This processed image shows excellent depiction of the lung field, retrocardiac area and spine simultaneously with optimum contrast. Our image processing technique may be useful for diagnosis of chest radiographs. (author)

  12. Fully automated drug screening of dried blood spots using online LC-MS/MS analysis

    Stefan Gaugler

    2018-01-01

    Full Text Available A new and fully automated workflow for the cost effective drug screening of large populations based on the dried blood spot (DBS technology was introduced in this study. DBS were prepared by spotting 15 μL of whole blood, previously spiked with alprazolam, amphetamine, cocaine, codeine, diazepam, fentanyl, lysergic acid diethylamide (LSD, 3,4-methylenedioxymethamphet-amine (MDMA, methadone, methamphetamine, morphine and oxycodone onto filter paper cards. The dried spots were scanned, spiked with deuterated standards and directly extracted. The extract was transferred online to an analytical LC column and then to the electrospray ionization tandem mass spectrometry system. All drugs were quantified at their cut-off level and good precision and correlation within the calibration range was obtained. The method was finally applied to DBS samples from two patients with back pain and codeine and oxycodone could be identified and quantified accurately below the level of misuse of 89.6 ng/mL and 39.6 ng/mL respectively.

  13. Fully automated VMAT treatment planning for advanced-stage NSCLC patients

    Della Gala, Giuseppe; Dirkx, Maarten L.P.; Hoekstra, Nienke; Fransen, Dennie; Pol, Marjan van de; Heijmen, Ben J.M.; Lanconelli, Nico; Petit, Steven F.

    2017-01-01

    To develop a fully automated procedure for multicriterial volumetric modulated arc therapy (VMAT) treatment planning (autoVMAT) for stage III/IV non-small cell lung cancer (NSCLC) patients treated with curative intent. After configuring the developed autoVMAT system for NSCLC, autoVMAT plans were compared with manually generated clinically delivered intensity-modulated radiotherapy (IMRT) plans for 41 patients. AutoVMAT plans were also compared to manually generated VMAT plans in the absence of time pressure. For 16 patients with reduced planning target volume (PTV) dose prescription in the clinical IMRT plan (to avoid violation of organs at risk tolerances), the potential for dose escalation with autoVMAT was explored. Two physicians evaluated 35/41 autoVMAT plans (85%) as clinically acceptable. Compared to the manually generated IMRT plans, autoVMAT plans showed statistically significant improved PTV coverage (V_9_5_% increased by 1.1% ± 1.1%), higher dose conformity (R_5_0 reduced by 12.2% ± 12.7%), and reduced mean lung, heart, and esophagus doses (reductions of 0.9 Gy ± 1.0 Gy, 1.5 Gy ± 1.8 Gy, 3.6 Gy ± 2.8 Gy, respectively, all p [de

  14. Fully automated deformable registration of breast DCE-MRI and PET/CT

    Dmitriev, I. D.; Loo, C. E.; Vogel, W. V.; Pengel, K. E.; Gilhuijs, K. G. A.

    2013-02-01

    Accurate characterization of breast tumors is important for the appropriate selection of therapy and monitoring of the response. For this purpose breast imaging and tissue biopsy are important aspects. In this study, a fully automated method for deformable registration of DCE-MRI and PET/CT of the breast is presented. The registration is performed using the CT component of the PET/CT and the pre-contrast T1-weighted non-fat suppressed MRI. Comparable patient setup protocols were used during the MRI and PET examinations in order to avoid having to make assumptions of biomedical properties of the breast during and after the application of chemotherapy. The registration uses a multi-resolution approach to speed up the process and to minimize the probability of converging to local minima. The validation was performed on 140 breasts (70 patients). From a total number of registration cases, 94.2% of the breasts were aligned within 4.0 mm accuracy (1 PET voxel). Fused information may be beneficial to obtain representative biopsy samples, which in turn will benefit the treatment of the patient.

  15. Radiation Planning Assistant - A Streamlined, Fully Automated Radiotherapy Treatment Planning System

    Court, Laurence E.; Kisling, Kelly; McCarroll, Rachel; Zhang, Lifei; Yang, Jinzhong; Simonds, Hannah; du Toit, Monique; Trauernicht, Chris; Burger, Hester; Parkes, Jeannette; Mejia, Mike; Bojador, Maureen; Balter, Peter; Branco, Daniela; Steinmann, Angela; Baltz, Garrett; Gay, Skylar; Anderson, Brian; Cardenas, Carlos; Jhingran, Anuja; Shaitelman, Simona; Bogler, Oliver; Schmeller, Kathleen; Followill, David; Howell, Rebecca; Nelson, Christopher; Peterson, Christine; Beadle, Beth

    2018-01-01

    The Radiation Planning Assistant (RPA) is a system developed for the fully automated creation of radiotherapy treatment plans, including volume-modulated arc therapy (VMAT) plans for patients with head/neck cancer and 4-field box plans for patients with cervical cancer. It is a combination of specially developed in-house software that uses an application programming interface to communicate with a commercial radiotherapy treatment planning system. It also interfaces with a commercial secondary dose verification software. The necessary inputs to the system are a Treatment Plan Order, approved by the radiation oncologist, and a simulation computed tomography (CT) image, approved by the radiographer. The RPA then generates a complete radiotherapy treatment plan. For the cervical cancer treatment plans, no additional user intervention is necessary until the plan is complete. For head/neck treatment plans, after the normal tissue and some of the target structures are automatically delineated on the CT image, the radiation oncologist must review the contours, making edits if necessary. They also delineate the gross tumor volume. The RPA then completes the treatment planning process, creating a VMAT plan. Finally, the completed plan must be reviewed by qualified clinical staff. PMID:29708544

  16. Validation of a fully automated robotic setup for preparation of whole blood samples for LC-MS toxicology analysis

    Andersen, David Wederkinck; Rasmussen, Brian; Linnet, Kristian

    2012-01-01

    A fully automated setup was developed for preparing whole blood samples using a Tecan Evo workstation. By integrating several add-ons to the robotic platform, the flexible setup was able to prepare samples from sample tubes to a 96-well sample plate ready for injection on liquid chromatography...

  17. Extension of a semi-implicit shock-capturing algorithm for 3-D fully coupled, chemically reacting flows in generalized coordinates

    Shinn, J.L.; Yee, H.C.; Uenishi, K.; NASA, Ames Research Center, Moffett Field, CA; Vigyan Research Associates, Inc., Hampton, VA)

    1987-01-01

    A semiimplicit high-resolution shock-capturing method for multidimensional systems of hyperbolic conservation laws with stiff source terms has been developed by Yee and Shinn (1987). The goal of this work is to extend this method to solve the three-dimensional fully coupled Navier-Stokes equations for a hypersonic chemically reacting flow in generalized coordinates. In this formulation, the global continuity equation was replaced by all the species continuity equations. The shock-capturing technique is a second-order-accurate, symmetric total-variation-diminishing method which accounts fully and directly for the coupling among the fluid and all the species. To verify the current approach, it was implemented into an existing computer code which contained the MacCormack method. Test results for a five-species reacting flow are shown to be oscillation-free around the shock, and the time spent per iteration only doubles when compared to the result using classical way of supplying numerical dissipation. The extra computation is more than justified by the elimination of spurious oscillation and nonlinear instability associated with the classical shock-capturing schemes in computing hypersonic reacting flows. 27 references

  18. A semi-automated 2D/3D marker-based registration algorithm modelling prostate shrinkage during radiotherapy for prostate cancer

    Budiharto, Tom; Slagmolen, Pieter; Hermans, Jeroen; Maes, Frederik; Verstraete, Jan; Heuvel, Frank Van den; Depuydt, Tom; Oyen, Raymond; Haustermans, Karin

    2009-01-01

    Background and purpose: Currently, most available patient alignment tools based on implanted markers use manual marker matching and rigid registration transformations to measure the needed translational shifts. To quantify the particular effect of prostate gland shrinkage, implanted gold markers were tracked during a course of radiotherapy including an isotropic scaling factor to model prostate shrinkage. Materials and methods: Eight patients with prostate cancer had gold markers implanted transrectally and seven were treated with (neo) adjuvant androgen deprivation therapy. After patient alignment to skin tattoos, orthogonal electronic portal images (EPIs) were taken. A semi-automated 2D/3D marker-based registration was performed to calculate the necessary couch shifts. The registration consists of a rigid transformation combined with an isotropic scaling to model prostate shrinkage. Results: The inclusion of an isotropic shrinkage model in the registration algorithm cancelled the corresponding increase in registration error. The mean scaling factor was 0.89 ± 0.09. For all but two patients, a decrease of the isotropic scaling factor during treatment was observed. However, there was almost no difference in the translation offset between the manual matching of the EPIs to the digitally reconstructed radiographs and the semi-automated 2D/3D registration. A decrease in the intermarker distance was found correlating with prostate shrinkage rather than with random marker migration. Conclusions: Inclusion of shrinkage in the registration process reduces registration errors during a course of radiotherapy. Nevertheless, this did not lead to a clinically significant change in the proposed table translations when compared to translations obtained with manual marker matching without a scaling correction

  19. Fluid Lensing, Applications to High-Resolution 3D Subaqueous Imaging & Automated Remote Biosphere Assessment from Airborne and Space-borne Platforms

    Chirayath, V.

    2014-12-01

    Fluid Lensing is a theoretical model and algorithm I present for fluid-optical interactions in turbulent flows as well as two-fluid surface boundaries that, when coupled with an unique computer vision and image-processing pipeline, may be used to significantly enhance the angular resolution of a remote sensing optical system with applicability to high-resolution 3D imaging of subaqueous regions and through turbulent fluid flows. This novel remote sensing technology has recently been implemented on a quadcopter-based UAS for imaging shallow benthic systems to create the first dataset of a biosphere with unprecedented sub-cm-level imagery in 3D over areas as large as 15 square kilometers. Perturbed two-fluid boundaries with different refractive indices, such as the surface between the ocean and air, may be exploited for use as lensing elements for imaging targets on either side of the interface with enhanced angular resolution. I present theoretical developments behind Fluid Lensing and experimental results from its recent implementation for the Reactive Reefs project to image shallow reef ecosystems at cm scales. Preliminary results from petabyte-scale aerial survey efforts using Fluid Lensing to image at-risk coral reefs in American Samoa (August, 2013) show broad applicability to large-scale automated species identification, morphology studies and reef ecosystem characterization for shallow marine environments and terrestrial biospheres, of crucial importance to understanding climate change's impact on coastal zones, global oxygen production and carbon sequestration.

  20. An automated device for the digitization and 3D modelling of insects, combining extended-depth-of-field and all-side multi-view imaging

    Bernhard Ströbel

    2018-05-01

    Full Text Available Digitization of natural history collections is a major challenge in archiving biodiversity. In recent years, several approaches have emerged, allowing either automated digitization, extended depth of field (EDOF or multi-view imaging of insects. Here, we present DISC3D: a new digitization device for pinned insects and other small objects that combines all these aspects. A PC and a microcontroller board control the device. It features a sample holder on a motorized two-axis gimbal, allowing the specimens to be imaged from virtually any view. Ambient, mostly reflection-free illumination is ascertained by two LED-stripes circularly installed in two hemispherical white-coated domes (front-light and back-light. The device is equipped with an industrial camera and a compact macro lens, mounted on a motorized macro rail. EDOF images are calculated from an image stack using a novel calibrated scaling algorithm that meets the requirements of the pinhole camera model (a unique central perspective. The images can be used to generate a calibrated and real color texturized 3Dmodel by ‘structure from motion’ with a visibility consistent mesh generation. Such models are ideal for obtaining morphometric measurement data in 1D, 2D and 3D, thereby opening new opportunities for trait-based research in taxonomy, phylogeny, eco-physiology, and functional ecology.

  1. Automated Visualization and Quantification of Spiral Artery Blood Flow Entering the First-Trimester Placenta, Using 3-D Power Doppler Ultrasound.

    Stevenson, Gordon N; Noble, J Alison; Welsh, Alec W; Impey, Lawrence; Collins, Sally L

    2018-03-01

    The goal of our research was to quantify the placental vascularity in 3-D at 11-13 + 6 wk of pregnancy at precise distances from the utero-placental interface (UPI) using 3-D power Doppler ultrasound. With this automated image analysis technique, differences in vascularity between normal and pathologic pregnancies may be observed. The algorithm was validated using a computer-generated image phantom and applied retrospectively in 143 patients. The following features from the PD data were recorded: The number of spiral artery jets into the inter-villous space, total geometric and PD area. These were automatically measured at discrete millimeter distances from the UPI. Differences in features were compared with pregnancy outcomes: Pre-eclamptic versus normal, all small-for-gestational age (SGA) to appropriate-for-gestational age (AGA) patients and AGA versus SGA in normotensives (Mann-Whitney). The Benjamini-Hochberg procedure was used (false discovery rate 10%) for multiple comparison testing. Features decreased with increasing distance from the UPI (Kruskal-Wallis test; p  0.05). This method provides a new in-vivo imaging tool for examining spiral artery development through pregnancy. Size and number of entrances of blood flow into the UPI could potentially be used to identify high-risk pregnancies and may provide a new imaging biomarker for placental insufficiency. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

  2. Breast Density Estimation with Fully Automated Volumetric Method: Comparison to Radiologists' Assessment by BI-RADS Categories.

    Singh, Tulika; Sharma, Madhurima; Singla, Veenu; Khandelwal, Niranjan

    2016-01-01

    The objective of our study was to calculate mammographic breast density with a fully automated volumetric breast density measurement method and to compare it to breast imaging reporting and data system (BI-RADS) breast density categories assigned by two radiologists. A total of 476 full-field digital mammography examinations with standard mediolateral oblique and craniocaudal views were evaluated by two blinded radiologists and BI-RADS density categories were assigned. Using a fully automated software, mean fibroglandular tissue volume, mean breast volume, and mean volumetric breast density were calculated. Based on percentage volumetric breast density, a volumetric density grade was assigned from 1 to 4. The weighted overall kappa was 0.895 (almost perfect agreement) for the two radiologists' BI-RADS density estimates. A statistically significant difference was seen in mean volumetric breast density among the BI-RADS density categories. With increased BI-RADS density category, increase in mean volumetric breast density was also seen (P BI-RADS categories and volumetric density grading by fully automated software (ρ = 0.728, P BI-RADS density category by two observers showed fair agreement (κ = 0.398 and 0.388, respectively). In our study, a good correlation was seen between density grading using fully automated volumetric method and density grading using BI-RADS density categories assigned by the two radiologists. Thus, the fully automated volumetric method may be used to quantify breast density on routine mammography. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  3. A novel fully automated molecular diagnostic system (AMDS for colorectal cancer mutation detection.

    Shiro Kitano

    Full Text Available BACKGROUND: KRAS, BRAF and PIK3CA mutations are frequently observed in colorectal cancer (CRC. In particular, KRAS mutations are strong predictors for clinical outcomes of EGFR-targeted treatments such as cetuximab and panitumumab in metastatic colorectal cancer (mCRC. For mutation analysis, the current methods are time-consuming, and not readily available to all oncologists and pathologists. We have developed a novel, simple, sensitive and fully automated molecular diagnostic system (AMDS for point of care testing (POCT. Here we report the results of a comparison study between AMDS and direct sequencing (DS in the detection of KRAS, BRAF and PI3KCA somatic mutations. METHODOLOGY/PRINCIPAL FINDING: DNA was extracted from a slice of either frozen (n = 89 or formalin-fixed and paraffin-embedded (FFPE CRC tissue (n = 70, and then used for mutation analysis by AMDS and DS. All mutations (n = 41 among frozen and 27 among FFPE samples detected by DS were also successfully (100% detected by the AMDS. However, 8 frozen and 6 FFPE samples detected as wild-type in the DS analysis were shown as mutants in the AMDS analysis. By cloning-sequencing assays, these discordant samples were confirmed as true mutants. One sample had simultaneous "hot spot" mutations of KRAS and PIK3CA, and cloning assay comfirmed that E542K and E545K were not on the same allele. Genotyping call rates for DS were 100.0% (89/89 and 74.3% (52/70 in frozen and FFPE samples, respectively, for the first attempt; whereas that of AMDS was 100.0% for both sample sets. For automated DNA extraction and mutation detection by AMDS, frozen tissues (n = 41 were successfully detected all mutations within 70 minutes. CONCLUSIONS/SIGNIFICANCE: AMDS has superior sensitivity and accuracy over DS, and is much easier to execute than conventional labor intensive manual mutation analysis. AMDS has great potential for POCT equipment for mutation analysis.

  4. A fully automated temperature-dependent resistance measurement setup using van der Pauw method

    Pandey, Shivendra Kumar; Manivannan, Anbarasu

    2018-03-01

    The van der Pauw (VDP) method is widely used to identify the resistance of planar homogeneous samples with four contacts placed on its periphery. We have developed a fully automated thin film resistance measurement setup using the VDP method with the capability of precisely measuring a wide range of thin film resistances from few mΩ up to 10 GΩ under controlled temperatures from room-temperature up to 600 °C. The setup utilizes a robust, custom-designed switching network board (SNB) for measuring current-voltage characteristics automatically at four different source-measure configurations based on the VDP method. Moreover, SNB is connected with low noise shielded coaxial cables that reduce the effect of leakage current as well as the capacitance in the circuit thereby enhancing the accuracy of measurement. In order to enable precise and accurate resistance measurement of the sample, wide range of sourcing currents/voltages are pre-determined with the capability of auto-tuning for ˜12 orders of variation in the resistances. Furthermore, the setup has been calibrated with standard samples and also employed to investigate temperature dependent resistance (few Ω-10 GΩ) measurements for various chalcogenide based phase change thin films (Ge2Sb2Te5, Ag5In5Sb60Te30, and In3SbTe2). This setup would be highly helpful for measurement of temperature-dependent resistance of wide range of materials, i.e., metals, semiconductors, and insulators illuminating information about structural change upon temperature as reflected by change in resistances, which are useful for numerous applications.

  5. Fully Automated Laser Ablation Liquid Capture Sample Analysis using NanoElectrospray Ionization Mass Spectrometry

    Lorenz, Matthias [ORNL; Ovchinnikova, Olga S [ORNL; Van Berkel, Gary J [ORNL

    2014-01-01

    RATIONALE: Laser ablation provides for the possibility of sampling a large variety of surfaces with high spatial resolution. This type of sampling when employed in conjunction with liquid capture followed by nanoelectrospray ionization provides the opportunity for sensitive and prolonged interrogation of samples by mass spectrometry as well as the ability to analyze surfaces not amenable to direct liquid extraction. METHODS: A fully automated, reflection geometry, laser ablation liquid capture spot sampling system was achieved by incorporating appropriate laser fiber optics and a focusing lens into a commercially available, liquid extraction surface analysis (LESA ) ready Advion TriVersa NanoMate system. RESULTS: Under optimized conditions about 10% of laser ablated material could be captured in a droplet positioned vertically over the ablation region using the NanoMate robot controlled pipette. The sampling spot size area with this laser ablation liquid capture surface analysis (LA/LCSA) mode of operation (typically about 120 m x 160 m) was approximately 50 times smaller than that achievable by direct liquid extraction using LESA (ca. 1 mm diameter liquid extraction spot). The set-up was successfully applied for the analysis of ink on glass and paper as well as the endogenous components in Alstroemeria Yellow King flower petals. In a second mode of operation with a comparable sampling spot size, termed laser ablation/LESA , the laser system was used to drill through, penetrate, or otherwise expose material beneath a solvent resistant surface. Once drilled, LESA was effective in sampling soluble material exposed at that location on the surface. CONCLUSIONS: Incorporating the capability for different laser ablation liquid capture spot sampling modes of operation into a LESA ready Advion TriVersa NanoMate enhanced the spot sampling spatial resolution of this device and broadened the surface types amenable to analysis to include absorbent and solvent resistant

  6. Fully automated whole-head segmentation with improved smoothness and continuity, with theory reviewed.

    Yu Huang

    Full Text Available Individualized current-flow models are needed for precise targeting of brain structures using transcranial electrical or magnetic stimulation (TES/TMS. The same is true for current-source reconstruction in electroencephalography and magnetoencephalography (EEG/MEG. The first step in generating such models is to obtain an accurate segmentation of individual head anatomy, including not only brain but also cerebrospinal fluid (CSF, skull and soft tissues, with a field of view (FOV that covers the whole head. Currently available automated segmentation tools only provide results for brain tissues, have a limited FOV, and do not guarantee continuity and smoothness of tissues, which is crucially important for accurate current-flow estimates. Here we present a tool that addresses these needs. It is based on a rigorous Bayesian inference framework that combines image intensity model, anatomical prior (atlas and morphological constraints using Markov random fields (MRF. The method is evaluated on 20 simulated and 8 real head volumes acquired with magnetic resonance imaging (MRI at 1 mm3 resolution. We find improved surface smoothness and continuity as compared to the segmentation algorithms currently implemented in Statistical Parametric Mapping (SPM. With this tool, accurate and morphologically correct modeling of the whole-head anatomy for individual subjects may now be feasible on a routine basis. Code and data are fully integrated into SPM software tool and are made publicly available. In addition, a review on the MRI segmentation using atlas and the MRF over the last 20 years is also provided, with the general mathematical framework clearly derived.

  7. Fully automated whole-head segmentation with improved smoothness and continuity, with theory reviewed.

    Huang, Yu; Parra, Lucas C

    2015-01-01

    Individualized current-flow models are needed for precise targeting of brain structures using transcranial electrical or magnetic stimulation (TES/TMS). The same is true for current-source reconstruction in electroencephalography and magnetoencephalography (EEG/MEG). The first step in generating such models is to obtain an accurate segmentation of individual head anatomy, including not only brain but also cerebrospinal fluid (CSF), skull and soft tissues, with a field of view (FOV) that covers the whole head. Currently available automated segmentation tools only provide results for brain tissues, have a limited FOV, and do not guarantee continuity and smoothness of tissues, which is crucially important for accurate current-flow estimates. Here we present a tool that addresses these needs. It is based on a rigorous Bayesian inference framework that combines image intensity model, anatomical prior (atlas) and morphological constraints using Markov random fields (MRF). The method is evaluated on 20 simulated and 8 real head volumes acquired with magnetic resonance imaging (MRI) at 1 mm3 resolution. We find improved surface smoothness and continuity as compared to the segmentation algorithms currently implemented in Statistical Parametric Mapping (SPM). With this tool, accurate and morphologically correct modeling of the whole-head anatomy for individual subjects may now be feasible on a routine basis. Code and data are fully integrated into SPM software tool and are made publicly available. In addition, a review on the MRI segmentation using atlas and the MRF over the last 20 years is also provided, with the general mathematical framework clearly derived.

  8. Fully automated intrinsic respiratory and cardiac gating for small animal CT

    Kuntz, J; Baeuerle, T; Semmler, W; Bartling, S H [Department of Medical Physics in Radiology, German Cancer Research Center, Heidelberg (Germany); Dinkel, J [Department of Radiology, German Cancer Research Center, Heidelberg (Germany); Zwick, S [Department of Diagnostic Radiology, Medical Physics, Freiburg University (Germany); Grasruck, M [Siemens Healthcare, Forchheim (Germany); Kiessling, F [Chair of Experimental Molecular Imaging, RWTH-Aachen University, Medical Faculty, Aachen (Germany); Gupta, R [Department of Radiology, Massachusetts General Hospital, Boston, MA (United States)], E-mail: j.kuntz@dkfz.de

    2010-04-07

    A fully automated, intrinsic gating algorithm for small animal cone-beam CT is described and evaluated. A parameter representing the organ motion, derived from the raw projection images, is used for both cardiac and respiratory gating. The proposed algorithm makes it possible to reconstruct motion-corrected still images as well as to generate four-dimensional (4D) datasets representing the cardiac and pulmonary anatomy of free-breathing animals without the use of electrocardiogram (ECG) or respiratory sensors. Variation analysis of projections from several rotations is used to place a region of interest (ROI) on the diaphragm. The ROI is cranially extended to include the heart. The centre of mass (COM) variation within this ROI, the filtered frequency response and the local maxima are used to derive a binary motion-gating parameter for phase-sensitive gated reconstruction. This algorithm was implemented on a flat-panel-based cone-beam CT scanner and evaluated using a moving phantom and animal scans (seven rats and eight mice). Volumes were determined using a semiautomatic segmentation. In all cases robust gating signals could be obtained. The maximum volume error in phantom studies was less than 6%. By utilizing extrinsic gating via externally placed cardiac and respiratory sensors, the functional parameters (e.g. cardiac ejection fraction) and image quality were equivalent to this current gold standard. This algorithm obviates the necessity of both gating hardware and user interaction. The simplicity of the proposed algorithm enables adoption in a wide range of small animal cone-beam CT scanners.

  9. Accuracy and reproducibility of aortic annular measurements obtained from echocardiographic 3D manual and semi-automated software analyses in patients referred for transcatheter aortic valve implantation: implication for prosthesis size selection.

    Stella, Stefano; Italia, Leonardo; Geremia, Giulia; Rosa, Isabella; Ancona, Francesco; Marini, Claudia; Capogrosso, Cristina; Giglio, Manuela; Montorfano, Matteo; Latib, Azeem; Margonato, Alberto; Colombo, Antonio; Agricola, Eustachio

    2018-02-06

    A 3D transoesophageal echocardiography (3D-TOE) reconstruction tool has recently been introduced. The system automatically configures a geometric model of the aortic root and performs quantitative analysis of these structures. We compared the measurements of the aortic annulus (AA) obtained by semi-automated 3D-TOE quantitative software and manual analysis vs. multislice computed tomography (MSCT) ones. One hundred and seventy-five patients (mean age 81.3 ± 6.3 years, 77 men) who underwent both MSCT and 3D-TOE for annulus assessment before transcatheter aortic valve implantation were analysed. Hypothetical prosthetic valve sizing was evaluated using the 3D manual, semi-automated measurements using manufacturer-recommended CT-based sizing algorithm as gold standard. Good correlation between 3D-TOE methods vs. MSCT measurements was found, but the semi-automated analysis demonstrated slightly better correlations for AA major diameter (r = 0.89), perimeter (r = 0.89), and area (r = 0.85) (all P 3D methods underestimated the MSCT measurements, but semi-automated measurements showed narrower limits of agreement and lesser bias than manual measurements for most of AA parameters. On average, 3D-TOE semi-automated major diameter, area, and perimeter underestimated the respective MSCT measurements by 7.4%, 3.5%, and 4.4%, respectively, whereas minor diameter was overestimated by 0.3%. Moderate agreement for valve sizing for both 3D-TOE techniques was found: Kappa agreement 0.5 for both semi-automated and manual analysis. Interobserver and intraobserver agreements for the AA measurements were excellent for both techniques (intraclass correlation coefficients for all parameters >0.80). The 3D-TOE semi-automated analysis of AA is feasible and reliable and can be used in clinical practice as an alternative to MSCT for AA assessment. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2018. For permissions, please

  10. 3D neuromelanin-sensitive magnetic resonance imaging with semi-automated volume measurement of the substantia nigra pars compacta for diagnosis of Parkinson's disease

    Ogisu, Kimihiro; Shirato, Hiroki [Hokkaido University Graduate School of Medicine, Department of Radiology, Hokkaido (Japan); Kudo, Kohsuke; Sasaki, Makoto [Iwate Medical University, Division of Ultrahigh Field MRI, Iwate (Japan); Sakushima, Ken; Yabe, Ichiro; Sasaki, Hidenao [Hokkaido University Hospital, Department of Neurology, Hokkaido (Japan); Terae, Satoshi; Nakanishi, Mitsuhiro [Hokkaido University Hospital, Department of Radiology, Hokkaido (Japan)

    2013-06-15

    Neuromelanin-sensitive MRI has been reported to be used in the diagnosis of Parkinson's disease (PD), which results from loss of dopamine-producing cells in the substantia nigra pars compacta (SNc). In this study, we aimed to apply a 3D turbo field echo (TFE) sequence for neuromelanin-sensitive MRI and to evaluate the diagnostic performance of semi-automated method for measurement of SNc volume in patients with PD. We examined 18 PD patients and 27 healthy volunteers (control subjects). A 3D TFE technique with off-resonance magnetization transfer pulse was used for neuromelanin-sensitive MRI on a 3T scanner. The SNc volume was semi-automatically measured using a region-growing technique at various thresholds (ranging from 1.66 to 2.48), with the signals measured relative to that for the superior cerebellar peduncle. Receiver operating characteristic (ROC) analysis was performed at all thresholds. Intra-rater reproducibility was evaluated by intraclass correlation coefficient (ICC). The average SNc volume in the PD group was significantly smaller than that in the control group at all the thresholds (P < 0.01, student t test). At higher thresholds (>2.0), the area under the curve of ROC (Az) increased (0.88). In addition, we observed balanced sensitivity and specificity (0.83 and 0.85, respectively). At lower thresholds, sensitivity tended to increase but specificity reduced in comparison with that at higher thresholds. ICC was larger than 0.9 when the threshold was over 1.86. Our method can distinguish the PD group from the control group with high sensitivity and specificity, especially for early stage of PD. (orig.)

  11. The Number Density Evolution of Extreme Emission Line Galaxies in 3D-HST: Results from a Novel Automated Line Search Technique for Slitless Spectroscopy

    Maseda, Michael V.; van der Wel, Arjen; Rix, Hans-Walter; Momcheva, Ivelina; Brammer, Gabriel B.; Franx, Marijn; Lundgren, Britt F.; Skelton, Rosalind E.; Whitaker, Katherine E.

    2018-02-01

    The multiplexing capability of slitless spectroscopy is a powerful asset in creating large spectroscopic data sets, but issues such as spectral confusion make the interpretation of the data challenging. Here we present a new method to search for emission lines in the slitless spectroscopic data from the 3D-HST survey utilizing the Wide-Field Camera 3 on board the Hubble Space Telescope. Using a novel statistical technique, we can detect compact (extended) emission lines at 90% completeness down to fluxes of 1.5(3.0)× {10}-17 {erg} {{{s}}}-1 {{cm}}-2, close to the noise level of the grism exposures, for objects detected in the deep ancillary photometric data. Unlike previous methods, the Bayesian nature allows for probabilistic line identifications, namely redshift estimates, based on secondary emission line detections and/or photometric redshift priors. As a first application, we measure the comoving number density of Extreme Emission Line Galaxies (restframe [O III] λ5007 equivalent widths in excess of 500 Å). We find that these galaxies are nearly 10× more common above z ∼ 1.5 than at z ≲ 0.5. With upcoming large grism surveys such as Euclid and WFIRST, as well as grisms featured prominently on the NIRISS and NIRCam instruments on the James Webb Space Telescope, methods like the one presented here will be crucial for constructing emission line redshift catalogs in an automated and well-understood manner. This work is based on observations taken by the 3D-HST Treasury Program and the CANDELS Multi-Cycle Treasury Program with the NASA/ESA HST, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS5-26555.

  12. Effectiveness of a Web-Based Screening and Fully Automated Brief Motivational Intervention for Adolescent Substance Use

    Arnaud, Nicolas; Baldus, Christiane; Elgán, Tobias H.

    2016-01-01

    ).Conclusions: Although the study is limited by a large drop-out, significant between-group effects for alcohol use indicate that targeted brief motivational intervention in a fully automated Web-based format can be effective to reduce drinking and lessen existing substance use service barriers for at...... of substance use among college students. However, the evidence is sparse among adolescents with at-risk use of alcohol and other drugs. Objective: This study evaluated the effectiveness of a targeted and fully automated Web-based brief motivational intervention with no face-to-face components on substance use......, and polydrug use. All outcome analyses were conducted with and without Expectation Maximization (EM) imputation of missing follow-up data. Results: In total, 2673 adolescents were screened and 1449 (54.2%) participants were randomized to the intervention or control group. After 3 months, 211 adolescents (14...

  13. Effectiveness of a Web-Based Screening and Fully Automated Brief Motivational Intervention for Adolescent Substance Use

    Arnaud, Nicolas; Baldus, Christiane; Elgán, Tobias H.

    2016-01-01

    of substance use among college students. However, the evidence is sparse among adolescents with at-risk use of alcohol and other drugs. Objective: This study evaluated the effectiveness of a targeted and fully automated Web-based brief motivational intervention with no face-to-face components on substance use...... methods and screened online for at-risk substance use using the CRAFFT (Car, Relax, Alone, Forget, Friends, Trouble) screening instrument. Participants were randomized to a single session brief motivational intervention group or an assessment-only control group but not blinded. Primary outcome......).Conclusions: Although the study is limited by a large drop-out, significant between-group effects for alcohol use indicate that targeted brief motivational intervention in a fully automated Web-based format can be effective to reduce drinking and lessen existing substance use service barriers for at...

  14. Fully automated treatment planning for head and neck radiotherapy using a voxel-based dose prediction and dose mimicking method

    McIntosh, Chris; Welch, Mattea; McNiven, Andrea; Jaffray, David A.; Purdie, Thomas G.

    2017-08-01

    Recent works in automated radiotherapy treatment planning have used machine learning based on historical treatment plans to infer the spatial dose distribution for a novel patient directly from the planning image. We present a probabilistic, atlas-based approach which predicts the dose for novel patients using a set of automatically selected most similar patients (atlases). The output is a spatial dose objective, which specifies the desired dose-per-voxel, and therefore replaces the need to specify and tune dose-volume objectives. Voxel-based dose mimicking optimization then converts the predicted dose distribution to a complete treatment plan with dose calculation using a collapsed cone convolution dose engine. In this study, we investigated automated planning for right-sided oropharaynx head and neck patients treated with IMRT and VMAT. We compare four versions of our dose prediction pipeline using a database of 54 training and 12 independent testing patients by evaluating 14 clinical dose evaluation criteria. Our preliminary results are promising and demonstrate that automated methods can generate comparable dose distributions to clinical. Overall, automated plans achieved an average of 0.6% higher dose for target coverage evaluation criteria, and 2.4% lower dose at the organs at risk criteria levels evaluated compared with clinical. There was no statistically significant difference detected in high-dose conformity between automated and clinical plans as measured by the conformation number. Automated plans achieved nine more unique criteria than clinical across the 12 patients tested and automated plans scored a significantly higher dose at the evaluation limit for two high-risk target coverage criteria and a significantly lower dose in one critical organ maximum dose. The novel dose prediction method with dose mimicking can generate complete treatment plans in 12-13 min without user interaction. It is a promising approach for fully automated treatment

  15. Gene Expression Measurement Module (GEMM) - a fully automated, miniaturized instrument for measuring gene expression in space

    Karouia, Fathi; Ricco, Antonio; Pohorille, Andrew; Peyvan, Kianoosh

    2012-07-01

    The capability to measure gene expression on board spacecrafts opens the doors to a large number of experiments on the influence of space environment on biological systems that will profoundly impact our ability to conduct safe and effective space travel, and might also shed light on terrestrial physiology or biological function and human disease and aging processes. Measurements of gene expression will help us to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment on a wide range of organisms from microbes to humans, develop effective countermeasures against these effects, determine metabolic basis of microbial pathogenicity and drug resistance, test our ability to sustain and grow in space organisms that can be used for life support and in situ resource utilization during long-duration space exploration, and monitor both the spacecraft environment and crew health. These and other applications hold significant potential for discoveries in space biology, biotechnology and medicine. Accordingly, supported by funding from the NASA Astrobiology Science and Technology Instrument Development Program, we are developing a fully automated, miniaturized, integrated fluidic system for small spacecraft capable of in-situ measuring microbial expression of thousands of genes from multiple samples. The instrument will be capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing it on a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. The prototype under development is suitable for deployment on nanosatellite platforms developed by the NASA Small Spacecraft Office. The first target application is to cultivate and measure gene expression of the photosynthetic bacterium Synechococcus elongatus, i.e. a cyanobacterium known to exhibit remarkable metabolic diversity and resilience to adverse conditions

  16. Gene Expression Measurement Module (GEMM) - A Fully Automated, Miniaturized Instrument for Measuring Gene Expression in Space

    Pohorille, Andrew; Peyvan, Kia; Karouia, Fathi; Ricco, Antonio

    2012-01-01

    The capability to measure gene expression on board spacecraft opens the door to a large number of high-value experiments on the influence of the space environment on biological systems. For example, measurements of gene expression will help us to understand adaptation of terrestrial life to conditions beyond the planet of origin, identify deleterious effects of the space environment on a wide range of organisms from microbes to humans, develop effective countermeasures against these effects, and determine the metabolic bases of microbial pathogenicity and drug resistance. These and other applications hold significant potential for discoveries in space biology, biotechnology, and medicine. Supported by funding from the NASA Astrobiology Science and Technology Instrument Development Program, we are developing a fully automated, miniaturized, integrated fluidic system for small spacecraft capable of in-situ measurement of expression of several hundreds of microbial genes from multiple samples. The instrument will be capable of (1) lysing cell walls of bacteria sampled from cultures grown in space, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA on a microarray and (4) providing readout of the microarray signal, all in a single microfluidics cartridge. The device is suitable for deployment on nanosatellite platforms developed by NASA Ames' Small Spacecraft Division. To meet space and other technical constraints imposed by these platforms, a number of technical innovations are being implemented. The integration and end-to-end technological and biological validation of the instrument are carried out using as a model the photosynthetic bacterium Synechococcus elongatus, known for its remarkable metabolic diversity and resilience to adverse conditions. Each step in the measurement process-lysis, nucleic acid extraction, purification, and hybridization to an array-is assessed through comparison of the results obtained using the instrument with

  17. Implementation of a fully automated process purge-and-trap gas chromatograph at an environmental remediation site

    Blair, D.S.; Morrison, D.J.

    1997-01-01

    The AQUASCAN, a commercially available, fully automated purge-and-trap gas chromatograph from Sentex Systems Inc., was implemented and evaluated as an in-field, automated monitoring system of contaminated groundwater at an active DOE remediation site in Pinellas, FL. Though the AQUASCAN is designed as a stand alone process analytical unit, implementation at this site required additional hardware. The hardware included a sample dilution system and a method for delivering standard solution to the gas chromatograph for automated calibration. As a result of the evaluation the system was determined to be a reliable and accurate instrument. The AQUASCAN reported concentration values for methylene chloride, trichloroethylene, and toluene in the Pinellas ground water were within 20% of reference laboratory values

  18. Fully automated VMAT treatment planning for advanced-stage NSCLC patients

    Della Gala, Giuseppe [Erasmus MC Cancer Institute, Department of Radiation Oncology, Rotterdam (Netherlands); Universita di Bologna, Scuola di Scienze, Alma Mater Studiorum, Bologna (Italy); Dirkx, Maarten L.P.; Hoekstra, Nienke; Fransen, Dennie; Pol, Marjan van de; Heijmen, Ben J.M. [Erasmus MC Cancer Institute, Department of Radiation Oncology, Rotterdam (Netherlands); Lanconelli, Nico [Universita di Bologna, Scuola di Scienze, Alma Mater Studiorum, Bologna (Italy); Petit, Steven F. [Erasmus MC Cancer Institute, Department of Radiation Oncology, Rotterdam (Netherlands); Massachusetts General Hospital - Harvard Medical School, Department of Radiation Oncology, Boston, MA (United States)

    2017-05-15

    To develop a fully automated procedure for multicriterial volumetric modulated arc therapy (VMAT) treatment planning (autoVMAT) for stage III/IV non-small cell lung cancer (NSCLC) patients treated with curative intent. After configuring the developed autoVMAT system for NSCLC, autoVMAT plans were compared with manually generated clinically delivered intensity-modulated radiotherapy (IMRT) plans for 41 patients. AutoVMAT plans were also compared to manually generated VMAT plans in the absence of time pressure. For 16 patients with reduced planning target volume (PTV) dose prescription in the clinical IMRT plan (to avoid violation of organs at risk tolerances), the potential for dose escalation with autoVMAT was explored. Two physicians evaluated 35/41 autoVMAT plans (85%) as clinically acceptable. Compared to the manually generated IMRT plans, autoVMAT plans showed statistically significant improved PTV coverage (V{sub 95%} increased by 1.1% ± 1.1%), higher dose conformity (R{sub 50} reduced by 12.2% ± 12.7%), and reduced mean lung, heart, and esophagus doses (reductions of 0.9 Gy ± 1.0 Gy, 1.5 Gy ± 1.8 Gy, 3.6 Gy ± 2.8 Gy, respectively, all p < 0.001). To render the six remaining autoVMAT plans clinically acceptable, a dosimetrist needed less than 10 min hands-on time for fine-tuning. AutoVMAT plans were also considered equivalent or better than manually optimized VMAT plans. For 6/16 patients, autoVMAT allowed tumor dose escalation of 5-10 Gy. Clinically deliverable, high-quality autoVMAT plans can be generated fully automatically for the vast majority of advanced-stage NSCLC patients. For a subset of patients, autoVMAT allowed for tumor dose escalation. (orig.) [German] Entwicklung einer vollautomatisierten, auf multiplen Kriterien basierenden volumenmodulierten Arc-Therapie-(VMAT-)Behandlungsplanung (autoVMAT) fuer kurativ behandelte Patienten mit nicht-kleinzelligem Bronchialkarzinom (NSCLC) im Stadium III/IV. Nach Konfiguration unseres auto

  19. Fully automated atlas-based hippocampal volumetry for detection of Alzheimer's disease in a memory clinic setting.

    Suppa, Per; Anker, Ulrich; Spies, Lothar; Bopp, Irene; Rüegger-Frey, Brigitte; Klaghofer, Richard; Gocke, Carola; Hampel, Harald; Beck, Sacha; Buchert, Ralph

    2015-01-01

    Hippocampal volume is a promising biomarker to enhance the accuracy of the diagnosis of dementia due to Alzheimer's disease (AD). However, whereas hippocampal volume is well studied in patient samples from clinical trials, its value in clinical routine patient care is still rather unclear. The aim of the present study, therefore, was to evaluate fully automated atlas-based hippocampal volumetry for detection of AD in the setting of a secondary care expert memory clinic for outpatients. One-hundred consecutive patients with memory complaints were clinically evaluated and categorized into three diagnostic groups: AD, intermediate AD, and non-AD. A software tool based on open source software (Statistical Parametric Mapping SPM8) was employed for fully automated tissue segmentation and stereotactical normalization of high-resolution three-dimensional T1-weighted magnetic resonance images. Predefined standard masks were used for computation of grey matter volume of the left and right hippocampus which then was scaled to the patient's total grey matter volume. The right hippocampal volume provided an area under the receiver operating characteristic curve of 84% for detection of AD patients in the whole sample. This indicates that fully automated MR-based hippocampal volumetry fulfills the requirements for a relevant core feasible biomarker for detection of AD in everyday patient care in a secondary care memory clinic for outpatients. The software used in the present study has been made freely available as an SPM8 toolbox. It is robust and fast so that it is easily integrated into routine workflow.

  20. SU-F-J-93: Automated Segmentation of High-Resolution 3D WholeBrain Spectroscopic MRI for Glioblastoma Treatment Planning

    Schreibmann, E; Shu, H [Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA (United States); Cordova, J; Gurbani, S; Holder, C; Cooper, L; Shim, H [Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA (United States)

    2016-06-15

    Purpose: We report on an automated segmentation algorithm for defining radiation therapy target volumes using spectroscopic MR images (sMRI) acquired at nominal voxel resolution of 100 microliters. Methods: Wholebrain sMRI combining 3D echo-planar spectroscopic imaging, generalized auto-calibrating partially-parallel acquisitions, and elliptical k-space encoding were conducted on 3T MRI scanner with 32-channel head coil array creating images. Metabolite maps generated include choline (Cho), creatine (Cr), and N-acetylaspartate (NAA), as well as Cho/NAA, Cho/Cr, and NAA/Cr ratio maps. Automated segmentation was achieved by concomitantly considering sMRI metabolite maps with standard contrast enhancing (CE) imaging in a pipeline that first uses the water signal for skull stripping. Subsequently, an initial blob of tumor region is identified by searching for regions of FLAIR abnormalities that also display reduced NAA activity using a mean ratio correlation and morphological filters. These regions are used as starting point for a geodesic level-set refinement that adapts the initial blob to the fine details specific to each metabolite. Results: Accuracy of the segmentation model was tested on a cohort of 12 patients that had sMRI datasets acquired pre, mid and post-treatment, providing a broad range of enhancement patterns. Compared to classical imaging, where heterogeneity in the tumor appearance and shape across posed a greater challenge to the algorithm, sMRI’s regions of abnormal activity were easily detected in the sMRI metabolite maps when combining the detail available in the standard imaging with the local enhancement produced by the metabolites. Results can be imported in the treatment planning, leading in general increase in the target volumes (GTV60) when using sMRI+CE MRI compared to the standard CE MRI alone. Conclusion: Integration of automated segmentation of sMRI metabolite maps into planning is feasible and will likely streamline acceptance of this

  1. Online fully automated three-dimensional surface reconstruction of unknown objects

    Khalfaoui, Souhaiel; Aigueperse, Antoine; Fougerolle, Yohan; Seulin, Ralph; Fofi, David

    2015-04-01

    This paper presents a novel scheme for automatic and intelligent 3D digitization using robotic cells. The advantage of our procedure is that it is generic since it is not performed for a specific scanning technology. Moreover, it is not dependent on the methods used to perform the tasks associated with each elementary process. The comparison of results between manual and automatic scanning of complex objects shows that our digitization strategy is very efficient and faster than trained experts. The 3D models of the different objects are obtained with a strongly reduced number of acquisitions while moving efficiently the ranging device.

  2. 3D-Pathology: a real-time system for quantitative diagnostic pathology and visualisation in 3D

    Gottrup, Christian; Beckett, Mark G.; Hager, Henrik; Locht, Peter

    2005-02-01

    This paper presents the results of the 3D-Pathology project conducted under the European EC Framework 5. The aim of the project was, through the application of 3D image reconstruction and visualization techniques, to improve the diagnostic and prognostic capabilities of medical personnel when analyzing pathological specimens using transmitted light microscopy. A fully automated, computer-controlled microscope system has been developed to capture 3D images of specimen content. 3D image reconstruction algorithms have been implemented and applied to the acquired volume data in order to facilitate the subsequent 3D visualization of the specimen. Three potential application fields, immunohistology, cromogenic in situ hybridization (CISH) and cytology, have been tested using the prototype system. For both immunohistology and CISH, use of the system furnished significant additional information to the pathologist.

  3. A fully automated conversational agent for promoting mental well-being: A pilot RCT using mixed methods

    Kien Hoa Ly

    2017-12-01

    Full Text Available Fully automated self-help interventions can serve as highly cost-effective mental health promotion tools for massive amounts of people. However, these interventions are often characterised by poor adherence. One way to address this problem is to mimic therapy support by a conversational agent. The objectives of this study were to assess the effectiveness and adherence of a smartphone app, delivering strategies used in positive psychology and CBT interventions via an automated chatbot (Shim for a non-clinical population — as well as to explore participants' views and experiences of interacting with this chatbot. A total of 28 participants were randomized to either receive the chatbot intervention (n = 14 or to a wait-list control group (n = 14. Findings revealed that participants who adhered to the intervention (n = 13 showed significant interaction effects of group and time on psychological well-being (FS and perceived stress (PSS-10 compared to the wait-list control group, with small to large between effect sizes (Cohen's d range 0.14–1.06. Also, the participants showed high engagement during the 2-week long intervention, with an average open app ratio of 17.71 times for the whole period. This is higher compared to other studies on fully automated interventions claiming to be highly engaging, such as Woebot and the Panoply app. The qualitative data revealed sub-themes which, to our knowledge, have not been found previously, such as the moderating format of the chatbot. The results of this study, in particular the good adherence rate, validated the usefulness of replicating this study in the future with a larger sample size and an active control group. This is important, as the search for fully automated, yet highly engaging and effective digital self-help interventions for promoting mental health is crucial for the public health.

  4. Performance of an Artificial Multi-observer Deep Neural Network for Fully Automated Segmentation of Polycystic Kidneys.

    Kline, Timothy L; Korfiatis, Panagiotis; Edwards, Marie E; Blais, Jaime D; Czerwiec, Frank S; Harris, Peter C; King, Bernard F; Torres, Vicente E; Erickson, Bradley J

    2017-08-01

    Deep learning techniques are being rapidly applied to medical imaging tasks-from organ and lesion segmentation to tissue and tumor classification. These techniques are becoming the leading algorithmic approaches to solve inherently difficult image processing tasks. Currently, the most critical requirement for successful implementation lies in the need for relatively large datasets that can be used for training the deep learning networks. Based on our initial studies of MR imaging examinations of the kidneys of patients affected by polycystic kidney disease (PKD), we have generated a unique database of imaging data and corresponding reference standard segmentations of polycystic kidneys. In the study of PKD, segmentation of the kidneys is needed in order to measure total kidney volume (TKV). Automated methods to segment the kidneys and measure TKV are needed to increase measurement throughput and alleviate the inherent variability of human-derived measurements. We hypothesize that deep learning techniques can be leveraged to perform fast, accurate, reproducible, and fully automated segmentation of polycystic kidneys. Here, we describe a fully automated approach for segmenting PKD kidneys within MR images that simulates a multi-observer approach in order to create an accurate and robust method for the task of segmentation and computation of TKV for PKD patients. A total of 2000 cases were used for training and validation, and 400 cases were used for testing. The multi-observer ensemble method had mean ± SD percent volume difference of 0.68 ± 2.2% compared with the reference standard segmentations. The complete framework performs fully automated segmentation at a level comparable with interobserver variability and could be considered as a replacement for the task of segmentation of PKD kidneys by a human.

  5. Quantification of common carotid artery and descending aorta vessel wall thickness from MR vessel wall imaging using a fully automated processing pipeline.

    Gao, Shan; van 't Klooster, Ronald; Brandts, Anne; Roes, Stijntje D; Alizadeh Dehnavi, Reza; de Roos, Albert; Westenberg, Jos J M; van der Geest, Rob J

    2017-01-01

    To develop and evaluate a method that can fully automatically identify the vessel wall boundaries and quantify the wall thickness for both common carotid artery (CCA) and descending aorta (DAO) from axial magnetic resonance (MR) images. 3T MRI data acquired with T 1 -weighted gradient-echo black-blood imaging sequence from carotid (39 subjects) and aorta (39 subjects) were used to develop and test the algorithm. The vessel wall segmentation was achieved by respectively fitting a 3D cylindrical B-spline surface to the boundaries of lumen and outer wall. The tube-fitting was based on the edge detection performed on the signal intensity (SI) profile along the surface normal. To achieve a fully automated process, Hough Transform (HT) was developed to estimate the lumen centerline and radii for the target vessel. Using the outputs of HT, a tube model for lumen segmentation was initialized and deformed to fit the image data. Finally, lumen segmentation was dilated to initiate the adaptation procedure of outer wall tube. The algorithm was validated by determining: 1) its performance against manual tracing; 2) its interscan reproducibility in quantifying vessel wall thickness (VWT); 3) its capability of detecting VWT difference in hypertensive patients compared with healthy controls. Statistical analysis including Bland-Altman analysis, t-test, and sample size calculation were performed for the purpose of algorithm evaluation. The mean distance between the manual and automatically detected lumen/outer wall contours was 0.00 ± 0.23/0.09 ± 0.21 mm for CCA and 0.12 ± 0.24/0.14 ± 0.35 mm for DAO. No significant difference was observed between the interscan VWT assessment using automated segmentation for both CCA (P = 0.19) and DAO (P = 0.94). Both manual and automated segmentation detected significantly higher carotid (P = 0.016 and P = 0.005) and aortic (P < 0.001 and P = 0.021) wall thickness in the hypertensive patients. A reliable and reproducible pipeline for fully

  6. A Novel Approach for Fully Automated, Personalized Health Coaching for Adults with Prediabetes: Pilot Clinical Trial.

    Everett, Estelle; Kane, Brian; Yoo, Ashley; Dobs, Adrian; Mathioudakis, Nestoras

    2018-02-27

    Prediabetes is a high-risk state for the future development of type 2 diabetes, which may be prevented through physical activity (PA), adherence to a healthy diet, and weight loss. Mobile health (mHealth) technology is a practical and cost-effective method of delivering diabetes prevention programs in a real-world setting. Sweetch (Sweetch Health, Ltd) is a fully automated, personalized mHealth platform designed to promote adherence to PA and weight reduction in people with prediabetes. The objective of this pilot study was to calibrate the Sweetch app and determine the feasibility, acceptability, safety, and effectiveness of the Sweetch app in combination with a digital body weight scale (DBWS) in adults with prediabetes. This was a 3-month prospective, single-arm, observational study of adults with a diagnosis of prediabetes and body mass index (BMI) between 24 kg/m 2 and 40 kg/m 2 . Feasibility was assessed by study retention. Acceptability of the mobile platform and DBWS were evaluated using validated questionnaires. Effectiveness measures included change in PA, weight, BMI, glycated hemoglobin (HbA 1c ), and fasting blood glucose from baseline to 3-month visit. The significance of changes in outcome measures was evaluated using paired t test or Wilcoxon matched pairs test. The study retention rate was 47 out of 55 (86%) participants. There was a high degree of acceptability of the Sweetch app, with a median (interquartile range [IQR]) score of 78% (73%-80%) out of 100% on the validated System Usability Scale. Satisfaction regarding the DBWS was also high, with median (IQR) score of 93% (83%-100%). PA increased by 2.8 metabolic equivalent of task (MET)-hours per week (SD 6.8; P=.02), with mean weight loss of 1.6 kg (SD 2.5; P<.001) from baseline. The median change in A 1c was -0.1% (IQR -0.2% to 0.1%; P=.04), with no significant change in fasting blood glucose (-1 mg/dL; P=.59). There were no adverse events reported. The Sweetch mobile

  7. Fully automated laboratory for the assay of plutonium in wastes and recoverable scraps

    Guiberteau, P.; Michaut, F.; Bergey, C.; Debruyne, T.

    1990-01-01

    To determine the plutonium content of wastes and recoverable scraps in intermediate size containers (ten liters) an automated laboratory has been carried out. Two passive methods of measurement are used. Gamma ray spectrometry allows plutonium isotopic analysis, americium determination and plutonium assay in wastes and poor scraps. Calorimetry is used for accurate (± 3%) plutonium determination in rich scraps. A full automation was realized with a barcode management and a supply robot to feed the eight assay set-ups. The laboratory works on a 24 hours per day and 365 days per year basis and has a capacity of 8,000 assays per year

  8. A two-dimensionally coincident second difference cosmic ray spike removal method for the fully automated processing of Raman spectra.

    Schulze, H Georg; Turner, Robin F B

    2014-01-01

    Charge-coupled device detectors are vulnerable to cosmic rays that can contaminate Raman spectra with positive going spikes. Because spikes can adversely affect spectral processing and data analyses, they must be removed. Although both hardware-based and software-based spike removal methods exist, they typically require parameter and threshold specification dependent on well-considered user input. Here, we present a fully automated spike removal algorithm that proceeds without requiring user input. It is minimally dependent on sample attributes, and those that are required (e.g., standard deviation of spectral noise) can be determined with other fully automated procedures. At the core of the method is the identification and location of spikes with coincident second derivatives along both the spectral and spatiotemporal dimensions of two-dimensional datasets. The method can be applied to spectra that are relatively inhomogeneous because it provides fairly effective and selective targeting of spikes resulting in minimal distortion of spectra. Relatively effective spike removal obtained with full automation could provide substantial benefits to users where large numbers of spectra must be processed.

  9. The development of a fully automated radioimmunoassay instrument - micromedic systems concept 4

    Painter, K.

    1977-01-01

    The fully automatic RIA system Concept 4 by Micromedic is described in detail. The system uses antibody-coated test tubes to take up the samples. It has a maximum capacity of 200 tubes including standards and control tubes. Its advantages are, in particular, high flow rate, reproducibility, and fully automatic testing i.e. low personnel requirements. Its disadvantage are difficulties in protein assays. (ORU) [de

  10. Rapid access to compound libraries through flow technology: fully automated synthesis of a 3-aminoindolizine library via orthogonal diversification.

    Lange, Paul P; James, Keith

    2012-10-08

    A novel methodology for the synthesis of druglike heterocycle libraries has been developed through the use of flow reactor technology. The strategy employs orthogonal modification of a heterocyclic core, which is generated in situ, and was used to construct both a 25-membered library of druglike 3-aminoindolizines, and selected examples of a 100-member virtual library. This general protocol allows a broad range of acylation, alkylation and sulfonamidation reactions to be performed in conjunction with a tandem Sonogashira coupling/cycloisomerization sequence. All three synthetic steps were conducted under full automation in the flow reactor, with no handling or isolation of intermediates, to afford the desired products in good yields. This fully automated, multistep flow approach opens the way to highly efficient generation of druglike heterocyclic systems as part of a lead discovery strategy or within a lead optimization program.

  11. Fully automated synthesis of 11C-acetate as tumor PET tracer by simple modified solid-phase extraction purification

    Tang, Xiaolan; Tang, Ganghua; Nie, Dahong

    2013-01-01

    Introduction: Automated synthesis of 11 C-acetate ( 11 C-AC) as the most commonly used radioactive fatty acid tracer is performed by a simple, rapid, and modified solid-phase extraction (SPE) purification. Methods: Automated synthesis of 11 C-AC was implemented by carboxylation reaction of MeMgBr on a polyethylene Teflon loop ring with 11 C-CO 2 , followed by acidic hydrolysis with acid and SCX cartridge, and purification on SCX, AG11A8 and C18 SPE cartridges using a commercially available 11 C-tracer synthesizer. Quality control test and animals positron emission tomography (PET) imaging were also carried out. Results: A high and reproducible decay-uncorrected radiochemical yield of (41.0±4.6)% (n=10) was obtained from 11 C-CO 2 within the whole synthesis time about 8 min. The radiochemical purity of 11 C-AC was over 95% by high-performance liquid chromatography (HPLC) analysis. Quality control test and PET imaging showed that 11 C-AC injection produced by the simple SPE procedure was safe and efficient, and was in agreement with the current Chinese radiopharmaceutical quality control guidelines. Conclusion: The novel, simple, and rapid method is readily adapted to the fully automated synthesis of 11 C-AC on several existing commercial synthesis module. The method can be used routinely to produce 11 C-AC for preclinical and clinical studies with PET imaging. - Highlights: • A fully automated synthesis of 11 C-acetate by simple modified solid-phase extraction purification has been developed. • Typical non-decay-corrected yields were (41.0±4.6)% (n=10) • Radiochemical purity was determined by radio-HPLC analysis on a C18 column using the gradient program, instead of expensive organic acid column or anion column. • QC testing (RCP>99%)

  12. A new TLD badge with machine readable ID for fully automated readout

    Kannan, S. Ratna P.; Kulkarni, M.S.

    2003-01-01

    The TLD badge currently being used for personnel monitoring of more than 40,000 radiation workers has a few drawbacks such as lack of on-badge machine readable ID code, delicate two-point clamping of dosimeters on an aluminium card with the chances of dosimeters falling off during handling or readout, projections on one side making automation of readout difficult etc. A new badge has been designed with a 8-digit identification code in the form of an array of holes and smooth exteriors to enable full automation of readout. The new badge also permits changing of dosimeters when necessary. The new design does not affect the readout time or the dosimetric characteristics. The salient features and the dosimetric characteristics are discussed. (author)

  13. A fully automated mass spectrometer for the analysis of organic solids

    Hillig, H.; Kueper, H.; Riepe, W.

    1979-01-01

    Automation of a mass spectrometer-computer system makes it possible to process up to 30 samples without attention after sample loading. An automatic sample changer introduces the samples successively into the ion source by means of a direct inlet probe. A process control unit determines the operation sequence. Computer programs are available for the hardware support, system supervision and evaluation of the spectrometer signals. The most essential precondition for automation - automatic evaporation of the sample material by electronic control of the total ion current - is confirmed to be satisfactory. The system operates routinely overnight in an industrial laboratory, so that day work can be devoted to difficult analytical problems. The cost of routine analyses is halved. (Auth.)

  14. A wearable device for a fully automated in-hospital staff and patient identification.

    Cavalleri, M; Morstabilini, R; Reni, G

    2004-01-01

    In the health care context, devices for automated staff / patient identification provide multiple benefits, including error reduction in drug administration, an easier and faster use of the Electronic Health Record, enhanced security and control features when accessing confidential data, etc. Current identification systems (e.g. smartcards, bar codes) are not completely seamless to users and require mechanical operations that sometimes are difficult to perform for impaired subjects. Emerging wireless RFID technologies are encouraging, but cannot still be introduced in health care environments due to their electromagnetic emissions and the need for large size antenna to operate at reasonable distances. The present work describes a prototype of wearable device for automated staff and patient identification which is small in size and complies with the in-hospital electromagnetic requirements. This prototype also implements an anti-counterfeit option. Its experimental application allowed the introduction of some security functions for confidential data management.

  15. Development of a fully automated network system for long-term health-care monitoring at home.

    Motoi, K; Kubota, S; Ikarashi, A; Nogawa, M; Tanaka, S; Nemoto, T; Yamakoshi, K

    2007-01-01

    Daily monitoring of health condition at home is very important not only as an effective scheme for early diagnosis and treatment of cardiovascular and other diseases, but also for prevention and control of such diseases. From this point of view, we have developed a prototype room for fully automated monitoring of various vital signs. From the results of preliminary experiments using this room, it was confirmed that (1) ECG and respiration during bathing, (2) excretion weight and blood pressure, and (3) respiration and cardiac beat during sleep could be monitored with reasonable accuracy by the sensor system installed in bathtub, toilet and bed, respectively.

  16. Evaluation of a Fully Automated Analyzer for Rapid Measurement of Water Vapor Sorption Isotherms for Applications in Soil Science

    Arthur, Emmanuel; Tuller, Markus; Moldrup, Per

    2014-01-01

    The characterization and description of important soil processes such as water vapor transport, volatilization of pesticides, and hysteresis require accurate means for measuring the soil water characteristic (SWC) at low water potentials. Until recently, measurement of the SWC at low water...... potentials was constrained by hydraulic decoupling and long equilibration times when pressure plates or single-point, chilled-mirror instruments were used. A new, fully automated Vapor Sorption Analyzer (VSA) helps to overcome these challenges and allows faster measurement of highly detailed water vapor...

  17. Comparison of subjective and fully automated methods for measuring mammographic density.

    Moshina, Nataliia; Roman, Marta; Sebuødegård, Sofie; Waade, Gunvor G; Ursin, Giske; Hofvind, Solveig

    2018-02-01

    Background Breast radiologists of the Norwegian Breast Cancer Screening Program subjectively classified mammographic density using a three-point scale between 1996 and 2012 and changed into the fourth edition of the BI-RADS classification since 2013. In 2015, an automated volumetric breast density assessment software was installed at two screening units. Purpose To compare volumetric breast density measurements from the automated method with two subjective methods: the three-point scale and the BI-RADS density classification. Material and Methods Information on subjective and automated density assessment was obtained from screening examinations of 3635 women recalled for further assessment due to positive screening mammography between 2007 and 2015. The score of the three-point scale (I = fatty; II = medium dense; III = dense) was available for 2310 women. The BI-RADS density score was provided for 1325 women. Mean volumetric breast density was estimated for each category of the subjective classifications. The automated software assigned volumetric breast density to four categories. The agreement between BI-RADS and volumetric breast density categories was assessed using weighted kappa (k w ). Results Mean volumetric breast density was 4.5%, 7.5%, and 13.4% for categories I, II, and III of the three-point scale, respectively, and 4.4%, 7.5%, 9.9%, and 13.9% for the BI-RADS density categories, respectively ( P for trend density categories was k w  = 0.5 (95% CI = 0.47-0.53; P density increased with increasing density category of the subjective classifications. The agreement between BI-RADS and volumetric breast density categories was moderate.

  18. A fully automated primary screening system for the discovery of therapeutic antibodies directly from B cells.

    Tickle, Simon; Howells, Louise; O'Dowd, Victoria; Starkie, Dale; Whale, Kevin; Saunders, Mark; Lee, David; Lightwood, Daniel

    2015-04-01

    For a therapeutic antibody to succeed, it must meet a range of potency, stability, and specificity criteria. Many of these characteristics are conferred by the amino acid sequence of the heavy and light chain variable regions and, for this reason, can be screened for during antibody selection. However, it is important to consider that antibodies satisfying all these criteria may be of low frequency in an immunized animal; for this reason, it is essential to have a mechanism that allows for efficient sampling of the immune repertoire. UCB's core antibody discovery platform combines high-throughput B cell culture screening and the identification and isolation of single, antigen-specific IgG-secreting B cells through a proprietary technique called the "fluorescent foci" method. Using state-of-the-art automation to facilitate primary screening, extremely efficient interrogation of the natural antibody repertoire is made possible; more than 1 billion immune B cells can now be screened to provide a useful starting point from which to identify the rare therapeutic antibody. This article will describe the design, construction, and commissioning of a bespoke automated screening platform and two examples of how it was used to screen for antibodies against two targets. © 2014 Society for Laboratory Automation and Screening.

  19. Designing a fully automated multi-bioreactor plant for fast DoE optimization of pharmaceutical protein production.

    Fricke, Jens; Pohlmann, Kristof; Jonescheit, Nils A; Ellert, Andree; Joksch, Burkhard; Luttmann, Reiner

    2013-06-01

    The identification of optimal expression conditions for state-of-the-art production of pharmaceutical proteins is a very time-consuming and expensive process. In this report a method for rapid and reproducible optimization of protein expression in an in-house designed small-scale BIOSTAT® multi-bioreactor plant is described. A newly developed BioPAT® MFCS/win Design of Experiments (DoE) module (Sartorius Stedim Systems, Germany) connects the process control system MFCS/win and the DoE software MODDE® (Umetrics AB, Sweden) and enables therefore the implementation of fully automated optimization procedures. As a proof of concept, a commercial Pichia pastoris strain KM71H has been transformed for the expression of potential malaria vaccines. This approach has allowed a doubling of intact protein secretion productivity due to the DoE optimization procedure compared to initial cultivation results. In a next step, robustness regarding the sensitivity to process parameter variability has been proven around the determined optimum. Thereby, a pharmaceutical production process that is significantly improved within seven 24-hour cultivation cycles was established. Specifically, regarding the regulatory demands pointed out in the process analytical technology (PAT) initiative of the United States Food and Drug Administration (FDA), the combination of a highly instrumented, fully automated multi-bioreactor platform with proper cultivation strategies and extended DoE software solutions opens up promising benefits and opportunities for pharmaceutical protein production. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Fully automated synthesis of [(18) F]fluoro-dihydrotestosterone ([(18) F]FDHT) using the FlexLab module.

    Ackermann, Uwe; Lewis, Jason S; Young, Kenneth; Morris, Michael J; Weickhardt, Andrew; Davis, Ian D; Scott, Andrew M

    2016-08-01

    Imaging of androgen receptor expression in prostate cancer using F-18 FDHT is becoming increasingly popular. With the radiolabelling precursor now commercially available, developing a fully automated synthesis of [(18) F] FDHT is important. We have fully automated the synthesis of F-18 FDHT using the iPhase FlexLab module using only commercially available components. Total synthesis time was 90 min, radiochemical yields were 25-33% (n = 11). Radiochemical purity of the final formulation was > 99% and specific activity was > 18.5 GBq/µmol for all batches. This method can be up-scaled as desired, thus making it possible to study multiple patients in a day. Furthermore, our procedure uses 4 mg of precursor only and is therefore cost-effective. The synthesis has now been validated at Austin Health and is currently used for [(18) F]FDHT studies in patients. We believe that this method can easily adapted by other modules to further widen the availability of [(18) F]FDHT. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Searching for prostate cancer by fully automated magnetic resonance imaging classification: deep learning versus non-deep learning.

    Wang, Xinggang; Yang, Wei; Weinreb, Jeffrey; Han, Juan; Li, Qiubai; Kong, Xiangchuang; Yan, Yongluan; Ke, Zan; Luo, Bo; Liu, Tao; Wang, Liang

    2017-11-13

    Prostate cancer (PCa) is a major cause of death since ancient time documented in Egyptian Ptolemaic mummy imaging. PCa detection is critical to personalized medicine and varies considerably under an MRI scan. 172 patients with 2,602 morphologic images (axial 2D T2-weighted imaging) of the prostate were obtained. A deep learning with deep convolutional neural network (DCNN) and a non-deep learning with SIFT image feature and bag-of-word (BoW), a representative method for image recognition and analysis, were used to distinguish pathologically confirmed PCa patients from prostate benign conditions (BCs) patients with prostatitis or prostate benign hyperplasia (BPH). In fully automated detection of PCa patients, deep learning had a statistically higher area under the receiver operating characteristics curve (AUC) than non-deep learning (P = 0.0007 deep learning method and 0.70 (95% CI 0.63-0.77) for non-deep learning method, respectively. Our results suggest that deep learning with DCNN is superior to non-deep learning with SIFT image feature and BoW model for fully automated PCa patients differentiation from prostate BCs patients. Our deep learning method is extensible to image modalities such as MR imaging, CT and PET of other organs.

  2. Fully automated laboratory and field-portable goniometer used for performing accurate and precise multiangular reflectance measurements

    Harms, Justin D.; Bachmann, Charles M.; Ambeau, Brittany L.; Faulring, Jason W.; Ruiz Torres, Andres J.; Badura, Gregory; Myers, Emily

    2017-10-01

    Field-portable goniometers are created for a wide variety of applications. Many of these applications require specific types of instruments and measurement schemes and must operate in challenging environments. Therefore, designs are based on the requirements that are specific to the application. We present a field-portable goniometer that was designed for measuring the hemispherical-conical reflectance factor (HCRF) of various soils and low-growing vegetation in austere coastal and desert environments and biconical reflectance factors in laboratory settings. Unlike some goniometers, this system features a requirement for "target-plane tracking" to ensure that measurements can be collected on sloped surfaces, without compromising angular accuracy. The system also features a second upward-looking spectrometer to measure the spatially dependent incoming illumination, an integrated software package to provide full automation, an automated leveling system to ensure a standard frame of reference, a design that minimizes the obscuration due to self-shading to measure the opposition effect, and the ability to record a digital elevation model of the target region. This fully automated and highly mobile system obtains accurate and precise measurements of HCRF in a wide variety of terrain and in less time than most other systems while not sacrificing consistency or repeatability in laboratory environments.

  3. Reliability of fully automated versus visually controlled pre- and post-processing of resting-state EEG.

    Hatz, F; Hardmeier, M; Bousleiman, H; Rüegg, S; Schindler, C; Fuhr, P

    2015-02-01

    To compare the reliability of a newly developed Matlab® toolbox for the fully automated, pre- and post-processing of resting state EEG (automated analysis, AA) with the reliability of analysis involving visually controlled pre- and post-processing (VA). 34 healthy volunteers (age: median 38.2 (20-49), 82% female) had three consecutive 256-channel resting-state EEG at one year intervals. Results of frequency analysis of AA and VA were compared with Pearson correlation coefficients, and reliability over time was assessed with intraclass correlation coefficients (ICC). Mean correlation coefficient between AA and VA was 0.94±0.07, mean ICC for AA 0.83±0.05 and for VA 0.84±0.07. AA and VA yield very similar results for spectral EEG analysis and are equally reliable. AA is less time-consuming, completely standardized, and independent of raters and their training. Automated processing of EEG facilitates workflow in quantitative EEG analysis. Copyright © 2014 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  4. Comparison of T1-weighted 2D TSE, 3D SPGR, and two-point 3D Dixon MRI for automated segmentation of visceral adipose tissue at 3 Tesla.

    Fallah, Faezeh; Machann, Jürgen; Martirosian, Petros; Bamberg, Fabian; Schick, Fritz; Yang, Bin

    2017-04-01

    To evaluate and compare conventional T1-weighted 2D turbo spin echo (TSE), T1-weighted 3D volumetric interpolated breath-hold examination (VIBE), and two-point 3D Dixon-VIBE sequences for automatic segmentation of visceral adipose tissue (VAT) volume at 3 Tesla by measuring and compensating for errors arising from intensity nonuniformity (INU) and partial volume effects (PVE). The body trunks of 28 volunteers with body mass index values ranging from 18 to 41.2 kg/m 2 (30.02 ± 6.63 kg/m 2 ) were scanned at 3 Tesla using three imaging techniques. Automatic methods were applied to reduce INU and PVE and to segment VAT. The automatically segmented VAT volumes obtained from all acquisitions were then statistically and objectively evaluated against the manually segmented (reference) VAT volumes. Comparing the reference volumes with the VAT volumes automatically segmented over the uncorrected images showed that INU led to an average relative volume difference of -59.22 ± 11.59, 2.21 ± 47.04, and -43.05 ± 5.01 % for the TSE, VIBE, and Dixon images, respectively, while PVE led to average differences of -34.85 ± 19.85, -15.13 ± 11.04, and -33.79 ± 20.38 %. After signal correction, differences of -2.72 ± 6.60, 34.02 ± 36.99, and -2.23 ± 7.58 % were obtained between the reference and the automatically segmented volumes. A paired-sample two-tailed t test revealed no significant difference between the reference and automatically segmented VAT volumes of the corrected TSE (p = 0.614) and Dixon (p = 0.969) images, but showed a significant VAT overestimation using the corrected VIBE images. Under similar imaging conditions and spatial resolution, automatically segmented VAT volumes obtained from the corrected TSE and Dixon images agreed with each other and with the reference volumes. These results demonstrate the efficacy of the signal correction methods and the similar accuracy of TSE and Dixon imaging for automatic volumetry of VAT at 3 Tesla.

  5. Construction and calibration of a low cost and fully automated vibrating sample magnetometer

    El-Alaily, T.M.; El-Nimr, M.K.; Saafan, S.A.; Kamel, M.M.; Meaz, T.M.; Assar, S.T.

    2015-01-01

    A low cost vibrating sample magnetometer (VSM) has been constructed by using an electromagnet and an audio loud speaker; where both are controlled by a data acquisition device. The constructed VSM records the magnetic hysteresis loop up to 8.3 KG at room temperature. The apparatus has been calibrated and tested by using magnetic hysteresis data of some ferrite samples measured by two scientifically calibrated magnetometers; model (Lake Shore 7410) and model (LDJ Electronics Inc. Troy, MI). Our VSM lab-built new design proved success and reliability. - Highlights: • A low cost automated vibrating sample magnetometer VSM has been constructed. • The VSM records the magnetic hysteresis loop up to 8.3 KG at room temperature. • The VSM has been calibrated and tested by using some measured ferrite samples. • Our VSM lab-built new design proved success and reliability

  6. Construction and calibration of a low cost and fully automated vibrating sample magnetometer

    El-Alaily, T.M., E-mail: toson_alaily@yahoo.com [Physics Department, Faculty of Science, Tanta University, Tanta (Egypt); El-Nimr, M.K.; Saafan, S.A.; Kamel, M.M.; Meaz, T.M. [Physics Department, Faculty of Science, Tanta University, Tanta (Egypt); Assar, S.T. [Engineering Physics and Mathematics Department, Faculty of Engineering, Tanta University, Tanta (Egypt)

    2015-07-15

    A low cost vibrating sample magnetometer (VSM) has been constructed by using an electromagnet and an audio loud speaker; where both are controlled by a data acquisition device. The constructed VSM records the magnetic hysteresis loop up to 8.3 KG at room temperature. The apparatus has been calibrated and tested by using magnetic hysteresis data of some ferrite samples measured by two scientifically calibrated magnetometers; model (Lake Shore 7410) and model (LDJ Electronics Inc. Troy, MI). Our VSM lab-built new design proved success and reliability. - Highlights: • A low cost automated vibrating sample magnetometer VSM has been constructed. • The VSM records the magnetic hysteresis loop up to 8.3 KG at room temperature. • The VSM has been calibrated and tested by using some measured ferrite samples. • Our VSM lab-built new design proved success and reliability.

  7. A fully automated contour detection algorithm the preliminary step for scatter and attenuation compensation in SPECT

    Younes, R.B.; Mas, J.; Bidet, R.

    1988-01-01

    Contour detection is an important step in information extraction from nuclear medicine images. In order to perform accurate quantitative studies in single photon emission computed tomography (SPECT) a new procedure is described which can rapidly derive the best fit contour of an attenuated medium. Some authors evaluate the influence of the detected contour on the reconstructed images with various attenuation correction techniques. Most of the methods are strongly affected by inaccurately detected contours. This approach uses the Compton window to redetermine the convex contour: It seems to be simpler and more practical in clinical SPECT studies. The main advantages of this procedure are the high speed of computation, the accuracy of the contour found and the programme's automation. Results obtained using computer simulated and real phantoms or clinical studies demonstrate the reliability of the present algorithm. (orig.)

  8. A FULLY AUTOMATED PIPELINE FOR CLASSIFICATION TASKS WITH AN APPLICATION TO REMOTE SENSING

    K. Suzuki

    2016-06-01

    Full Text Available Nowadays deep learning has been intensively in spotlight owing to its great victories at major competitions, which undeservedly pushed ‘shallow’ machine learning methods, relatively naive/handy algorithms commonly used by industrial engineers, to the background in spite of their facilities such as small requisite amount of time/dataset for training. We, with a practical point of view, utilized shallow learning algorithms to construct a learning pipeline such that operators can utilize machine learning without any special knowledge, expensive computation environment, and a large amount of labelled data. The proposed pipeline automates a whole classification process, namely feature-selection, weighting features and the selection of the most suitable classifier with optimized hyperparameters. The configuration facilitates particle swarm optimization, one of well-known metaheuristic algorithms for the sake of generally fast and fine optimization, which enables us not only to optimize (hyperparameters but also to determine appropriate features/classifier to the problem, which has conventionally been a priori based on domain knowledge and remained untouched or dealt with naïve algorithms such as grid search. Through experiments with the MNIST and CIFAR-10 datasets, common datasets in computer vision field for character recognition and object recognition problems respectively, our automated learning approach provides high performance considering its simple setting (i.e. non-specialized setting depending on dataset, small amount of training data, and practical learning time. Moreover, compared to deep learning the performance stays robust without almost any modification even with a remote sensing object recognition problem, which in turn indicates that there is a high possibility that our approach contributes to general classification problems.

  9. Comparisons of fully automated syphilis tests with conventional VDRL and FTA-ABS tests.

    Choi, Seung Jun; Park, Yongjung; Lee, Eun Young; Kim, Sinyoung; Kim, Hyon-Suk

    2013-06-01

    Serologic tests are widely used for the diagnosis of syphilis. However, conventional methods require well-trained technicians to produce reliable results. We compared automated nontreponemal and treponemal tests with conventional methods. The HiSens Auto Rapid Plasma Reagin (AutoRPR) and Treponema Pallidum particle agglutination (AutoTPPA) tests, which utilize latex turbidimetric immunoassay, were assessed. A total of 504 sera were assayed by AutoRPR, AutoTPPA, conventional VDRL and FTA-ABS. Among them, 250 samples were also tested by conventional TPPA. The concordance rate between the results of VDRL and AutoRPR was 67.5%, and 164 discrepant cases were all VDRL reactive but AutoRPR negative. In the 164 cases, 133 showed FTA-ABS reactivity. Medical records of 106 among the 133 cases were reviewed, and 82 among 106 specimens were found to be collected from patients already treated for syphilis. The concordance rate between the results of AutoTPPA and FTA-ABS was 97.8%. The results of conventional TPPA and AutoTPPA for 250 samples were concordant in 241 cases (96.4%). AutoRPR showed higher specificity than that of VDRL, while VDRL demonstrated higher sensitivity than that of AutoRPR regardless of whether the patients had been already treated for syphilis or not. Both FTA-ABS and AutoTPPA showed high sensitivities and specificities greater than 98.0%. Automated RPR and TPPA tests could be alternatives to conventional syphilis tests, and AutoRPR would be particularly suitable in treatment monitoring, since results by AutoRPR in cases after treatment became negative more rapidly than by VDRL. Copyright © 2013. Published by Elsevier Inc.

  10. Validation of a Fully Automated HER2 Staining Kit in Breast Cancer

    Cathy B. Moelans

    2010-01-01

    Full Text Available Background: Testing for HER2 amplification and/or overexpression is currently routine practice to guide Herceptin therapy in invasive breast cancer. At present, HER2 status is most commonly assessed by immunohistochemistry (IHC. Standardization of HER2 IHC assays is of utmost clinical and economical importance. At present, HER2 IHC is most commonly performed with the HercepTest which contains a polyclonal antibody and applies a manual staining procedure. Analytical variability in HER2 IHC testing could be diminished by a fully automatic staining system with a monoclonal antibody.

  11. Fully automated processing of buffy-coat-derived pooled platelet concentrates.

    Janetzko, Karin; Klüter, Harald; van Waeg, Geert; Eichler, Hermann

    2004-07-01

    The OrbiSac device, which was developed to automate the manufacture of buffy-coat PLT concentrates (BC-PCs), was evaluated. In-vitro characteristics of BC-PC preparations using the OrbiSac device were compared with manually prepared BC-PCs. For standard processing (Std-PC, n = 20), four BC-PCs were pooled using 300 mL of PLT AS (PAS) followed by soft-spin centrifugation and WBC filtration. The OrbiSac preparation (OS-PC, n = 20) was performed by automated pooling of four BC-PCs with 300 mL PAS followed by centrifugation and inline WBC filtration. All PCs were stored at 22 degrees C. Samples were withdrawn on Day 1, 5, and 7 evaluating PTL count, blood gas analysis, glucose, lactate, LDH, beta-thromboglobulin, hypotonic shock response, and CD62p expression. A PLT content of 3.1 +/- 0.4 x 10(11) (OS-PCs) versus 2.7 +/- 0.5 x 10(11) (Std-PCs, p < 0.05) was found. A CV of 19 percent (Std-PC) versus 14 percent (OS-PC) suggests more standardization in the OS group. At Day 7, the Std-PCs versus OS-PCs showed a glucose consumption of 1.03 +/- 0.32 micro mol per 10(9) PLT versus 0.75 +/- 0.25 micro mol per 10(9) PLT (p < 0.001), and a lactate production of 1.50 +/- 0.86 micro mol per 10(9) versus 1.11 +/- 0.61 micro mol per 10(9) (p < 0.001). The pH (7.00 +/- 0.19 vs. 7.23 +/- 0.06; p < 0.001), pO(2) (45.3 +/- 18 vs. 31.3 +/- 10.4 mmHg; p < 0.01), and HCO(3) levels (4.91 +/- 1.49 vs. 7.14 +/- 0.95 mmol/L; p < 0.001) suggest a slightly better aerobic metabolism within the OS group. Only small differences in CD62p expression was observed (37.3 +/- 12.9% Std-PC vs. 44.8 +/- 6.6% OS-PC; p < 0.05). The OrbiSac device allows an improved PLT yield without affecting PLT in-vitro characteristics and may enable an improved consistency in product volume and yield.

  12. Fully Automated Detection of Corticospinal Tract Damage in Chronic Stroke Patients

    Ming Yang

    2014-01-01

    Full Text Available Structural integrity of the corticospinal tract (CST after stroke is closely linked to the degree of motor impairment. However, current methods for measurement of fractional atrophy (FA of CST based on region of interest (ROI are time-consuming and open to bias. Here, we used tract-based spatial statistics (TBSS together with a CST template with healthy volunteers to quantify structural integrity of CST automatically. Two groups of patients after ischemic stroke were enrolled, group 1 (10 patients, 7 men, and Fugl-Meyer assessment (FMA scores ⩽ 50 and group 2 (12 patients, 12 men, and FMA scores = 100. CST of FAipsi, FAcontra, and FAratio was compared between the two groups. Relative to group 2, FA was decreased in group 1 in the ipsilesional CST (P<0.01, as well as the FAratio (P<0.01. There was no significant difference between the two subgroups in the contralesional CST (P=0.23. Compared with contralesional CST, FA of ipsilesional CST decreased in group 1 (P<0.01. These results suggest that the automated method used in our study could detect a surrogate biomarker to quantify the CST after stroke, which would facilitate implementation of clinical practice.

  13. Atmospheric ozone measurement with an inexpensive and fully automated porous tube collector-colorimeter.

    Li, Jianzhong; Li, Qingyang; Dyke, Jason V; Dasgupta, Purnendu K

    2008-01-15

    The bleaching action of ozone on indigo and related compounds is well known. We describe sensitive automated instrumentation for measuring ambient ozone. Air is sampled around a porous polypropylene tube filled with a solution of indigotrisulfonate. Light transmission through the tube is measured. Light transmission increases as O(3) diffuses through the membrane and bleaches the indigo. Evaporation of the solution, a function of the RH and the air temperature, can, however cause major errors. We solve this problem by adding an O(3)-inert dye that absorbs at a different wavelength. Here we provide a new algorithm for this correction and show that this very inexpensive instrument package (controlled by a BASIC Stamp Microcontroller with an on-board data logger, total parts cost US$ 300) provides data highly comparable to commercial ozone monitors over an extended period. The instrument displays an LOD of 1.2ppbv and a linear span up to 300ppbv for a sampling time of 1min. For a sampling time of 5min, the respective values are 0.24ppbv and 100ppbv O(3).

  14. A Fully Automated and Robust Method to Incorporate Stamping Data in Crash, NVH and Durability Analysis

    Palaniswamy, Hariharasudhan; Kanthadai, Narayan; Roy, Subir; Beauchesne, Erwan

    2011-08-01

    Crash, NVH (Noise, Vibration, Harshness), and durability analysis are commonly deployed in structural CAE analysis for mechanical design of components especially in the automotive industry. Components manufactured by stamping constitute a major portion of the automotive structure. In CAE analysis they are modeled at a nominal state with uniform thickness and no residual stresses and strains. However, in reality the stamped components have non-uniformly distributed thickness and residual stresses and strains resulting from stamping. It is essential to consider the stamping information in CAE analysis to accurately model the behavior of the sheet metal structures under different loading conditions. Especially with the current emphasis on weight reduction by replacing conventional steels with aluminum and advanced high strength steels it is imperative to avoid over design. Considering this growing need in industry, a highly automated and robust method has been integrated within Altair Hyperworks® to initialize sheet metal components in CAE models with stamping data. This paper demonstrates this new feature and the influence of stamping data for a full car frontal crash analysis.

  15. Grid-Competitive Residential and Commercial Fully Automated PV Systems Technology: Final technical Report, August 2011

    Brown, Katie E.; Cousins, Peter; Culligan, Matt; Jonathan Botkin; DeGraaff, David; Bunea, Gabriella; Rose, Douglas; Bourne, Ben; Koehler, Oliver

    2011-08-26

    Under DOE's Technology Pathway Partnership program, SunPower Corporation developed turn-key, high-efficiency residential and commercial systems that are cost effective. Key program objectives include a reduction in LCOE values to 9-12 cents/kWh and 13-18 cents/kWh respectively for the commercial and residential markets. Target LCOE values for the commercial ground, commercial roof, and residential markets are 10, 11, and 13 cents/kWh. For this effort, SunPower collaborated with a variety of suppliers and partners to complete the tasks below. Subcontractors included: Solaicx, SiGen, Ribbon Technology, Dow Corning, Xantrex, Tigo Energy, and Solar Bridge. SunPower's TPP addressed nearly the complete PV value chain: from ingot growth through system deployment. Throughout the award period of performance, SunPower has made progress toward achieving these reduced costs through the development of 20%+ efficient modules, increased cell efficiency through the understanding of loss mechanisms and improved manufacturing technologies, novel module development, automated design tools and techniques, and reduced system development and installation time. Based on an LCOE assessment using NREL's Solar Advisor Model, SunPower achieved the 2010 target range, as well as progress toward 2015 targets.

  16. Fully automated segmentation of oncological PET volumes using a combined multiscale and statistical model

    Montgomery, David W. G.; Amira, Abbes; Zaidi, Habib

    2007-01-01

    The widespread application of positron emission tomography (PET) in clinical oncology has driven this imaging technology into a number of new research and clinical arenas. Increasing numbers of patient scans have led to an urgent need for efficient data handling and the development of new image analysis techniques to aid clinicians in the diagnosis of disease and planning of treatment. Automatic quantitative assessment of metabolic PET data is attractive and will certainly revolutionize the practice of functional imaging since it can lower variability across institutions and may enhance the consistency of image interpretation independent of reader experience. In this paper, a novel automated system for the segmentation of oncological PET data aiming at providing an accurate quantitative analysis tool is proposed. The initial step involves expectation maximization (EM)-based mixture modeling using a k-means clustering procedure, which varies voxel order for initialization. A multiscale Markov model is then used to refine this segmentation by modeling spatial correlations between neighboring image voxels. An experimental study using an anthropomorphic thorax phantom was conducted for quantitative evaluation of the performance of the proposed segmentation algorithm. The comparison of actual tumor volumes to the volumes calculated using different segmentation methodologies including standard k-means, spatial domain Markov Random Field Model (MRFM), and the new multiscale MRFM proposed in this paper showed that the latter dramatically reduces the relative error to less than 8% for small lesions (7 mm radii) and less than 3.5% for larger lesions (9 mm radii). The analysis of the resulting segmentations of clinical oncologic PET data seems to confirm that this methodology shows promise and can successfully segment patient lesions. For problematic images, this technique enables the identification of tumors situated very close to nearby high normal physiologic uptake. The

  17. Real-time direct cell concentration and viability determination using a fully automated microfluidic platform for standalone process monitoring

    Rodrigues de Sousa Nunes, Pedro André; Kjaerulff, S.; Dufva, Martin

    2015-01-01

    system performance by monitoring in real time the cell concentration and viability of yeast extracted directly from an in-house made bioreactor. This is the first demonstration of using the Dean drag force, generated due to the implementation of a curved microchannel geometry in conjunction with high...... flow rates, to promote passive mixing of cell samples and thus homogenization of the diluted cell plug. The autonomous operation of the fluidics furthermore allows implementation of intelligent protocols for administering air bubbles from the bioreactor in the microfluidic system, so...... and thereby ensure optimal cell production, by prolonging the fermentation cycle and increasing the bioreactor output. In this work, we report on the development of a fully automated microfluidic system capable of extracting samples directly from a bioreactor, diluting the sample, staining the cells...

  18. A fully-automated multiscale kernel graph cuts based particle localization scheme for temporal focusing two-photon microscopy

    Huang, Xia; Li, Chunqiang; Xiao, Chuan; Sun, Wenqing; Qian, Wei

    2017-03-01

    The temporal focusing two-photon microscope (TFM) is developed to perform depth resolved wide field fluorescence imaging by capturing frames sequentially. However, due to strong nonignorable noises and diffraction rings surrounding particles, further researches are extremely formidable without a precise particle localization technique. In this paper, we developed a fully-automated scheme to locate particles positions with high noise tolerance. Our scheme includes the following procedures: noise reduction using a hybrid Kalman filter method, particle segmentation based on a multiscale kernel graph cuts global and local segmentation algorithm, and a kinematic estimation based particle tracking method. Both isolated and partial-overlapped particles can be accurately identified with removal of unrelated pixels. Based on our quantitative analysis, 96.22% isolated particles and 84.19% partial-overlapped particles were successfully detected.

  19. A fully-automated neural network analysis of AFM force-distance curves for cancer tissue diagnosis

    Minelli, Eleonora; Ciasca, Gabriele; Sassun, Tanya Enny; Antonelli, Manila; Palmieri, Valentina; Papi, Massimiliano; Maulucci, Giuseppe; Santoro, Antonio; Giangaspero, Felice; Delfini, Roberto; Campi, Gaetano; De Spirito, Marco

    2017-10-01

    Atomic Force Microscopy (AFM) has the unique capability of probing the nanoscale mechanical properties of biological systems that affect and are affected by the occurrence of many pathologies, including cancer. This capability has triggered growing interest in the translational process of AFM from physics laboratories to clinical practice. A factor still hindering the current use of AFM in diagnostics is related to the complexity of AFM data analysis, which is time-consuming and needs highly specialized personnel with a strong physical and mathematical background. In this work, we demonstrate an operator-independent neural-network approach for the analysis of surgically removed brain cancer tissues. This approach allowed us to distinguish—in a fully automated fashion—cancer from healthy tissues with high accuracy, also highlighting the presence and the location of infiltrating tumor cells.

  20. Automated red blood cells extraction from holographic images using fully convolutional neural networks

    Yi, Faliu; Moon, Inkyu; Javidi, Bahram

    2017-01-01

    In this paper, we present two models for automatically extracting red blood cells (RBCs) from RBCs holographic images based on a deep learning fully convolutional neural network (FCN) algorithm. The first model, called FCN-1, only uses the FCN algorithm to carry out RBCs prediction, whereas the second model, called FCN-2, combines the FCN approach with the marker-controlled watershed transform segmentation scheme to achieve RBCs extraction. Both models achieve good segmentation accuracy. In addition, the second model has much better performance in terms of cell separation than traditional segmentation methods. In the proposed methods, the RBCs phase images are first numerically reconstructed from RBCs holograms recorded with off-axis digital holographic microscopy. Then, some RBCs phase images are manually segmented and used as training data to fine-tune the FCN. Finally, each pixel in new input RBCs phase images is predicted into either foreground or background using the trained FCN models. The RBCs prediction result from the first model is the final segmentation result, whereas the result from the second model is used as the internal markers of the marker-controlled transform algorithm for further segmentation. Experimental results show that the given schemes can automatically extract RBCs from RBCs phase images and much better RBCs separation results are obtained when the FCN technique is combined with the marker-controlled watershed segmentation algorithm. PMID:29082078

  1. Fully automated motion correction in first-pass myocardial perfusion MR image sequences.

    Milles, Julien; van der Geest, Rob J; Jerosch-Herold, Michael; Reiber, Johan H C; Lelieveldt, Boudewijn P F

    2008-11-01

    This paper presents a novel method for registration of cardiac perfusion magnetic resonance imaging (MRI). The presented method is capable of automatically registering perfusion data, using independent component analysis (ICA) to extract physiologically relevant features together with their time-intensity behavior. A time-varying reference image mimicking intensity changes in the data of interest is computed based on the results of that ICA. This reference image is used in a two-pass registration framework. Qualitative and quantitative validation of the method is carried out using 46 clinical quality, short-axis, perfusion MR datasets comprising 100 images each. Despite varying image quality and motion patterns in the evaluation set, validation of the method showed a reduction of the average right ventricle (LV) motion from 1.26+/-0.87 to 0.64+/-0.46 pixels. Time-intensity curves are also improved after registration with an average error reduced from 2.65+/-7.89% to 0.87+/-3.88% between registered data and manual gold standard. Comparison of clinically relevant parameters computed using registered data and the manual gold standard show a good agreement. Additional tests with a simulated free-breathing protocol showed robustness against considerable deviations from a standard breathing protocol. We conclude that this fully automatic ICA-based method shows an accuracy, a robustness and a computation speed adequate for use in a clinical environment.

  2. Screening for anabolic steroids in urine of forensic cases using fully automated solid phase extraction and LC-MS-MS.

    Andersen, David W; Linnet, Kristian

    2014-01-01

    A screening method for 18 frequently measured exogenous anabolic steroids and the testosterone/epitestosterone (T/E) ratio in forensic cases has been developed and validated. The method involves a fully automated sample preparation including enzyme treatment, addition of internal standards and solid phase extraction followed by analysis by liquid chromatography-tandem mass spectrometry (LC-MS-MS) using electrospray ionization with adduct formation for two compounds. Urine samples from 580 forensic cases were analyzed to determine the T/E ratio and occurrence of exogenous anabolic steroids. Extraction recoveries ranged from 77 to 95%, matrix effects from 48 to 78%, overall process efficiencies from 40 to 54% and the lower limit of identification ranged from 2 to 40 ng/mL. In the 580 urine samples analyzed from routine forensic cases, 17 (2.9%) were found positive for one or more anabolic steroids. Only seven different steroids including testosterone were found in the material, suggesting that only a small number of common steroids are likely to occur in a forensic context. The steroids were often in high concentrations (>100 ng/mL), and a combination of steroids and/or other drugs of abuse were seen in the majority of cases. The method presented serves as a fast and automated screening procedure, proving the suitability of LC-MS-MS for analyzing anabolic steroids. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Comparison and clinical utility evaluation of four multiple allergen simultaneous tests including two newly introduced fully automated analyzers

    John Hoon Rim

    2016-04-01

    Full Text Available Background: We compared the diagnostic performances of two newly introduced fully automated multiple allergen simultaneous tests (MAST analyzers with two conventional MAST assays. Methods: The serum samples from a total of 53 and 104 patients were tested for food panels and inhalant panels, respectively, in four analyzers including AdvanSure AlloScreen (LG Life Science, Korea, AdvanSure Allostation Smart II (LG Life Science, PROTIA Allergy-Q (ProteomeTech, Korea, and RIDA Allergy Screen (R-Biopharm, Germany. We compared not only the total agreement percentages but also positive propensities among four analyzers. Results: Evaluation of AdvanSure Allostation Smart II as upgraded version of AdvanSure AlloScreen revealed good concordance with total agreement percentages of 93.0% and 92.2% in food and inhalant panel, respectively. Comparisons of AdvanSure Allostation Smart II or PROTIA Allergy-Q with RIDA Allergy Screen also showed good concordance performance with positive propensities of two new analyzers for common allergens (Dermatophagoides farina and Dermatophagoides pteronyssinus. The changes of cut-off level resulted in various total agreement percentage fluctuations among allergens by different analyzers, although current cut-off level of class 2 appeared to be generally suitable. Conclusions: AdvanSure Allostation Smart II and PROTIA Allergy-Q presented favorable agreement performances with RIDA Allergy Screen, although positive propensities were noticed in common allergens. Keywords: Multiple allergen simultaneous test, Automated analyzer

  4. NIF Ignition Target 3D Point Design

    Jones, O; Marinak, M; Milovich, J; Callahan, D

    2008-11-05

    We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

  5. Semantic focusing allows fully automated single-layer slide scanning of cervical cytology slides.

    Bernd Lahrmann

    Full Text Available Liquid-based cytology (LBC in conjunction with Whole-Slide Imaging (WSI enables the objective and sensitive and quantitative evaluation of biomarkers in cytology. However, the complex three-dimensional distribution of cells on LBC slides requires manual focusing, long scanning-times, and multi-layer scanning. Here, we present a solution that overcomes these limitations in two steps: first, we make sure that focus points are only set on cells. Secondly, we check the total slide focus quality. From a first analysis we detected that superficial dust can be separated from the cell layer (thin layer of cells on the glass slide itself. Then we analyzed 2,295 individual focus points from 51 LBC slides stained for p16 and Ki67. Using the number of edges in a focus point image, specific color values and size-inclusion filters, focus points detecting cells could be distinguished from focus points on artifacts (accuracy 98.6%. Sharpness as total focus quality of a virtual LBC slide is computed from 5 sharpness features. We trained a multi-parameter SVM classifier on 1,600 images. On an independent validation set of 3,232 cell images we achieved an accuracy of 94.8% for classifying images as focused. Our results show that single-layer scanning of LBC slides is possible and how it can be achieved. We assembled focus point analysis and sharpness classification into a fully automatic, iterative workflow, free of user intervention, which performs repetitive slide scanning as necessary. On 400 LBC slides we achieved a scanning-time of 13.9±10.1 min with 29.1±15.5 focus points. In summary, the integration of semantic focus information into whole-slide imaging allows automatic high-quality imaging of LBC slides and subsequent biomarker analysis.

  6. Semantic focusing allows fully automated single-layer slide scanning of cervical cytology slides.

    Lahrmann, Bernd; Valous, Nektarios A; Eisenmann, Urs; Wentzensen, Nicolas; Grabe, Niels

    2013-01-01

    Liquid-based cytology (LBC) in conjunction with Whole-Slide Imaging (WSI) enables the objective and sensitive and quantitative evaluation of biomarkers in cytology. However, the complex three-dimensional distribution of cells on LBC slides requires manual focusing, long scanning-times, and multi-layer scanning. Here, we present a solution that overcomes these limitations in two steps: first, we make sure that focus points are only set on cells. Secondly, we check the total slide focus quality. From a first analysis we detected that superficial dust can be separated from the cell layer (thin layer of cells on the glass slide) itself. Then we analyzed 2,295 individual focus points from 51 LBC slides stained for p16 and Ki67. Using the number of edges in a focus point image, specific color values and size-inclusion filters, focus points detecting cells could be distinguished from focus points on artifacts (accuracy 98.6%). Sharpness as total focus quality of a virtual LBC slide is computed from 5 sharpness features. We trained a multi-parameter SVM classifier on 1,600 images. On an independent validation set of 3,232 cell images we achieved an accuracy of 94.8% for classifying images as focused. Our results show that single-layer scanning of LBC slides is possible and how it can be achieved. We assembled focus point analysis and sharpness classification into a fully automatic, iterative workflow, free of user intervention, which performs repetitive slide scanning as necessary. On 400 LBC slides we achieved a scanning-time of 13.9±10.1 min with 29.1±15.5 focus points. In summary, the integration of semantic focus information into whole-slide imaging allows automatic high-quality imaging of LBC slides and subsequent biomarker analysis.

  7. A fully automated non-external marker 4D-CT sorting algorithm using a serial cine scanning protocol.

    Carnes, Greg; Gaede, Stewart; Yu, Edward; Van Dyk, Jake; Battista, Jerry; Lee, Ting-Yim

    2009-04-07

    Current 4D-CT methods require external marker data to retrospectively sort image data and generate CT volumes. In this work we develop an automated 4D-CT sorting algorithm that performs without the aid of data collected from an external respiratory surrogate. The sorting algorithm requires an overlapping cine scan protocol. The overlapping protocol provides a spatial link between couch positions. Beginning with a starting scan position, images from the adjacent scan position (which spatial match the starting scan position) are selected by maximizing the normalized cross correlation (NCC) of the images at the overlapping slice position. The process was continued by 'daisy chaining' all couch positions using the selected images until an entire 3D volume was produced. The algorithm produced 16 phase volumes to complete a 4D-CT dataset. Additional 4D-CT datasets were also produced using external marker amplitude and phase angle sorting methods. The image quality of the volumes produced by the different methods was quantified by calculating the mean difference of the sorted overlapping slices from adjacent couch positions. The NCC sorted images showed a significant decrease in the mean difference (p < 0.01) for the five patients.

  8. Fully Automated On-Chip Imaging Flow Cytometry System with Disposable Contamination-Free Plastic Re-Cultivation Chip

    Tomoyuki Kaneko

    2011-06-01

    Full Text Available We have developed a novel imaging cytometry system using a poly(methyl methacrylate (PMMA based microfluidic chip. The system was contamination-free, because sample suspensions contacted only with a flammable PMMA chip and no other component of the system. The transparency and low-fluorescence of PMMA was suitable for microscopic imaging of cells flowing through microchannels on the chip. Sample particles flowing through microchannels on the chip were discriminated by an image-recognition unit with a high-speed camera in real time at the rate of 200 event/s, e.g., microparticles 2.5 μm and 3.0 μm in diameter were differentiated with an error rate of less than 2%. Desired cells were separated automatically from other cells by electrophoretic or dielectrophoretic force one by one with a separation efficiency of 90%. Cells in suspension with fluorescent dye were separated using the same kind of microfluidic chip. Sample of 5 μL with 1 × 106 particle/mL was processed within 40 min. Separated cells could be cultured on the microfluidic chip without contamination. The whole operation of sample handling was automated using 3D micropipetting system. These results showed that the novel imaging flow cytometry system is practically applicable for biological research and clinical diagnostics.

  9. The role of 3-D interactive visualization in blind surveys of H I in galaxies

    Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

    2015-09-01

    Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

  10. 3D Animation Essentials

    Beane, Andy

    2012-01-01

    The essential fundamentals of 3D animation for aspiring 3D artists 3D is everywhere--video games, movie and television special effects, mobile devices, etc. Many aspiring artists and animators have grown up with 3D and computers, and naturally gravitate to this field as their area of interest. Bringing a blend of studio and classroom experience to offer you thorough coverage of the 3D animation industry, this must-have book shows you what it takes to create compelling and realistic 3D imagery. Serves as the first step to understanding the language of 3D and computer graphics (CG)Covers 3D anim

  11. 3D video

    Lucas, Laurent; Loscos, Céline

    2013-01-01

    While 3D vision has existed for many years, the use of 3D cameras and video-based modeling by the film industry has induced an explosion of interest for 3D acquisition technology, 3D content and 3D displays. As such, 3D video has become one of the new technology trends of this century.The chapters in this book cover a large spectrum of areas connected to 3D video, which are presented both theoretically and technologically, while taking into account both physiological and perceptual aspects. Stepping away from traditional 3D vision, the authors, all currently involved in these areas, provide th

  12. A fully automated multi-modal computer aided diagnosis approach to coronary calcium scoring of MSCT images

    Wu, Jing; Ferns, Gordon; Giles, John; Lewis, Emma

    2012-03-01

    Inter- and intra- observer variability is a problem often faced when an expert or observer is tasked with assessing the severity of a disease. This issue is keenly felt in coronary calcium scoring of patients suffering from atherosclerosis where in clinical practice, the observer must identify firstly the presence, followed by the location of candidate calcified plaques found within the coronary arteries that may prevent oxygenated blood flow to the heart muscle. However, it can be difficult for a human observer to differentiate calcified plaques that are located in the coronary arteries from those found in surrounding anatomy such as the mitral valve or pericardium. In addition to the benefits to scoring accuracy, the use of fast, low dose multi-slice CT imaging to perform the cardiac scan is capable of acquiring the entire heart within a single breath hold. Thus exposing the patient to lower radiation dose, which for a progressive disease such as atherosclerosis where multiple scans may be required, is beneficial to their health. Presented here is a fully automated method for calcium scoring using both the traditional Agatston method, as well as the volume scoring method. Elimination of the unwanted regions of the cardiac image slices such as lungs, ribs, and vertebrae is carried out using adaptive heart isolation. Such regions cannot contain calcified plaques but can be of a similar intensity and their removal will aid detection. Removal of both the ascending and descending aortas, as they contain clinical insignificant plaques, is necessary before the final calcium scores are calculated and examined against ground truth scores of three averaged expert observer results. The results presented here are intended to show the feasibility and requirement for an automated scoring method to reduce the subjectivity and reproducibility error inherent with manual clinical calcium scoring.

  13. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    Jang, Richard; Gao, Xin; Li, Ming

    2011-01-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg's contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  14. Towards fully automated structure-based NMR resonance assignment of 15N-labeled proteins from automatically picked peaks

    Jang, Richard

    2011-03-01

    In NMR resonance assignment, an indispensable step in NMR protein studies, manually processed peaks from both N-labeled and C-labeled spectra are typically used as inputs. However, the use of homologous structures can allow one to use only N-labeled NMR data and avoid the added expense of using C-labeled data. We propose a novel integer programming framework for structure-based backbone resonance assignment using N-labeled data. The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment. The goal is to perform the assignment directly from spectra without any manual intervention via automatically picked peaks, which are much noisier than manually picked peaks, so methods must be error-tolerant. In the case of semi-automated/manually processed peak data, we compare our system with the Xiong-Pandurangan-Bailey- Kellogg\\'s contact replacement (CR) method, which is the most error-tolerant method for structure-based resonance assignment. Our system, on average, reduces the error rate of the CR method by five folds on their data set. In addition, by using an iterative algorithm, our system has the added capability of using the NOESY data to correct assignment errors due to errors in predicting the amino acid and secondary structure type of each spin system. On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors. In the case of automatically picked peaks, using assignment information from yeast ubiquitin, we achieve a fully automatic assignment with 97% accuracy. To our knowledge, this is the first system that can achieve fully automatic structure-based assignment directly from spectra. This has implications in NMR protein mutant studies, where the assignment step is repeated for each mutant. © Copyright 2011, Mary Ann Liebert, Inc.

  15. Fully automated dual-frequency three-pulse-echo 2DIR spectrometer accessing spectral range from 800 to 4000 wavenumbers

    Leger, Joel D.; Nyby, Clara M.; Varner, Clyde; Tang, Jianan; Rubtsova, Natalia I.; Yue, Yuankai; Kireev, Victor V.; Burtsev, Viacheslav D.; Qasim, Layla N.; Rubtsov, Igor V., E-mail: irubtsov@tulane.edu [Department of Chemistry, Tulane University, New Orleans, Louisiana 70118 (United States); Rubtsov, Grigory I. [Institute for Nuclear Research of the Russian Academy of Sciences, Moscow 117312 (Russian Federation)

    2014-08-15

    A novel dual-frequency two-dimensional infrared instrument is designed and built that permits three-pulse heterodyned echo measurements of any cross-peak within a spectral range from 800 to 4000 cm{sup −1} to be performed in a fully automated fashion. The superior sensitivity of the instrument is achieved by a combination of spectral interferometry, phase cycling, and closed-loop phase stabilization accurate to ∼70 as. The anharmonicity of smaller than 10{sup −4} cm{sup −1} was recorded for strong carbonyl stretching modes using 800 laser shot accumulations. The novel design of the phase stabilization scheme permits tuning polarizations of the mid-infrared (m-IR) pulses, thus supporting measurements of the angles between vibrational transition dipoles. The automatic frequency tuning is achieved by implementing beam direction stabilization schemes for each m-IR beam, providing better than 50 μrad beam stability, and novel scheme for setting the phase-matching geometry for the m-IR beams at the sample. The errors in the cross-peak amplitudes associated with imperfect phase matching conditions and alignment are found to be at the level of 20%. The instrument can be used by non-specialists in ultrafast spectroscopy.

  16. Fully-automated in-syringe dispersive liquid-liquid microextraction for the determination of caffeine in coffee beverages.

    Frizzarin, Rejane M; Maya, Fernando; Estela, José M; Cerdà, Víctor

    2016-12-01

    A novel fully-automated magnetic stirring-assisted lab-in-syringe analytical procedure has been developed for the fast and efficient dispersive liquid-liquid microextraction (DLLME) of caffeine in coffee beverages. The procedure is based on the microextraction of caffeine with a minute amount of dichloromethane, isolating caffeine from the sample matrix with no further sample pretreatment. Selection of the relevant extraction parameters such as the dispersive solvent, proportion of aqueous/organic phase, pH and flow rates have been carefully evaluated. Caffeine quantification was linear from 2 to 75mgL(-1), with detection and quantification limits of 0.46mgL(-1) and 1.54mgL(-1), respectively. A coefficient of variation (n=8; 5mgL(-1)) of a 2.1% and a sampling rate of 16h(-1), were obtained. The procedure was satisfactorily applied to the determination of caffeine in brewed, instant and decaf coffee samples, being the results for the sample analysis validated using high-performance liquid chromatography. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Validation of the fully automated A&D TM-2656 blood pressure monitor according to the British Hypertension Society Protocol.

    Zeng, Wei-Fang; Liu, Ming; Kang, Yuan-Yuan; Li, Yan; Wang, Ji-Guang

    2013-08-01

    The present study aimed to evaluate the accuracy of the fully automated oscillometric upper-arm blood pressure monitor TM-2656 according to the British Hypertension Society (BHS) Protocol 1993. We recruited individuals until there were 85 eligible participants and their blood pressure could meet the blood pressure distribution requirements specified by the BHS Protocol. For each individual, we sequentially measured the systolic and diastolic blood pressures using a mercury sphygmomanometer (two observers) and the TM-2656 device (one supervisor). Data analysis was carried out according to the BHS Protocol. The device achieved grade A. The percentage of blood pressure differences within 5, 10, and 15 mmHg was 62, 85, and 96%, respectively, for systolic blood pressure, and 71, 93, and 99%, respectively, for diastolic blood pressure. The average (±SD) of the device-observer differences was -2.1±7.8 mmHg (P<0.0001) and -1.1±5.8 mmHg (P<0.0001) for systolic and diastolic blood pressures, respectively. The A&D upper-arm blood pressure monitor TM-2656 has passed the requirements of the BHS Protocol, and can thus be recommended for blood pressure measurement.

  18. A fully automated and scalable timing probe-based method for time alignment of the LabPET II scanners

    Samson, Arnaud; Thibaudeau, Christian; Bouchard, Jonathan; Gaudin, Émilie; Paulin, Caroline; Lecomte, Roger; Fontaine, Réjean

    2018-05-01

    A fully automated time alignment method based on a positron timing probe was developed to correct the channel-to-channel coincidence time dispersion of the LabPET II avalanche photodiode-based positron emission tomography (PET) scanners. The timing probe was designed to directly detect positrons and generate an absolute time reference. The probe-to-channel coincidences are recorded and processed using firmware embedded in the scanner hardware to compute the time differences between detector channels. The time corrections are then applied in real-time to each event in every channel during PET data acquisition to align all coincidence time spectra, thus enhancing the scanner time resolution. When applied to the mouse version of the LabPET II scanner, the calibration of 6 144 channels was performed in less than 15 min and showed a 47% improvement on the overall time resolution of the scanner, decreasing from 7 ns to 3.7 ns full width at half maximum (FWHM).

  19. DEWS (DEep White matter hyperintensity Segmentation framework): A fully automated pipeline for detecting small deep white matter hyperintensities in migraineurs.

    Park, Bo-Yong; Lee, Mi Ji; Lee, Seung-Hak; Cha, Jihoon; Chung, Chin-Sang; Kim, Sung Tae; Park, Hyunjin

    2018-01-01

    Migraineurs show an increased load of white matter hyperintensities (WMHs) and more rapid deep WMH progression. Previous methods for WMH segmentation have limited efficacy to detect small deep WMHs. We developed a new fully automated detection pipeline, DEWS (DEep White matter hyperintensity Segmentation framework), for small and superficially-located deep WMHs. A total of 148 non-elderly subjects with migraine were included in this study. The pipeline consists of three components: 1) white matter (WM) extraction, 2) WMH detection, and 3) false positive reduction. In WM extraction, we adjusted the WM mask to re-assign misclassified WMHs back to WM using many sequential low-level image processing steps. In WMH detection, the potential WMH clusters were detected using an intensity based threshold and region growing approach. For false positive reduction, the detected WMH clusters were classified into final WMHs and non-WMHs using the random forest (RF) classifier. Size, texture, and multi-scale deep features were used to train the RF classifier. DEWS successfully detected small deep WMHs with a high positive predictive value (PPV) of 0.98 and true positive rate (TPR) of 0.70 in the training and test sets. Similar performance of PPV (0.96) and TPR (0.68) was attained in the validation set. DEWS showed a superior performance in comparison with other methods. Our proposed pipeline is freely available online to help the research community in quantifying deep WMHs in non-elderly adults.

  20. Experimental optimization of a direct injection homogeneous charge compression ignition gasoline engine using split injections with fully automated microgenetic algorithms

    Canakci, M. [Kocaeli Univ., Izmit (Turkey); Reitz, R.D. [Wisconsin Univ., Dept. of Mechanical Engineering, Madison, WI (United States)

    2003-03-01

    Homogeneous charge compression ignition (HCCI) is receiving attention as a new low-emission engine concept. Little is known about the optimal operating conditions for this engine operation mode. Combustion under homogeneous, low equivalence ratio conditions results in modest temperature combustion products, containing very low concentrations of NO{sub x} and particulate matter (PM) as well as providing high thermal efficiency. However, this combustion mode can produce higher HC and CO emissions than those of conventional engines. An electronically controlled Caterpillar single-cylinder oil test engine (SCOTE), originally designed for heavy-duty diesel applications, was converted to an HCCI direct injection (DI) gasoline engine. The engine features an electronically controlled low-pressure direct injection gasoline (DI-G) injector with a 60 deg spray angle that is capable of multiple injections. The use of double injection was explored for emission control and the engine was optimized using fully automated experiments and a microgenetic algorithm optimization code. The variables changed during the optimization include the intake air temperature, start of injection timing and the split injection parameters (per cent mass of fuel in each injection, dwell between the pulses). The engine performance and emissions were determined at 700 r/min with a constant fuel flowrate at 10 MPa fuel injection pressure. The results show that significant emissions reductions are possible with the use of optimal injection strategies. (Author)

  1. Computer-aided liver volumetry: performance of a fully-automated, prototype post-processing solution for whole-organ and lobar segmentation based on MDCT imaging.

    Fananapazir, Ghaneh; Bashir, Mustafa R; Marin, Daniele; Boll, Daniel T

    2015-06-01

    To evaluate the performance of a prototype, fully-automated post-processing solution for whole-liver and lobar segmentation based on MDCT datasets. A polymer liver phantom was used to assess accuracy of post-processing applications comparing phantom volumes determined via Archimedes' principle with MDCT segmented datasets. For the IRB-approved, HIPAA-compliant study, 25 patients were enrolled. Volumetry performance compared the manual approach with the automated prototype, assessing intraobserver variability, and interclass correlation for whole-organ and lobar segmentation using ANOVA comparison. Fidelity of segmentation was evaluated qualitatively. Phantom volume was 1581.0 ± 44.7 mL, manually segmented datasets estimated 1628.0 ± 47.8 mL, representing a mean overestimation of 3.0%, automatically segmented datasets estimated 1601.9 ± 0 mL, representing a mean overestimation of 1.3%. Whole-liver and segmental volumetry demonstrated no significant intraobserver variability for neither manual nor automated measurements. For whole-liver volumetry, automated measurement repetitions resulted in identical values; reproducible whole-organ volumetry was also achieved with manual segmentation, p(ANOVA) 0.98. For lobar volumetry, automated segmentation improved reproducibility over manual approach, without significant measurement differences for either methodology, p(ANOVA) 0.95-0.99. Whole-organ and lobar segmentation results from manual and automated segmentation showed no significant differences, p(ANOVA) 0.96-1.00. Assessment of segmentation fidelity found that segments I-IV/VI showed greater segmentation inaccuracies compared to the remaining right hepatic lobe segments. Automated whole-liver segmentation showed non-inferiority of fully-automated whole-liver segmentation compared to manual approaches with improved reproducibility and post-processing duration; automated dual-seed lobar segmentation showed slight tendencies for underestimating the right hepatic lobe

  2. Assessment of pulmonary vasculature volume with automated threshold-based 3D quantitative CT volumetry: In vitro and in vivo validation

    Liu Jingzhe; Wu Qingyu; Xu Yufeng; Bai Yan; Liu Zhibo; Li Hongyin; Zhu Jiemin

    2012-01-01

    Objectives: To validate the ability of threshold-based 3D CT volumetry to enable measurement of volume of visible pulmonary vessels on CT. Materials and methods: In vivo, 3D CT volumetry was validated in seven phantoms that consisted of silicone tubes embedded in a foam block. With the true volume value as reference standard, the accuracy of CT measurement at various lower thresholds of −600 HU, −500 HU, −300 HU and −200 HU were compared. The volume measurements obtained when filled with varied concentration of iodinated contrast media (1:100, 1:200 and 1:500) were also compared. In vivo validation was performed in sixteen patients (9 men, 7 women; mean age, 52.1 years). Inter-scan and inter-observer agreement and reproducibility for pulmonary vasculature volume measurement were evaluated with Bland–Altman analysis. Results: In vitro, the mean value measured under lower threshold of −300 HU (relative error = 1.5%) were the closest to the true values and have no significant difference (P = 0.375). There were no significant differences among the phantom measurement values with different filled concentration (1:100, 1:200 and 1:500). In vivo, the inter-scan reproducibility of volume measurements was good, with a correlation coefficient of 0.82 and ICC (intraclass correlation coefficient) of 0.86. Inter-observer agreement was excellent with a correlation coefficient of 0.91 and ICC of 0.95. Conclusions: The threshold-based 3D quantitative CT volumetry enables accurate and reproducible measurement of pulmonary vessels volume.

  3. Fully automated SPE-based synthesis and purification of 2-[{sup 18}F]fluoroethyl-choline for human use

    Schmaljohann, Joern [Department of Nuclear Medicine, University of Bonn, Bonn (Germany); Department of Nuclear Medicine, University of Aachen, Aachen (Germany); Schirrmacher, Esther [McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec (Canada); Waengler, Bjoern; Waengler, Carmen [Department of Nuclear Medicine, Ludwig-Maximilians University, Munich (Germany); Schirrmacher, Ralf, E-mail: ralf.schirrmacher@mcgill.c [McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec (Canada); Guhlke, Stefan, E-mail: stefan.guhlke@ukb.uni-bonn.d [Department of Nuclear Medicine, University of Bonn, Bonn (Germany)

    2011-02-15

    Introduction: 2-[{sup 18}F]Fluoroethyl-choline ([{sup 18}F]FECH) is a promising tracer for the detection of prostate cancer as well as brain tumors with positron emission tomography (PET). [{sup 18}F]FECH is actively transported into mammalian cells, becomes phosphorylated by choline kinase and gets incorporated into the cell membrane after being metabolized to phosphatidylcholine. So far, its synthesis is a two-step procedure involving at least one HPLC purification step. To allow a wider dissemination of this tracer, finding a purification method avoiding HPLC is highly desirable and would result in easier accessibility and more reliable production of [{sup 18}F]FECH. Methods: [{sup 18}F]FECH was synthesized by reaction of 2-bromo-1-[{sup 18}F]fluoroethane ([{sup 18}F]BFE) with dimethylaminoethanol (DMAE) in DMSO. We applied a novel and very reliable work-up procedure for the synthesis of [{sup 18}F]BFE. Based on a combination of three different solid-phase cartridges, the purification of [{sup 18}F]BFE from its precursor 2-bromoethyl-4-nitrobenzenesulfonate (BENos) could be achieved without using HPLC. Following the subsequent reaction of the purified [{sup 18}F]BFE with DMAE, the final product [{sup 18}F]FECH was obtained as a sterile solution by passing the crude reaction mixture through a combination of two CM plus cartridges and a sterile filter. The fully automated synthesis was performed using as well a Raytest SynChrom module (Raytest, Germany) or a Scintomics HotboxIII module (Scintomics, Germany). Results: The radiotracer [{sup 18}F]FECH can be synthesized in reliable radiochemical yields (RCY) of 37{+-}5% (Synchrom module) and 33{+-}5% (Hotbox III unit) in less than 1 h using these two fully automated commercially available synthesis units without HPLC involvement for purification. Detailed quality control of the final injectable [{sup 18}F]FECH solution proved the high radiochemical purity and the absence of Kryptofix2.2.2, DMAE and DMSO used in the

  4. UmUTracker: A versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data

    Zhang, Hanqing; Stangner, Tim; Wiklund, Krister; Rodriguez, Alvaro; Andersson, Magnus

    2017-10-01

    We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the 2D lateral positions of particles with an algorithm based on the isosceles triangle transform, and reconstructs their 3D axial positions by a fast implementation of the Rayleigh-Sommerfeld model using a radial intensity profile. To validate the accuracy and performance of our program, we first track the 2D position of polystyrene particles using bright field and digital holographic microscopy. Second, we determine the 3D particle position by analyzing synthetic and experimentally acquired holograms. Finally, to highlight the full program features, we profile the microfluidic flow in a 100 μm high flow chamber. This result agrees with computational fluid dynamic simulations. On a regular desktop computer UmUTracker can detect, analyze, and track multiple particles at 5 frames per second for a template size of 201 ×201 in a 1024 × 1024 image. To enhance usability and to make it easy to implement new functions we used object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement. Program Files doi : http://dx.doi.org/10.17632/fkprs4s6xp.1 Licensing provisions : Creative Commons by 4.0 (CC by 4.0) Programming language : MATLAB Nature of problem: 3D multi-particle tracking is a common technique in physics, chemistry and biology. However, in terms of accuracy, reliable particle tracking is a challenging task since results depend on sample illumination, particle overlap, motion blur and noise from recording sensors. Additionally, the computational performance is also an issue if, for example, a computationally expensive process is executed, such as axial particle position reconstruction from digital holographic microscopy data. Versatile

  5. EUROPEANA AND 3D

    D. Pletinckx

    2012-09-01

    Full Text Available The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

  6. Automated volumetric assessment of the Achilles tendon (AVAT) using a 3D T2 weighted SPACE sequence at 3 T in healthy and pathologic cases

    Syha, R.; Würslin, C.; Ketelsen, D.; Martirosian, P.; Grosse, U.; Schick, F.; Claussen, C.D.; Springer, F.

    2012-01-01

    Purpose: Achilles tendinopathy has been reported to be frequently associated with increasing volume of the tendon. This work aims at reliable and accurate volumetric quantification of the Achilles tendon using a newly developed contour detection algorithm applied on high resolution MRI data sets recorded at 3 T. Materials and methods: A total of 26 healthy tendons and 4 degenerated tendons were examined for this study. Automated identification (AI) of tendon boundaries was performed in transverse slices with isotropic resolution (0.8 mm) gained with a T2-weighted SPACE sequence at 3 T. For AI a snake algorithm was applied and compared to manual tracing (MT). Results: AI was feasible in all examined tendons without further correction. AI of both tendons was performed in each participant within 2 min (2 × 37 slices) compared to MT lasting 20 min. MT and AI showed excellent agreement and correlation (R 2 = 0.99, p 3 vs. 0.5 cm 3 ) and coefficient of variation (1% vs. 2%). Discussion: Compared to MT the AI allows assessment of tendon volumes in highly resolved MRI data in a more accurate and reliable time-saving way. Therefore automated volume detection is seen as a helpful clinical tool for evaluation of small volumetric changes of the Achilles tendon.

  7. Co-Deposition of a Hydrogel/Calcium Phosphate Hybrid Layer on 3D Printed Poly(Lactic Acid Scaffolds via Dip Coating: Towards Automated Biomaterials Fabrication

    Matthias Schneider

    2018-03-01

    Full Text Available The article describes the surface modification of 3D printed poly(lactic acid (PLA scaffolds with calcium phosphate (CP/gelatin and CP/chitosan hybrid coating layers. The presence of gelatin or chitosan significantly enhances CP co-deposition and adhesion of the mineral layer on the PLA scaffolds. The hydrogel/CP coating layers are fairly thick and the mineral is a mixture of brushite, octacalcium phosphate, and hydroxyapatite. Mineral formation is uniform throughout the printed architectures and all steps (printing, hydrogel deposition, and mineralization are in principle amenable to automatization. Overall, the process reported here therefore has a high application potential for the controlled synthesis of biomimetic coatings on polymeric biomaterials.

  8. Automating the design of resection guides specific to patient anatomy in knee replacement surgery by enhanced 3D curvature and surface modeling of distal femur shape models.

    Cerveri, Pietro; Manzotti, Alfonso; Confalonieri, Norberto; Baroni, Guido

    2014-12-01

    Personalized resection guides (PRG) have been recently proposed in the domain of knee replacement, demonstrating clinical outcome similar or even superior to both manual and navigated interventions. Among the mandatory pre-surgical steps for PRG prototyping, the measurement of clinical landmarks (CL) on the bony surfaces is recognized as a key issue due to lack of standardized methodologies, operator-dependent variability and time expenditure. In this paper, we focus on the reliability and repeatability of an anterior-posterior axis, also known as Whiteside line (WL), of the distal femur proposing automatic surface processing and modeling methods aimed at overcoming some of the major concerns related to the manual identification of such CL on 2D images and 3D models. We show that the measurement of WL, exploiting the principle of mean-shifting surface curvature, is highly repeatable and coherent with clinical knowledge. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Association between fully automated MRI-based volumetry of different brain regions and neuropsychological test performance in patients with amnestic mild cognitive impairment and Alzheimer's disease.

    Arlt, Sönke; Buchert, Ralph; Spies, Lothar; Eichenlaub, Martin; Lehmbeck, Jan T; Jahn, Holger

    2013-06-01

    Fully automated magnetic resonance imaging (MRI)-based volumetry may serve as biomarker for the diagnosis in patients with mild cognitive impairment (MCI) or dementia. We aimed at investigating the relation between fully automated MRI-based volumetric measures and neuropsychological test performance in amnestic MCI and patients with mild dementia due to Alzheimer's disease (AD) in a cross-sectional and longitudinal study. In order to assess a possible prognostic value of fully automated MRI-based volumetry for future cognitive performance, the rate of change of neuropsychological test performance over time was also tested for its correlation with fully automated MRI-based volumetry at baseline. In 50 subjects, 18 with amnestic MCI, 21 with mild AD, and 11 controls, neuropsychological testing and T1-weighted MRI were performed at baseline and at a mean follow-up interval of 2.1 ± 0.5 years (n = 19). Fully automated MRI volumetry of the grey matter volume (GMV) was performed using a combined stereotactic normalisation and segmentation approach as provided by SPM8 and a set of pre-defined binary lobe masks. Left and right hippocampus masks were derived from probabilistic cytoarchitectonic maps. Volumes of the inner and outer liquor space were also determined automatically from the MRI. Pearson's test was used for the correlation analyses. Left hippocampal GMV was significantly correlated with performance in memory tasks, and left temporal GMV was related to performance in language tasks. Bilateral frontal, parietal and occipital GMVs were correlated to performance in neuropsychological tests comprising multiple domains. Rate of GMV change in the left hippocampus was correlated with decline of performance in the Boston Naming Test (BNT), Mini-Mental Status Examination, and trail making test B (TMT-B). The decrease of BNT and TMT-A performance over time correlated with the loss of grey matter in multiple brain regions. We conclude that fully automated MRI

  10. A device for fully automated on-site process monitoring and control of trihalomethane concentrations in drinking water

    Brown, Aaron W.; Simone, Paul S.; York, J.C.; Emmert, Gary L.

    2015-01-01

    Highlights: • Commercial device for on-line monitoring of trihalomethanes in drinking water. • Method detection limits for individual trihalomethanes range from 0.01–0.04 μg L –1 . • Rugged and robust device operates automatically for on-site process control. • Used for process mapping and process optimization to reduce treatment costs. • Hourly measurements of trihalomethanes made continuously for ten months. - Abstract: An instrument designed for fully automated on-line monitoring of trihalomethane concentrations in chlorinated drinking water is presented. The patented capillary membrane sampling device automatically samples directly from a water tap followed by injection of the sample into a gas chromatograph equipped with a nickel-63 electron capture detector. Detailed studies using individual trihalomethane species exhibited method detection limits ranging from 0.01–0.04 μg L −1 . Mean percent recoveries ranged from 77.1 to 86.5% with percent relative standard deviation values ranging from 1.2 to 4.6%. Out of more than 5200 samples analyzed, 95% of the concentration ranges were detectable, 86.5% were quantifiable. The failure rate was less than 2%. Using the data from the instrument, two different treatment processes were optimized so that total trihalomethane concentrations were maintained at acceptable levels while reducing treatment costs significantly. This ongoing trihalomethane monitoring program has been operating for more than ten months and has produced the longest continuous and most finely time-resolved data on trihalomethane concentrations reported in the literature

  11. Review: Behavioral signs of estrus and the potential of fully automated systems for detection of estrus in dairy cattle.

    Reith, S; Hoy, S

    2018-02-01

    Efficient detection of estrus is a permanent challenge for successful reproductive performance in dairy cattle. In this context, comprehensive knowledge of estrus-related behaviors is fundamental to achieve optimal estrus detection rates. This review was designed to identify the characteristics of behavioral estrus as a necessary basis for developing strategies and technologies to improve the reproductive management on dairy farms. The focus is on secondary symptoms of estrus (mounting, activity, aggressive and agonistic behaviors) which seem more indicative than standing behavior. The consequences of management, housing conditions and cow- and environmental-related factors impacting expression and detection of estrus as well as their relative importance are described in order to increase efficiency and accuracy of estrus detection. As traditional estrus detection via visual observation is time-consuming and ineffective, there has been a considerable advancement of detection aids during the last 10 years. By now, a number of fully automated technologies including pressure sensing systems, activity meters, video cameras, recordings of vocalization as well as measurements of body temperature and milk progesterone concentration are available. These systems differ in many aspects regarding sustainability and efficiency as keys to their adoption for farm use. As being most practical for estrus detection a high priority - according to the current research - is given to the detection based on sensor-supported activity monitoring, especially accelerometer systems. Due to differences in individual intensity and duration of estrus multivariate analysis can support herd managers in determining the onset of estrus. Actually, there is increasing interest in investigating the potential of combining data of activity monitoring and information of several other methods, which may lead to the best results concerning sensitivity and specificity of detection. Future improvements will

  12. A device for fully automated on-site process monitoring and control of trihalomethane concentrations in drinking water

    Brown, Aaron W. [The University of Memphis, Department of Chemistry, Memphis, TN 38152 (United States); Simone, Paul S. [The University of Memphis, Department of Chemistry, Memphis, TN 38152 (United States); Foundation Instruments, Inc., Collierville, TN 38017 (United States); York, J.C. [City of Lebanon, TN Water Treatment Plant, 7 Gilmore Hill Rd., Lebanon, TN 37087 (United States); Emmert, Gary L., E-mail: gemmert@memphis.edu [The University of Memphis, Department of Chemistry, Memphis, TN 38152 (United States); Foundation Instruments, Inc., Collierville, TN 38017 (United States)

    2015-01-01

    Highlights: • Commercial device for on-line monitoring of trihalomethanes in drinking water. • Method detection limits for individual trihalomethanes range from 0.01–0.04 μg L{sup –1}. • Rugged and robust device operates automatically for on-site process control. • Used for process mapping and process optimization to reduce treatment costs. • Hourly measurements of trihalomethanes made continuously for ten months. - Abstract: An instrument designed for fully automated on-line monitoring of trihalomethane concentrations in chlorinated drinking water is presented. The patented capillary membrane sampling device automatically samples directly from a water tap followed by injection of the sample into a gas chromatograph equipped with a nickel-63 electron capture detector. Detailed studies using individual trihalomethane species exhibited method detection limits ranging from 0.01–0.04 μg L{sup −1}. Mean percent recoveries ranged from 77.1 to 86.5% with percent relative standard deviation values ranging from 1.2 to 4.6%. Out of more than 5200 samples analyzed, 95% of the concentration ranges were detectable, 86.5% were quantifiable. The failure rate was less than 2%. Using the data from the instrument, two different treatment processes were optimized so that total trihalomethane concentrations were maintained at acceptable levels while reducing treatment costs significantly. This ongoing trihalomethane monitoring program has been operating for more than ten months and has produced the longest continuous and most finely time-resolved data on trihalomethane concentrations reported in the literature.

  13. Open 3D Projects

    Felician ALECU

    2010-01-01

    Full Text Available Many professionals and 3D artists consider Blender as being the best open source solution for 3D computer graphics. The main features are related to modeling, rendering, shading, imaging, compositing, animation, physics and particles and realtime 3D/game creation.

  14. 3D DOCUMENTATION OF 40 KILOMETERS OF HISTORICAL PORTICOES – THE CHALLENGE

    F. Remondino

    2016-06-01

    Full Text Available In the last years the image-based pipeline for 3D reconstruction purposes has received large interest leading to fully automated methodologies able to process large image datasets and deliver 3D products with a level of detail and precision variable according to the applications. Different open issues still exist, in particular when dealing with the 3D surveying and modeling of large and complex scenarios, like historical porticoes. The paper presents an evaluation of various surveying methods for the geometric documentation of ca 40km of historical porticoes in Bologna (Italy. Finally, terrestrial photogrammetry was chosen as the most flexible and productive technique in order to deliver 3D results in form of colored point clouds or textured 3D meshes accessible on the web. The presented digital products are a complementary material for the final candidature of the porticoes as UNESCO WHS.

  15. Recent advancements in mechanical characterisation of 3D woven composites

    Saleh, Mohamed Nasr; Soutis, Constantinos

    2017-12-01

    Three dimensional (3D) woven composites have attracted the interest of academia and industry thanks to their damage tolerance characteristics and automated fabric manufacturing. Although much research has been conducted to investigate their out-of-plane "through thickness" properties, still their in-plane properties are not fully understood and rely on extensive experimentation. To date, the literature lacks an inclusive summary of the mechanical characterisation for 3D woven composites. Therefore, the objective of this paper is to provide a comprehensive review of the available research studies on 3D woven composites mechanical characterisation, with less emphasis on the out-of-plane response, but an in-depth review of the in-plane response "un-notched vs. notched". The paper highlights the knowledge gap in the literature of 3D woven composites, suggesting opportunities for future research in this field and a room for improvement in utilising Non-Destructive Techniques (NDT), such as Digital Image Correlation (DIC), Acoustic Emission (AE) and X-ray Computed Tomography (CT), for observing damage initiation and evolution in 3D woven composites that could be used to calibrate and evaluate analytical and numerical models.

  16. 3D Printing of Organs-On-Chips

    Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

    2017-01-01

    Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms. PMID:28952489

  17. 3D Printing of Organs-On-Chips.

    Yi, Hee-Gyeong; Lee, Hyungseok; Cho, Dong-Woo

    2017-01-25

    Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM) and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms.

  18. 3D Printing of Organs-On-Chips

    Hee-Gyeong Yi

    2017-01-01

    Full Text Available Organ-on-a-chip engineering aims to create artificial living organs that mimic the complex and physiological responses of real organs, in order to test drugs by precisely manipulating the cells and their microenvironments. To achieve this, the artificial organs should to be microfabricated with an extracellular matrix (ECM and various types of cells, and should recapitulate morphogenesis, cell differentiation, and functions according to the native organ. A promising strategy is 3D printing, which precisely controls the spatial distribution and layer-by-layer assembly of cells, ECMs, and other biomaterials. Owing to this unique advantage, integration of 3D printing into organ-on-a-chip engineering can facilitate the creation of micro-organs with heterogeneity, a desired 3D cellular arrangement, tissue-specific functions, or even cyclic movement within a microfluidic device. Moreover, fully 3D-printed organs-on-chips more easily incorporate other mechanical and electrical components with the chips, and can be commercialized via automated massive production. Herein, we discuss the recent advances and the potential of 3D cell-printing technology in engineering organs-on-chips, and provides the future perspectives of this technology to establish the highly reliable and useful drug-screening platforms.

  19. Evaluation of brain perfusion in specific Brodmann areas in Frontotemporal dementia and Alzheimer disease using automated 3-D voxel based analysis

    Valotassiou, V; Tsougos, I; Tzavara, C; Georgoulias, P [Nuclear Medicine Dpt, University Hospital of Larissa, Larissa (Greece); Papatriantafyllou, J; Karageorgiou, C [Neurology Dpt, General Hospital ' G. Gennimatas' , Athens (Greece); Sifakis, N; Zerva, C [Nuclear Medicine Dpt, ' Alexandra' University Hospital, Athens (Greece)], E-mail: vanvalot@yahoo.gr

    2009-05-15

    Introduction. Brain perfusion studies with single-photon emission computed tomography (SPECT) have been applied in demented patients to provide better discrimination between frontotemporal dementia (FTD) and Alzheimer's disease (AD). Aim. To assess the perfusion of specific Brodmann (Br) areas of the brain cortex in FTD and AD patients, using NeuroGam processing program to provide 3D voxel-by-voxel cerebral SPECT analysis. Material and methods. We studied 34 consecutive patients. We used the established criteria for the diagnosis of dementia and the specific established criteria for the diagnosis of FTD and AD. All the patients had a neuropsychological evaluation with a battery of tests including the mini-mental state examination (MMSE).Twenty-six patients (16 males, 10 females, mean age 68.76{+-}6.51 years, education 11.81{+-}4.25 years, MMSE 16.69{+-}9.89) received the diagnosis of FTD and 8 patients (all females, mean age 71.25{+-}10.48 years, education 10{+-}4.6 years, MMSE 12.5{+-}3.89) the diagnosis of AD. All the patients underwent a brain SPECT. We applied the NeuroGam Software for the evaluation of brain perfusion in specific Br areas in the left (L) and right (R) hemispheres. Results. Statistically significant hypoperfusion in FTD compared to AD patients, was found in the following Br areas: 11L (p<0.0001), 11R, 20L, 20R, 32L, 38L, 38R, 44L (p<0.001), 32R, 36L, 36R, 45L, 45R, 47R (p<0.01), 9L, 21L, 39R, 44R, 46R, 47L (p<0.05). On the contrary, AD patients presented significant (p<0.05) hypoperfusion in 7R and 39R Br areas. Conclusion. NeuroGam processing program of brain perfusion SPECT could result in enhanced accuracy for the differential diagnosis between AD and FTD patients.

  20. Evaluation of brain perfusion in specific Brodmann areas in Frontotemporal dementia and Alzheimer disease using automated 3-D voxel based analysis

    Valotassiou, V; Tsougos, I; Tzavara, C; Georgoulias, P; Papatriantafyllou, J; Karageorgiou, C; Sifakis, N; Zerva, C

    2009-01-01

    Introduction. Brain perfusion studies with single-photon emission computed tomography (SPECT) have been applied in demented patients to provide better discrimination between frontotemporal dementia (FTD) and Alzheimer's disease (AD). Aim. To assess the perfusion of specific Brodmann (Br) areas of the brain cortex in FTD and AD patients, using NeuroGam processing program to provide 3D voxel-by-voxel cerebral SPECT analysis. Material and methods. We studied 34 consecutive patients. We used the established criteria for the diagnosis of dementia and the specific established criteria for the diagnosis of FTD and AD. All the patients had a neuropsychological evaluation with a battery of tests including the mini-mental state examination (MMSE).Twenty-six patients (16 males, 10 females, mean age 68.76±6.51 years, education 11.81±4.25 years, MMSE 16.69±9.89) received the diagnosis of FTD and 8 patients (all females, mean age 71.25±10.48 years, education 10±4.6 years, MMSE 12.5±3.89) the diagnosis of AD. All the patients underwent a brain SPECT. We applied the NeuroGam Software for the evaluation of brain perfusion in specific Br areas in the left (L) and right (R) hemispheres. Results. Statistically significant hypoperfusion in FTD compared to AD patients, was found in the following Br areas: 11L (p<0.0001), 11R, 20L, 20R, 32L, 38L, 38R, 44L (p<0.001), 32R, 36L, 36R, 45L, 45R, 47R (p<0.01), 9L, 21L, 39R, 44R, 46R, 47L (p<0.05). On the contrary, AD patients presented significant (p<0.05) hypoperfusion in 7R and 39R Br areas. Conclusion. NeuroGam processing program of brain perfusion SPECT could result in enhanced accuracy for the differential diagnosis between AD and FTD patients.

  1. Evaluation of brain perfusion in specific Brodmann areas in Frontotemporal dementia and Alzheimer disease using automated 3-D voxel based analysis

    Valotassiou, V.; Papatriantafyllou, J.; Sifakis, N.; Karageorgiou, C.; Tsougos, I.; Tzavara, C.; Zerva, C.; Georgoulias, P.

    2009-05-01

    Introduction. Brain perfusion studies with single-photon emission computed tomography (SPECT) have been applied in demented patients to provide better discrimination between frontotemporal dementia (FTD) and Alzheimer's disease (AD). Aim. To assess the perfusion of specific Brodmann (Br) areas of the brain cortex in FTD and AD patients, using NeuroGam processing program to provide 3D voxel-by-voxel cerebral SPECT analysis. Material and methods. We studied 34 consecutive patients. We used the established criteria for the diagnosis of dementia and the specific established criteria for the diagnosis of FTD and AD. All the patients had a neuropsychological evaluation with a battery of tests including the mini-mental state examination (MMSE).Twenty-six patients (16 males, 10 females, mean age 68.76±6.51 years, education 11.81±4.25 years, MMSE 16.69±9.89) received the diagnosis of FTD and 8 patients (all females, mean age 71.25±10.48 years, education 10±4.6 years, MMSE 12.5±3.89) the diagnosis of AD. All the patients underwent a brain SPECT. We applied the NeuroGam Software for the evaluation of brain perfusion in specific Br areas in the left (L) and right (R) hemispheres. Results. Statistically significant hypoperfusion in FTD compared to AD patients, was found in the following Br areas: 11L (p<0.0001), 11R, 20L, 20R, 32L, 38L, 38R, 44L (p<0.001), 32R, 36L, 36R, 45L, 45R, 47R (p<0.01), 9L, 21L, 39R, 44R, 46R, 47L (p<0.05). On the contrary, AD patients presented significant (p<0.05) hypoperfusion in 7R and 39R Br areas. Conclusion. NeuroGam processing program of brain perfusion SPECT could result in enhanced accuracy for the differential diagnosis between AD and FTD patients.

  2. Refined 3d-3d correspondence

    Alday, Luis F.; Genolini, Pietro Benetti; Bullimore, Mathew; Loon, Mark van [Mathematical Institute, University of Oxford, Andrew Wiles Building,Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG (United Kingdom)

    2017-04-28

    We explore aspects of the correspondence between Seifert 3-manifolds and 3d N=2 supersymmetric theories with a distinguished abelian flavour symmetry. We give a prescription for computing the squashed three-sphere partition functions of such 3d N=2 theories constructed from boundary conditions and interfaces in a 4d N=2{sup ∗} theory, mirroring the construction of Seifert manifold invariants via Dehn surgery. This is extended to include links in the Seifert manifold by the insertion of supersymmetric Wilson-’t Hooft loops in the 4d N=2{sup ∗} theory. In the presence of a mass parameter for the distinguished flavour symmetry, we recover aspects of refined Chern-Simons theory with complex gauge group, and in particular construct an analytic continuation of the S-matrix of refined Chern-Simons theory.

  3. Fully automated calculation of image-derived input function in simultaneous PET/MRI in a sheep model

    Jochimsen, Thies H.; Zeisig, Vilia; Schulz, Jessica; Werner, Peter; Patt, Marianne; Patt, Jörg; Dreyer, Antje Y.; Boltze, Johannes; Barthel, Henryk; Sabri, Osama; Sattler, Bernhard

    2016-01-01

    Obtaining the arterial input function (AIF) from image data in dynamic positron emission tomography (PET) examinations is a non-invasive alternative to arterial blood sampling. In simultaneous PET/magnetic resonance imaging (PET/MRI), high-resolution MRI angiographies can be used to define major arteries for correction of partial-volume effects (PVE) and point spread function (PSF) response in the PET data. The present study describes a fully automated method to obtain the image-derived input function (IDIF) in PET/MRI. Results are compared to those obtained by arterial blood sampling. To segment the trunk of the major arteries in the neck, a high-resolution time-of-flight MRI angiography was postprocessed by a vessel-enhancement filter based on the inertia tensor. Together with the measured PSF of the PET subsystem, the arterial mask was used for geometrical deconvolution, yielding the time-resolved activity concentration averaged over a major artery. The method was compared to manual arterial blood sampling at the hind leg of 21 sheep (animal stroke model) during measurement of blood flow with O15-water. Absolute quantification of activity concentration was compared after bolus passage during steady state, i.e., between 2.5- and 5-min post injection. Cerebral blood flow (CBF) values from blood sampling and IDIF were also compared. The cross-calibration factor obtained by comparing activity concentrations in blood samples and IDIF during steady state is 0.98 ± 0.10. In all examinations, the IDIF provided a much earlier and sharper bolus peak than in the time course of activity concentration obtained by arterial blood sampling. CBF using the IDIF was 22 % higher than CBF obtained by using the AIF yielded by blood sampling. The small deviation between arterial blood sampling and IDIF during steady state indicates that correction of PVE and PSF is possible with the method presented. The differences in bolus dynamics and, hence, CBF values can be explained by the

  4. Fully automated calculation of image-derived input function in simultaneous PET/MRI in a sheep model

    Jochimsen, Thies H.; Zeisig, Vilia [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany); Schulz, Jessica [Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstr. 1a, Leipzig, D-04103 (Germany); Werner, Peter; Patt, Marianne; Patt, Jörg [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany); Dreyer, Antje Y. [Fraunhofer Institute of Cell Therapy and Immunology, Perlickstr. 1, Leipzig, D-04103 (Germany); Translational Centre for Regenerative Medicine, University Leipzig, Philipp-Rosenthal-Str. 55, Leipzig, D-04103 (Germany); Boltze, Johannes [Fraunhofer Institute of Cell Therapy and Immunology, Perlickstr. 1, Leipzig, D-04103 (Germany); Translational Centre for Regenerative Medicine, University Leipzig, Philipp-Rosenthal-Str. 55, Leipzig, D-04103 (Germany); Fraunhofer Research Institution of Marine Biotechnology and Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck (Germany); Barthel, Henryk; Sabri, Osama; Sattler, Bernhard [Department of Nuclear Medicine, Leipzig University Hospital, Liebigstr. 18, Leipzig (Germany)

    2016-02-13

    Obtaining the arterial input function (AIF) from image data in dynamic positron emission tomography (PET) examinations is a non-invasive alternative to arterial blood sampling. In simultaneous PET/magnetic resonance imaging (PET/MRI), high-resolution MRI angiographies can be used to define major arteries for correction of partial-volume effects (PVE) and point spread function (PSF) response in the PET data. The present study describes a fully automated method to obtain the image-derived input function (IDIF) in PET/MRI. Results are compared to those obtained by arterial blood sampling. To segment the trunk of the major arteries in the neck, a high-resolution time-of-flight MRI angiography was postprocessed by a vessel-enhancement filter based on the inertia tensor. Together with the measured PSF of the PET subsystem, the arterial mask was used for geometrical deconvolution, yielding the time-resolved activity concentration averaged over a major artery. The method was compared to manual arterial blood sampling at the hind leg of 21 sheep (animal stroke model) during measurement of blood flow with O15-water. Absolute quantification of activity concentration was compared after bolus passage during steady state, i.e., between 2.5- and 5-min post injection. Cerebral blood flow (CBF) values from blood sampling and IDIF were also compared. The cross-calibration factor obtained by comparing activity concentrations in blood samples and IDIF during steady state is 0.98 ± 0.10. In all examinations, the IDIF provided a much earlier and sharper bolus peak than in the time course of activity concentration obtained by arterial blood sampling. CBF using the IDIF was 22 % higher than CBF obtained by using the AIF yielded by blood sampling. The small deviation between arterial blood sampling and IDIF during steady state indicates that correction of PVE and PSF is possible with the method presented. The differences in bolus dynamics and, hence, CBF values can be explained by the

  5. A 3d-3d appetizer

    Pei, Du; Ye, Ke [Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA, 91125 (United States)

    2016-11-02

    We test the 3d-3d correspondence for theories that are labeled by Lens spaces. We find a full agreement between the index of the 3d N=2 “Lens space theory” T[L(p,1)] and the partition function of complex Chern-Simons theory on L(p,1). In particular, for p=1, we show how the familiar S{sup 3} partition function of Chern-Simons theory arises from the index of a free theory. For large p, we find that the index of T[L(p,1)] becomes a constant independent of p. In addition, we study T[L(p,1)] on the squashed three-sphere S{sub b}{sup 3}. This enables us to see clearly, at the level of partition function, to what extent G{sub ℂ} complex Chern-Simons theory can be thought of as two copies of Chern-Simons theory with compact gauge group G.

  6. Reliability of a semi-automated 3D-CT measuring method for tunnel diameters after anterior cruciate ligament reconstruction: A comparison between soft-tissue single-bundle allograft vs. autograft.

    Robbrecht, Cedric; Claes, Steven; Cromheecke, Michiel; Mahieu, Peter; Kakavelakis, Kyriakos; Victor, Jan; Bellemans, Johan; Verdonk, Peter

    2014-10-01

    Post-operative widening of tibial and/or femoral bone tunnels is a common observation after ACL reconstruction, especially with soft-tissue grafts. There are no studies comparing tunnel widening in hamstring autografts versus tibialis anterior allografts. The goal of this study was to observe the difference in tunnel widening after the use of allograft vs. autograft for ACL reconstruction, by measuring it with a novel 3-D computed tomography based method. Thirty-five ACL-deficient subjects were included, underwent anatomic single-bundle ACL reconstruction and were evaluated at one year after surgery with the use of 3-D CT imaging. Three independent observers semi-automatically delineated femoral and tibial tunnel outlines, after which a best-fit cylinder was derived and the tunnel diameter was determined. Finally, intra- and inter-observer reliability of this novel measurement protocol was defined. In femoral tunnels, the intra-observer ICC was 0.973 (95% CI: 0.922-0.991) and the inter-observer ICC was 0.992 (95% CI: 0.982-0.996). In tibial tunnels, the intra-observer ICC was 0.955 (95% CI: 0.875-0.985). The combined inter-observer ICC was 0.970 (95% CI: 0.987-0.917). Tunnel widening was significantly higher in allografts compared to autografts, in the tibial tunnels (p=0.013) as well as in the femoral tunnels (p=0.007). To our knowledge, this novel, semi-automated 3D-computed tomography image processing method has shown to yield highly reproducible results for the measurement of bone tunnel diameter and area. This series showed a significantly higher amount of tunnel widening observed in the allograft group at one-year follow-up. Level II, Prospective comparative study. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. 3D virtuel udstilling

    Tournay, Bruno; Rüdiger, Bjarne

    2006-01-01

    3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s.......3d digital model af Arkitektskolens gård med virtuel udstilling af afgangsprojekter fra afgangen sommer 2006. 10 s....

  8. Underwater 3D filming

    Roberto Rinaldi

    2014-12-01

    Full Text Available After an experimental phase of many years, 3D filming is now effective and successful. Improvements are still possible, but the film industry achieved memorable success on 3D movie’s box offices due to the overall quality of its products. Special environments such as space (“Gravity” and the underwater realm look perfect to be reproduced in 3D. “Filming in space” was possible in “Gravity” using special effects and computer graphic. The underwater realm is still difficult to be handled. Underwater filming in 3D was not that easy and effective as filming in 2D, since not long ago. After almost 3 years of research, a French, Austrian and Italian team realized a perfect tool to film underwater, in 3D, without any constrains. This allows filmmakers to bring the audience deep inside an environment where they most probably will never have the chance to be.

  9. Underwater 3D filming

    Rinaldi, Roberto

    2014-01-01

    After an experimental phase of many years, 3D filming is now effective and successful. Improvements are still possible, but the film industry achieved memorable success on 3D movie’s box offices due to the overall quality of its products. Special environments such as space (“Gravity” ) and the underwater realm look perfect to be reproduced in 3D. “Filming in space” was possible in “Gravity” using special effects and computer graphic. The underwater realm is still difficult to be handled. Unde...

  10. Blender 3D cookbook

    Valenza, Enrico

    2015-01-01

    This book is aimed at the professionals that already have good 3D CGI experience with commercial packages and have now decided to try the open source Blender and want to experiment with something more complex than the average tutorials on the web. However, it's also aimed at the intermediate Blender users who simply want to go some steps further.It's taken for granted that you already know how to move inside the Blender interface, that you already have 3D modeling knowledge, and also that of basic 3D modeling and rendering concepts, for example, edge-loops, n-gons, or samples. In any case, it'

  11. Fully Automated Electro Membrane Extraction Autosampler for LC-MS Systems Allowing Soft Extractions for High-Throughput Applications

    Fuchs, David; Pedersen-Bjergaard, Stig; Jensen, Henrik

    2016-01-01

    was optimized for soft extraction of analytes and high sample throughput. Further, it was demonstrated that by flushing the EME-syringe with acidic wash buffer and reverting the applied electric potential, carry-over between samples can be reduced to below 1%. Performance of the system was characterized (RSD......, a complete analytical workflow of purification, separation, and analysis of sample could be achieved within only 5.5 min. With the developed system large sequences of samples could be analyzed in a completely automated manner. This high degree of automation makes the developed EME-autosampler a powerful tool...

  12. Performance evaluation of vertical feed fully automated TLD badge reader using 0.8 and 0.4 mm teflon embedded CaSO4:Dy dosimeters

    Ratna, P.; More, Vinay; Kulkarni, M.S.

    2012-01-01

    The personnel monitoring of more than 80,000 radiation workers in India is at present carried out by semi-automated TLD badge Reader systems (TLDBR-7B) developed by Radiation Safety Systems Division, Bhabha Atomic Research Centre. More than 60 such reader systems are in use in all the personnel monitoring centers in the country. Radiation Safety Systems Division also developed the fully automated TLD badge reader based on a new TLD badge having built-in machine readable ID code (in the form of 16x3 hole pattern). This automated reader is designed with minimum of changes in the electronics and mechanical hardware in the semiautomatic version (TLDBR-7B) so that such semi-automatic readers can be easily upgraded to the fully automated versions by using the new TLD badge with ID code. The reader was capable of reading 50 TLD cards in 90 minutes. Based on the feedback from the users, a new model of frilly automated TLD badge Reader (model VEFFA-10) is designed which is an improved version of the previously reported fully Automated TLD badge reader. This VEFFA-10 PC based Reader incorporates vertical loading of TLD bards having machine readable ID code. In this new reader, a vertical rack, which can hold 100 such cards, is mounted from the right side of the reader system. The TLD card falls into the channel by gravity from where it is taken to the reading position by rack and pinion method. After the readout, the TLD card is dropped in a eject tray. The reader employs hot N 2 gas heating method and the gas flow is controlled by a specially designed digital gas flow meter on the front panel of the reader system. The system design is very compact and simple and card stuck up problem is totally eliminated in the reader system. The reader has a number of self-diagnostic features to ensure a high degree of reliability. This paper reports the performance evaluation of the Reader using 0.4 mm thick Teflon embedded CaSO 4 :Dy TLD cards instead of 0.8 mm cards

  13. Visual Versus Fully Automated Analyses of 18F-FDG and Amyloid PET for Prediction of Dementia Due to Alzheimer Disease in Mild Cognitive Impairment.

    Grimmer, Timo; Wutz, Carolin; Alexopoulos, Panagiotis; Drzezga, Alexander; Förster, Stefan; Förstl, Hans; Goldhardt, Oliver; Ortner, Marion; Sorg, Christian; Kurz, Alexander

    2016-02-01

    Biomarkers of Alzheimer disease (AD) can be imaged in vivo and can be used for diagnostic and prognostic purposes in people with cognitive decline and dementia. Indicators of amyloid deposition such as (11)C-Pittsburgh compound B ((11)C-PiB) PET are primarily used to identify or rule out brain diseases that are associated with amyloid pathology but have also been deployed to forecast the clinical course. Indicators of neuronal metabolism including (18)F-FDG PET demonstrate the localization and severity of neuronal dysfunction and are valuable for differential diagnosis and for predicting the progression from mild cognitive impairment (MCI) to dementia. It is a matter of debate whether to analyze these images visually or using automated techniques. Therefore, we compared the usefulness of both imaging methods and both analyzing strategies to predict dementia due to AD. In MCI participants, a baseline examination, including clinical and imaging assessments, and a clinical follow-up examination after a planned interval of 24 mo were performed. Of 28 MCI patients, 9 developed dementia due to AD, 2 developed frontotemporal dementia, and 1 developed moderate dementia of unknown etiology. The positive and negative predictive values and the accuracy of visual and fully automated analyses of (11)C-PiB for the prediction of progression to dementia due to AD were 0.50, 1.00, and 0.68, respectively, for the visual and 0.53, 1.00, and 0.71, respectively, for the automated analyses. Positive predictive value, negative predictive value, and accuracy of fully automated analyses of (18)F-FDG PET were 0.37, 0.78, and 0.50, respectively. Results of visual analyses were highly variable between raters but were superior to automated analyses. Both (18)F-FDG and (11)C-PiB imaging appear to be of limited use for predicting the progression from MCI to dementia due to AD in short-term follow-up, irrespective of the strategy of analysis. On the other hand, amyloid PET is extremely useful to

  14. The Traveling Optical Scanner – Case Study on 3D Shape Models of Ancient Brazilian Skulls

    Trinderup, Camilla Himmelstrup; Dahl, Vedrana Andersen; Gregersen, Kristian Murphy

    2016-01-01

    , inoffensive and inexpensive 3D scanning modality based on structured light, suitable for capturing the morphology and the appearance of specimens. Benefits of having 3D models are manifold. The 3D models are easy to share among researchers and can be made available to the general public. Advanced...... morphological modelling is possible with accurate description of the specimens provided by the models. Furthermore, performing studies on models reduces the risk of damage to the original specimen. In our work we employ a high resolution structured light scanner for digitalizing a collection of 8500 year old...... human skulls from Brazil. To evaluate the precision of our setup we compare the structured light scan to micro-CT and achieve submillimetre difference. We analyse morphological features of the Brazilian skulls using manual landmarks, but a research goal is to automate this, fully utilize the dense 3D...

  15. DELTA 3D PRINTER

    ȘOVĂILĂ Florin

    2016-07-01

    Full Text Available 3D printing is a very used process in industry, the generic name being “rapid prototyping”. The essential advantage of a 3D printer is that it allows the designers to produce a prototype in a very short time, which is tested and quickly remodeled, considerably reducing the required time to get from the prototype phase to the final product. At the same time, through this technique we can achieve components with very precise forms, complex pieces that, through classical methods, could have been accomplished only in a large amount of time. In this paper, there are presented the stages of a 3D model execution, also the physical achievement after of a Delta 3D printer after the model.

  16. Professional Papervision3D

    Lively, Michael

    2010-01-01

    Professional Papervision3D describes how Papervision3D works and how real world applications are built, with a clear look at essential topics such as building websites and games, creating virtual tours, and Adobe's Flash 10. Readers learn important techniques through hands-on applications, and build on those skills as the book progresses. The companion website contains all code examples, video step-by-step explanations, and a collada repository.

  17. Toward fully automated genotyping: Allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy

    Perlin, M.W.; Burks, M.B. [Carnegie Mellon Univ., Pittsburgh, PA (United States); Hoop, R.C.; Hoffman, E.P. [Univ. of Pittsburgh School of Medicine, PA (United States)

    1994-10-01

    Human genetic maps have made quantum leaps in the past few years, because of the characterization of >2,000 CA dinucleotide repeat loci: these PCR-based markers offer extraordinarily high PIC, and within the next year their density is expected to reach intervals of a few centimorgans per marker. These new genetic maps open new avenues for disease gene research, including large-scale genotyping for both simple and complex disease loci. However, the allele patterns of many dinucleotide repeat loci can be complex and difficult to interpret, with genotyping errors a recognized problem. Furthermore, the possibility of genotyping individuals at hundreds or thousands of polymorphic loci requires improvements in data handling and analysis. The automation of genotyping and analysis of computer-derived haplotypes would remove many of the barriers preventing optimal use of dense and informative dinucleotide genetic maps. Toward this end, we have automated the allele identification, genotyping, phase determinations, and inheritance consistency checks generated by four CA repeats within the 2.5-Mbp, 10-cM X-linked dystrophin gene, using fluorescein-labeled multiplexed PCR products analyzed on automated sequencers. The described algorithms can deconvolute and resolve closely spaced alleles, despite interfering stutter noise; set phase in females; propagate the phase through the family; and identify recombination events. We show the implementation of these algorithms for the completely automated interpretation of allele data and risk assessment for five Duchenne/Becker muscular dystrophy families. The described approach can be scaled up to perform genome-based analyses with hundreds or thousands of CA-repeat loci, using multiple fluorophors on automated sequencers. 16 refs., 5 figs., 1 tab.

  18. A fully-automated computer-assisted method of CT brain scan analysis for the measurement of cerebrospinal fluid spaces and brain absorption density

    Baldy, R.E.; Brindley, G.S.; Jacobson, R.R.; Reveley, M.A.; Lishman, W.A.; Ewusi-Mensah, I.; Turner, S.W.

    1986-01-01

    Computer-assisted methods of CT brain scan analysis offer considerable advantages over visual inspection, particularly in research; and several semi-automated methods are currently available. A new computer-assisted program is presented which provides fully automated processing of CT brain scans, depending on ''anatomical knowledge'' of where cerebrospinal fluid (CSF)-containing spaces are likely to lie. After identifying these regions of interest quantitative estimates are then provided of CSF content in each slice in cisterns, ventricles, Sylvian fissure and interhemispheric fissure. Separate measures are also provided of mean brain density in each slice. These estimates can be summated to provide total ventricular and total brain volumes. The program shows a high correlation with measures derived from mechanical planimetry and visual grading procedures, also when tested against a phantom brain of known ventricular volume. The advantages and limitations of the present program are discussed. (orig.)

  19. Fully automated one-pot radiosynthesis of O-(2-[{sup 18}F]fluoroethyl)-L-tyrosine on the TracerLab FX{sub FN} module

    Bourdier, Thomas, E-mail: bts@ansto.gov.au [LifeSciences, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC NSW 2232, Sydney (Australia); Greguric, Ivan [LifeSciences, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC NSW 2232, Sydney (Australia); Roselt, Peter [Centre for Molecular Imaging, Peter MacCallum Cancer Centre, 12 St Andrew' s Place, East Melbourne, VIC, 3002 (Australia); Jackson, Tim; Faragalla, Jane; Katsifis, Andrew [LifeSciences, Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC NSW 2232, Sydney (Australia)

    2011-07-15

    Introduction: An efficient fully automated method for the radiosynthesis of enantiomerically pure O-(2-[{sup 18}F]fluoroethyl)-L-tyrosine ([{sup 18}F]FET) using the GE TracerLab FX{sub FN} synthesis module via the O-(2-tosyloxyethyl)-N-trityl-L-tyrosine tert-butylester precursor has been developed. Methods: The radiolabelling of [{sup 18}F]FET involved a classical [{sup 18}F]fluoride nucleophilic substitution performed in acetonitrile using potassium carbonate and Kryptofix 222, followed by acid hydrolysis using 2N hydrochloric acid. Results: [{sup 18}F]FET was produced in 35{+-}5% (n=22) yield non-decay-corrected (55{+-}5% decay-corrected) and with radiochemical and enantiomeric purity of >99% with a specific activity of >90 GBq/{mu}mol after 63 min of radiosynthesis including HPLC purification and formulation. Conclusion: The automated radiosynthesis provides high and reproducible yields suitable for routine clinical use.

  20. Fully-automated computer-assisted method of CT brain scan analysis for the measurement of cerebrospinal fluid spaces and brain absorption density

    Baldy, R.E.; Brindley, G.S.; Jacobson, R.R.; Reveley, M.A.; Lishman, W.A.; Ewusi-Mensah, I.; Turner, S.W.

    1986-03-01

    Computer-assisted methods of CT brain scan analysis offer considerable advantages over visual inspection, particularly in research; and several semi-automated methods are currently available. A new computer-assisted program is presented which provides fully automated processing of CT brain scans, depending on ''anatomical knowledge'' of where cerebrospinal fluid (CSF)-containing spaces are likely to lie. After identifying these regions of interest quantitative estimates are then provided of CSF content in each slice in cisterns, ventricles, Sylvian fissure and interhemispheric fissure. Separate measures are also provided of mean brain density in each slice. These estimates can be summated to provide total ventricular and total brain volumes. The program shows a high correlation with measures derived from mechanical planimetry and visual grading procedures, also when tested against a phantom brain of known ventricular volume. The advantages and limitations of the present program are discussed.

  1. Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).

    Salimi, Nima; Loh, Kar Hoe; Kaur Dhillon, Sarinder; Chong, Ving Ching

    2016-01-01

    Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

  2. Deep convolutional neural network and 3D deformable approach for tissue segmentation in musculoskeletal magnetic resonance imaging.

    Liu, Fang; Zhou, Zhaoye; Jang, Hyungseok; Samsonov, Alexey; Zhao, Gengyan; Kijowski, Richard

    2018-04-01

    To describe and evaluate a new fully automated musculoskeletal tissue segmentation method using deep convolutional neural network (CNN) and three-dimensional (3D) simplex deformable modeling to improve the accuracy and efficiency of cartilage and bone segmentation within the knee joint. A fully automated segmentation pipeline was built by combining a semantic segmentation CNN and 3D simplex deformable modeling. A CNN technique called SegNet was applied as the core of the segmentation method to perform high resolution pixel-wise multi-class tissue classification. The 3D simplex deformable modeling refined the output from SegNet to preserve the overall shape and maintain a desirable smooth surface for musculoskeletal structure. The fully automated segmentation method was tested using a publicly available knee image data set to compare with currently used state-of-the-art segmentation methods. The fully automated method was also evaluated on two different data sets, which include morphological and quantitative MR images with different tissue contrasts. The proposed fully automated segmentation method provided good segmentation performance with segmentation accuracy superior to most of state-of-the-art methods in the publicly available knee image data set. The method also demonstrated versatile segmentation performance on both morphological and quantitative musculoskeletal MR images with different tissue contrasts and spatial resolutions. The study demonstrates that the combined CNN and 3D deformable modeling approach is useful for performing rapid and accurate cartilage and bone segmentation within the knee joint. The CNN has promising potential applications in musculoskeletal imaging. Magn Reson Med 79:2379-2391, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  3. 3-D interactive visualisation tools for Hi spectral line imaging

    van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

    2016-01-01

    Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is

  4. The MMP inhibitor (R)-2-(N-benzyl-4-(2-[18F]fluoroethoxy)phenylsulphonamido) -N-hydroxy-3-methylbutanamide: Improved precursor synthesis and fully automated radiosynthesis

    Wagner, Stefan; Faust, Andreas; Breyholz, Hans-Joerg; Schober, Otmar; Schaefers, Michael; Kopka, Klaus

    2011-01-01

    Summary: The CGS 25966 derivative (R)-2-(N-Benzyl-4-(2-[ 18 F]fluoroethoxy)phenyl-sulphonamido) -N-hydroxy-3-methylbutanamide [ 18 F]9 represents a very potent radiolabelled matrix metalloproteinase inhibitor. For first human PET studies it is mandatory to have a fully automated radiosynthesis and a straightforward precursor synthesis available. The realisation of both requirements is reported herein. In particular, the corresponding precursor 8 was obtained in a reliable 7 step synthesis with an overall chemical yield of 2.3%. Furthermore, the target compound [ 18 F]9 was prepared with a radiochemical yield of 14.8±3.9% (not corrected for decay).

  5. Advances toward fully automated in vivo assessment of oral epithelial dysplasia by nuclear endomicroscopy-A pilot study.

    Liese, Jan; Winter, Karsten; Glass, Änne; Bertolini, Julia; Kämmerer, Peer Wolfgang; Frerich, Bernhard; Schiefke, Ingolf; Remmerbach, Torsten W

    2017-11-01

    Uncertainties in detection of oral epithelial dysplasia (OED) frequently result from sampling error especially in inflammatory oral lesions. Endomicroscopy allows non-invasive, "en face" imaging of upper oral epithelium, but parameters of OED are unknown. Mucosal nuclei were imaged in 34 toluidine blue-stained oral lesions with a commercial endomicroscopy. Histopathological diagnosis showed four biopsies in "dys-/neoplastic," 23 in "inflammatory," and seven in "others" disease groups. Strength of different assessment strategies of nuclear scoring, nuclear count, and automated nuclear analysis were measured by area under ROC curve (AUC) to identify histopathological "dys-/neoplastic" group. Nuclear objects from automated image analysis were visually corrected. Best-performing parameters of nuclear-to-image ratios were the count of large nuclei (AUC=0.986) and 6-nearest neighborhood relation (AUC=0.896), and best parameters of nuclear polymorphism were the count of atypical nuclei (AUC=0.996) and compactness of nuclei (AUC=0.922). Excluding low-grade OED, nuclear scoring and count reached 100% sensitivity and 98% specificity for detection of dys-/neoplastic lesions. In automated analysis, combination of parameters enhanced diagnostic strength. Sensitivity of 100% and specificity of 87% were seen for distances of 6-nearest neighbors and aspect ratios even in uncorrected objects. Correction improved measures of nuclear polymorphism only. The hue of background color was stronger than nuclear density (AUC=0.779 vs 0.687) to detect dys-/neoplastic group indicating that macroscopic aspect is biased. Nuclear-to-image ratios are applicable for automated optical in vivo diagnostics for oral potentially malignant disorders. Nuclear endomicroscopy may promote non-invasive, early detection of dys-/neoplastic lesions by reducing sampling error. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Wearable 3D measurement

    Manabe, Yoshitsugu; Imura, Masataka; Tsuchiya, Masanobu; Yasumuro, Yoshihiro; Chihara, Kunihiro

    2003-01-01

    Wearable 3D measurement realizes to acquire 3D information of an objects or an environment using a wearable computer. Recently, we can send voice and sound as well as pictures by mobile phone in Japan. Moreover it will become easy to capture and send data of short movie by it. On the other hand, the computers become compact and high performance. And it can easy connect to Internet by wireless LAN. Near future, we can use the wearable computer always and everywhere. So we will be able to send the three-dimensional data that is measured by wearable computer as a next new data. This paper proposes the measurement method and system of three-dimensional data of an object with the using of wearable computer. This method uses slit light projection for 3D measurement and user"s motion instead of scanning system.

  7. 3D Digital Modelling

    Hundebøl, Jesper

    wave of new building information modelling tools demands further investigation, not least because of industry representatives' somewhat coarse parlance: Now the word is spreading -3D digital modelling is nothing less than a revolution, a shift of paradigm, a new alphabet... Research qeustions. Based...... on empirical probes (interviews, observations, written inscriptions) within the Danish construction industry this paper explores the organizational and managerial dynamics of 3D Digital Modelling. The paper intends to - Illustrate how the network of (non-)human actors engaged in the promotion (and arrest) of 3...... important to appreciate the analysis. Before turning to the presentation of preliminary findings and a discussion of 3D digital modelling, it begins, however, with an outline of industry specific ICT strategic issues. Paper type. Multi-site field study...

  8. 3D ARCHITECTURAL VIDEOMAPPING

    R. Catanese

    2013-07-01

    Full Text Available 3D architectural mapping is a video projection technique that can be done with a survey of a chosen building in order to realize a perfect correspondence between its shapes and the images in projection. As a performative kind of audiovisual artifact, the real event of the 3D mapping is a combination of a registered video animation file with a real architecture. This new kind of visual art is becoming very popular and its big audience success testifies new expressive chances in the field of urban design. My case study has been experienced in Pisa for the Luminara feast in 2012.

  9. Interaktiv 3D design

    Villaume, René Domine; Ørstrup, Finn Rude

    2002-01-01

    Projektet undersøger potentialet for interaktiv 3D design via Internettet. Arkitekt Jørn Utzons projekt til Espansiva blev udviklet som et byggesystem med det mål, at kunne skabe mangfoldige planmuligheder og mangfoldige facade- og rumudformninger. Systemets bygningskomponenter er digitaliseret som...... 3D elementer og gjort tilgængelige. Via Internettet er det nu muligt at sammenstille og afprøve en uendelig  række bygningstyper som  systemet blev tænkt og udviklet til....

  10. 3D Projection Installations

    Halskov, Kim; Johansen, Stine Liv; Bach Mikkelsen, Michelle

    2014-01-01

    Three-dimensional projection installations are particular kinds of augmented spaces in which a digital 3-D model is projected onto a physical three-dimensional object, thereby fusing the digital content and the physical object. Based on interaction design research and media studies, this article ...... Fingerplan to Loop City, is a 3-D projection installation presenting the history and future of city planning for the Copenhagen area in Denmark. The installation was presented as part of the 12th Architecture Biennale in Venice in 2010....

  11. Herramientas SIG 3D

    Francisco R. Feito Higueruela

    2010-04-01

    Full Text Available Applications of Geographical Information Systems on several Archeology fields have been increasing during the last years. Recent avances in these technologies make possible to work with more realistic 3D models. In this paper we introduce a new paradigm for this system, the GIS Thetrahedron, in which we define the fundamental elements of GIS, in order to provide a better understanding of their capabilities. At the same time the basic 3D characteristics of some comercial and open source software are described, as well as the application to some samples on archeological researchs

  12. Bootstrapping 3D fermions

    Iliesiu, Luca [Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544 (United States); Kos, Filip; Poland, David [Department of Physics, Yale University, New Haven, CT 06520 (United States); Pufu, Silviu S. [Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544 (United States); Simmons-Duffin, David [School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540 (United States); Yacoby, Ran [Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544 (United States)

    2016-03-17

    We study the conformal bootstrap for a 4-point function of fermions 〈ψψψψ〉 in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ×ψ OPE, and also on the central charge C{sub T}. We observe features in our bounds that coincide with scaling dimensions in the Gross-Neveu models at large N. We also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  13. Towards a fully automated lab-on-a-disc system integrating sample enrichment and detection of analytes from complex matrices

    Andreasen, Sune Zoëga

    the technology on a large scale from fulfilling its potential for maturing into applied technologies and products. In this work, we have taken the first steps towards realizing a capable and truly automated “sample-to-answer” analysis system, aimed at small molecule detection and quantification from a complex...... sample matrix. The main result is a working prototype of a microfluidic system, integrating both centrifugal microfluidics for sample handling, supported liquid membrane extraction (SLM) for selective and effective sample treatment, as well as in-situ electrochemical detection. As a case study...

  14. Shaping 3-D boxes

    Stenholt, Rasmus; Madsen, Claus B.

    2011-01-01

    Enabling users to shape 3-D boxes in immersive virtual environments is a non-trivial problem. In this paper, a new family of techniques for creating rectangular boxes of arbitrary position, orientation, and size is presented and evaluated. These new techniques are based solely on position data...

  15. 3D Wire 2015

    Jordi, Moréton; F, Escribano; J. L., Farias

    This document is a general report on the implementation of gamification in 3D Wire 2015 event. As the second gamification experience in this event, we have delved deeply in the previous objectives (attracting public areas less frequented exhibition in previous years and enhance networking) and have...

  16. 3D Harmonic Echocardiography:

    M.M. Voormolen (Marco)

    2007-01-01

    textabstractThree dimensional (3D) echocardiography has recently developed from an experimental technique in the ’90 towards an imaging modality for the daily clinical practice. This dissertation describes the considerations, implementation, validation and clinical application of a unique

  17. DNA origami design of 3D nanostructures

    Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

    2009-01-01

    [8]. We have recently developed a semi-automated DNA origami software package [9] that uses a 2D sequence editor in conjunction with several automated tools to facilitate the design process. Here we extend the use of the program for designing DNA origami structures in 3D and show the application......Structural DNA nanotechnology has been heavily dependent on the development of dedicated software tools for the design of unique helical junctions, to define unique sticky-ends for tile assembly, and for predicting the products of the self-assembly reaction of multiple DNA strands [1-3]. Recently......, several dedicated 3D editors for computer-aided design of DNA structures have been developed [4-7]. However, many of these tools are not efficient for designing DNA origami structures that requires the design of more than 200 unique DNA strands to be folded along a scaffold strand into a defined 3D shape...

  18. DNA origami design of 3D nanostructures

    Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

    2009-01-01

    , several dedicated 3D editors for computer-aided design of DNA structures have been developed [4-7]. However, many of these tools are not efficient for designing DNA origami structures that requires the design of more than 200 unique DNA strands to be folded along a scaffold strand into a defined 3D shape...... [8]. We have recently developed a semi-automated DNA origami software package [9] that uses a 2D sequence editor in conjunction with several automated tools to facilitate the design process. Here we extend the use of the program for designing DNA origami structures in 3D and show the application...... by the construction of a DNA box with dimensions of 42 × 36 × 36 nm3. The software is available at www.cdna.dk/origami/ ....

  19. A user-friendly robotic sample preparation program for fully automated biological sample pipetting and dilution to benefit the regulated bioanalysis.

    Jiang, Hao; Ouyang, Zheng; Zeng, Jianing; Yuan, Long; Zheng, Naiyu; Jemal, Mohammed; Arnold, Mark E

    2012-06-01

    Biological sample dilution is a rate-limiting step in bioanalytical sample preparation when the concentrations of samples are beyond standard curve ranges, especially when multiple dilution factors are needed in an analytical run. We have developed and validated a Microsoft Excel-based robotic sample preparation program (RSPP) that automatically transforms Watson worklist sample information (identification, sequence and dilution factor) to comma-separated value (CSV) files. The Freedom EVO liquid handler software imports and transforms the CSV files to executable worklists (.gwl files), allowing the robot to perform sample dilutions at variable dilution factors. The dynamic dilution range is 1- to 1000-fold and divided into three dilution steps: 1- to 10-, 11- to 100-, and 101- to 1000-fold. The whole process, including pipetting samples, diluting samples, and adding internal standard(s), is accomplished within 1 h for two racks of samples (96 samples/rack). This platform also supports online sample extraction (liquid-liquid extraction, solid-phase extraction, protein precipitation, etc.) using 96 multichannel arms. This fully automated and validated sample dilution and preparation process has been applied to several drug development programs. The results demonstrate that application of the RSPP for fully automated sample processing is efficient and rugged. The RSPP not only saved more than 50% of the time in sample pipetting and dilution but also reduced human errors. The generated bioanalytical data are accurate and precise; therefore, this application can be used in regulated bioanalysis.

  20. Fully automated radiosynthesis of [11C]PBR28, a radiopharmaceutical for the translocator protein (TSPO) 18 kDa, using a GE TRACERlab FXC-Pro

    Hoareau, Raphaël; Shao, Xia; Henderson, Bradford D.; Scott, Peter J.H.

    2012-01-01

    In order to image the translocator protein (TSPO) 18 kDa in the clinic using positron emission tomography (PET) imaging, we had a cause to prepare [ 11 C]PBR28. In this communication we highlight our novel, recently developed, one-pot synthesis of the desmethyl-PBR28 precursor, as well as present an optimized fully automated preparation of [ 11 C]PBR28 using a GE TRACERlab FX C-Pro . Following radiolabelling, purification is achieved by HPLC and, to the best of our knowledge, the first reported example of reconstituting [ 11 C]PBR28 into ethanolic saline using solid-phase extraction (SPE). This procedure is operationally simple, and provides high quality doses of [ 11 C]PBR28 suitable for use in clinical PET imaging studies. Typical radiochemical yield using the optimized method is 3.6% yield (EOS, n=3), radiochemical and chemical purity are consistently >99%, and specific activities are 14,523 Ci/mmol. Highlights: ► This paper reports a fully automated synthesis of [ 11 C]PBR28 using a TRACERlab FXc-pro. ► We report a solid-phase extraction technique for the reconstitution of [ 11 C]PBR28. ► ICP-MS data for PBR28 precursor is reported confirming suitability for clinical use.

  1. Fully Automated Atlas-Based Hippocampus Volumetry for Clinical Routine: Validation in Subjects with Mild Cognitive Impairment from the ADNI Cohort.

    Suppa, Per; Hampel, Harald; Spies, Lothar; Fiebach, Jochen B; Dubois, Bruno; Buchert, Ralph

    2015-01-01

    Hippocampus volumetry based on magnetic resonance imaging (MRI) has not yet been translated into everyday clinical diagnostic patient care, at least in part due to limited availability of appropriate software tools. In the present study, we evaluate a fully-automated and computationally efficient processing pipeline for atlas based hippocampal volumetry using freely available Statistical Parametric Mapping (SPM) software in 198 amnestic mild cognitive impairment (MCI) subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI1). Subjects were grouped into MCI stable and MCI to probable Alzheimer's disease (AD) converters according to follow-up diagnoses at 12, 24, and 36 months. Hippocampal grey matter volume (HGMV) was obtained from baseline T1-weighted MRI and then corrected for total intracranial volume and age. Average processing time per subject was less than 4 minutes on a standard PC. The area under the receiver operator characteristic curve of the corrected HGMV for identification of MCI to probable AD converters within 12, 24, and 36 months was 0.78, 0.72, and 0.71, respectively. Thus, hippocampal volume computed with the fully-automated processing pipeline provides similar power for prediction of MCI to probable AD conversion as computationally more expensive methods. The whole processing pipeline has been made freely available as an SPM8 toolbox. It is easily set up and integrated into everyday clinical patient care.

  2. Development of a fully automated open-column chemical-separation system—COLUMNSPIDER—and its application to Sr-Nd-Pb isotope analyses of igneous rock samples

    Miyazaki, Takashi; Vaglarov, Bogdan Stefanov; Takei, Masakazu; Suzuki, Masahiro; Suzuki, Hiroaki; Ohsawa, Kouzou; Chang, Qing; Takahashi, Toshiro; Hirahara, Yuka; Hanyu, Takeshi; Kimura, Jun-Ichi; Tatsumi, Yoshiyuki

    A fully automated open-column resin-bed chemical-separation system, named COLUMNSPIDER, has been developed. The system consists of a programmable micropipetting robot that dispenses chemical reagents and sample solutions into an open-column resin bed for elemental separation. After the initial set up of resin columns, chemical reagents, and beakers for the separated chemical components, all separation procedures are automated. As many as ten samples can be eluted in parallel in a single automated run. Many separation procedures, such as radiogenic isotope ratio analyses for Sr and Nd, involve the use of multiple column separations with different resin columns, chemical reagents, and beakers of various volumes. COLUMNSPIDER completes these separations using multiple runs. Programmable functions, including the positioning of the micropipetter, reagent volume, and elution time, enable flexible operation. Optimized m