WorldWideScience

Sample records for video-tracking 3d-reconstructions bioinformatics-based

  1. 3D Reconstruction of NMR Images

    Directory of Open Access Journals (Sweden)

    Peter Izak

    2007-01-01

    Full Text Available This paper introduces experiment of 3D reconstruction NMR images scanned from magnetic resonance device. There are described methods which can be used for 3D reconstruction magnetic resonance images in biomedical application. The main idea is based on marching cubes algorithm. For this task was chosen sophistication method by program Vision Assistant, which is a part of program LabVIEW.

  2. Research on 3D reconstruction of concrete

    Directory of Open Access Journals (Sweden)

    Shi Pan-fei

    2015-01-01

    Full Text Available In order to associate with using acoustic emission, ultrasonic or other means to locate damage of concrete, based on the concrete CT image information, the research of 3D reconstruction of concrete crack structure was completed by using Amira 5.2.1 3D reconstruction software. Experiments showed that: three dimensional reconstruction of concrete can reflect the real crack structure, and distribution of aggregate concrete of three dimensional model established was basically in accordance with the original CT image, which laid the good foundation to simulate and analysis by using ANSYS finite element software in the future.

  3. 3-D Reconstruction From Satellite Images

    DEFF Research Database (Denmark)

    Denver, Troelz

    1999-01-01

    The aim of this project has been to implement a software system, that is able to create a 3-D reconstruction from two or more 2-D photographic images made from different positions. The height is determined from the disparity difference of the images. The general purpose of the system is mapping o......, where various methods have been tested in order to optimize the performance. The match results are used in the reconstruction part to establish a 3-D digital representation and finally, different presentation forms are discussed....

  4. 3D Reconstruction of NMR Images by LabVIEW

    Directory of Open Access Journals (Sweden)

    Peter IZAK

    2007-01-01

    Full Text Available This paper introduces the experiment of 3D reconstruction NMR images via virtual instrumentation - LabVIEW. The main idea is based on marching cubes algorithm and image processing implemented by module of Vision assistant. The two dimensional images shot by the magnetic resonance device provide information about the surface properties of human body. There is implemented algorithm which can be used for 3D reconstruction of magnetic resonance images in biomedical application.

  5. Array antenna diagnostics with the 3D reconstruction algorithm

    DEFF Research Database (Denmark)

    Cappellin, Cecilia; Meincke, Peter; Pivnenko, Sergey

    2012-01-01

    The 3D reconstruction algorithm is applied to a slotted waveguide array measured at the DTU-ESA Spherical Near-Field Antenna Test Facility. One slot of the array is covered by conductive tape and an error is present in the array excitation. Results show the accuracy obtainable by the 3D...... reconstruction algorithm. Considerations on the measurement sampling, the obtainable spatial resolution, and the possibility of taking full advantage of the reconstruction geometry are provided....

  6. DCT and DST Based Image Compression for 3D Reconstruction

    Science.gov (United States)

    Siddeq, Mohammed M.; Rodrigues, Marcos A.

    2017-03-01

    This paper introduces a new method for 2D image compression whose quality is demonstrated through accurate 3D reconstruction using structured light techniques and 3D reconstruction from multiple viewpoints. The method is based on two discrete transforms: (1) A one-dimensional Discrete Cosine Transform (DCT) is applied to each row of the image. (2) The output from the previous step is transformed again by a one-dimensional Discrete Sine Transform (DST), which is applied to each column of data generating new sets of high-frequency components followed by quantization of the higher frequencies. The output is then divided into two parts where the low-frequency components are compressed by arithmetic coding and the high frequency ones by an efficient minimization encoding algorithm. At decompression stage, a binary search algorithm is used to recover the original high frequency components. The technique is demonstrated by compressing 2D images up to 99% compression ratio. The decompressed images, which include images with structured light patterns for 3D reconstruction and from multiple viewpoints, are of high perceptual quality yielding accurate 3D reconstruction. Perceptual assessment and objective quality of compression are compared with JPEG and JPEG2000 through 2D and 3D RMSE. Results show that the proposed compression method is superior to both JPEG and JPEG2000 concerning 3D reconstruction, and with equivalent perceptual quality to JPEG2000.

  7. Filtering of measurement noise with the 3D reconstruction algorithm

    DEFF Research Database (Denmark)

    Cappellin, Cecilia; Pivnenko, Sergey

    2014-01-01

    Two different antenna models are set up in GRASP and CHAMP, and noise is added to the radiated field. The noisy field is then given as input to the 3D reconstruction of DIATOOL and the SWE coefficients and the far-field radiated by the reconstructed currents are compared with the noise-free results...

  8. Improving automated 3D reconstruction methods via vision metrology

    Science.gov (United States)

    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.

  9. Facial-paralysis diagnostic system based on 3D reconstruction

    Science.gov (United States)

    Khairunnisaa, Aida; Basah, Shafriza Nisha; Yazid, Haniza; Basri, Hassrizal Hassan; Yaacob, Sazali; Chin, Lim Chee

    2015-05-01

    The diagnostic process of facial paralysis requires qualitative assessment for the classification and treatment planning. This result is inconsistent assessment that potential affect treatment planning. We developed a facial-paralysis diagnostic system based on 3D reconstruction of RGB and depth data using a standard structured-light camera - Kinect 360 - and implementation of Active Appearance Models (AAM). We also proposed a quantitative assessment for facial paralysis based on triangular model. In this paper, we report on the design and development process, including preliminary experimental results. Our preliminary experimental results demonstrate the feasibility of our quantitative assessment system to diagnose facial paralysis.

  10. Automating 3D reconstruction using a probabilistic grammar

    Science.gov (United States)

    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. Dose fractionation theorem in 3-D reconstruction (tomography)

    Energy Technology Data Exchange (ETDEWEB)

    Glaeser, R.M. [Lawrence Berkeley National Lab., CA (United States)

    1997-02-01

    It is commonly assumed that the large number of projections for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3-D reconstruction is the same as that required to obtain a single 2-D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3-D image can be computed from statistically insignificant projections, as along as the total dosage that is distributed among these projections is high enough that it would have resulted in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3-D model created from an electron micrograph. The simulations verify the basic conclusions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Furthermore, the simulations demonstrate that individual projections in the series of fractionated-dose images can be aligned by cross-correlation because they contain significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3-D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results, in combination with dose estimates for imaging single voxels and measurements of radiation damage in the electron microscope, demonstrate that it is feasible to use single-axis tomography with soft X-ray microscopy of frozen-hydrated specimens.

  12. Self-expressive Dictionary Learning for Dynamic 3D Reconstruction.

    Science.gov (United States)

    Zheng, Enliang; Ji, Dinghuang; Dunn, Enrique; Frahm, Jan-Michael

    2017-08-22

    We target the problem of sparse 3D reconstruction of dynamic objects observed by multiple unsynchronized video cameras with unknown temporal overlap. To this end, we develop a framework to recover the unknown structure without sequencing information across video sequences. Our proposed compressed sensing framework poses the estimation of 3D structure as the problem of dictionary learning, where the dictionary is defined as an aggregation of the temporally varying 3D structures. Given the smooth motion of dynamic objects, we observe any element in the dictionary can be well approximated by a sparse linear combination of other elements in the same dictionary (i.e. self-expression). Our formulation optimizes a biconvex cost function that leverages a compressed sensing formulation and enforces both structural dependency coherence across video streams, as well as motion smoothness across estimates from common video sources. We further analyze the reconstructability of our approach under different capture scenarios, and its comparison and relation to existing methods. Experimental results on large amounts of synthetic data as well as real imagery demonstrate the effectiveness of our approach.

  13. 3D reconstruction of elastin fibres in coronary adventitia.

    Science.gov (United States)

    Luo, T; Chen, H; Kassab, G S

    2017-01-01

    A 3D reconstruction of individual fibres in vascular tissue is necessary to understand the microstructure properties of the vessel wall.  The objective of this study is to determine the 3D microstructure of elastin fibres in the adventitia of coronary arteries.  Quantification of fibre geometry is challenging due to the complex interwoven structure of the fibres.  In particular, accurate linking of gaps remains a significant challenge, and complex features such as long gaps and interwoven fibres have not been adequately addressed by current fibre reconstruction algorithms.  We use a novel line Laplacian deformation method, which better deals with fibre shape uncertainty to reconstruct elastin fibres in the coronary adventitia of five swine. A cost function, based on entropy and Euler Spiral, was used in the shortest path search. We find that mean diameter of elastin fibres is 1.67 ± 1.42 μm and fibre orientation is clustered around two major angles of 8.9˚ and 81.8˚.  Comparing with CT-FIRE, we find that our method gives more accurate estimation of fibre width.  To our knowledge, the measurements obtained using our algorithm represent the first investigation focused on the reconstruction of full elastin fibre length.  Our data provide a foundation for a 3D microstructural model of the coronary adventitia to elucidate the structure-function relationship of elastin fibres. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  14. Preoperative Planning Using 3D Reconstructions and Virtual Endoscopy for Location of the Frontal Sinus

    Directory of Open Access Journals (Sweden)

    Abreu, João Paulo Saraiva

    2011-01-01

    Full Text Available Introduction: Computed tomography (TC generated tridimensional (3D reconstructions allow the observation of cavities and anatomic structures of our body with detail. In our specialty there have been attempts to carry out virtual endoscopies and laryngoscopies. However, such application has been practically abandoned due to its complexity and need for computers with high power of graphic processing. Objective: To demonstrate the production of 3D reconstructions from CTs of patients in personal computers, with a free specific program and compare them to the surgery actual endoscopic images. Method: Prospective study in which the CTs proper files of 10 patients were reconstructed with the program Intage Realia, version 2009, 0, 0, 702 (KGT Inc., Japan. The reconstructions were carried out before the surgeries and a virtual endoscopy was made to assess the recess and frontal sinus region. After this study, the surgery was digitally performed and stored. The actual endoscopic images of the recess and frontal sinus region were compared to the virtual images. Results: The 3D reconstruction and virtual endoscopy were made in 10 patients submitted to the surgery. The virtual images had a large resemblance with the actual surgical images. Conclusion: With relatively simple tools and personal computer, we demonstrated the possibility to generate 3D reconstructions and virtual endoscopies. The preoperative knowledge of the frontal sinus natural draining path location may generate benefits during the performance of surgeries. However, more studies must be developed for the evaluation of the real roles of such 3D reconstructions and virtual endoscopies.

  15. Brachial plexus 3D reconstruction from MRI with dissection validation: a baseline study for clinical applications.

    Science.gov (United States)

    Van de Velde, Joris; Bogaert, Stephanie; Vandemaele, Pieter; Huysse, Wouter; Achten, Eric; Leijnse, Joris; De Neve, Wilfried; Van Hoof, Tom

    2016-03-01

    The present study aimed to establish a baseline for detailed 3D brachial plexus reconstruction from magnetic resonance imaging (MRI). Concretely, the goal was to determine the individual brachial plexus anatomy with maximum detail and accuracy achievable, as yet irrespective of whether the methods used could be economically and practically applied in the clinical setting. Six embalmed cadavers were randomly taken for MRI imaging of the brachial plexus. Detailed two-dimensional (2D) segmentation for all brachial plexus parts was done. The 2D brachial plexus segmentations were 3D reconstructed using Mimics(®) software. Then, these 3D reconstructions were anatomically validated by dissection of the cadavers. After finalising the cadaver experiments, brachial plexus MRIs were obtained in three healthy male volunteers and the same reconstruction procedure as in vitro was followed. A procedure was developed for brachial plexus 3D reconstruction based on MRI without the use of any contrast agent. Anatomical validation of six cadaver brachial plexus reconstructions showed high correspondence with the dissected brachial plexuses. Anatomical variations of the main branches were equally present in the 3D reconstructions generated. However, there were also some differences that related to the difference between the surface anatomy of the nerve and the internal nerve structure. In vivo, it was possible to reconstruct the complete brachial plexus in such a manner that normal-appearing BPs were derived in a reproducible way. This study showed that the described procedure results in accurate and reproducible brachial plexus 3D reconstructions.

  16. Benchmarking Close-range Structure from Motion 3D Reconstruction Software under Varying Capturing Conditions

    DEFF Research Database (Denmark)

    Nikolov, Ivan Adriyanov; Madsen, Claus B.

    2016-01-01

    Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique. In this ......Structure from Motion 3D reconstruction has become widely used in recent years in a number of fields such as industrial surface in- inspection, archeology, cultural heritage preservation and geomapping. A number of software solutions have been released using variations of this technique...

  17. Reliable Gait Recognition Using 3D Reconstructions and Random Forests - An Anthropometric Approach

    DEFF Research Database (Denmark)

    Sandau, Martin; Heimbürger, Rikke V.; Jensen, Karl E.

    2016-01-01

    Photogrammetric measurements of bodily dimensions and analysis of gait patterns in CCTV are important tools in forensic investigations but accurate extraction of the measurements are challenging. This study tested whether manual annotation of the joint centers on 3D reconstructions could provide...... expert annotated the data. Recognition based on data annotated by different experts was less reliable achieving 72.6% correct recognitions as some parameters were heavily affected by interobserver variability. This study verified that 3D reconstructions are feasible for forensic gait analysis...

  18. An automatic 3D reconstruction system based on binocular vision measurement

    Science.gov (United States)

    Liu, Shuangyin; Wang, Zhenwei; Fan, Fang

    2017-10-01

    With the rapid development of computer vision, vision measurement and 3D reconstruction have become a hot research trend. However, it is still a problem to reconstruct the weak texture surface in engineering. In this paper, we present the systematic design and implementation of an automatic measurement system based on binocular vision. The hardware configuration of the verification platform is presented, including CCD cameras, stepper motors, laser displacement sensors and so on. Binocular-vision algorithms including camera calibration, feature extraction, stereo match and 3D reconstruction are prompted to reconstruct the weak texture surface. An experiment demonstrates the effectiveness and feasibility of this platform.

  19. Array diagnostics, spatial resolution, and filtering of undesired radiation with the 3D reconstruction algorithm

    DEFF Research Database (Denmark)

    Cappellin, C.; Pivnenko, Sergey; Jørgensen, E.

    2013-01-01

    This paper focuses on three important features of the 3D reconstruction algorithm of DIATOOL: the identification of array elements improper functioning and failure, the obtainable spatial resolution of the reconstructed fields and currents, and the filtering of undesired radiation and scattering...

  20. Improved 3D reconstruction in smart-room environments using ToF imaging

    DEFF Research Database (Denmark)

    Guðmundsson, Sigurjón Árni; Pardas, Montse; Casas, Josep R.

    2010-01-01

    This paper presents the use of Time-of-Flight (ToF) cameras in smart-rooms and how this leads to improved results in segmenting the people in the room from the background and consequently better 3D reconstruction of foreground objects. A calibrated rig consisting of one Swissranger SR3100 Time-of...

  1. A Hierarchical Building Segmentation in Digital Surface Models for 3D Reconstruction

    Directory of Open Access Journals (Sweden)

    Yiming Yan

    2017-01-01

    Full Text Available In this study, a hierarchical method for segmenting buildings in a digital surface model (DSM, which is used in a novel framework for 3D reconstruction, is proposed. Most 3D reconstructions of buildings are model-based. However, the limitations of these methods are overreliance on completeness of the offline-constructed models of buildings, and the completeness is not easily guaranteed since in modern cities buildings can be of a variety of types. Therefore, a model-free framework using high precision DSM and texture-images buildings was introduced. There are two key problems with this framework. The first one is how to accurately extract the buildings from the DSM. Most segmentation methods are limited by either the terrain factors or the difficult choice of parameter-settings. A level-set method are employed to roughly find the building regions in the DSM, and then a recently proposed ‘occlusions of random textures model’ are used to enhance the local segmentation of the buildings. The second problem is how to generate the facades of buildings. Synergizing with the corresponding texture-images, we propose a roof-contour guided interpolation of building facades. The 3D reconstruction results achieved by airborne-like images and satellites are compared. Experiments show that the segmentation method has good performance, and 3D reconstruction is easily performed by our framework, and better visualization results can be obtained by airborne-like images, which can be further replaced by UAV images.

  2. On the 3D reconstruction of diatom frustules : a novel method, applications, and limitations

    NARCIS (Netherlands)

    Mansilla, Catalina; Novais, Maria Helena; Faber, Enne; Martinez-Martinez, Diego; De Hosson, J. Th.

    Because of the importance of diatoms and the lack of information about their third dimension, a new method for the 3D reconstruction is explored, based on digital image correlation of several scanning electron microscope images. The accuracy of the method to reconstruct both centric and pennate

  3. Imaging Techniques for Dense 3D reconstruction of Swimming Aquatic Life using Multi-view Stereo

    Science.gov (United States)

    Daily, David; Kiser, Jillian; McQueen, Sarah

    2016-11-01

    Understanding the movement characteristics of how various species of fish swim is an important step to uncovering how they propel themselves through the water. Previous methods have focused on profile capture methods or sparse 3D manual feature point tracking. This research uses an array of 30 cameras to automatically track hundreds of points on a fish as they swim in 3D using multi-view stereo. Blacktip sharks, sting rays, puffer fish, turtles and more were imaged in collaboration with the National Aquarium in Baltimore, Maryland using the multi-view stereo technique. The processes for data collection, camera synchronization, feature point extraction, 3D reconstruction, 3D alignment, biological considerations, and lessons learned will be presented. Preliminary results of the 3D reconstructions will be shown and future research into mathematically characterizing various bio-locomotive maneuvers will be discussed.

  4. 3D reconstruction and digitalization of an archeological site, Itanos, Crete

    Directory of Open Access Journals (Sweden)

    Rudy Ercek

    2010-04-01

    Full Text Available The city of Itanos is situated in the North-East of Crete. Between 1994 and 2005, the French School of Archaeology at Athens (Efa and the Center for Mediterranean Studies in Rethymnon carried out excavation campaigns during which a necropolis and an Archaic building have been explored by a team of the CReA. A very close collaboration between archeologists, engineers and computer graphic designers allowed the 3D reconstruction of these remains. The archeologist was able to directly verify his hypotheses during the reconstruction process. In summer 2007 and 2008, a 3D digitalization of Itanos was made in order to insert the 3D reconstructions into the actual landscape.

  5. 3D RECONSTRUCTION WITH A COLLABORATIVE APPROACH BASED ON SMARTPHONES AND A CLOUD-BASED SERVER

    Directory of Open Access Journals (Sweden)

    E. Nocerino

    2017-11-01

    Full Text Available The paper presents a collaborative image-based 3D reconstruction pipeline to perform image acquisition with a smartphone and geometric 3D reconstruction on a server during concurrent or disjoint acquisition sessions. Images are selected from the video feed of the smartphone’s camera based on their quality and novelty. The smartphone’s app provides on-the-fly reconstruction feedback to users co-involved in the acquisitions. The server is composed of an incremental SfM algorithm that processes the received images by seamlessly merging them into a single sparse point cloud using bundle adjustment. Dense image matching algorithm can be lunched to derive denser point clouds. The reconstruction details, experiments and performance evaluation are presented and discussed.

  6. Application aspects of advanced antenna diagnostics with the 3D reconstruction algorithm

    DEFF Research Database (Denmark)

    Cappellin, Cecilia; Pivnenko, Sergey

    2015-01-01

    This paper focuses on two important applications of the 3D reconstruction algorithm of the commercial software DIATOOL for antenna diagnostics. The first one is the accurate and detailed identification of array malfunctioning, thanks to the available enhanced spatial resolution of the reconstructed...... fields and currents. The second one is the filtering of the scattering from support structures and feed network leakage. Representative experimental results are presented and guidelines on the recommended measurement parameters for obtaining the best diagnostics results are provided....

  7. 3D Reconstruction from X-ray Fluoroscopy for Clinical Veterinary Medicine using Differential Volume Rendering

    Science.gov (United States)

    Khongsomboon, Khamphong; Hamamoto, Kazuhiko; Kondo, Shozo

    3D reconstruction from ordinary X-ray equipment which is not CT or MRI is required in clinical veterinary medicine. Authors have already proposed a 3D reconstruction technique from X-ray photograph to present bone structure. Although the reconstruction is useful for veterinary medicine, the thechnique has two problems. One is about exposure of X-ray and the other is about data acquisition process. An x-ray equipment which is not special one but can solve the problems is X-ray fluoroscopy. Therefore, in this paper, we propose a method for 3D-reconstruction from X-ray fluoroscopy for clinical veterinary medicine. Fluoroscopy is usually used to observe a movement of organ or to identify a position of organ for surgery by weak X-ray intensity. Since fluoroscopy can output a observed result as movie, the previous two problems which are caused by use of X-ray photograph can be solved. However, a new problem arises due to weak X-ray intensity. Although fluoroscopy can present information of not only bone structure but soft tissues, the contrast is very low and it is very difficult to recognize some soft tissues. It is very useful to be able to observe not only bone structure but soft tissues clearly by ordinary X-ray equipment in the field of clinical veterinary medicine. To solve this problem, this paper proposes a new method to determine opacity in volume rendering process. The opacity is determined according to 3D differential coefficient of 3D reconstruction. This differential volume rendering can present a 3D structure image of multiple organs volumetrically and clearly for clinical veterinary medicine. This paper shows results of simulation and experimental investigation of small dog and evaluation by veterinarians.

  8. Dense soft tissue 3D reconstruction refined with super-pixel segmentation for robotic abdominal surgery.

    Science.gov (United States)

    Penza, Veronica; Ortiz, Jesús; Mattos, Leonardo S; Forgione, Antonello; De Momi, Elena

    2016-02-01

    Single-incision laparoscopic surgery decreases postoperative infections, but introduces limitations in the surgeon's maneuverability and in the surgical field of view. This work aims at enhancing intra-operative surgical visualization by exploiting the 3D information about the surgical site. An interactive guidance system is proposed wherein the pose of preoperative tissue models is updated online. A critical process involves the intra-operative acquisition of tissue surfaces. It can be achieved using stereoscopic imaging and 3D reconstruction techniques. This work contributes to this process by proposing new methods for improved dense 3D reconstruction of soft tissues, which allows a more accurate deformation identification and facilitates the registration process. Two methods for soft tissue 3D reconstruction are proposed: Method 1 follows the traditional approach of the block matching algorithm. Method 2 performs a nonparametric modified census transform to be more robust to illumination variation. The simple linear iterative clustering (SLIC) super-pixel algorithm is exploited for disparity refinement by filling holes in the disparity images. The methods were validated using two video datasets from the Hamlyn Centre, achieving an accuracy of 2.95 and 1.66 mm, respectively. A comparison with ground-truth data demonstrated the disparity refinement procedure: (1) increases the number of reconstructed points by up to 43 % and (2) does not affect the accuracy of the 3D reconstructions significantly. Both methods give results that compare favorably with the state-of-the-art methods. The computational time constraints their applicability in real time, but can be greatly improved by using a GPU implementation.

  9. A practical approach to test the scope of FIB-SEM 3D reconstruction

    Science.gov (United States)

    Ritter, M.; Midgley, P. A.

    2010-07-01

    State-of-the-art focused ion beam (FIB) instruments have an ion column for sample modification and an electron column for scanning electron microscopy (SEM). 3D reconstruction of a sample volume can be achieved by serial sectioning using the FIB in combination with high-resolution SEM imaging of each cross-section. Usually, the resolution in the direction in which the sections are milled (z-direction) is much lower than in the plane of the cross-section (xy-direction) itself. Increased sampling in the z-direction can only be achieved by decreasing the distance between single sections. For a constant volume this is equivalent to increasing the number of sections, i.e. time and effort. To perform efficient 3D reconstructions the effect of the reduced sampling in the z-direction to the overall accuracy of the 3D reconstruction has to be known. We tested this approach with FIB conical test structures that were slice-and-view processed and subsequently reconstructed. Using a reference data set with a slice thickness (z-resolution) of 22 nm, data with z-resolutions ranging from 44 nm to 440 nm were created and reconstructed with commercial software. The calculated volumes for the simulated z-resolutions and their deviations from the reference volume are shown. Deviations of up to 35% occur and reach about 10% once the z-resolution was one fifth of the upper diameter of the conical structures.

  10. Near-infrared optical imaging of human brain based on the semi-3D reconstruction algorithm

    Science.gov (United States)

    Liu, Ming; Meng, Wei; Qin, Zhuanping; Zhou, Xiaoqing; Zhao, Huijuan; Gao, Feng

    2013-03-01

    In the non-invasive brain imaging with near-infrared light, precise head model is of great significance to the forward model and the image reconstruction. To deal with the individual difference of human head tissues and the problem of the irregular curvature, in this paper, we extracted head structure with Mimics software from the MRI image of a volunteer. This scheme makes it possible to assign the optical parameters to every layer of the head tissues reasonably and solve the diffusion equation with the finite-element analysis. During the solution of the inverse problem, a semi-3D reconstruction algorithm is adopted to trade off the computation cost and accuracy between the full 3-D and the 2-D reconstructions. In this scheme, the changes in the optical properties of the inclusions are assumed either axially invariable or confined to the imaging plane, while the 3-D nature of the photon migration is still retained. This therefore leads to a 2-D inverse issue with the matched 3-D forward model. Simulation results show that comparing to the 3-D reconstruction algorithm, the Semi-3D reconstruction algorithm cut 27% the calculation time consumption.

  11. Procedure and algorithm of 3D reconstruction of large-scale ancient architecture

    Science.gov (United States)

    Xia, Song; Zhu, Yixuan; Li, Xin

    2006-02-01

    3D reconstruction plays an essential role in the documentation and protection of ancient architecture. 3D reconstruction and photogrammetry are mainly used to conserve the datum and restore the 3D model of large-scale ancient architecture in our work. The whole procedure and an algorithm on space polyhedron are investigated in this paper. Firstly lots of conspicuous feature points are laid around the huge granite in order to construct a local and temporary 3D controlling field with sufficiently high precision. And feature points on the granite are obtained by means of photogrammetry. We use DLT (Direct Linear Transform) to calculate coordinates of feature points and accuracy evaluation of all feature points can be obtained simultaneously. A new generation algorithm for spatial convex polyhedron is presented and realized efficiently in our research. And we can get 3D model of the granite. In order to reduce duplicate storage of points and edges of the model, model connection and optimization are performed to complete the modeling process. Realistic material can be attached to the 3D model in 3DMAX. At last rendering and animation of the 3D model are completed and we got the reconstructive model of the granite. We use the approach mentioned above to realize the 3D reconstruction of large-scale ancient architecture successfully.

  12. A Simple and Cheap 3D Reconstruction System of Embryonic Structures from Serial Sections

    Directory of Open Access Journals (Sweden)

    Johanna Suárez-Rairán

    2007-01-01

    Full Text Available This work explaines how to setup and use a very cheap and simple 3D reconstruction system, for embryonic structures, using as an example the innervation of E19 hindlimb rat embryo. It also shows how results of good level can be achieved, such as, form, location and distribution of the structures of interest, obtaining additionally quantitative data of the size (volume and superficial area, and form. All the results mentioned above were obtained from the operation of free software available at the Internet.

  13. The Transformations of the Central Area of Nora: the 3D Reconstruction of the Central Baths

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    Daniele Capuzzo

    2013-11-01

    Full Text Available The 3D reconstruction of the Central Baths of Nora has required a long and reasoned analysis. On the basis of precise comparisons, a planimetric study of the complex has been first carried out, followed by the more difficult one of the elevations and the roofs, in order to create a model that allows to appreciate the building not only in its structural complexity, but also in the relationship with the spatial context in which it stood. This work represents only a part of a larger project that lead to the creation of a 3D model of the whole central district of Nora.

  14. JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

    Directory of Open Access Journals (Sweden)

    Delphine Ribes

    Full Text Available In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

  15. On the use of orientation filters for 3D reconstruction in event-driven stereo vision.

    Science.gov (United States)

    Camuñas-Mesa, Luis A; Serrano-Gotarredona, Teresa; Ieng, Sio H; Benosman, Ryad B; Linares-Barranco, Bernabe

    2014-01-01

    The recently developed Dynamic Vision Sensors (DVS) sense visual information asynchronously and code it into trains of events with sub-micro second temporal resolution. This high temporal precision makes the output of these sensors especially suited for dynamic 3D visual reconstruction, by matching corresponding events generated by two different sensors in a stereo setup. This paper explores the use of Gabor filters to extract information about the orientation of the object edges that produce the events, therefore increasing the number of constraints applied to the matching algorithm. This strategy provides more reliably matched pairs of events, improving the final 3D reconstruction.

  16. The Return of the Siegesburg - 3D-RECONSTRUCTION of a Disappeared and Forgotten Monument

    Science.gov (United States)

    Deggim, S.; Kersten, T. P.; Lindstaedt, M.; Hinrichsen, N.

    2017-02-01

    Many Cultural Heritage (CH) monuments are destroyed in the past and they are often lost forever. If there is no contemporary metric documentation of the historic objects available, the monument and the information about this monument could be disappeared and forgotten forever. The Siegesburg (also known as Segeberg castle) located on the "Kalkberg" (Chalk Mountain) in Bad Segeberg in Northern Germany, is a typical example for such a monument, which was destroyed by Swedish troops at the end of the Thirty Years' War in 1644. This important monument was only documented by a few historic isometric maps, but the castle and even the later castle ruin were totally destructed and demolished over the last centuries and disappeared forever. Furthermore, this significant memorial is even forgotten in many people's mind. This contribution describes the physical and virtual return of the Siegesburg by 3D reconstruction using historic sources. The laboratory for Photogrammetry & Laser Scanning of the HafenCity University Hamburg conducted this project in co-operation with the museum Alt-Segeberger Bürgerhaus (Old-Segeberg town house). The process of the 3D reconstruction and visualisation of both the Kalkberg and the castle is presented in this paper.

  17. Fast and Easy 3D Reconstruction with the Help of Geometric Constraints and Genetic Algorithms

    Science.gov (United States)

    Annich, Afafe; El Abderrahmani, Abdellatif; Satori, Khalid

    2017-09-01

    The purpose of the work presented in this paper is to describe new method of 3D reconstruction from one or more uncalibrated images. This method is based on two important concepts: geometric constraints and genetic algorithms (GAs). At first, we are going to discuss the combination between bundle adjustment and GAs that we have proposed in order to improve 3D reconstruction efficiency and success. We used GAs in order to improve fitness quality of initial values that are used in the optimization problem. It will increase surely convergence rate. Extracted geometric constraints are used first to obtain an estimated value of focal length that helps us in the initialization step. Matching homologous points and constraints is used to estimate the 3D model. In fact, our new method gives us a lot of advantages: reducing the estimated parameter number in optimization step, decreasing used image number, winning time and stabilizing good quality of 3D results. At the end, without any prior information about our 3D scene, we obtain an accurate calibration of the cameras, and a realistic 3D model that strictly respects the geometric constraints defined before in an easy way. Various data and examples will be used to highlight the efficiency and competitiveness of our present approach.

  18. The Effect of Underwater Imagery Radiometry on 3d Reconstruction and Orthoimagery

    Science.gov (United States)

    Agrafiotis, P.; Drakonakis, G. I.; Georgopoulos, A.; Skarlatos, D.

    2017-02-01

    The work presented in this paper investigates the effect of the radiometry of the underwater imagery on automating the 3D reconstruction and the produced orthoimagery. Main aim is to investigate whether pre-processing of the underwater imagery improves the 3D reconstruction using automated SfM - MVS software or not. Since the processing of images either separately or in batch is a time-consuming procedure, it is critical to determine the necessity of implementing colour correction and enhancement before the SfM - MVS procedure or directly to the final orthoimage when the orthoimagery is the deliverable. Two different test sites were used to capture imagery ensuring different environmental conditions, depth and complexity. Three different image correction methods are applied: A very simple automated method using Adobe Photoshop, a developed colour correction algorithm using the CLAHE (Zuiderveld, 1994) method and an implementation of the algorithm described in Bianco et al., (2015). The produced point clouds using the initial and the corrected imagery are then being compared and evaluated.

  19. A topology-based strategy for 3D reconstruction of complicated buildings

    Science.gov (United States)

    Shao, Zhenfeng; Li, Deren; Cheng, Qimin; Ye, Huanzhuo

    2004-04-01

    In this paper, a topology-based strategy for 3D reconstruction of complicated buildings from stereo image pair is put forward. It comes from our investigation on the applicability of topology analysis and a strongly topology-driven process that combines different levels of geometrical description with different levels of topological abstraction. The authors emphasize the topology-based strategy on different levels of geometrical description: Firstly a topology-based 3D data model is presented in which the topological relationships within a building or between geometrical objects are described implicitly or explicitly. Secondly based on description of vertexes level, interested vertexes are collected from stereo image pair and saturated attribute of each interior vertex is defined, furthermore an adjacency table is defined to store the connection attributes of verges automatically. Thirdly surfaces are looked on as polygons with closed verges on the basis of bi-directional querying of the adjacency table. Finally complicated buildings are described as graphs with interior and exterior topological attributes. Based on the strategy mentioned above, a software platform for 3D reconstruction of complicated buildings is built up. The efficiency of suggested method is examined through practical experiments.

  20. Toward 3D reconstruction of outdoor scenes using an MMW radar and a monocular vision sensor.

    Science.gov (United States)

    Natour, Ghina El; Ait-Aider, Omar; Rouveure, Raphael; Berry, François; Faure, Patrice

    2015-10-14

    In this paper, we introduce a geometric method for 3D reconstruction of the exterior environment using a panoramic microwave radar and a camera. We rely on the complementarity of these two sensors considering the robustness to the environmental conditions and depth detection ability of the radar, on the one hand, and the high spatial resolution of a vision sensor, on the other. Firstly, geometric modeling of each sensor and of the entire system is presented. Secondly, we address the global calibration problem, which consists of finding the exact transformation between the sensors' coordinate systems. Two implementation methods are proposed and compared, based on the optimization of a non-linear criterion obtained from a set of radar-to-image target correspondences. Unlike existing methods, no special configuration of the 3D points is required for calibration. This makes the methods flexible and easy to use by a non-expert operator. Finally, we present a very simple, yet robust 3D reconstruction method based on the sensors' geometry. This method enables one to reconstruct observed features in 3D using one acquisition (static sensor), which is not always met in the state of the art for outdoor scene reconstruction. The proposed methods have been validated with synthetic and real data.

  1. Toward 3D Reconstruction of Outdoor Scenes Using an MMW Radar and a Monocular Vision Sensor

    Directory of Open Access Journals (Sweden)

    Ghina El Natour

    2015-10-01

    Full Text Available In this paper, we introduce a geometric method for 3D reconstruction of the exterior environment using a panoramic microwave radar and a camera. We rely on the complementarity of these two sensors considering the robustness to the environmental conditions and depth detection ability of the radar, on the one hand, and the high spatial resolution of a vision sensor, on the other. Firstly, geometric modeling of each sensor and of the entire system is presented. Secondly, we address the global calibration problem, which consists of finding the exact transformation between the sensors’ coordinate systems. Two implementation methods are proposed and compared, based on the optimization of a non-linear criterion obtained from a set of radar-to-image target correspondences. Unlike existing methods, no special configuration of the 3D points is required for calibration. This makes the methods flexible and easy to use by a non-expert operator. Finally, we present a very simple, yet robust 3D reconstruction method based on the sensors’ geometry. This method enables one to reconstruct observed features in 3D using one acquisition (static sensor, which is not always met in the state of the art for outdoor scene reconstruction. The proposed methods have been validated with synthetic and real data.

  2. Enhanced imaging colonoscopy facilitates dense motion-based 3D reconstruction.

    Science.gov (United States)

    Alcantarilla, Pablo F; Bartoli, Adrien; Chadebecq, Francois; Tilmant, Christophe; Lepilliez, Vincent

    2013-01-01

    We propose a novel approach for estimating a dense 3D model of neoplasia in colonoscopy using enhanced imaging endoscopy modalities. Estimating a dense 3D model of neoplasia is important to make 3D measurements and to classify the superficial lesions in standard frameworks such as the Paris classification. However, it is challenging to obtain decent dense 3D models using computer vision techniques such as Structure-from-Motion due to the lack of texture in conventional (white light) colonoscopy. Therefore, we propose to use enhanced imaging endoscopy modalities such as Narrow Band Imaging and chromoendoscopy to facilitate the 3D reconstruction process. Thanks to the use of these enhanced endoscopy techniques, visualization is improved, resulting in more reliable feature tracks and 3D reconstruction results. We first build a sparse 3D model of neoplasia using Structure-from-Motion from enhanced endoscopy imagery. Then, the sparse reconstruction is densified using a Multi-View Stereo approach, and finally the dense 3D point cloud is transformed into a mesh by means of Poisson surface reconstruction. The obtained dense 3D models facilitate classification of neoplasia in the Paris classification, in which the 3D size and the shape of the neoplasia play a major role in the diagnosis.

  3. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.

    Science.gov (United States)

    Yu, Guimei; Yan, Rui; Zhang, Chuan; Mao, Chengde; Jiang, Wen

    2015-10-01

    Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Use of 3D reconstruction cloacagrams and 3D printing in cloacal malformations.

    Science.gov (United States)

    Ahn, Jennifer J; Shnorhavorian, Margarett; Amies Oelschlager, Anne-Marie E; Ripley, Beth; Shivaram, Giridhar M; Avansino, Jeffrey R; Merguerian, Paul A

    2017-08-01

    Cloacal anomalies are complex to manage, and the anatomy affects prognosis and management. Assessment historically includes examination under anesthesia, and genitography is often performed, but these do not consistently capture three-dimensional (3D) detail or spatial relationships of the anatomic structures. Three-dimensional reconstruction cloacagrams can provide a high level of detail including channel measurements and the level of the cloaca (3 cm), which typically determines the approach for surgical reconstruction and can impact long-term prognosis. Yet this imaging modality has not yet been directly compared with intra-operative or endoscopic findings. Our objective was to compare 3D reconstruction cloacagrams with endoscopic and intraoperative findings, as well as to describe the use of 3D printing to create models for surgical planning and education. An IRB-approved retrospective review of all cloaca patients seen by our multi-disciplinary program from 2014 to 2016 was performed. All patients underwent examination under anesthesia, endoscopy, 3D reconstruction cloacagram, and subsequent reconstructive surgery at a later date. Patient characteristics, intraoperative details, and measurements from endoscopy and cloacagram were reviewed and compared. One of the 3D cloacagrams was reformatted for 3D printing to create a model for surgical planning. Four patients were included for review, with the Figure illustrating 3D cloacagram results. Measurements of common channel length and urethral length were similar between modalities, particularly with confirming the level of cloaca. No patient experienced any complications or adverse effects from cloacagram or endoscopy. A model was successfully created from cloacagram images with the use of 3D printing technology. Accurate preoperative assessment for cloacal anomalies is important for counseling and surgical planning. Three-dimensional cloacagrams have been shown to yield a high level of anatomic detail. Here

  5. WASS: an open-source stereo processing pipeline for sea waves 3D reconstruction

    Science.gov (United States)

    Bergamasco, Filippo; Benetazzo, Alvise; Torsello, Andrea; Barbariol, Francesco; Carniel, Sandro; Sclavo, Mauro

    2017-04-01

    Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community. In fact, recent advances of both computer vision algorithms and CPU processing power can now allow the study of the spatio-temporal wave fields with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner so that the implementation of a 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well-tested software package that automates the steps from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS, a completely Open-Source stereo processing pipeline for sea waves 3D reconstruction, available at http://www.dais.unive.it/wass/. Our tool completely automates the recovery of dense point clouds from stereo images by providing three main functionalities. First, WASS can automatically recover the extrinsic parameters of the stereo rig (up to scale) so that no delicate calibration has to be performed on the field. Second, WASS implements a fast 3D dense stereo reconstruction procedure so that an accurate 3D point cloud can be computed from each stereo pair. We rely on the well-consolidated OpenCV library both for the image stereo rectification and disparity map recovery. Lastly, a set of 2D and 3D filtering techniques both on the disparity map and the produced point cloud are implemented to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface (examples are sun-glares, large white-capped areas, fog and water areosol, etc). Developed to be as fast as possible, WASS

  6. 3D reconstruction of a human heart fascicle using SurfDriver

    Science.gov (United States)

    Rader, Robert J.; Phillips, Steven J.; LaFollette, Paul S., Jr.

    2000-06-01

    The Temple University Medical School has a sequence of over 400 serial sections of adult normal ventricular human heart tissue, cut at 25 micrometer thickness. We used a Zeiss Ultraphot with a 4x planapo objective and a Pixera digital camera to make a series of 45 sequential montages to use in the 3D reconstruction of a fascicle (muscle bundle). We wrote custom software to merge 4 smaller image fields from each section into one composite image. We used SurfDriver software, developed by Scott Lozanoff of the University of Hawaii and David Moody of the University of Alberta, for registration, object boundary identification, and 3D surface reconstruction. We used an Epson Stylus Color 900 printer to get photo-quality prints. We describe the challenge and our solution to the following problems: image acquisition and digitization, image merge, alignment and registration, boundary identification, 3D surface reconstruction, 3D visualization and orientation, snapshot, and photo-quality prints.

  7. Streaming video-based 3D reconstruction method compatible with existing monoscopic and stereoscopic endoscopy systems

    Science.gov (United States)

    Bouma, Henri; van der Mark, Wannes; Eendebak, Pieter T.; Landsmeer, Sander H.; van Eekeren, Adam W. M.; ter Haar, Frank B.; Wieringa, F. Pieter; van Basten, Jean-Paul

    2012-06-01

    Compared to open surgery, minimal invasive surgery offers reduced trauma and faster recovery. However, lack of direct view limits space perception. Stereo-endoscopy improves depth perception, but is still restricted to the direct endoscopic field-of-view. We describe a novel technology that reconstructs 3D-panoramas from endoscopic video streams providing a much wider cumulative overview. The method is compatible with any endoscope. We demonstrate that it is possible to generate photorealistic 3D-environments from mono- and stereoscopic endoscopy. The resulting 3D-reconstructions can be directly applied in simulators and e-learning. Extended to real-time processing, the method looks promising for telesurgery or other remote vision-guided tasks.

  8. Interdisciplinary Data Fusion for Diachronic 3d Reconstruction of Historic Sites

    Science.gov (United States)

    Micoli, L. L.; Gonizzi Barsanti, S.; Guidi, G.

    2017-02-01

    In recent decades, 3D reconstruction has progressively become a tool to show archaeological and architectural monuments in their current state, presumed past aspect and to predict their future evolution. The 3D representations trough time can be useful in order to study and preserve the memory of Cultural Heritage and to plan maintenance and promotion of the historical sites. This paper represent a case study, at architectonic and urbanistic scale, based on methodological approach for CH time-varying representations proposed by JPI-CH European Project called Cultural Heritage Through Time (CHT2). The work is focused on the area of Milan Roman circus, relatively to which was conducted both a thorough philological research based on several sources and a 3D survey campaign of still accessible remains, aiming at obtaining the monumental representation of the area in 3 different ages.

  9. 3D reconstruction of the source and scale of buried young flood channels on Mars.

    Science.gov (United States)

    Morgan, Gareth A; Campbell, Bruce A; Carter, Lynn M; Plaut, Jeffrey J; Phillips, Roger J

    2013-05-03

    Outflow channels on Mars are interpreted as the product of gigantic floods due to the catastrophic eruption of groundwater that may also have initiated episodes of climate change. Marte Vallis, the largest of the young martian outflow channels (Mars hydrologic activity during a period otherwise considered to be cold and dry. Using data from the Shallow Radar sounder on the Mars Reconnaissance Orbiter, we present a three-dimensional (3D) reconstruction of buried channels on Mars and provide estimates of paleohydrologic parameters. Our work shows that Cerberus Fossae provided the waters that carved Marte Vallis, and it extended an additional 180 kilometers to the east before the emplacement of the younger lava flows. We identified two stages of channel incision and determined that channel depths were more than twice those of previous estimates.

  10. CUDA based Level Set Method for 3D Reconstruction of Fishes from Large Acoustic Data

    DEFF Research Database (Denmark)

    Sharma, Ojaswa; Anton, François

    2009-01-01

    identification is highly desirable for planning sustainable fisheries. Main hurdles in analysing acoustic images are the presence of speckle noise and the vast amount of acoustic data. This paper presents a level set formulation for simultaneous fish reconstruction and noise suppression from raw acoustic images......Acoustic images present views of underwater dynamics, even in high depths. With multi-beam echo sounders (SONARs), it is possible to capture series of 2D high resolution acoustic images. 3D reconstruction of the water column and subsequent estimation of fish abundance and fish species....... Despite the presence of speckle noise blobs, actual fish intensity values can be distinguished by extremely high values, varying exponentially from the background. Edge detection generally gives excessive false edges that are not reliable. Our approach to reconstruction is based on level set evolution...

  11. EFFECT OF DIGITAL FRINGE PROJECTION PARAMETERS ON 3D RECONSTRUCTION ACCURACY

    Directory of Open Access Journals (Sweden)

    A. Babaei

    2013-09-01

    This paper aims to evaluate different parameters which affect the accuracy of the final results. For this purpose, some test were designed and implemented. These tests assess the number of phase shifts, spatial frequency of the fringe pattern, light condition, noise level of images, and the color and material of target objects on the quality of resulted phase map. The evaluation results demonstrate that digital fringe projection method is capable of obtaining depth map of complicated object with high accuracy. The contrast test results showed that this method is able to work under different ambient light condition; although at places with high light condition will not work properly. The results of implementation on different objects with various materials, color and shapes demonstrate the high capability of this method of 3D reconstruction.

  12. 3D Reconstruction of Tree-Crown Based on the UAV Aerial Images

    Directory of Open Access Journals (Sweden)

    Chao Xu

    2015-01-01

    Full Text Available The algorithm for 3D reconstruction of tree-crown is presented with the UAV aerial images from a mountainous area in China. Considering the fact that the aerial images consist of little tree-crown texture and contour information, a feature area extraction method is proposed based on watershed segmentation, and the local area correlation coefficient is calculated to match the feature areas, in order to fully extract the characteristics that can reflect the structure of tree-crown. Then, the depth of feature points is calculated using the stereo vision theory. Finally, the L-system theory is applied to construct the 3D model of tree. The experiments are conducted with the tree-crown images from UAV aerial images manually. The experiment result showed that the method proposed in this paper can fully extract and match the feature points of tree-crown that can reconstruct the 3D model of the tree-crown correctly.

  13. A predictive model of asymmetric morphogenesis from 3D reconstructions of mouse heart looping dynamics

    Science.gov (United States)

    Le Garrec, Jean-François; Ivanovitch, Kenzo D; Raphaël, Etienne; Bangham, J Andrew; Torres, Miguel; Coen, Enrico; Mohun, Timothy J

    2017-01-01

    How left-right patterning drives asymmetric morphogenesis is unclear. Here, we have quantified shape changes during mouse heart looping, from 3D reconstructions by HREM. In combination with cell labelling and computer simulations, we propose a novel model of heart looping. Buckling, when the cardiac tube grows between fixed poles, is modulated by the progressive breakdown of the dorsal mesocardium. We have identified sequential left-right asymmetries at the poles, which bias the buckling in opposite directions, thus leading to a helical shape. Our predictive model is useful to explore the parameter space generating shape variations. The role of the dorsal mesocardium was validated in Shh-/- mutants, which recapitulate heart shape changes expected from a persistent dorsal mesocardium. Our computer and quantitative tools provide novel insight into the mechanism of heart looping and the contribution of different factors, beyond the simple description of looping direction. This is relevant to congenital heart defects. PMID:29179813

  14. Research on 3D reconstruction measurement and parameter of cavitation bubble based on stereo vision

    Science.gov (United States)

    Li, Shengyong; Ai, Xiaochuan; Wu, Ronghua; Cao, Jing

    2017-02-01

    The problems caused by the cavitation bubble and caused many adverse effects on the ship propeller, hydraulic machinery and equipment. In order to research the production mechanism of cavitation bubble under different conditions, cavitation bubble zone parameter fine measurement and analysis technology is indispensable, this paper adopts a non-contact measurement method of optical autonomous construction of binocular stereo vision measurement system according to the characteristics of cavitation bubble, the texture features are not clear, transparent and difficult to obtain, 3D imaging measurement of cavitation bubble using composite dynamic lighting, and 3D reconstruction of cavitation bubble region and obtained the characteristics of more accurate parameters, test results show that the cavitation bubble characteristics of the fine technology can obtain and analyze cavitation bubble region and instability.

  15. 3D reconstruction of digitized histological sections for vasculature quantification in the mouse hind limb

    Science.gov (United States)

    Xu, Yiwen; Pickering, J. Geoffrey; Nong, Zengxuan; Gibson, Eli; Ward, Aaron D.

    2014-03-01

    In contrast to imaging modalities such as magnetic resonance imaging and micro computed tomography, digital histology reveals multiple stained tissue features at high resolution (0.25μm/pixel). However, the two-dimensional (2D) nature of histology challenges three-dimensional (3D) quantification and visualization of the different tissue components, cellular structures, and subcellular elements. This limitation is particularly relevant to the vasculature, which has a complex and variable structure within tissues. The objective of this study was to perform a fully automated 3D reconstruction of histology tissue in the mouse hind limb preserving the accurate systemic orientation of the tissues, stained with hematoxylin and immunostained for smooth muscle α actin. We performed a 3D reconstruction using pairwise rigid registrations of 5μm thick, paraffin-embedded serial sections, digitized at 0.25μm/pixel. Each registration was performed using the iterative closest points algorithm on blood vessel landmarks. Landmarks were vessel centroids, determined according to a signed distance map of each pixel to a decision boundary in hue-saturation-value color space; this decision boundary was determined based on manual annotation of a separate training set. Cell nuclei were then automatically extracted and corresponded to refine the vessel landmark registration. Homologous nucleus landmark pairs appearing on not more than two adjacent slides were chosen to avoid registrations which force curved or non-sectionorthogonal structures to be straight and section-orthogonal. The median accumulated target registration errors ± interquartile ranges for the vessel landmark registration, and the nucleus landmark refinement were 43.4+/-42.8μm and 2.9+/-1.7μm, respectively (phistology imaging is feasible based on extracted vasculature and nuclei.

  16. Rapid 3D Reconstruction for Image Sequence Acquired from UAV Camera

    Directory of Open Access Journals (Sweden)

    Yufu Qu

    2018-01-01

    Full Text Available In order to reconstruct three-dimensional (3D structures from an image sequence captured by unmanned aerial vehicles’ camera (UAVs and improve the processing speed, we propose a rapid 3D reconstruction method that is based on an image queue, considering the continuity and relevance of UAV camera images. The proposed approach first compresses the feature points of each image into three principal component points by using the principal component analysis method. In order to select the key images suitable for 3D reconstruction, the principal component points are used to estimate the interrelationships between images. Second, these key images are inserted into a fixed-length image queue. The positions and orientations of the images are calculated, and the 3D coordinates of the feature points are estimated using weighted bundle adjustment. With this structural information, the depth maps of these images can be calculated. Next, we update the image queue by deleting some of the old images and inserting some new images into the queue, and a structural calculation of all the images can be performed by repeating the previous steps. Finally, a dense 3D point cloud can be obtained using the depth–map fusion method. The experimental results indicate that when the texture of the images is complex and the number of images exceeds 100, the proposed method can improve the calculation speed by more than a factor of four with almost no loss of precision. Furthermore, as the number of images increases, the improvement in the calculation speed will become more noticeable.

  17. Rapid 3D Reconstruction for Image Sequence Acquired from UAV Camera.

    Science.gov (United States)

    Qu, Yufu; Huang, Jianyu; Zhang, Xuan

    2018-01-14

    In order to reconstruct three-dimensional (3D) structures from an image sequence captured by unmanned aerial vehicles' camera (UAVs) and improve the processing speed, we propose a rapid 3D reconstruction method that is based on an image queue, considering the continuity and relevance of UAV camera images. The proposed approach first compresses the feature points of each image into three principal component points by using the principal component analysis method. In order to select the key images suitable for 3D reconstruction, the principal component points are used to estimate the interrelationships between images. Second, these key images are inserted into a fixed-length image queue. The positions and orientations of the images are calculated, and the 3D coordinates of the feature points are estimated using weighted bundle adjustment. With this structural information, the depth maps of these images can be calculated. Next, we update the image queue by deleting some of the old images and inserting some new images into the queue, and a structural calculation of all the images can be performed by repeating the previous steps. Finally, a dense 3D point cloud can be obtained using the depth-map fusion method. The experimental results indicate that when the texture of the images is complex and the number of images exceeds 100, the proposed method can improve the calculation speed by more than a factor of four with almost no loss of precision. Furthermore, as the number of images increases, the improvement in the calculation speed will become more noticeable.

  18. A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction.

    Science.gov (United States)

    Yin, Zhye; Zheng, Yili; Doerschuk, Peter C; Natarajan, Padmaja; Johnson, John E

    2003-01-01

    The scattering density of the virus is represented as a truncated weighted sum of orthonormal basis functions in spherical coordinates, where the angular dependence of each basis function has icosahedral symmetry. A statistical model of the image formation process is proposed and the maximum likelihood estimation method computed by an expectation-maximization algorithm is used to estimate the weights in the sum and thereby compute a 3-D reconstruction of the virus particle. If multiple types of virus particle are represented in the boxed images then multiple 3-D reconstructions are computed simultaneously without first requiring that the type of particle shown in each boxed image be determined. Examples of the procedure are described for viruses with known structure: (1). 3-D reconstruction of Flockhouse Virus from experimental images, (2). 3-D reconstruction of the capsid of Nudaurelia Omega Capensis Virus from synthetic images, and (3). 3-D reconstruction of both the capsid and the procapsid of Nudaurelia Omega Capensis Virus from a mixture of unclassified synthetic images.

  19. Implementation of a close range photogrammetric system for 3D reconstruction of a scoliotic torso

    Science.gov (United States)

    Detchev, Ivan Denislavov

    Scoliosis is a deformity of the human spine most commonly encountered with children. After being detected, periodic examinations via x-rays are traditionally used to measure its progression. However, due to the increased risk of cancer, a non-invasive and radiation-free scoliosis detection and progression monitoring methodology is needed. Quantifying the scoliotic deformity through the torso surface is a valid alternative, because of its high correlation with the internal spine curvature. This work proposes a low-cost multi-camera photogrammetric system for semi-automated 3D reconstruction of a torso surface with sub-millimetre level accuracy. The thesis describes the system design and calibration for optimal accuracy. It also covers the methodology behind the reconstruction and registration procedures. The experimental results include the complete reconstruction of a scoliotic torso mannequin. The final accuracy is evaluated through the goodness of fit between the reconstructed surface and a more accurate set of points measured by a coordinate measuring machine.

  20. Fine-Scale Population Estimation by 3D Reconstruction of Urban Residential Buildings

    Directory of Open Access Journals (Sweden)

    Shixin Wang

    2016-10-01

    Full Text Available Fine-scale population estimation is essential in emergency response and epidemiological applications as well as urban planning and management. However, representing populations in heterogeneous urban regions with a finer resolution is a challenge. This study aims to obtain fine-scale population distribution based on 3D reconstruction of urban residential buildings with morphological operations using optical high-resolution (HR images from the Chinese No. 3 Resources Satellite (ZY-3. Specifically, the research area was first divided into three categories when dasymetric mapping was taken into consideration. The results demonstrate that the morphological building index (MBI yielded better results than built-up presence index (PanTex in building detection, and the morphological shadow index (MSI outperformed color invariant indices (CIIT in shadow extraction and height retrieval. Building extraction and height retrieval were then combined to reconstruct 3D models and to estimate population. Final results show that this approach is effective in fine-scale population estimation, with a mean relative error of 16.46% and an overall Relative Total Absolute Error (RATE of 0.158. This study gives significant insights into fine-scale population estimation in complicated urban landscapes, when detailed 3D information of buildings is unavailable.

  1. Influence of Stereoscopic Camera System Alignment Error on the Accuracy of 3D Reconstruction

    Directory of Open Access Journals (Sweden)

    L. Bolecek

    2015-06-01

    Full Text Available The article deals with the influence of inaccurate rotation of cameras in camera system alignment on 3D reconstruction accuracy. The accuracy of the all three spatial coordinates is analyzed for two alignments (setups of 3D cameras. In the first setup, a 3D system with parallel optical axes of the cameras is analyzed. In this stereoscopic setup, the deterministic relations are derived by the trigonometry and basic stereoscopic formulas. The second alignment is a generalized setup with cameras in arbitrary positions. The analysis of the situation in the general setup is closely related with the influence of errors of the points' correspondences. Therefore the relation between errors of points' correspondences and reconstruction of the spatial position of the point was investigated. This issue is very complex. The worst case analysis was executed with the use of Monte Carlo method. The aim is to estimate a critical situation and the possible extent of these errors. Analysis of the generalized system and derived relations for normal system represent a significant improvement of the spatial coordinates accuracy analysis. A practical experiment was executed which confirmed the proposed relations.

  2. Processing of MRI images weighted in TOF for blood vessels analysis: 3-D reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez D, J.; Cordova F, T. [Universidad de Guanajuato, Campus Leon, Departamento de Ingenieria Fisica, Loma del Bosque No. 103, Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Cruz A, I., E-mail: hernandezdj.gto@gmail.com [CONACYT, Centro de Investigacion en Matematicas, A. C., Jalisco s/n, Col. Valenciana, 36000 Guanajuato, Gto. (Mexico)

    2015-10-15

    This paper presents a novel presents an approach based on differences of intensities for the identification of vascular structures in medical images from MRI studies of type time of flight method (TOF). The plating method hypothesis gave high intensities belonging to the vascular system image type TOF can be segmented by thresholding of the histogram. The enhanced vascular structures is performed using the filter Vesselness, upon completion of a decision based on fuzzy thresholding minimizes error in the selection of vascular structures. It will give a brief introduction to the vascular system problems and how the images have helped diagnosis, is summarized the physical history of the different imaging modalities and the evolution of digital images with computers. Segmentation and 3-D reconstruction became image type time of flight; these images are typically used in medical diagnosis of cerebrovascular diseases. The proposed method has less error in segmentation and reconstruction of volumes related to the vascular system, clear images and less noise compared with edge detection methods. (Author)

  3. Underwater 3D Reconstruction Based on Geometric Transformation of Sonar and Depth Information

    Science.gov (United States)

    Dong, Mingjie; Chou, Wusheng; Yao, Guodong

    2017-10-01

    3D reconstruction is of vital importance to detect and monitor the underwater environment. A method based on geometric transformation of mechanical scanning sonar and depth information is proposed, in which the point cloud data from sonar and depth gauge are acquired to reconstruct the underwater 3D environment. However, noise and interference can affect the measurement of sonar, and movement of sonar during measurement can lead to distortion of the received data. Meanwhile, translation and rotation movement of sonar head may happen when ROV dives which can lead to different body reference coordinates of different scanning. To solve this, pre-processing and motion compensation are implemented at first, and underwater matching correction algorithm is used to calculate the translation and rotation of the sonar head. Then the inverse operation is implemented to convert the scan data of every depth into the same coordinate reference system. Finally, surface reconstruction of point clouds from sonar the depth information are used to reconstruct underwater environment based on MLS (Moving Least Square Method) using PCL (Point Cloud Library). Water tank experiments verify the effectiveness of the proposed method.

  4. Orthotic Design through 3D Reconstruction: A Passive-Assistance Ankle–Foot Orthotic

    Directory of Open Access Journals (Sweden)

    A. L. Darling

    2006-01-01

    Full Text Available Current methods of designing and manufacturing custom orthotics include manual techniques such as casting a limb in plaster, making a plaster duplicate of the limb to be treated and forming a polymer orthotic directly onto the plaster model. Such techniques are usually accompanied with numerous postmanufacture alterations to adapt the orthotic for patient comfort. External modeling techniques rely heavily on the skill of the clinician, as the axes of rotation of any joint are partially specified by the skeletal structure and are not completely inferable from the skin, especially in cases where edema is present. Clinicians could benefit from a simultaneous view of external and skeletal patient-specific geometry. In addition to providing more information to clinicians, quantification of patient-specific data would allow rapid production of advanced orthotics, requiring machining rather than casting. This paper presents a supplemental method of orthotic design and fitting, through 3D reconstruction of medical imaging data to parameterise an orthotic design based on a major axis of rotation, shape of rigid components and placement of skin contact surfaces. An example of this design approach is shown in the design of an ankle–foot orthotic designed around the computed tomography data from the Visible Human Project.

  5. Sensor Fusion of Cameras and a Laser for City-Scale 3D Reconstruction

    Directory of Open Access Journals (Sweden)

    Yunsu Bok

    2014-11-01

    Full Text Available This paper presents a sensor fusion system of cameras and a 2D laser sensorfor large-scale 3D reconstruction. The proposed system is designed to capture data on afast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor,and they are synchronized by a hardware trigger. Reconstruction of 3D structures is doneby estimating frame-by-frame motion and accumulating vertical laser scans, as in previousworks. However, our approach does not assume near 2D motion, but estimates free motion(including absolute scale in 3D space using both laser data and image features. In orderto avoid the degeneration associated with typical three-point algorithms, we present a newalgorithm that selects 3D points from two frames captured by multiple cameras. The problemof error accumulation is solved by loop closing, not by GPS. The experimental resultsshow that the estimated path is successfully overlaid on the satellite images, such that thereconstruction result is very accurate.

  6. 3D reconstruction of synapses with deep learning based on EM Images

    Science.gov (United States)

    Xiao, Chi; Rao, Qiang; Zhang, Dandan; Chen, Xi; Han, Hua; Xie, Qiwei

    2017-03-01

    Recently, due to the rapid development of electron microscope (EM) with its high resolution, stacks delivered by EM can be used to analyze a variety of components that are critical to understand brain function. Since synaptic study is essential in neurobiology and can be analyzed by EM stacks, the automated routines for reconstruction of synapses based on EM Images can become a very useful tool for analyzing large volumes of brain tissue and providing the ability to understand the mechanism of brain. In this article, we propose a novel automated method to realize 3D reconstruction of synapses for Automated Tapecollecting Ultra Microtome Scanning Electron Microscopy (ATUM-SEM) with deep learning. Being different from other reconstruction algorithms, which employ classifier to segment synaptic clefts directly. We utilize deep learning method and segmentation algorithm to obtain synaptic clefts as well as promote the accuracy of reconstruction. The proposed method contains five parts: (1) using modified Moving Least Square (MLS) deformation algorithm and Scale Invariant Feature Transform (SIFT) features to register adjacent sections, (2) adopting Faster Region Convolutional Neural Networks (Faster R-CNN) algorithm to detect synapses, (3) utilizing screening method which takes context cues of synapses into consideration to reduce the false positive rate, (4) combining a practical morphology algorithm with a suitable fitting function to segment synaptic clefts and optimize the shape of them, (5) applying the plugin in FIJI to show the final 3D visualization of synapses. Experimental results on ATUM-SEM images demonstrate the effectiveness of our proposed method.

  7. Evaluating Dense 3d Reconstruction Software Packages for Oblique Monitoring of Crop Canopy Surface

    Science.gov (United States)

    Brocks, S.; Bareth, G.

    2016-06-01

    Crop Surface Models (CSMs) are 2.5D raster surfaces representing absolute plant canopy height. Using multiple CMSs generated from data acquired at multiple time steps, a crop surface monitoring is enabled. This makes it possible to monitor crop growth over time and can be used for monitoring in-field crop growth variability which is useful in the context of high-throughput phenotyping. This study aims to evaluate several software packages for dense 3D reconstruction from multiple overlapping RGB images on field and plot-scale. A summer barley field experiment located at the Campus Klein-Altendorf of University of Bonn was observed by acquiring stereo images from an oblique angle using consumer-grade smart cameras. Two such cameras were mounted at an elevation of 10 m and acquired images for a period of two months during the growing period of 2014. The field experiment consisted of nine barley cultivars that were cultivated in multiple repetitions and nitrogen treatments. Manual plant height measurements were carried out at four dates during the observation period. The software packages Agisoft PhotoScan, VisualSfM with CMVS/PMVS2 and SURE are investigated. The point clouds are georeferenced through a set of ground control points. Where adequate results are reached, a statistical analysis is performed.

  8. 3D reconstruction of a compressible flow by synchronized multi-camera BOS

    Science.gov (United States)

    Nicolas, F.; Donjat, D.; Léon, O.; Le Besnerais, G.; Champagnat, F.; Micheli, F.

    2017-05-01

    This paper investigates the application of a 3D density reconstruction from a limited number of background-oriented schlieren (BOS) images as recently proposed in Nicolas et al. (Exp Fluids 57(1):1-21, 2016), to the case of compressible flows, such as underexpanded jets. First, an optimization of a 2D BOS setup is conducted to mitigate the intense local blurs observed in raw BOS images and caused by strong density gradients present in the jets. It is demonstrated that a careful choice of experimental conditions enables one to obtain sharp deviation fields from 2D BOS images. Second, a 3DBOS experimental bench involving 12 synchronized cameras is specifically designed for the present study. It is shown that the 3DBOS method can provide physically consistent 3D reconstructions of instantaneous and mean density fields for various underexpanded jet flows issued into quiescent air. Finally, an analysis of the density structure of a moderately underexpanded jet is conducted through phase-averaging, highlighting the development of a large-scale coherent structure associated with a jet shear layer instability.

  9. A fast stereo matching algorithm for 3D reconstruction of internal organs in laparoscopic surgery

    Science.gov (United States)

    Okada, Yoshimichi; Koishi, Takeshi; Ushiki, Suguru; Nakaguchi, Toshiya; Tsumura, Norimichi; Miyake, Yoichi

    2008-03-01

    We propose a fast stereo matching algorithm for 3D reconstruction of internal organs using a stereoscopic laparoscope. Stoyanov et al. have proposed a technique for recovering the 3D depth of internal organs from images taken by a stereoscopic laparoscope. In their technique, the dense stereo correspondence is solved by registration of the entire image. However, the computational cost is very high because registration of the entire image requires multidimensional optimization. In this paper, we propose a new algorithm based on a local area registration method that requires only low-dimensional optimization for reduction of computational cost. We evaluated the computational cost of the proposed algorithm using a stereoscopic laparoscope. We also evaluated the accuracy of the proposed algorithm using three types of images of abdominal models taken by a 3D laser scanner. In the matching step, the size of the template used to calculate the correlation coefficient, on which the computational cost is strongly dependent, was reduced by a factor of 16 as compared with the conventional algorithm. On the other hand, the average depth errors were 4.68 mm, 7.18 mm, and 7.44 mm respectively, and accuracy was approximately as same as the conventional algorithm.

  10. 3D reconstruction of SEM images by use of optical photogrammetry software.

    Science.gov (United States)

    Eulitz, Mona; Reiss, Gebhard

    2015-08-01

    Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Melanoma Is Skin Deep: A 3D Reconstruction Technique for Computerized Dermoscopic Skin Lesion Classification.

    Science.gov (United States)

    Satheesha, T Y; Satyanarayana, D; Prasad, M N Giri; Dhruve, Kashyap D

    2017-01-01

    Melanoma mortality rates are the highest amongst skin cancer patients. Melanoma is life threating when it grows beyond the dermis of the skin. Hence, depth is an important factor to diagnose melanoma. This paper introduces a non-invasive computerized dermoscopy system that considers the estimated depth of skin lesions for diagnosis. A 3-D skin lesion reconstruction technique using the estimated depth obtained from regular dermoscopic images is presented. On basis of the 3-D reconstruction, depth and 3-D shape features are extracted. In addition to 3-D features, regular color, texture, and 2-D shape features are also extracted. Feature extraction is critical to achieve accurate results. Apart from melanoma, in-situ melanoma the proposed system is designed to diagnose basal cell carcinoma, blue nevus, dermatofibroma, haemangioma, seborrhoeic keratosis, and normal mole lesions. For experimental evaluations, the PH2, ISIC: Melanoma Project, and ATLAS dermoscopy data sets is considered. Different feature set combinations is considered and performance is evaluated. Significant performance improvement is reported the post inclusion of estimated depth and 3-D features. The good classification scores of sensitivity = 96%, specificity = 97% on PH2 data set and sensitivity = 98%, specificity = 99% on the ATLAS data set is achieved. Experiments conducted to estimate tumor depth from 3-D lesion reconstruction is presented. Experimental results achieved prove that the proposed computerized dermoscopy system is efficient and can be used to diagnose varied skin lesion dermoscopy images.

  12. 3D Reconstruction of Static Human Body with a Digital Camera

    Science.gov (United States)

    Remondino, Fabio

    2003-01-01

    Nowadays the interest in 3D reconstruction and modeling of real humans is one of the most challenging problems and a topic of great interest. The human models are used for movies, video games or ergonomics applications and they are usually created with 3D scanner devices. In this paper a new method to reconstruct the shape of a static human is presented. Our approach is based on photogrammetric techniques and uses a sequence of images acquired around a standing person with a digital still video camera or with a camcorder. First the images are calibrated and orientated using a bundle adjustment. After the establishment of a stable adjusted image block, an image matching process is performed between consecutive triplets of images. Finally the 3D coordinates of the matched points are computed with a mean accuracy of ca 2 mm by forward ray intersection. The obtained point cloud can then be triangulated to generate a surface model of the body or a virtual human model can be fitted to the recovered 3D data. Results of the 3D human point cloud with pixel color information are presented.

  13. EVALUATING DENSE 3D RECONSTRUCTION SOFTWARE PACKAGES FOR OBLIQUE MONITORING OF CROP CANOPY SURFACE

    Directory of Open Access Journals (Sweden)

    S. Brocks

    2016-06-01

    Full Text Available Crop Surface Models (CSMs are 2.5D raster surfaces representing absolute plant canopy height. Using multiple CMSs generated from data acquired at multiple time steps, a crop surface monitoring is enabled. This makes it possible to monitor crop growth over time and can be used for monitoring in-field crop growth variability which is useful in the context of high-throughput phenotyping. This study aims to evaluate several software packages for dense 3D reconstruction from multiple overlapping RGB images on field and plot-scale. A summer barley field experiment located at the Campus Klein-Altendorf of University of Bonn was observed by acquiring stereo images from an oblique angle using consumer-grade smart cameras. Two such cameras were mounted at an elevation of 10 m and acquired images for a period of two months during the growing period of 2014. The field experiment consisted of nine barley cultivars that were cultivated in multiple repetitions and nitrogen treatments. Manual plant height measurements were carried out at four dates during the observation period. The software packages Agisoft PhotoScan, VisualSfM with CMVS/PMVS2 and SURE are investigated. The point clouds are georeferenced through a set of ground control points. Where adequate results are reached, a statistical analysis is performed.

  14. Video Tracking dalam Digital Compositing untuk Paska Produksi Video

    Directory of Open Access Journals (Sweden)

    Ardiyan Ardiyan

    2012-04-01

    Full Text Available Video Tracking is one of the processes in video postproduction and motion picture digitally. The ability of video tracking method in the production is helpful to realize the concept of the visual. It is considered in the process of visual effects making. This paper presents how the tracking process and its benefits in visual needs, especially for video and motion picture production. Some of the things involved in the process of tracking such as failure to do so are made clear in this discussion. 

  15. Adaptive geometric tessellation for 3D reconstruction of anisotropically developing cells in multilayer tissues from sparse volumetric microscopy images.

    Directory of Open Access Journals (Sweden)

    Anirban Chakraborty

    Full Text Available The need for quantification of cell growth patterns in a multilayer, multi-cellular tissue necessitates the development of a 3D reconstruction technique that can estimate 3D shapes and sizes of individual cells from Confocal Microscopy (CLSM image slices. However, the current methods of 3D reconstruction using CLSM imaging require large number of image slices per cell. But, in case of Live Cell Imaging of an actively developing tissue, large depth resolution is not feasible in order to avoid damage to cells from prolonged exposure to laser radiation. In the present work, we have proposed an anisotropic Voronoi tessellation based 3D reconstruction framework for a tightly packed multilayer tissue with extreme z-sparsity (2-4 slices/cell and wide range of cell shapes and sizes. The proposed method, named as the 'Adaptive Quadratic Voronoi Tessellation' (AQVT, is capable of handling both the sparsity problem and the non-uniformity in cell shapes by estimating the tessellation parameters for each cell from the sparse data-points on its boundaries. We have tested the proposed 3D reconstruction method on time-lapse CLSM image stacks of the Arabidopsis Shoot Apical Meristem (SAM and have shown that the AQVT based reconstruction method can correctly estimate the 3D shapes of a large number of SAM cells.

  16. GOTHIC CHURCHES IN PARIS ST GERVAIS ET ST PROTAIS IMAGE MATCHING 3D RECONSTRUCTION TO UNDERSTAND THE VAULTS SYSTEM GEOMETRY

    Directory of Open Access Journals (Sweden)

    M. Capone

    2015-02-01

    benefits and the troubles. From a methodological point of view this is our workflow: - theoretical study about geometrical configuration of rib vault systems; - 3D model based on theoretical hypothesis about geometric definition of the vaults' form; - 3D model based on image matching 3D reconstruction methods; - comparison between 3D theoretical model and 3D model based on image matching;

  17. 3D RECONSTRUCTION FROM MULTI-VIEW MEDICAL X-RAY IMAGES – REVIEW AND EVALUATION OF EXISTING METHODS

    Directory of Open Access Journals (Sweden)

    S. Hosseinian

    2015-12-01

    Full Text Available The 3D concept is extremely important in clinical studies of human body. Accurate 3D models of bony structures are currently required in clinical routine for diagnosis, patient follow-up, surgical planning, computer assisted surgery and biomechanical applications. However, 3D conventional medical imaging techniques such as computed tomography (CT scan and magnetic resonance imaging (MRI have serious limitations such as using in non-weight-bearing positions, costs and high radiation dose(for CT. Therefore, 3D reconstruction methods from biplanar X-ray images have been taken into consideration as reliable alternative methods in order to achieve accurate 3D models with low dose radiation in weight-bearing positions. Different methods have been offered for 3D reconstruction from X-ray images using photogrammetry which should be assessed. In this paper, after demonstrating the principles of 3D reconstruction from X-ray images, different existing methods of 3D reconstruction of bony structures from radiographs are classified and evaluated with various metrics and their advantages and disadvantages are mentioned. Finally, a comparison has been done on the presented methods with respect to several metrics such as accuracy, reconstruction time and their applications. With regards to the research, each method has several advantages and disadvantages which should be considered for a specific application.

  18. Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education.

    Science.gov (United States)

    Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M

    2017-01-01

    Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce

  19. Rigorous accuracy assessment for 3D reconstruction using time-series Dual Fluoroscopy (DF) image pairs

    Science.gov (United States)

    Al-Durgham, Kaleel; Lichti, Derek D.; Kuntze, Gregor; Ronsky, Janet

    2017-06-01

    High-speed biplanar videoradiography, or clinically referred to as dual fluoroscopy (DF), imaging systems are being used increasingly for skeletal kinematics analysis. Typically, a DF system comprises two X-ray sources, two image intensifiers and two high-speed video cameras. The combination of these elements provides time-series image pairs of articulating bones of a joint, which permits the measurement of bony rotation and translation in 3D at high temporal resolution (e.g., 120-250 Hz). Assessment of the accuracy of 3D measurements derived from DF imaging has been the subject of recent research efforts by several groups, however with methodological limitations. This paper presents a novel and simple accuracy assessment procedure based on using precise photogrammetric tools. We address the fundamental photogrammetry principles for the accuracy evaluation of an imaging system. Bundle adjustment with selfcalibration is used for the estimation of the system parameters. The bundle adjustment calibration uses an appropriate sensor model and applies free-network constraints and relative orientation stability constraints for a precise estimation of the system parameters. A photogrammetric intersection of time-series image pairs is used for the 3D reconstruction of a rotating planar object. A point-based registration method is used to combine the 3D coordinates from the intersection and independently surveyed coordinates. The final DF accuracy measure is reported as the distance between 3D coordinates from image intersection and the independently surveyed coordinates. The accuracy assessment procedure is designed to evaluate the accuracy over the full DF image format and a wide range of object rotation. Experiment of reconstruction of a rotating planar object reported an average positional error of 0.44 +/- 0.2 mm in the derived 3D coordinates (minimum 0.05 and maximum 1.2 mm).

  20. Digital 3D reconstructions using histological serial sections of lung tissue including the alveolar capillary network.

    Science.gov (United States)

    Grothausmann, Roman; Knudsen, Lars; Ochs, Matthias; Mühlfeld, Christian

    2017-02-01

    Grothausmann R, Knudsen L, Ochs M, Mühlfeld C. Digital 3D reconstructions using histological serial sections of lung tissue including the alveolar capillary network. Am J Physiol Lung Cell Mol Physiol 312: L243-L257, 2017. First published December 2, 2016; doi:10.1152/ajplung.00326.2016-The alveolar capillary network (ACN) provides an enormously large surface area that is necessary for pulmonary gas exchange. Changes of the ACN during normal or pathological development or in pulmonary diseases are of great functional impact and warrant further analysis. Due to the complexity of the three-dimensional (3D) architecture of the ACN, 2D approaches are limited in providing a comprehensive impression of the characteristics of the normal ACN or the nature of its alterations. Stereological methods offer a quantitative way to assess the ACN in 3D in terms of capillary volume, surface area, or number but lack a 3D visualization to interpret the data. Hence, the necessity to visualize the ACN in 3D and to correlate this with data from the same set of data arises. Such an approach requires a large sample volume combined with a high resolution. Here, we present a technically simple and cost-efficient approach to create 3D representations of lung tissue ranging from bronchioles over alveolar ducts and alveoli up to the ACN from more than 1 mm sample extent to a resolution of less than 1 μm. The method is based on automated image acquisition of serially sectioned epoxy resin-embedded lung tissue fixed by vascular perfusion and subsequent automated digital reconstruction and analysis of the 3D data. This efficient method may help to better understand mechanisms of vascular development and pathology of the lung. Copyright © 2017 the American Physiological Society.

  1. Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education.

    Directory of Open Access Journals (Sweden)

    Hazel Raffan

    Full Text Available Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this

  2. [Measurement study of MDCT 3D reconstruction and microanatomy related to individual piston shaping on malleostapedotomy].

    Science.gov (United States)

    Ge, Runmei; Wu, Peina; Liu, Hui; Cui, Yong; Xu, Mimi; Wang, Xiaoqian; Fu, Min; Chen, Liangsi

    2009-01-01

    To study the management of basic parameters related to individual piston shaping on malleostapedotomy by MDST 3D reconstruction and microanatomy and to assess the accuracy of MDST method. Ten Chinese temporal bones without ear diseases were numbered randomly and scanned by GE Light Speed Ultra 64 rows of spiral CT. 3D structure of ossicular chain were reconstructed by MPR and VR methods in AW4. 1 workstation. Then measurements of distances between stapes head to stapes footplate (A line), and manubrium to stapes head (B line), and manubrium to stapes footplate (C line), angle between line A and line B (angle AB) are completed. After that, all samples of temporal bone were undergone canal wall down mastoidectomy under microscope and the relevant measurements were completed. The MPR and VR technique of MDCT reconstructed ossicular chain clearly, and revealed the spatial relationship between every structure stereoscopically. Respectively, lengths of A, B, C line by MDST and microanatomy are (3.42 +/- 0.86) mm and (3.60 +/- 0.94) mm, (3.42 +/- 0.80) mm and (2.96 +/- 0.42) mm, (5.86 +/- 0.60) mm and (6.22 +/- 1.10) mm, while angle AB (141.05 +/- 30.07) degrees and (144.57 +/- 41.86) degrees. There are no statistically significant differences between two groups (P>0.05). The MPR and VR technique of MDCT can clearly reconstructed the 3D shapes of the temporal bone and finish the exactly managements on A, B, C lines and AB angel which is crucial for shaping a individual piston on malleus-to-oval window surgery.

  3. Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction.

    Science.gov (United States)

    Mollink, J; van Baarsen, K M; Dederen, P J W C; Foxley, S; Miller, K L; Jbabdi, S; Slump, C H; Grotenhuis, J A; Kleinnijenhuis, M; van Cappellen van Walsum, A M

    2016-09-01

    Diffusion-weighted imaging (DWI) tractography is a technique with great potential to characterize the in vivo anatomical position and integrity of white matter tracts. Tractography, however, remains an estimation of white matter tracts, and false-positive and false-negative rates are not available. The goal of the present study was to compare postmortem tractography of the dentatorubrothalamic tract (DRTT) by its 3D histological reconstruction, to estimate the reliability of the tractography algorithm in this specific tract. Recent studies have shown that the cerebellum is involved in cognitive, language and emotional functions besides its role in motor control. However, the exact working mechanism of the cerebellum is still to be elucidated. As the DRTT is the main output tract it is of special interest for the neuroscience and clinical community. A postmortem human brain specimen was scanned on a 7T MRI scanner using a diffusion-weighted steady-state free precession sequence. Tractography was performed with PROBTRACKX. The specimen was subsequently serially sectioned and stained for myelin using a modified Heidenhain-Woelke staining. Image registration permitted the 3D reconstruction of the histological sections and comparison with MRI. The spatial concordance between the two modalities was evaluated using ROC analysis and a similarity index (SI). ROC curves showed a high sensitivity and specificity in general. Highest measures were observed in the superior cerebellar peduncle with an SI of 0.72. Less overlap was found in the decussation of the DRTT at the level of the mesencephalon. The study demonstrates high spatial accuracy of postmortem probabilistic tractography of the DRTT when compared to a 3D histological reconstruction. This gives hopeful prospect for studying structure-function correlations in patients with cerebellar disorders using tractography of the DRTT.

  4. 3D RECONSTRUCTION OF AN UNDERWATER ARCHAELOGICAL SITE: COMPARISON BETWEEN LOW COST CAMERAS

    Directory of Open Access Journals (Sweden)

    A. Capra

    2015-04-01

    Full Text Available The 3D reconstruction with a metric content of a submerged area, where objects and structures of archaeological interest are found, could play an important role in the research and study activities and even in the digitization of the cultural heritage. The reconstruction of 3D object, of interest for archaeologists, constitutes a starting point in the classification and description of object in digital format and for successive fruition by user after delivering through several media. The starting point is a metric evaluation of the site obtained with photogrammetric surveying and appropriate 3D restitution. The authors have been applying the underwater photogrammetric technique since several years using underwater digital cameras and, in this paper, digital low cost cameras (off-the-shelf. Results of tests made on submerged objects with three cameras are presented: © Canon Power Shot G12, © Intova Sport HD e © GoPro HERO 2. The experimentation had the goal to evaluate the precision in self-calibration procedures, essential for multimedia underwater photogrammetry, and to analyze the quality of 3D restitution. Precisions obtained in the calibration and orientation procedures was assessed by using three cameras, and an homogeneous set control points. Data were processed with © Agisoft Photoscan. Successively, 3D models were created and the comparison of the models derived from the use of different cameras was performed. Different potentialities of the used cameras are reported in the discussion section. The 3D restitution of objects and structures was integrated with sea bottom floor morphology in order to achieve a comprehensive description of the site. A possible methodology of survey and representation of submerged objects is therefore illustrated, considering an automatic and a semi-automatic approach.

  5. First report of fossil "keratose" demosponges in Phanerozoic carbonates: preservation and 3-D reconstruction.

    Science.gov (United States)

    Luo, Cui; Reitner, Joachim

    2014-06-01

    Fossil record of Phanerozoic non-spicular sponges, beside of being important with respect to the lineage evolution per se, could provide valuable references for the investigation of Precambrian ancestral animal fossils. However, although modern phylogenomic studies resolve non-spicular demosponges as the sister group of the remaining spiculate demosponges, the fossil record of the former is extremely sparse or unexplored compared to that of the latter; the Middle Cambrian Vauxiidae Walcott 1920, is the only confirmed fossil taxon of non-spicular demosponges. Here, we describe carbonate materials from Devonian (Upper Givetian to Lower Frasnian) bioherms of northern France and Triassic (Anisian) microbialites of Poland that most likely represent fossil remnants of keratose demosponges. These putative fossils of keratose demosponges are preserved as automicritic clumps. They are morphologically distinguishable from microbial fabrics but similar to other spiculate sponge fossils, except that the skeletal elements consist of fibrous networks instead of assembled spicules. Consistent with the immunological behavior of sponges, these fibrous skeletons often form a rim at the edge of the automicritic aggregate, separating the inner part of the aggregate from foreign objects. To confirm the architecture of these fibrous networks, two fossil specimens and a modern thorectid sponge for comparison were processed for three-dimensional (3-D) reconstruction using serial grinding tomography. The resulting fossil reconstructions are three-dimensionally anastomosing, like modern keratose demosponges, but their irregular and nonhierarchical meshes indicate a likely verongid affinity, although a precise taxonomic conclusion cannot be made based on the skeletal architecture alone. This study is a preliminary effort, but an important start to identify fossil non-spicular demosponges in carbonates and to re-evaluate their fossilization potential.

  6. MDCT in the assessment of laryngeal trauma: value of 2D multiplanar and 3D reconstructions.

    Science.gov (United States)

    Becker, Minerva; Duboé, Pier-Olivier; Platon, Alexandra; Kohler, Romain; Tasu, Jean-Pierre; Becker, Christoph D; Poletti, Pierre-Alexandre

    2013-10-01

    The purpose of this study was to analyze fracture patterns and related effects of laryngeal trauma and to assess the value of 2D multiplanar reformation (MPR) and 3D reconstruction. Among 4222 consecutively registered trauma patients who underwent emergency MDCT, 38 patients had presented with laryngeal trauma. Axial, 2D MPR, 3D volume-rendered, and virtual endoscopic images were analyzed retrospectively by two blinded observers according to predefined criteria. Laryngeal fractures, soft-tissue injuries, and airway compromise were evaluated and correlated with clinical, endoscopic, surgical, and follow-up findings. Fifty-nine fractures (37 thyroid, 13 cricoid, nine arytenoid) were present in 38 patients. They were isolated in 21 (55%) patients. The other 17 (45%) patients had additional injuries to the neck, face, brain, chest, or abdomen. Laryngeal fractures were bilateral in 31 (82%) patients and were associated with hyoid bone fractures in nine (24%) patients. Arytenoid luxation was present in eight cartilages. Axial imaging missed 7 of 59 (12%) laryngeal fractures, six of eight (75%) arytenoid luxations, and four of nine (44%) hyoid bone fractures. Additional 2D MPR imaging missed 5 of 59 (8%) laryngeal fractures, five of eight (62.5%) arytenoid luxations, and two of nine (22%) hyoid bone fractures, whereas 3D volume-rendered images depicted them all. Virtual endoscopy and 3D volume rendering added diagnostic accuracy with respect to the length, width, shape, and spatial orientation of fractures in 22 of 38 (58%) patients; arytenoid luxation in six of eight (75%) luxations; and the evaluation of airway narrowing in 19 of 38 (50%) patients. Three-dimensional volume rendering was not of additional value in evaluation of the cricoid cartilage. The use of 2D MPR and 3D volume rendering with or without virtual endoscopy improved assessment of thyroid and hyoid bone fractures, arytenoid luxations, and laryngotracheal narrowing, providing helpful data for optimal

  7. Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI.

    Science.gov (United States)

    Scott, Julia A; Habas, Piotr A; Kim, Kio; Rajagopalan, Vidya; Hamzelou, Kia S; Corbett-Detig, James M; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2011-08-01

    In the latter half of gestation (20-40 gestational weeks), human brain growth accelerates in conjunction with cortical folding and the deceleration of ventricular zone progenitor cell proliferation. These processes are reflected in changes in the volume of respective fetal tissue zones. Thus far, growth trajectories of the fetal tissue zones have been extracted primarily from 2D measurements on histological sections and magnetic resonance imaging (MRI). In this study, the volumes of major fetal zones-cortical plate (CP), subplate and intermediate zone (SP+IZ), germinal matrix (GMAT), deep gray nuclei (DG), and ventricles (VENT)--are calculated from automatic segmentation of motion-corrected, 3D reconstructed MRI. We analyzed 48 T2-weighted MRI scans from 39 normally developing fetuses in utero between 20.57 and 31.14 gestational weeks (GW). The supratentorial volume (STV) increased linearly at a rate of 15.22% per week. The SP+IZ (14.75% per week) and DG (15.56% per week) volumes increased at similar rates. The CP increased at a greater relative rate (18.00% per week), while the VENT (9.18% per week) changed more slowly. Therefore, CP increased as a fraction of STV and the VENT fraction declined. The total GMAT volume slightly increased then decreased after 25 GW. We did not detect volumetric sexual dimorphisms or total hemispheric volume asymmetries, which may emerge later in gestation. Further application of the automated fetal brain segmentation to later gestational ages will bridge the gap between volumetric studies of premature brain development and normal brain development in utero. Published by Elsevier Ltd.

  8. Multi-view 3D reconstruction with volumetric registration in a freehand ultrasound imaging system

    Science.gov (United States)

    Yu, Honggang; Pattichis, Marios S.; Goens, M. Beth

    2006-03-01

    In this paper, we describe a new freehand ultrasound imaging system for reconstructing the left ventricle from 2D echocardiography slices. An important contribution of the proposed system is its ability to reconstruct from multiple standard views. The multi-view reconstruction procedure results in significant reduction in reconstruction error over single view reconstructions. The system uses object-based 3D volumetric registration, allowing for arbitrary rigid object movements in inter-view acquisition. Furthermore, a new segmentation procedure that combines level set methods with gradient vector flow(GVF) is used for automatically segmenting the 2D ultrasound images, in which low level of contrast, high level of speckle noise, and weak boundaries are common. The new segmentation approach is shown to be robust to these artifacts and is found to converge to the boundary from a wider range of initial conditions than competitive methods. The proposed system has been validated on a physical, 3D ultrasound calibration phantom and evaluated on one actual cardiac echocardiography data set. In the phantom experiment, two calibrated volumetric egg-shape objects were scanned from the top and side windows and reconstructed using the new method. The volume error was measured to be less than 4%. In a real heart data set experiment, qualitative results of 3D surface reconstruction from parasternal and apical views appear significantly improved over single view reconstructions. The estimated volumes from the 3D reconstructions were also found to be in agreement with the manual clinical measurements from 2D slices. Further extension of this work is to compare the quantitative results with more accuracy MRI data.

  9. In-air versus underwater comparison of 3D reconstruction accuracy using action sport cameras.

    Science.gov (United States)

    Bernardina, Gustavo R D; Cerveri, Pietro; Barros, Ricardo M L; Marins, João C B; Silvatti, Amanda P

    2017-01-25

    Action sport cameras (ASC) have achieved a large consensus for recreational purposes due to ongoing cost decrease, image resolution and frame rate increase, along with plug-and-play usability. Consequently, they have been recently considered for sport gesture studies and quantitative athletic performance evaluation. In this paper, we evaluated the potential of two ASCs (GoPro Hero3+) for in-air (laboratory) and underwater (swimming pool) three-dimensional (3D) motion analysis as a function of different camera setups involving the acquisition frequency, image resolution and field of view. This is motivated by the fact that in swimming, movement cycles are characterized by underwater and in-air phases what imposes the technical challenge of having a split volume configuration: an underwater measurement volume observed by underwater cameras and an in-air measurement volume observed by in-air cameras. The reconstruction of whole swimming cycles requires thus merging of simultaneous measurements acquired in both volumes. Characterizing and optimizing the instrumental errors of such a configuration makes mandatory the assessment of the instrumental errors of both volumes. In order to calibrate the camera stereo pair, black spherical markers placed on two calibration tools, used both in-air and underwater, and a two-step nonlinear optimization were exploited. The 3D reconstruction accuracy of testing markers and the repeatability of the estimated camera parameters accounted for system performance. For both environments, statistical tests were focused on the comparison of the different camera configurations. Then, each camera configuration was compared across the two environments. In all assessed resolutions, and in both environments, the reconstruction error (true distance between the two testing markers) was less than 3mm and the error related to the working volume diagonal was in the range of 1:2000 (3×1.3×1.5m3) to 1:7000 (4.5×2.2×1.5m3) in agreement with the

  10. Analysis of bite marks in foodstuffs by computer tomography (cone beam CT)--3D reconstruction.

    Science.gov (United States)

    Marques, Jeidson; Musse, Jamilly; Caetano, Catarina; Corte-Real, Francisco; Corte-Real, Ana Teresa

    2013-12-01

    The use of three-dimensional (3D) analysis of forensic evidence is highlighted in comparison with traditional methods. This three-dimensional analysis is based on the registration of the surface from a bitten object. The authors propose to use Cone Beam Computed Tomography (CBCT), which is used in dental practice, in order to study the surface and interior of bitten objects and dental casts of suspects. In this study, CBCT is applied to the analysis of bite marks in foodstuffs, which may be found in a forensic case scenario. 6 different types of foodstuffs were used: chocolate, cheese, apple, chewing gum, pizza and tart (flaky pastry and custard). The food was bitten into and dental casts of the possible suspects were made. The dental casts and bitten objects were registered using an x-ray source and the CBCT equipment iCAT® (Pennsylvania, EUA). The software InVivo5® (Anatomage Inc, EUA) was used to visualize and analyze the tomographic slices and 3D reconstructions of the objects. For each material an estimate of its density was assessed by two methods: HU values and specific gravity. All the used materials were successfully reconstructed as good quality 3D images. The relative densities of the materials in study were compared. Amongst the foodstuffs, the chocolate had the highest density (median value 100.5 HU and 1,36 g/cm(3)), while the pizza showed to have the lowest (median value -775 HU and 0,39 g/cm(3)), on both scales. Through tomographic slices and three-dimensional reconstructions it was possible to perform the metric analysis of the bite marks in all the foodstuffs, except for the pizza. These measurements could also be obtained from the dental casts. The depth of the bite mark was also successfully determined in all the foodstuffs except for the pizza. Cone Beam Computed Tomography has the potential to become an important tool for forensic sciences, namely for the registration and analysis of bite marks in foodstuffs that may be found in a crime

  11. Middle and inner ear modelling: from microCT images to 3D reconstruction and coupling of models.

    Science.gov (United States)

    Tachos, N S; Sakellarios, A I; Rigas, G; Isailovic, V; Ni, G; Bohnke, F; Filipovic, N; Bibas, T; Fotiadis, D I

    2016-08-01

    We present finite element (FE) modeling approaches of ear mechanics including 3-dimensional (3D) reconstruction of the human middle and inner ear. Specifically, we demonstrate a semi-automatic methodology for the 3D reconstruction of the inner ear structures, a FE harmonic response model of the middle ear to predict the stapes footplate frequency response, a 2D FE slice model of the cochlea for the coupled response at the micromechanical level for either acoustic or electrical excitation and a coupled FE middle ear model with a simplified cochlea box model to simulate the basilar membrane velocity in response to acoustic excitation. The proposed methodologies are validated against experimental and literature data and the results are in good agreement.

  12. THE COMPLETE VIRTUAL 3D RECONSTRUCTION OF THE EAST PEDIMENT OF THE TEMPLE OF ZEUS AT OLYMPIA

    OpenAIRE

    Patay-Horváth, A.

    2012-01-01

    The arrangement of the five central figures of the east pediment of the temple of Zeus at Olympia has been the subject of scholarly debates since the discovery of the fragments more than a century ago. In theory, there are four substantially different arrangements, all of which have already been selected by certain scholars for various aesthetic, technical and other considerations. The present project tries to approach this controversy in a new way, by producing a virtual 3D reconstruction of...

  13. Breast volume estimation from systematic series of CT scans using the Cavalieri principle and 3D reconstruction.

    Science.gov (United States)

    Erić, Mirela; Anderla, Andraš; Stefanović, Darko; Drapšin, Miodrag

    2014-01-01

    Preoperative breast volume estimation is very important for the success of the breast surgery. In the present study, two different breast volume determination methods, Cavalieri principle and 3D reconstruction were compared. Consecutive sections were taken in slice thickness of 5 mm. Every 2nd breast section in a set of consecutive sections was selected. We marked breast tissue with blue line on each selected section, and so prepared CT scans used for breast volume estimation. The volumes of the 60 breasts were estimated using the Cavalieri principle and 3D reconstruction. The mean breast volume value was established to be 467.79 ± 188.90 cm(3) with Cavalieri method and 465.91 ± 191.41 cm(3) with 3D reconstruction. The mean CE for the estimates in this study was calculated as 0.25%. Skin-sparing volume was about 91.64% of the whole breast volume. Both methods are very accurate and have a strong linear association. Our results suggest that the calculation of breast volume or its part in vivo from systematic series of CT scans using the Cavalieri principle or 3D breast reconstruction is accurate enough to have a significant clinical benefit in planning reconstructive breast surgery. These methods can help the surgeon guide the choice of the most appropriate implant or/and flap preoperatively. Copyright © 2014 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

  14. Gothic Churches in Paris ST Gervais et ST Protais Image Matching 3d Reconstruction to Understand the Vaults System Geometry

    Science.gov (United States)

    Capone, M.; Campi, M.; Catuogno, R.

    2015-02-01

    This paper is part of a research about ribbed vaults systems in French Gothic Cathedrals. Our goal is to compare some different gothic cathedrals to understand the complex geometry of the ribbed vaults. The survey isn't the main objective but it is the way to verify the theoretical hypotheses about geometric configuration of the flamboyant churches in Paris. The survey method's choice generally depends on the goal; in this case we had to study many churches in a short time, so we chose 3D reconstruction method based on image dense stereo matching. This method allowed us to obtain the necessary information to our study without bringing special equipment, such as the laser scanner. The goal of this paper is to test image matching 3D reconstruction method in relation to some particular study cases and to show the benefits and the troubles. From a methodological point of view this is our workflow: - theoretical study about geometrical configuration of rib vault systems; - 3D model based on theoretical hypothesis about geometric definition of the vaults' form; - 3D model based on image matching 3D reconstruction methods; - comparison between 3D theoretical model and 3D model based on image matching;

  15. The Performance Evaluation of Multi-Image 3d Reconstruction Software with Different Sensors

    Science.gov (United States)

    Mousavi, V.; Khosravi, M.; Ahmadi, M.; Noori, N.; Naveh, A. Hosseini; Varshosaz, M.

    2015-12-01

    Today, multi-image 3D reconstruction is an active research field and generating three dimensional model of the objects is one the most discussed issues in Photogrammetry and Computer Vision that can be accomplished using range-based or image-based methods. Very accurate and dense point clouds generated by range-based methods such as structured light systems and laser scanners has introduced them as reliable tools in the industry. Image-based 3D digitization methodologies offer the option of reconstructing an object by a set of unordered images that depict it from different viewpoints. As their hardware requirements are narrowed down to a digital camera and a computer system, they compose an attractive 3D digitization approach, consequently, although range-based methods are generally very accurate, image-based methods are low-cost and can be easily used by non-professional users. One of the factors affecting the accuracy of the obtained model in image-based methods is the software and algorithm used to generate three dimensional model. These algorithms are provided in the form of commercial software, open source and web-based services. Another important factor in the accuracy of the obtained model is the type of sensor used. Due to availability of mobile sensors to the public, popularity of professional sensors and the advent of stereo sensors, a comparison of these three sensors plays an effective role in evaluating and finding the optimized method to generate three-dimensional models. Lots of research has been accomplished to identify a suitable software and algorithm to achieve an accurate and complete model, however little attention is paid to the type of sensors used and its effects on the quality of the final model. The purpose of this paper is deliberation and the introduction of an appropriate combination of a sensor and software to provide a complete model with the highest accuracy. To do this, different software, used in previous studies, were compared and

  16. A new multiresolution method applied to the 3D reconstruction of small bodies

    Science.gov (United States)

    Capanna, C.; Jorda, L.; Lamy, P. L.; Gesquiere, G.

    2012-12-01

    model of its surface and compare it with models obtained with the SPG and SPC methods. We finally illustrate the practical interest of our approach in geomorphological studies through an analysis of depth to diameter ratio of several craters and topographic properties of other features. Botsch, M., et al., "Geometric modeling based on polygonal meshes," Proc. ACM SIGGRAPH Course Notes, 2007 Capanna, C., et al.: 3D Reconstruction of small solar system bodies using photoclinometry by deformation, IADIS International Journal on Computer Science and Information Systems, in press, 2012. Gaskell, R. W., et al.: Characterizing and navigating small bodies with imaging data, Meteoritics and Planetary Science, vol 43, p. 1049, 2008. Jorda, L., et al: Asteroid (2867) Steins: Shape, Topography and Global Physical Properties from OSIRIS observations, Icarus, in press, 2012. Oberst, J., et al.: The nucleus of Comet Borrelly: a study of morphology and surface brightness, Icarus, vol. 167, 2004. Preusker, F., et al.: The northern hemisphere of asteroid 21 Lutetia topography and orthoimages from Rosetta OSIRIS NAC image data, Planetary and Space Science, vol. 66, p. 54-63, 2012. Thomas, P. C., et al.: The shape, topography, and geology of Tempel 1 from Deep Impact observations, Icarus, vol. 187, Issue 1, p. 4-15, 2007

  17. Video tracking analysis of behavioral patterns during estrus in goats

    Science.gov (United States)

    ENDO, Natsumi; RAHAYU, Larasati Puji; ARAKAWA, Toshiya; TANAKA, Tomomi

    2015-01-01

    Here, we report a new method for measuring behavioral patterns during estrus in goats based on video tracking analysis. Data were collected from cycling goats, which were in estrus (n = 8) or not in estrus (n = 8). An observation pen (2.5 m × 2.5 m) was set up in the corner of the female paddock with one side adjacent to a male paddock. The positions and movements of goats were tracked every 0.5 sec for 10 min by using a video tracking software, and the trajectory data were used for the analysis. There were no significant differences in the durations of standing and walking or the total length of movement. However, the number of approaches to a male and the duration of staying near the male were higher in goats in estrus than in goats not in estrus. The proposed evaluation method may be suitable for detailed monitoring of behavioral changes during estrus in goats. PMID:26560676

  18. A quick guide to video-tracking birds

    OpenAIRE

    Bluff, Lucas A; Rutz, Christian

    2008-01-01

    Video tracking is a powerful new tool for studying natural undisturbed behaviour in a wide range of birds, mammals and reptiles. Using integrated animal-borne video tags, video footage and positional data are recorded simultaneously from wild free-ranging animals. At the analysis stage, video scenes are linked to radio fixes, yielding an animal's eye view of resource use and social interactions along a known movement trajectory. Here, we provide a brief description of our basic equipment and ...

  19. Differential geometry measures of nonlinearity for the video tracking problem

    Science.gov (United States)

    Mallick, Mahendra; La Scala, Barbara F.

    2006-05-01

    Tracking people and vehicles in an urban environment using video cameras onboard unmanned aerial vehicles has drawn a great deal of interest in recent years due to their low cost compared with expensive radar systems. Video cameras onboard a number of small UAVs can provide inexpensive, effective, and highly flexible airborne intelligence, surveillance and reconnaissance as well as situational awareness functions. The perspective transformation is a commonly used general measurement model for the video camera when the variation in terrain height in the object scene is not negligible and the distance between the camera and the scene is not large. The perspective transformation is a nonlinear function of the object position. Most video tracking applications use a nearly constant velocity model (NCVM) of the target in the local horizontal plane. The filtering problem is nonlinear due to nonlinearity in the measurement model. In this paper, we present algorithms for quantifying the degree of nonlinearity (DoN) by calculating the differential geometry based parameter-effects curvature and intrinsic curvature measures of nonlinearity for the video tracking problem. We use the constant velocity model (CVM) of a target in 2D with simulated video measurements in the image plane. We have presented preliminary results using 200 Monte Carlo simulations and future work will focus on detailed numerical results. Our results for the chosen video tracking problem indicate that the DoN is low and therefore, we expect the extended Kalman filter to be reasonable choice.

  20. Workflows and the Role of Images for Virtual 3d Reconstruction of no Longer Extant Historic Objects

    Science.gov (United States)

    Münster, S.

    2013-07-01

    3D reconstruction technologies have gained importance as tools for the research and visualization of no longer extant historic objects during the last decade. Within such reconstruction processes, visual media assumes several important roles: as the most important sources especially for a reconstruction of no longer extant objects, as a tool for communication and cooperation within the production process, as well as for a communication and visualization of results. While there are many discourses about theoretical issues of depiction as sources and as visualization outcomes of such projects, there is no systematic research about the importance of depiction during a 3D reconstruction process and based on empirical findings. Moreover, from a methodological perspective, it would be necessary to understand which role visual media plays during the production process and how it is affected by disciplinary boundaries and challenges specific to historic topics. Research includes an analysis of published work and case studies investigating reconstruction projects. This study uses methods taken from social sciences to gain a grounded view of how production processes would take place in practice and which functions and roles images would play within them. For the investigation of these topics, a content analysis of 452 conference proceedings and journal articles related to 3D reconstruction modeling in the field of humanities has been completed. Most of the projects described in those publications dealt with data acquisition and model building for existing objects. Only a small number of projects focused on structures that no longer or never existed physically. Especially that type of project seems to be interesting for a study of the importance of pictures as sources and as tools for interdisciplinary cooperation during the production process. In the course of the examination the authors of this paper applied a qualitative content analysis for a sample of 26 previously

  1. The 3D reconstruction of greenhouse tomato plant based on real organ samples and parametric L-system

    Science.gov (United States)

    Xin, Longjiao; Xu, Lihong; Li, Dawei; Fu, Daichang

    2014-04-01

    In this paper, a fast and effective 3D reconstruction method for the growth of greenhouse tomato plant is proposed by using real organ samples and a parametric L-system. By analyzing the stereo structure of tomato plant, we extracts rules and parameters to assemble an L-system that is able to simulate the plant growth, and then the components of the L-system are translated into plant organ entities via image processing and computer graphics techniques. This method can efficiently and faithfully simulate the growing process of the greenhouse tomato plant.

  2. A Post-Rectification Approach of Depth Images of Kinect v2 for 3D Reconstruction of Indoor Scenes

    Directory of Open Access Journals (Sweden)

    Jichao Jiao

    2017-11-01

    Full Text Available 3D reconstruction of indoor scenes is a hot research topic in computer vision. Reconstructing fast, low-cost, and accurate dense 3D maps of indoor scenes have applications in indoor robot positioning, navigation, and semantic mapping. In other studies, the Microsoft Kinect for Windows v2 (Kinect v2 is utilized to complete this task, however, the accuracy and precision of depth information and the accuracy of correspondence between the RGB and depth (RGB-D images still remain to be improved. In this paper, we propose a post-rectification approach of the depth images to improve the accuracy and precision of depth information. Firstly, we calibrate the Kinect v2 with a planar checkerboard pattern. Secondly, we propose a post-rectification approach of the depth images according to the reflectivity-related depth error. Finally, we conduct tests to evaluate this post-rectification approach from the perspectives of accuracy and precision. In order to validate the effect of our post-rectification approach, we apply it to RGB-D simultaneous localization and mapping (SLAM in an indoor environment. Experimental results show that once our post-rectification approach is employed, the RGB-D SLAM system can perform a more accurate and better visual effect 3D reconstruction of indoor scenes than other state-of-the-art methods.

  3. See-through Detection and 3D Reconstruction Using Terahertz Leaky-Wave Radar Based on Sparse Signal Processing

    Science.gov (United States)

    Murata, Koji; Murano, Kosuke; Watanabe, Issei; Kasamatsu, Akifumi; Tanaka, Toshiyuki; Monnai, Yasuaki

    2018-02-01

    We experimentally demonstrate see-through detection and 3D reconstruction using terahertz leaky-wave radar based on sparse signal processing. The application of terahertz waves to radar has received increasing attention in recent years for its potential to high-resolution and see-through detection. Among others, the implementation using a leaky-wave antenna is promising for compact system integration with beam steering capability based on frequency sweep. However, the use of a leaky-wave antenna poses a challenge on signal processing. Since a leaky-wave antenna combines the entire signal captured by each part of the aperture into a single output, the conventional array signal processing assuming access to a respective antenna element is not applicable. In this paper, we apply an iterative recovery algorithm "CoSaMP" to signals acquired with terahertz leaky-wave radar for clutter mitigation and aperture synthesis. We firstly demonstrate see-through detection of target location even when the radar is covered with an opaque screen, and therefore, the radar signal is disturbed by clutter. Furthermore, leveraging the robustness of the algorithm against noise, we also demonstrate 3D reconstruction of distributed targets by synthesizing signals collected from different orientations. The proposed approach will contribute to the smart implementation of terahertz leaky-wave radar.

  4. Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

    Energy Technology Data Exchange (ETDEWEB)

    Chen Yong [College of Medicine, University of Illinois, Chicago, IL 60612 (United States) and Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China)]. E-mail: drychen@uic.edu; Cai Jiye [Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China)]. E-mail: tjycai@jnu.edu.cn; Zhao Tao [Department of Chemistry, Jinan University, Shipai Street, Guangzhou 510632 (China); Wang Chenxi [Department of Physics, Jinan University, Guangzhou 510632 (China); Dong Shuo [Department of BME, Capital University of Medical Sciences, Beijing (China); Luo Shuqian [Department of BME, Capital University of Medical Sciences, Beijing (China); Chen, Zheng W. [College of Medicine, University of Illinois, Chicago, IL 60612 (United States); Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States)

    2005-06-15

    The thin sectioning has been widely applied in electron microscopy (EM), and successfully used for an in situ observation of inner ultrastructure of cells. This powerful technique has recently been extended to the research field of atomic force microscopy (AFM). However, there have been no reports describing AFM imaging of serial thin sections and three-dimensional (3-D) reconstruction of cells and their inner structures. In the present study, we used AFM to scan serial thin sections approximately 60 nm thick of a mouse embryonic stem (ES) cell, and to observe the in situ inner ultrastructure including cell membrane, cytoplasm, mitochondria, nucleus membrane, and linear chromatin. The high-magnification AFM imaging of single mitochondria clearly demonstrated the outer membrane, inner boundary membrane and cristal membrane of mitochondria in the cellular compartment. Importantly, AFM imaging on six serial thin sections of a single mouse ES cell showed that mitochondria underwent sequential changes in the number, morphology and distribution. These nanoscale images allowed us to perform 3-D surface reconstruction of interested interior structures in cells. Based on the serial in situ images, 3-D models of morphological characteristics, numbers and distributions of interior structures of the single ES cells were validated and reconstructed. Our results suggest that the combined AFM and serial-thin-section technique is useful for the nanoscale imaging and 3-D reconstruction of single cells and their inner structures. This technique may facilitate studies of proliferating and differentiating stages of stem cells or somatic cells at a nanoscale.

  5. High-resolution 3D reconstruction of microtubule structures by quantitative multi-angle total internal reflection fluorescence microscopy

    Science.gov (United States)

    Jin, Luhong; Wu, Jian; Xiu, Peng; Fan, Jiannan; Hu, Miao; Kuang, Cuifang; Xu, Yingke; Zheng, Xiaoxiang; Liu, Xu

    2017-07-01

    Total internal reflection fluorescence microscopy (TIRFM) has been widely used in biomedical research to visualize cellular processes near the cell surface. In this study, a novel multi-angle ring-illuminated TIRFM system, equipped with two galvo mirrors that are on conjugate plan of a 4f optical system was developed. Multi-angle TIRFM generates images with different penetration depths through the controlled variation of the incident angle of illuminating laser. We presented a method to perform three-dimensional (3-D) reconstruction of microtubules from multi-angle TIRFM images. The performance of our method was validated in simulated microtubules with variable signal-to-noise ratios (SNR) and the axial resolution and accuracy of reconstruction were evaluated in selecting different numbers of illumination angles or in different SNR conditions. In U373 cells, we reconstructed the 3-D localization of microtubules near the cell surface with high resolution using over a hundred different angles. Theoretically, the presented TIRFM setup and 3-D reconstruction method can achieve 40 nm axial resolution in experimental conditions where SNR is as low as 2, with 35 different illumination angles. Moreover, our system and reconstruction method have the potential to be used in live cells to track membrane dynamics in 3-D.

  6. Online C-arm calibration using a marked guide wire for 3D reconstruction of pulmonary arteries

    Science.gov (United States)

    Vachon, Étienne; Miró, Joaquim; Duong, Luc

    2017-03-01

    3D reconstruction of vessels from 2D X-ray angiography is highly relevant to improve the visualization and the assessment of vascular structures such as pulmonary arteries by interventional cardiologists. However, to ensure a robust and accurate reconstruction, C-arm gantry parameters must be properly calibrated to provide clinically acceptable results. Calibration procedures often rely on calibration objects and complex protocol which is not adapted to an intervention context. In this study, a novel calibration algorithm for C-arm gantry is presented using the instrumentation such as catheters and guide wire. This ensures the availability of a minimum set of correspondences and implies minimal changes to the clinical workflow. The method was evaluated on simulated data and on retrospective patient datasets. Experimental results on simulated datasets demonstrate a calibration that allows a 3D reconstruction of the guide wire up to a geometric transformation. Experiments with patients datasets show a significant decrease of the retro projection error to 0.17 mm 2D RMS. Consequently, such procedure might contribute to identify any calibration drift during the intervention.

  7. Atomic force microscopy imaging and 3-D reconstructions of serial thin sections of a single cell and its interior structures

    Science.gov (United States)

    Chen, Yong; Cai, Jiye; Zhao, Tao; Wang, Chenxi; Dong, Shuo; Luo, Shuqian; Chen, Zheng W.

    2010-01-01

    The thin sectioning has been widely applied in electron microscopy (EM), and successfully used for an in situ observation of inner ultrastructure of cells. This powerful technique has recently been extended to the research field of atomic force microscopy (AFM). However, there have been no reports describing AFM imaging of serial thin sections and three-dimensional (3-D) reconstruction of cells and their inner structures. In the present study, we used AFM to scan serial thin sections approximately 60nm thick of a mouse embryonic stem (ES) cell, and to observe the in situ inner ultrastructure including cell membrane, cytoplasm, mitochondria, nucleus membrane, and linear chromatin. The high-magnification AFM imaging of single mitochondria clearly demonstrated the outer membrane, inner boundary membrane and cristal membrane of mitochondria in the cellular compartment. Importantly, AFM imaging on six serial thin sections of a single mouse ES cell showed that mitochondria underwent sequential changes in the number, morphology and distribution. These nanoscale images allowed us to perform 3-D surface reconstruction of interested interior structures in cells. Based on the serial in situ images, 3-D models of morphological characteristics, numbers and distributions of interior structures of the single ES cells were validated and reconstructed. Our results suggest that the combined AFM and serial-thin-section technique is useful for the nanoscale imaging and 3-D reconstruction of single cells and their inner structures. This technique may facilitate studies of proliferating and differentiating stages of stem cells or somatic cells at a nanoscale. PMID:15850704

  8. Validation of PSF-based 3D reconstruction for myocardial blood flow measurements with Rb-82 PET

    DEFF Research Database (Denmark)

    Tolbod, Lars Poulsen; Christensen, Nana Louise; Møller, Lone W.

    Aim:The use of PSF-based 3D reconstruction algorithms (PSF) is desirable in most clinical PET-exams due to their superior image quality. Rb-82 cardiac PET is inherently noisy due to short half-life and prompt gammas and would presumably benefit from PSF. However, the quantitative behavior of PSF...... is not well validated and problems with both edge-effects and unphysical contrast-recovery have been reported.1 In this study, we compare myocardial blood flow (MBF) and coronary flow reserve (CFR) obtained using GEs implementation of PSF, SharpIR, with the conventional method for reconstruction of dynamic...... images, filtered backprojection (FBP). Furthermore, since myocardial segmentation might be affected by image quality, two different approaches to segmentation implemented in standard software (Carimas (Turku PET Centre) and QPET (Cedar Sinai)) are utilized. Method:14 dynamic rest-stress Rb-82 patient...

  9. GPU-enabled FREALIGN: accelerating single particle 3D reconstruction and refinement in Fourier space on graphics processors.

    Science.gov (United States)

    Li, Xueming; Grigorieff, Nikolaus; Cheng, Yifan

    2010-12-01

    Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we modified the computer program, FREALIGN, to execute the computationally most intensive procedures on Graphics Processing Units (GPUs). Using the modified program, the execution speed increased between 10 and 240-fold depending on the task performed by FREALIGN. Here we report the steps necessary to parallelize critical FREALIGN subroutines and evaluate its performance on computers with multiple GPUs. Copyright © 2010 Elsevier Inc. All rights reserved.

  10. Investigation of orientation inhomogeneities in polycrystalline materials by means of FEG-SEM, FIB, EBSD and 3-D reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Kantor, M. M., E-mail: Kantor@imet.ac.ru; Vorkachev, K. G., E-mail: KGV@imet.ac.ru [A.A. Baikov Institute of Metallurgy and Materials Science RAS, Moscow, 119991, Leninskiy pr-t 49 (Russian Federation)

    2016-06-17

    The efficiency of different techniques application for the investigation of orientation inhomogeneities in polycrystalline materials was studied using FEG SEM-FIB dual beam station equipped with EBSD. It is shown that for the visualization of pearlitic ferrite fragments it is more appropriate to acquire the images in secondary electrons induced by Ga ions. At the same time for the visualization of nano-sized particles it is more prospective to use images in forward scatter electrons in combination with IQ maps. It is established that pearlitic ferrite fragments are not flat. Complicated spatial configuration of orientation inhomogeneities in pearlitic ferrite is shown by means of 3-d reconstruction. The features of ferrites aggregation are revealed depending on pearlitic ferrite fragmentation criterion. The existence of long-range misorientations in the aggregation area of proeutectoid and pearlitic ferrites is shown.

  11. Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

    Science.gov (United States)

    Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

    2016-12-01

    3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

  12. Visualization of ground truth tracks for the video 'Tracking a "facer's" behavior in a public plaza'

    DEFF Research Database (Denmark)

    2015-01-01

    The video shows the ground truth tracks in GIS of all pedestrians in the video 'Tracking a 'facer's" behavior in a public plaza'. The visualization was made using QGIS TimeManager.......The video shows the ground truth tracks in GIS of all pedestrians in the video 'Tracking a 'facer's" behavior in a public plaza'. The visualization was made using QGIS TimeManager....

  13. A comparison of multi-view 3D reconstruction of a rock wall using several cameras and a laser scanner

    Science.gov (United States)

    Thoeni, K.; Giacomini, A.; Murtagh, R.; Kniest, E.

    2014-06-01

    This work presents a comparative study between multi-view 3D reconstruction using various digital cameras and a terrestrial laser scanner (TLS). Five different digital cameras were used in order to estimate the limits related to the camera type and to establish the minimum camera requirements to obtain comparable results to the ones of the TLS. The cameras used for this study range from commercial grade to professional grade and included a GoPro Hero 1080 (5 Mp), iPhone 4S (8 Mp), Panasonic Lumix LX5 (9.5 Mp), Panasonic Lumix ZS20 (14.1 Mp) and Canon EOS 7D (18 Mp). The TLS used for this work was a FARO Focus 3D laser scanner with a range accuracy of ±2 mm. The study area is a small rock wall of about 6 m height and 20 m length. The wall is partly smooth with some evident geological features, such as non-persistent joints and sharp edges. Eight control points were placed on the wall and their coordinates were measured by using a total station. These coordinates were then used to georeference all models. A similar number of images was acquired from a distance of between approximately 5 to 10 m, depending on field of view of each camera. The commercial software package PhotoScan was used to process the images, georeference and scale the models, and to generate the dense point clouds. Finally, the open-source package CloudCompare was used to assess the accuracy of the multi-view results. Each point cloud obtained from a specific camera was compared to the point cloud obtained with the TLS. The latter is taken as ground truth. The result is a coloured point cloud for each camera showing the deviation in relation to the TLS data. The main goal of this study is to quantify the quality of the multi-view 3D reconstruction results obtained with various cameras as objectively as possible and to evaluate its applicability to geotechnical problems.

  14. Deformation analysis of a sinkhole in Thuringia using multi-temporal multi-view stereo 3D reconstruction data

    Science.gov (United States)

    Petschko, Helene; Goetz, Jason; Schmidt, Sven

    2017-04-01

    Sinkholes are a serious threat on life, personal property and infrastructure in large parts of Thuringia. Over 9000 sinkholes have been documented by the Geological Survey of Thuringia, which are caused by collapsing hollows which formed due to solution processes within the local bedrock material. However, little is known about surface processes and their dynamics at the flanks of the sinkhole once the sinkhole has shaped. These processes are of high interest as they might lead to dangerous situations at or within the vicinity of the sinkhole. Our objective was the analysis of these deformations over time in 3D by applying terrestrial photogrammetry with a simple DSLR camera. Within this study, we performed an analysis of deformations within a sinkhole close to Bad Frankenhausen (Thuringia) using terrestrial photogrammetry and multi-view stereo 3D reconstruction to obtain a 3D point cloud describing the morphology of the sinkhole. This was performed for multiple data collection campaigns over a 6-month period. The photos of the sinkhole were taken with a Nikon D3000 SLR Camera. For the comparison of the point clouds the Multiscale Model to Model Comparison (M3C2) plugin of the software CloudCompare was used. It allows to apply advanced methods of point cloud difference calculation which considers the co-registration error between two point clouds for assessing the significance of the calculated difference (given in meters). Three Styrofoam cuboids of known dimensions (16 cm wide/29 cm high/11.5 cm deep) were placed within the sinkhole to test the accuracy of the point cloud difference calculation. The multi-view stereo 3D reconstruction was performed with Agisoft Photoscan. Preliminary analysis indicates that about 26% of the sinkhole showed changes exceeding the co-registration error of the point clouds. The areas of change can mainly be detected on the flanks of the sinkhole and on an earth pillar that formed in the center of the sinkhole. These changes describe

  15. A comparison of multi-view 3D reconstruction of a rock wall using several cameras and a laser scanner

    Directory of Open Access Journals (Sweden)

    K. Thoeni

    2014-06-01

    Full Text Available This work presents a comparative study between multi-view 3D reconstruction using various digital cameras and a terrestrial laser scanner (TLS. Five different digital cameras were used in order to estimate the limits related to the camera type and to establish the minimum camera requirements to obtain comparable results to the ones of the TLS. The cameras used for this study range from commercial grade to professional grade and included a GoPro Hero 1080 (5 Mp, iPhone 4S (8 Mp, Panasonic Lumix LX5 (9.5 Mp, Panasonic Lumix ZS20 (14.1 Mp and Canon EOS 7D (18 Mp. The TLS used for this work was a FARO Focus 3D laser scanner with a range accuracy of ±2 mm. The study area is a small rock wall of about 6 m height and 20 m length. The wall is partly smooth with some evident geological features, such as non-persistent joints and sharp edges. Eight control points were placed on the wall and their coordinates were measured by using a total station. These coordinates were then used to georeference all models. A similar number of images was acquired from a distance of between approximately 5 to 10 m, depending on field of view of each camera. The commercial software package PhotoScan was used to process the images, georeference and scale the models, and to generate the dense point clouds. Finally, the open-source package CloudCompare was used to assess the accuracy of the multi-view results. Each point cloud obtained from a specific camera was compared to the point cloud obtained with the TLS. The latter is taken as ground truth. The result is a coloured point cloud for each camera showing the deviation in relation to the TLS data. The main goal of this study is to quantify the quality of the multi-view 3D reconstruction results obtained with various cameras as objectively as possible and to evaluate its applicability to geotechnical problems.

  16. The Complete Virtual 3d Reconstruction of the East Pediment of the Temple of ZEUS at Olympia

    Science.gov (United States)

    Patay-Horváth, A.

    2011-09-01

    The arrangement of the five central figures of the east pediment of the temple of Zeus at Olympia has been the subject of scholarly debates since the discovery of the fragments more than a century ago. In theory, there are four substantially different arrangements, all of which have already been selected by certain scholars for various aesthetic, technical and other considerations. The present project tries to approach this controversy in a new way, by producing a virtual 3D reconstruction of the group. Digital models of the statues were produced by scanning the original fragments and by reconstructing them virtually. For this purpose an innovative new software (Leonar3Do) has also been employed. The virtual model of the pediment surrounding the sculptures was prepared on the basis of the latest architectural studies and afterwards the reconstructed models were inserted in this frame, in order to test the technical feasibility and aesthetic effects the four possible arrangements. The paper gives an overview of the entire work and presents the final results suggesting that two arrangements can be ruled out due to the limited space available in the pediment.

  17. The effect of CT dose on glenohumeral joint congruency measurements using 3D reconstructed patient-specific bone models

    Energy Technology Data Exchange (ETDEWEB)

    Lalone, Emily A; Fox, Anne-Marie V; Jenkyn, Thomas R; King, Graham J W; Johnson, James A; Peters, Terry M [Biomedical Engineering, University of Western Ontario, London (Canada); Kedgley, Angela E [Wolf Orthopaedic Biomechanics Lab, Fowler Kennedy Sports Medicine Clinic, London (Canada); Athwal, George S, E-mail: tpeters@robarts.ca [Hand and Upper Limb Centre, St. Joseph' s Hospital, London, Canada (CT Scanning Location) (Canada)

    2011-10-21

    The study of joint congruency at the glenohumeral joint of the shoulder using computed tomography (CT) and three-dimensional (3D) reconstructions of joint surfaces is an area of significant clinical interest. However, ionizing radiation delivered to patients during CT examinations is much higher than other types of radiological imaging. The shoulder represents a significant challenge for this modality as it is adjacent to the thyroid gland and breast tissue. The objective of this study was to determine the optimal CT scanning techniques that would minimize radiation dose while accurately quantifying joint congruency of the shoulder. The results suggest that only one-tenth of the standard applied total current (mA) and a pitch ratio of 1.375:1 was necessary to produce joint congruency values consistent with that of the higher dose scans. Using the CT scanning techniques examined in this study, the effective dose applied to the shoulder to quantify joint congruency was reduced by 88.9% compared to standard clinical CT imaging techniques.

  18. Feasibility Assessment of a MALDI FTICR Imaging Approach for the 3D Reconstruction of a Mouse Lung

    Science.gov (United States)

    Jones, E. Ellen; Quiason, Cristine; Dale, Stephanie; Shahidi-Latham, Sheerin K.

    2017-08-01

    Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has proven to be a quick, robust, and label-free tool to produce two-dimensional (2D) ion-density maps representing the distribution of a variety of analytes across a tissue section of interest. In addition, three-dimensional (3D) imaging mass spectrometry workflows have been developed that are capable of visualizing these same analytes throughout an entire volume of a tissue rather than a single cross-section. Until recently, the use of Fourier transform ion cyclotron resonance (FTICR) mass spectrometers for 3D volume reconstruction has been impractical due to software limitations, such as inadequate capacity to manipulate the extremely large data files produced during an imaging experiment. Fortunately with recent software and hardware advancements, 3D reconstruction from MALDI FTICR IMS datasets is now feasible. Here we describe the first proof of principle study for a 3D volume reconstruction of an entire mouse lung using data collected on a FTICR mass spectrometer. Each lung tissue section was analyzed with high mass resolution and mass accuracy, and considered as an independent dataset. Each subsequent lung section image, or lung dataset, was then co-registered to its adjacent section to reconstruct a 3D volume. Volumes representing various endogenous lipid species were constructed, including sphingolipids and phosphatidylcholines (PC), and species confirmation was performed with on-tissue collision induced dissociation (CID).

  19. THE COMPLETE VIRTUAL 3D RECONSTRUCTION OF THE EAST PEDIMENT OF THE TEMPLE OF ZEUS AT OLYMPIA

    Directory of Open Access Journals (Sweden)

    A. Patay-Horváth

    2012-09-01

    Full Text Available The arrangement of the five central figures of the east pediment of the temple of Zeus at Olympia has been the subject of scholarly debates since the discovery of the fragments more than a century ago. In theory, there are four substantially different arrangements, all of which have already been selected by certain scholars for various aesthetic, technical and other considerations. The present project tries to approach this controversy in a new way, by producing a virtual 3D reconstruction of the group. Digital models of the statues were produced by scanning the original fragments and by reconstructing them virtually. For this purpose an innovative new software (Leonar3Do has also been employed. The virtual model of the pediment surrounding the sculptures was prepared on the basis of the latest architectural studies and afterwards the reconstructed models were inserted in this frame, in order to test the technical feasibility and aesthetic effects the four possible arrangements. The paper gives an overview of the entire work and presents the final results suggesting that two arrangements can be ruled out due to the limited space available in the pediment.

  20. Comparison between standard radiography and spiral CT with 3D reconstruction in the evaluation, classification and management of tibial plateau fractures

    Energy Technology Data Exchange (ETDEWEB)

    Wicky, S.; Schnyder, P.; Meuli, R.A. [Department of Diagnostic and Interventional Radiology, University Hospital, Lausanne (Switzerland); Blaser, P.F.; Blanc, C.H.; Leyvraz, P.F. [Department of Orthopedics and Traumatology, University Hospital, Lausanne (Switzerland)

    2000-08-01

    The aim of this study was to compare the diagnostic efficiency of plain film and spiral CT examinations with 3D reconstructions of 42 tibial plateau fractures and to assess the accuracy of these two techniques in the pre-operative surgical plan in 22 cases. Forty-two tibial plateau fractures were examined with plain film (anteroposterior, lateral, two obliques) and spiral CT with surface-shaded-display 3D reconstructions. The Swiss AO-ASIF classification system of bone fracture from Mueller was used. In 22 cases the surgical plans and the sequence of reconstruction of the fragments were prospectively determined with both techniques, successively, and then correlated with the surgical reports and post-operative plain film. The fractures were underestimated with plain film in 18 of 42 cases (43%). Due to the spiral CT 3D reconstructions, and precise pre-operative information, the surgical plans based on plain film were modified and adjusted in 13 cases among 22 (59%). Spiral CT 3D reconstructions give a better and more accurate demonstration of the tibial plateau fracture and allows a more precise pre-operative surgical plan. (orig.)

  1. Anatomical study to the vessels of the lower limb by using CT scan and 3D reconstructions of the injected material.

    Science.gov (United States)

    Chen, Sheng-hua; Chen, Mei-mei; Xu, Da-chuan; He, Hui; Peng, Tian-hong; Tan, Jian-guo; Xiang, Yu-yan

    2011-01-01

    To find out the advantages and insufficiency of the 3D reconstruction and traditional anatomy by comparing them with each other. 1. Infused with the radio-opaque material from the arteries and veins, respectively, fresh lower extremity specimens were subjected to spiral CT scanning and then 3D reconstruction was conducted to obtain 3D vessels. 2. Anatomizing the specimens to show the vessel system. 3. Comparing the images of 3D reconstruction and photos of the dissected specimens. 3D software could dissect and reconstruct the bones, vessels, skin and muscles, and the reconstructed photos could be shown, respectively or combinedly. On the other hand, the course, distribution, and anastomoses of the vessels could be viewed from different aspects and different layers, but the results were not completely correct, so they were not suitable for data acquisition. While the vessel systems could be observed clearly on the dissected specimens, so could the origin, course, distribution and the anastomoses of any vessel. The data acquisition could be conducted. The method of angiography with 3D reconstruction is very good and has considerable advantages for observing the 3D state of human blood vessels, and their distribution at different angles and different levels, but it cannot totally represent or replace the traditional dissected specimens.

  2. 3-D reconstructions of the early-November 2004 CDAW geomagnetic storms: analysis of Ooty IPS speed and density data

    Directory of Open Access Journals (Sweden)

    M. M. Bisi

    2009-12-01

    Full Text Available Interplanetary scintillation (IPS remote-sensing observations provide a view of the solar wind covering a wide range of heliographic latitudes and heliocentric distances from the Sun between ~0.1 AU and 3.0 AU. Such observations are used to study the development of solar coronal transients and the solar wind while propagating out through interplanetary space. They can also be used to measure the inner-heliospheric response to the passage of coronal mass ejections (CMEs and co-rotating heliospheric structures. IPS observations can, in general, provide a speed estimate of the heliospheric material crossing the observing line of site; some radio antennas/arrays can also provide a radio scintillation level. We use a three-dimensional (3-D reconstruction technique which obtains perspective views from outward-flowing solar wind and co-rotating structure as observed from Earth by iteratively fitting a kinematic solar wind model to these data. Using this 3-D modelling technique, we are able to reconstruct the velocity and density of CMEs as they travel through interplanetary space. For the time-dependent model used here with IPS data taken from the Ootacamund (Ooty Radio Telescope (ORT in India, the digital resolution of the tomography is 10° by 10° in both latitude and longitude with a half-day time cadence. Typically however, the resolutions range from 10° to 20° in latitude and longitude, with a half- to one-day time cadence for IPS data dependant upon how much data are used as input to the tomography. We compare reconstructed structures during early-November 2004 with in-situ measurements from the Wind spacecraft orbiting the Sun-Earth L1-Point to validate the 3-D tomographic reconstruction results and comment on how these improve upon prior reconstructions.

  3. 3-D reconstructions of the early-November 2004 CDAW geomagnetic storms: analysis of Ooty IPS speed and density data

    Directory of Open Access Journals (Sweden)

    M. M. Bisi

    2009-12-01

    Full Text Available Interplanetary scintillation (IPS remote-sensing observations provide a view of the solar wind covering a wide range of heliographic latitudes and heliocentric distances from the Sun between ~0.1 AU and 3.0 AU. Such observations are used to study the development of solar coronal transients and the solar wind while propagating out through interplanetary space. They can also be used to measure the inner-heliospheric response to the passage of coronal mass ejections (CMEs and co-rotating heliospheric structures. IPS observations can, in general, provide a speed estimate of the heliospheric material crossing the observing line of site; some radio antennas/arrays can also provide a radio scintillation level. We use a three-dimensional (3-D reconstruction technique which obtains perspective views from outward-flowing solar wind and co-rotating structure as observed from Earth by iteratively fitting a kinematic solar wind model to these data. Using this 3-D modelling technique, we are able to reconstruct the velocity and density of CMEs as they travel through interplanetary space. For the time-dependent model used here with IPS data taken from the Ootacamund (Ooty Radio Telescope (ORT in India, the digital resolution of the tomography is 10° by 10° in both latitude and longitude with a half-day time cadence. Typically however, the resolutions range from 10° to 20° in latitude and longitude, with a half- to one-day time cadence for IPS data dependant upon how much data are used as input to the tomography. We compare reconstructed structures during early-November 2004 with in-situ measurements from the Wind spacecraft orbiting the Sun-Earth L1-Point to validate the 3-D tomographic reconstruction results and comment on how these improve upon prior reconstructions.

  4. Chrysotile effects on human lung cell carcinoma in culture: 3-D reconstruction and DNA quantification by image analysis

    Directory of Open Access Journals (Sweden)

    Machado-Santelli Glaucia M

    2008-06-01

    Full Text Available Abstract Background Chrysotile is considered less harmful to human health than other types of asbestos fibers. Its clearance from the lung is faster and, in comparison to amphibole forms of asbestos, chrysotile asbestos fail to accumulate in the lung tissue due to a mechanism involving fibers fragmentation in short pieces. Short exposure to chrysotile has not been associated with any histopathological alteration of lung tissue. Methods The present work focuses on the association of small chrysotile fibers with interphasic and mitotic human lung cancer cells in culture, using for analyses confocal laser scanning microscopy and 3D reconstructions. The main goal was to perform the analysis of abnormalities in mitosis of fibers-containing cells as well as to quantify nuclear DNA content of treated cells during their recovery in fiber-free culture medium. Results HK2 cells treated with chrysotile for 48 h and recovered in additional periods of 24, 48 and 72 h in normal medium showed increased frequency of multinucleated and apoptotic cells. DNA ploidy of the cells submitted to the same chrysotile treatment schedules showed enhanced aneuploidy values. The results were consistent with the high frequency of multipolar spindles observed and with the presence of fibers in the intercellular bridge during cytokinesis. Conclusion The present data show that 48 h chrysotile exposure can cause centrosome amplification, apoptosis and aneuploid cell formation even when long periods of recovery were provided. Internalized fibers seem to interact with the chromatin during mitosis, and they could also interfere in cytokinesis, leading to cytokinesis failure which forms aneuploid or multinucleated cells with centrosome amplification.

  5. Potential Synaptic Connectivity of Different Neurons onto Pyramidal Cells in a 3D Reconstruction of the Rat Hippocampus

    Directory of Open Access Journals (Sweden)

    Deepak eRopireddy

    2011-07-01

    Full Text Available Most existing connectomic data and ongoing efforts focus either on individual synapses (e.g. with electron microscopy or on regional connectivity (tract tracing. An individual pyramidal cell extends thousands of synapses over macroscopic distances (~cm. The contrasting requirements of high resolution and large field of view make it too challenging to acquire the entire synaptic connectivity for even a single typical cortical neuron. Light microscopy can image whole neuronal arbors and resolve dendritic branches. Analyzing connectivity in terms of close spatial appositions between axons and dendrites could thus bridge the opposite scales, from synaptic level to whole systems. In the mammalian cortex, structural plasticity of spines and boutons makes these ‘potential synapses’ functionally relevant to learning capability and memory capacity. To date, however, potential synapses have only been mapped in the surrounding of a neuron and relative to its local orientation rather than in a system-level anatomical reference. Here we overcome this limitation by estimating the potential connectivity of different neurons embedded into a detailed 3D reconstruction of the rat hippocampus. Axonal and dendritic trees were oriented with respect to hippocampal cytoarchitecture according to longitudinal and transversal curvatures. We report the potential connectivity onto pyramidal cell dendrites from the axons of a dentate granule cell, three CA3 pyramidal cells, one CA2 pyramidal cell, and 13 CA3b interneurons. The numbers, densities, and distributions of potential synapses were analyzed in each sub-region (e.g. CA3 vs. CA1, layer (e.g. oriens vs. radiatum, and septo-temporal location (e.g. dorsal vs. ventral. The overall ratio between the numbers of actual and potential synapses was ~0.20 for the granule and CA3 pyramidal cells. All potential connectivity patterns are strikingly dependent on the anatomical location of both pre-synaptic and post

  6. High-throughput phenotyping of plant resistance to aphids by automated video tracking.

    Science.gov (United States)

    Kloth, Karen J; Ten Broeke, Cindy Jm; Thoen, Manus Pm; Hanhart-van den Brink, Marianne; Wiegers, Gerrie L; Krips, Olga E; Noldus, Lucas Pjj; Dicke, Marcel; Jongsma, Maarten A

    2015-01-01

    Piercing-sucking insects are major vectors of plant viruses causing significant yield losses in crops. Functional genomics of plant resistance to these insects would greatly benefit from the availability of high-throughput, quantitative phenotyping methods. We have developed an automated video tracking platform that quantifies aphid feeding behaviour on leaf discs to assess the level of plant resistance. Through the analysis of aphid movement, the start and duration of plant penetrations by aphids were estimated. As a case study, video tracking confirmed the near-complete resistance of lettuce cultivar 'Corbana' against Nasonovia ribisnigri (Mosely), biotype Nr:0, and revealed quantitative resistance in Arabidopsis accession Co-2 against Myzus persicae (Sulzer). The video tracking platform was benchmarked against Electrical Penetration Graph (EPG) recordings and aphid population development assays. The use of leaf discs instead of intact plants reduced the intensity of the resistance effect in video tracking, but sufficiently replicated experiments resulted in similar conclusions as EPG recordings and aphid population assays. One video tracking platform could screen 100 samples in parallel. Automated video tracking can be used to screen large plant populations for resistance to aphids and other piercing-sucking insects.

  7. A detailed description of the development of the hemichordate Saccoglossus kowalevskii using SEM, TEM, Histology and 3D-reconstructions.

    Science.gov (United States)

    Kaul-Strehlow, Sabrina; Stach, Thomas

    2013-09-06

    Traditionally, the origin of the third germ layer and its special formation of coelomic cavities by enterocoely is regarded to be an informative character in phylogenetic analyses. In early deuterostomes such as sea urchins, the mesoderm forms through a single evagination pinching off from the apical end of the archenteron which then gives off mesocoela and metacoela on each side. This echinoid-type coelom formation has conventionally been assumed to be ancestral for Deuterostomia. However, recent phylogenetic analyses show that Echinodermata hold a more derived position within Deuterostomia. In this regard a subgroup of Hemichordata, namely enteropneusts, seem to host promising candidates, because they are supposed to have retained many ancestral deuterostome features on the one hand, and furthermore share some characteristics with chordates on the other hand. In enteropneusts a wide range of different modes of coelom formation has been reported and in many cases authors of the original observations carefully detailed the limitations of their descriptions, while these doubts disappeared in subsequent reviews. In the present study, we investigated the development of all tissues in an enteropneust, Saccoglossus kowalevskii by using modern morphological techniques such as complete serial sectioning for LM and TEM, and 3D-reconstructions, in order to contribute new data to the elucidation of deuterostome evolution. Our data show that in the enteropneust S. kowalevskii all main coelomic cavities (single protocoel, paired mesocoela and metacoela) derive from the endoderm via enterocoely as separate evaginations, in contrast to the aforementioned echinoid-type. The anlagen of the first pair of gill slits emerge at the late kink stage (~96 h pf). From that time onwards, we documented a temporal left-first development of the gill slits and skeletal gill rods in S. kowalevskii until the 2 gill slit juvenile stage. The condition of coelom formation from separate

  8. Assessment of landmark measurements of craniofacial images from 2D and 3D reconstructions of spiral CT

    Science.gov (United States)

    Cavalcanti, Marcelo G.; Haller, John W.; Vannier, Michael W.

    1998-06-01

    Purpose: The purpose of this study is to compare the accuracy of facial linear measurements obtained from volumetric spiral CT using 2D versus 3D reconstruction, and test the repeatability of these measurements. Material and Methods: The population consisted of 5 cadaver heads that were scanned to a Spiral CT scanner (120 Kvp and 200 mA, Toshiba Xpress S/X Toshiba-America, Medical System Inc., Tustin, CA) with high- resolution contiguous slices. Heads were scanned with 3 mm thick axial slices and a 2 mm/sec table feed. The CT data were archived on optical disks, and then transferred to a networked computer workstation (Sun Microsystems with Cemax version 1.4 software, Fremont, CA), to generate 2D and 3D images for manipulation and analyses. Repeated measurements were done on 2D and 3D images reconstructed from spiral CT scans on the workstation. Linear measurements were done by 2 observers with 2 sessions each, using several unique and conventional craniometric anatomic landmarks. The soft tissues were then partially removed and physical measurements of the same landmarks were repeated by an electromagnetic (3 space) digitizer (Polhemus Navigation Sciences Division, Mc Donnell Douglas Electronic Company, Colchester, VE). Analyses of variance were done to compare 2D versus 3D methods, and the accuracy of measurements between both imaging techniques. Results: The results showed statistically significant differences between 2D and 3D images for the majority of measurements. The 3D image measurements were not statistically different from the physical measurements. However, some of the 2D image landmarks differed from physical measurements. The repeatability of measurements was high by spiral CT-based craniofacial imaging. Conclusion: New computer graphics technology combined with 3D volumetric imaging by spiral CT can distinguish the craniofacial anatomy with greater accuracy than previously reported measurements and with greater accuracy than measurements from 2DCT

  9. 3D reconstruction of emergency cranial computed tomography scans as a tool in clinical forensic radiology after survived blunt head trauma--report of two cases.

    Science.gov (United States)

    Grassberger, M; Gehl, A; Püschel, K; Turk, E E

    2011-04-15

    When requested to evaluate surviving victims of blunt head trauma the forensic expert has to draw mainly on medical documentation from the time of hospital admission. In many cases these consist of written clinical records, radiographs and in some cases photographic documentation of the injuries. We report two cases of survived severe blunt head trauma where CT images, which had primarily been obtained for clinical diagnostic purposes, were used for forensic assessment. 3D reconstructions of the clinical CT-images yielded valuable information regarding the sequence, number and direction of the impacts to the head, their gross morphology and the inflicting weapon. We conclude that computed tomography and related imaging methods, along with their 3D reconstruction capabilities, provide a useful tool to approach questions in clinical forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  10. Influence of patient axial malpositioning on the trueness and precision of pelvic parameters obtained from 3D reconstructions based on biplanar radiographs

    Energy Technology Data Exchange (ETDEWEB)

    Ghostine, Bachir; Assi, Ayman [Institut de Biomecanique Humaine Georges Charpak, Arts et Metiers ParisTech, Paris (France); University of Saint-Joseph, Laboratory of Biomechanics and Medical Imaging, Faculty of Medicine, Beirut (Lebanon); Sauret, Christophe; Skalli, Wafa [Institut de Biomecanique Humaine Georges Charpak, Arts et Metiers ParisTech, Paris (France); Bakouny, Ziad; Khalil, Nour [University of Saint-Joseph, Laboratory of Biomechanics and Medical Imaging, Faculty of Medicine, Beirut (Lebanon); Ghanem, Ismat [University of Saint-Joseph, Laboratory of Biomechanics and Medical Imaging, Faculty of Medicine, Beirut (Lebanon); University of Saint-Joseph, Hotel-Dieu de France Hospital, Beirut (Lebanon)

    2017-03-15

    Radiographs are often performed to assess pelvic and hip parameters, but results depend upon correct pelvis positioning. Three-dimensional (3D) reconstruction from biplanar-radiographs should provide parameters that are less sensitive to pelvic orientation, but this remained to be evaluated. Computerized-tomographic scans of six patients were used both as a reference and for generating simulated frontal and lateral radiographs. These simulated radiographs were generated while introducing axial rotations of the pelvis ranging from 0 to 20 . Simulated biplanar-radiographs were utilized by four operators, three times each, to perform pelvic 3D-reconstructions. These reconstructions were used to assess the trueness, precision and global uncertainty of radiological pelvic and hip parameters for each position. In the neutral position, global uncertainty ranged between ± 2 for pelvic tilt and ± 9 for acetabular posterior sector angle and was mainly related to precision errors (ranging from 1.5 to 7 ). With increasing axial rotation, global uncertainty increased and ranged between ± 5 for pelvic tilt and ± 11 for pelvic incidence, sacral slope and acetabular anterior sector angle, mainly due to precision errors. Radiological parameters obtained from 3D-reconstructions, based on biplanar-radiographs, are less sensitive to axial rotation compared to plain radiographs. However, the axial rotation should nonetheless not exceed 10 . (orig.)

  11. Weapon identification using antemortem CT with 3D reconstruction, is it always possible?--A report in a case of facial blunt and sharp injuries using an ashtray.

    Science.gov (United States)

    Aromatario, Mariarosaria; Cappelletti, Simone; Bottoni, Edoardo; Fiore, Paola Antonella; Ciallella, Costantino

    2016-01-01

    An interesting case of homicide involving the use of a heavy glass ashtray is described. The victim, a 81-years-old woman, has survived for few days and died in hospital. The external examination of the victim showed extensive blunt and sharp facial injuries and defense injuries on both the hands. The autopsy examination showed numerous tears on the face, as well as multiple fractures of the facial bones. Computer tomography scan, with 3D reconstruction, performed in hospital before death, was used to identify the weapon used for the crime. In recent years new diagnostics tools such as computer tomography has been widely used, especially in cases involving sharp and blunt forces. Computer tomography has proven to be very valuable in analyzing fractures of the cranial teca for forensic purpose, in particular antemortem computer tomography with 3D reconstruction is becoming an important tool in the process of weapon identification, thanks to the possibility to identify and make comparison between the shape of the object used to commit the crime, the injury and the objects found during the investigations. No previous reports on the use of this technique, for the weapon identification process, in cases of isolated facial fractures were described. We report a case in which, despite the correct use of this technique, it was not possible for the forensic pathologist to identify the weapon used to commit the crime. Authors wants to highlight the limits encountered in the use of computer tomography with 3D reconstruction as a tool for weapon identification when facial fractures occurred. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Validation of a statistical shape model-based 2D/3D reconstruction method for determination of cup orientation after THA.

    Science.gov (United States)

    Zheng, G; von Recum, J; Nolte, L-P; Grützner, P A; Steppacher, S D; Franke, J

    2012-03-01

    The aim of this study was to validate the accuracy and reproducibility of a statistical shape model-based 2D/3D reconstruction method for determining cup orientation after total hip arthroplasty. With a statistical shape model, this method allows reconstructing a patient-specific 3D-model of the pelvis from a standard AP X-ray radiograph. Cup orientation (inclination and anteversion) is then calculated with respect to the anterior pelvic plane that is derived from the reconstructed model. The validation study was conducted retrospectively on datasets of 29 patients (31 hips). Among them, there were 15 men (15 hips) and 14 women (16 hips). The average age of the patients was 69.4±8.5 (49-82) years. Each dataset has one postoperative X-ray radiograph and one postoperative CT scan. The postoperative CT scan for each patient was used to establish the ground truth for the cup orientation. The cup anteversion and inclination that were calculated from the 2D/3D reconstruction method were compared to the associated ground truth. To validate reproducibility and reliability, two observers performed measurements for each dataset twice in order to measure the reproducibility and the reliability of the 2D/3D reconstruction method. Our validation study demonstrated a mean accuracy of 0.4 ± 1.8° (-2.6° to 3.3°) for inclination and a mean accuracy of 0.6±1.5° (-2.0° to 3.9°) for anteversion. Through the Bland-Altman analysis, no systematic errors in accuracy were detected. The method showed very good consistency for both parameters. Our validation results demonstrate that the statistical shape model-based 2D/3D reconstruction-based method is an accurate, consistent, and reproducible technique to measure cup orientation from postoperative X-ray radiographs. The best results were achieved with radiographs including the bilateral anterior superior iliac spines and the cranial part of non-fractured pelvises.

  13. FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

    Directory of Open Access Journals (Sweden)

    Carles eBosch

    2015-05-01

    Full Text Available The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs in mice. 3D reconstruction of spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of spine development and unexpected features of synapse formation, including vacant and branched spines and presynaptic terminals establishing synapses with up to 10 spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner.

  14. FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons

    Science.gov (United States)

    Bosch, Carles; Martínez, Albert; Masachs, Nuria; Teixeira, Cátia M.; Fernaud, Isabel; Ulloa, Fausto; Pérez-Martínez, Esther; Lois, Carlos; Comella, Joan X.; DeFelipe, Javier; Merchán-Pérez, Angel; Soriano, Eduardo

    2015-01-01

    The fine analysis of synaptic contacts is usually performed using transmission electron microscopy (TEM) and its combination with neuronal labeling techniques. However, the complex 3D architecture of neuronal samples calls for their reconstruction from serial sections. Here we show that focused ion beam/scanning electron microscopy (FIB/SEM) allows efficient, complete, and automatic 3D reconstruction of identified dendrites, including their spines and synapses, from GFP/DAB-labeled neurons, with a resolution comparable to that of TEM. We applied this technology to analyze the synaptogenesis of labeled adult-generated granule cells (GCs) in mice. 3D reconstruction of dendritic spines in GCs aged 3–4 and 8–9 weeks revealed two different stages of dendritic spine development and unexpected features of synapse formation, including vacant and branched dendritic spines and presynaptic terminals establishing synapses with up to 10 dendritic spines. Given the reliability, efficiency, and high resolution of FIB/SEM technology and the wide use of DAB in conventional EM, we consider FIB/SEM fundamental for the detailed characterization of identified synaptic contacts in neurons in a high-throughput manner. PMID:26052271

  15. Classification and segmentation of orbital space based objects against terrestrial distractors for the purpose of finding holes in shape from motion 3D reconstruction

    Science.gov (United States)

    Mundhenk, T. Nathan; Flores, Arturo; Hoffman, Heiko

    2013-12-01

    3D reconstruction of objects via Shape from Motion (SFM) has made great strides recently. Utilizing images from a variety of poses, objects can be reconstructed in 3D without knowing a priori the camera pose. These feature points can then be bundled together to create large scale scene reconstructions automatically. A shortcoming of current methods of SFM reconstruction is in dealing with specular or flat low feature surfaces. The inability of SFM to handle these places creates holes in a 3D reconstruction. This can cause problems when the 3D reconstruction is used for proximity detection and collision avoidance by a space vehicle working around another space vehicle. As such, we would like the automatic ability to recognize when a hole in a 3D reconstruction is in fact not a hole, but is a place where reconstruction has failed. Once we know about such a location, methods can be used to try to either more vigorously fill in that region or to instruct a space vehicle to proceed with more caution around that area. Detecting such areas in earth orbiting objects is non-trivial since we need to parse out complex vehicle features from complex earth features, particularly when the observing vehicle is overhead the target vehicle. To do this, we have created a Space Object Classifier and Segmenter (SOCS) hole finder. The general principle we use is to classify image features into three categories (earth, man-made, space). Classified regions are then clustered into probabilistic regions which can then be segmented out. Our categorization method uses an augmentation of a state of the art bag of visual words method for object categorization. This method works by first extracting PHOW (dense SIFT like) features which are computed over an image and then quantized via KD Tree. The quantization results are then binned into histograms and results classified by the PEGASOS support vector machine solver. This gives a probability that a patch in the image corresponds to one of three

  16. COMBINING PUBLIC DOMAIN AND PROFESSIONAL PANORAMIC IMAGERY FOR THE ACCURATE AND DENSE 3D RECONSTRUCTION OF THE DESTROYED BEL TEMPLE IN PALMYRA

    Directory of Open Access Journals (Sweden)

    W. Wahbeh

    2016-06-01

    Full Text Available This paper exploits the potential of dense multi-image 3d reconstruction of destroyed cultural heritage monuments by either using public domain touristic imagery only or by combining the public domain imagery with professional panoramic imagery. The focus of our work is placed on the reconstruction of the temple of Bel, one of the Syrian heritage monuments, which was destroyed in September 2015 by the so called "Islamic State". The great temple of Bel is considered as one of the most important religious buildings of the 1st century AD in the East with a unique design. The investigations and the reconstruction were carried out using two types of imagery. The first are freely available generic touristic photos collected from the web. The second are panoramic images captured in 2010 for documenting those monuments. In the paper we present a 3d reconstruction workflow for both types of imagery using state-of-the art dense image matching software, addressing the non-trivial challenges of combining uncalibrated public domain imagery with panoramic images with very wide base-lines. We subsequently investigate the aspects of accuracy and completeness obtainable from the public domain touristic images alone and from the combination with spherical panoramas. We furthermore discuss the challenges of co-registering the weakly connected 3d point cloud fragments resulting from the limited coverage of the touristic photos. We then describe an approach using spherical photogrammetry as a virtual topographic survey allowing the co-registration of a detailed and accurate single 3d model of the temple interior and exterior.

  17. Combining Public Domain and Professional Panoramic Imagery for the Accurate and Dense 3d Reconstruction of the Destroyed Bel Temple in Palmyra

    Science.gov (United States)

    Wahbeh, W.; Nebiker, S.; Fangi, G.

    2016-06-01

    This paper exploits the potential of dense multi-image 3d reconstruction of destroyed cultural heritage monuments by either using public domain touristic imagery only or by combining the public domain imagery with professional panoramic imagery. The focus of our work is placed on the reconstruction of the temple of Bel, one of the Syrian heritage monuments, which was destroyed in September 2015 by the so called "Islamic State". The great temple of Bel is considered as one of the most important religious buildings of the 1st century AD in the East with a unique design. The investigations and the reconstruction were carried out using two types of imagery. The first are freely available generic touristic photos collected from the web. The second are panoramic images captured in 2010 for documenting those monuments. In the paper we present a 3d reconstruction workflow for both types of imagery using state-of-the art dense image matching software, addressing the non-trivial challenges of combining uncalibrated public domain imagery with panoramic images with very wide base-lines. We subsequently investigate the aspects of accuracy and completeness obtainable from the public domain touristic images alone and from the combination with spherical panoramas. We furthermore discuss the challenges of co-registering the weakly connected 3d point cloud fragments resulting from the limited coverage of the touristic photos. We then describe an approach using spherical photogrammetry as a virtual topographic survey allowing the co-registration of a detailed and accurate single 3d model of the temple interior and exterior.

  18. Evaluation of Simulated Clinical Breast Exam Motion Patterns Using Marker-Less Video Tracking.

    Science.gov (United States)

    Azari, David P; Pugh, Carla M; Laufer, Shlomi; Kwan, Calvin; Chen, Chia-Hsiung; Yen, Thomas Y; Hu, Yu Hen; Radwin, Robert G

    2016-05-01

    This study investigates using marker-less video tracking to evaluate hands-on clinical skills during simulated clinical breast examinations (CBEs). There are currently no standardized and widely accepted CBE screening techniques. Experienced physicians attending a national conference conducted simulated CBEs presenting different pathologies with distinct tumorous lesions. Single hand exam motion was recorded and analyzed using marker-less video tracking. Four kinematic measures were developed to describe temporal (time pressing and time searching) and spatial (area covered and distance explored) patterns. Mean differences between time pressing, area covered, and distance explored varied across the simulated lesions. Exams were objectively categorized as either sporadic, localized, thorough, or efficient for both temporal and spatial categories based on spatiotemporal characteristics. The majority of trials were temporally or spatially thorough (78% and 91%), exhibiting proportionally greater time pressing and time searching (temporally thorough) and greater area probed with greater distance explored (spatially thorough). More efficient exams exhibited proportionally more time pressing with less time searching (temporally efficient) and greater area probed with less distance explored (spatially efficient). Just two (5.9 %) of the trials exhibited both high temporal and spatial efficiency. Marker-less video tracking was used to discriminate different examination techniques and measure when an exam changes from general searching to specific probing. The majority of participants exhibited more thorough than efficient patterns. Marker-less video kinematic tracking may be useful for quantifying clinical skills for training and assessment. © 2015, Human Factors and Ergonomics Society.

  19. ‘PhysTrack’: a Matlab based environment for video tracking of kinematics in the physics laboratory

    Science.gov (United States)

    Umar Hassan, Muhammad; Sabieh Anwar, Muhammad

    2017-07-01

    In the past two decades, several computer software tools have been developed to investigate the motion of moving bodies in physics laboratories. In this article we report a Matlab based video tracking library, PhysTrack, primarily designed to investigate kinematics. We compare PhysTrack with other commonly available video tracking tools and outline its salient features. The general methodology of the whole video tracking process is described with a step by step explanation of several functionalities. Furthermore, results of some real physics experiments are also provided to demonstrate the working of the automated video tracking, data extraction, data analysis and presentation tools that come with this development environment. We believe that PhysTrack will be valuable for the large community of physics teachers and students already employing Matlab.

  20. The role of target 3D-reconstructions when analysyng qualitative characteristics of the surface of circular-shaped growth in the lungs

    Directory of Open Access Journals (Sweden)

    V. G. Kolmogorov

    2016-01-01

    Full Text Available The purpose of this paper is to improve the accuracy of X-ray diagnostics of circular-shaped growth (CSG by developing computed tomographic semiotics of qualitative characteristics of its surface and the state of the surrounding bronchi using target 3D-reconstruction.Material and methods. 560 patients at the age of 3–89 years were examined. Target 3D reconstruction was carried out with the use of 3D Fly Through program (Toshiba Medical Systems, Japan which removed the tissue surrounding CSG at a distance of 5–10 mm from the outer boundaries.CSG was inscribed into a cube. In case of the primary central and peripheral lung cancer a number of patients with severe rough surface of CSG prevailed over a number of patients with slightly rough surface was detected. In case of infiltrative tuberculosis, pneumonia, echinococcus, retention cysts the prevalence of a number of patients with slightly rough surface of CSG over a number of patients with rough surface was identified. In case of single cancer metastases, single and multiple tuberculomas the prevalence of a number of patients with non-uniform smooth surface of CSG over a number of patients with uniform smooth surface was identified. In case of multiple cancer metastasis, focal tuberculosis, cysticercosis the prevalence of a number of patients with a uniform smooth surface of CSG over a number of patients with uneven smooth surface was identified. In case of benign tumors, eosinophilic infiltrate, gamartohondroma, aspergilloma, chronic abscess, intrapulmonary hematoma there was not difference between the number of patients with a uniform smooth surface of CSG and a number of patients with uneven smooth surface. In case of primary lung cancer metastasis, single and multiple tuberkulomas, echinococcus, cysticercosis there was a prevalence of the number of patients with expressed deformed bronchi surrounding CSL over a number of patients with moderately deformed bronchi. In case of infiltrative

  1. Quantitative analysis of spider locomotion employing computer-automated video tracking

    DEFF Research Database (Denmark)

    Baatrup, E; Bayley, M

    1993-01-01

    The locomotor activity of adult specimens of the wolf spider Pardosa amentata was measured in an open-field setup, using computer-automated colour object video tracking. The x,y coordinates of the animal in the digitized image of the test arena were recorded three times per second during four...... consecutive 12-h periods, alternating between white and red (lambda > 600 nm) illumination. Male spiders were significantly more locomotor active than female spiders under both lighting conditions. They walked, on average, twice the distance of females, employed higher velocities, and spent less time...

  2. 3D-Reconstructions and Virtual 4D-Visualization to Study Metamorphic Brain Development in the Sphinx Moth Manduca Sexta.

    Science.gov (United States)

    Huetteroth, Wolf; El Jundi, Basil; El Jundi, Sirri; Schachtner, Joachim

    2010-01-01

    DURING METAMORPHOSIS, THE TRANSITION FROM THE LARVA TO THE ADULT, THE INSECT BRAIN UNDERGOES CONSIDERABLE REMODELING: new neurons are integrated while larval neurons are remodeled or eliminated. One well acknowledged model to study metamorphic brain development is the sphinx moth Manduca sexta. To further understand mechanisms involved in the metamorphic transition of the brain we generated a 3D standard brain based on selected brain areas of adult females and 3D reconstructed the same areas during defined stages of pupal development. Selected brain areas include for example mushroom bodies, central complex, antennal- and optic lobes. With this approach we eventually want to quantify developmental changes in neuropilar architecture, but also quantify changes in the neuronal complement and monitor the development of selected neuronal populations. Furthermore, we used a modeling software (Cinema 4D) to create a virtual 4D brain, morphing through its developmental stages. Thus the didactical advantages of 3D visualization are expanded to better comprehend complex processes of neuropil formation and remodeling during development. To obtain datasets of the M. sexta brain areas, we stained whole brains with an antiserum against the synaptic vesicle protein synapsin. Such labeled brains were then scanned with a confocal laser scanning microscope and selected neuropils were reconstructed with the 3D software AMIRA 4.1.

  3. 3D-reconstructions and virtual 4D-visualization to study metamorphic brain development in the sphinx moth Manduca sexta

    Directory of Open Access Journals (Sweden)

    Wolf Huetteroth

    2010-03-01

    Full Text Available During metamorphosis, the transition from the larva to the adult, the insect brain undergoes considerable remodeling: New neurons are integrated while larval neurons are remodeled or eliminated. One well acknowledged model to study metamorphic brain development is the sphinx moth Manduca sexta. To further understand mechanisms involved in the metamorphic transition of the brain we generated a 3D standard brain based on selected brain areas of adult females and 3D reconstructed the same areas during defined stages of pupal development. Selected brain areas include for example mushroom bodies, central complex, antennal- and optic lobes. With this approach we eventually want to quantify developmental changes in neuropilar architecture, but also quantify changes in the neuronal complement and monitor the development of selected neuronal populations. Furthermore, we used a modeling software (Cinema 4D to create a virtual 4D brain, morphing through its developmental stages. Thus the didactical advantages of 3D visualization are expanded to better comprehend complex processes of neuropil formation and remodeling during development. To obtain datasets of the M. sexta brain areas, we stained whole brains with an antiserum against the synaptic vesicle protein synapsin. Such labeled brains were then scanned with a confocal laser scanning microscope and selected neuropils were reconstructed with the 3D software AMIRA 4.1.

  4. Development of an in vitro cytotoxicity model for aerosol exposure using 3D reconstructed human airway tissue; application for assessment of e-cigarette aerosol.

    Science.gov (United States)

    Neilson, Louise; Mankus, Courtney; Thorne, David; Jackson, George; DeBay, Jason; Meredith, Clive

    2015-10-01

    Development of physiologically relevant test methods to analyse potential irritant effects to the respiratory tract caused by e-cigarette aerosols is required. This paper reports the method development and optimisation of an acute in vitro MTT cytotoxicity assay using human 3D reconstructed airway tissues and an aerosol exposure system. The EpiAirway™ tissue is a highly differentiated in vitro human airway culture derived from primary human tracheal/bronchial epithelial cells grown at the air-liquid interface, which can be exposed to aerosols generated by the VITROCELL® smoking robot. Method development was supported by understanding the compatibility of these tissues within the VITROCELL® system, in terms of airflow (L/min), vacuum rate (mL/min) and exposure time. Dosimetry tools (QCM) were used to measure deposited mass, to confirm the provision of e-cigarette aerosol to the tissues. EpiAirway™ tissues were exposed to cigarette smoke and aerosol generated from two commercial e-cigarettes for up to 6 h. Cigarette smoke reduced cell viability in a time dependent manner to 12% at 6 h. E-cigarette aerosol showed no such decrease in cell viability and displayed similar results to that of the untreated air controls. Applicability of the EpiAirway™ model and exposure system was demonstrated, showing little cytotoxicity from e-cigarette aerosol and different aerosol formulations when compared directly with reference cigarette smoke, over the same exposure time. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Automatic Association of Chats and Video Tracks for Activity Learning and Recognition in Aerial Video Surveillance

    Directory of Open Access Journals (Sweden)

    Riad I. Hammoud

    2014-10-01

    Full Text Available We describe two advanced video analysis techniques, including video-indexed by voice annotations (VIVA and multi-media indexing and explorer (MINER. VIVA utilizes analyst call-outs (ACOs in the form of chat messages (voice-to-text to associate labels with video target tracks, to designate spatial-temporal activity boundaries and to augment video tracking in challenging scenarios. Challenging scenarios include low-resolution sensors, moving targets and target trajectories obscured by natural and man-made clutter. MINER includes: (1 a fusion of graphical track and text data using probabilistic methods; (2 an activity pattern learning framework to support querying an index of activities of interest (AOIs and targets of interest (TOIs by movement type and geolocation; and (3 a user interface to support streaming multi-intelligence data processing. We also present an activity pattern learning framework that uses the multi-source associated data as training to index a large archive of full-motion videos (FMV. VIVA and MINER examples are demonstrated for wide aerial/overhead imagery over common data sets affording an improvement in tracking from video data alone, leading to 84% detection with modest misdetection/false alarm results due to the complexity of the scenario. The novel use of ACOs and chat Sensors 2014, 14 19844 messages in video tracking paves the way for user interaction, correction and preparation of situation awareness reports.

  6. Comprehensive Non-Destructive Conservation Documentation of Lunar Samples Using High-Resolution Image-Based 3D Reconstructions and X-Ray CT Data

    Science.gov (United States)

    Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Hanna, R. D.; Ketcham, R. A.

    2015-01-01

    Established contemporary conservation methods within the fields of Natural and Cultural Heritage encourage an interdisciplinary approach to preservation of heritage material (both tangible and intangible) that holds "Outstanding Universal Value" for our global community. NASA's lunar samples were acquired from the moon for the primary purpose of intensive scientific investigation. These samples, however, also invoke cultural significance, as evidenced by the millions of people per year that visit lunar displays in museums and heritage centers around the world. Being both scientifically and culturally significant, the lunar samples require a unique conservation approach. Government mandate dictates that NASA's Astromaterials Acquisition and Curation Office develop and maintain protocols for "documentation, preservation, preparation and distribution of samples for research, education and public outreach" for both current and future collections of astromaterials. Documentation, considered the first stage within the conservation methodology, has evolved many new techniques since curation protocols for the lunar samples were first implemented, and the development of new documentation strategies for current and future astromaterials is beneficial to keeping curation protocols up to date. We have developed and tested a comprehensive non-destructive documentation technique using high-resolution image-based 3D reconstruction and X-ray CT (XCT) data in order to create interactive 3D models of lunar samples that would ultimately be served to both researchers and the public. These data enhance preliminary scientific investigations including targeted sample requests, and also provide a new visual platform for the public to experience and interact with the lunar samples. We intend to serve these data as they are acquired on NASA's Astromaterials Acquisistion and Curation website at http://curator.jsc.nasa.gov/. Providing 3D interior and exterior documentation of astromaterial

  7. Wavelet-based 3D reconstruction of microcalcification clusters from two mammographic views: new evidence that fractal tumors are malignant and Euclidean tumors are benign.

    Directory of Open Access Journals (Sweden)

    Kendra A Batchelder

    Full Text Available The 2D Wavelet-Transform Modulus Maxima (WTMM method was used to detect microcalcifications (MC in human breast tissue seen in mammograms and to characterize the fractal geometry of benign and malignant MC clusters. This was done in the context of a preliminary analysis of a small dataset, via a novel way to partition the wavelet-transform space-scale skeleton. For the first time, the estimated 3D fractal structure of a breast lesion was inferred by pairing the information from two separate 2D projected mammographic views of the same breast, i.e. the cranial-caudal (CC and mediolateral-oblique (MLO views. As a novelty, we define the "CC-MLO fractal dimension plot", where a "fractal zone" and "Euclidean zones" (non-fractal are defined. 118 images (59 cases, 25 malignant and 34 benign obtained from a digital databank of mammograms with known radiologist diagnostics were analyzed to determine which cases would be plotted in the fractal zone and which cases would fall in the Euclidean zones. 92% of malignant breast lesions studied (23 out of 25 cases were in the fractal zone while 88% of the benign lesions were in the Euclidean zones (30 out of 34 cases. Furthermore, a Bayesian statistical analysis shows that, with 95% credibility, the probability that fractal breast lesions are malignant is between 74% and 98%. Alternatively, with 95% credibility, the probability that Euclidean breast lesions are benign is between 76% and 96%. These results support the notion that the fractal structure of malignant tumors is more likely to be associated with an invasive behavior into the surrounding tissue compared to the less invasive, Euclidean structure of benign tumors. Finally, based on indirect 3D reconstructions from the 2D views, we conjecture that all breast tumors considered in this study, benign and malignant, fractal or Euclidean, restrict their growth to 2-dimensional manifolds within the breast tissue.

  8. Wavelet-based 3D reconstruction of microcalcification clusters from two mammographic views: new evidence that fractal tumors are malignant and Euclidean tumors are benign.

    Science.gov (United States)

    Batchelder, Kendra A; Tanenbaum, Aaron B; Albert, Seth; Guimond, Lyne; Kestener, Pierre; Arneodo, Alain; Khalil, Andre

    2014-01-01

    The 2D Wavelet-Transform Modulus Maxima (WTMM) method was used to detect microcalcifications (MC) in human breast tissue seen in mammograms and to characterize the fractal geometry of benign and malignant MC clusters. This was done in the context of a preliminary analysis of a small dataset, via a novel way to partition the wavelet-transform space-scale skeleton. For the first time, the estimated 3D fractal structure of a breast lesion was inferred by pairing the information from two separate 2D projected mammographic views of the same breast, i.e. the cranial-caudal (CC) and mediolateral-oblique (MLO) views. As a novelty, we define the "CC-MLO fractal dimension plot", where a "fractal zone" and "Euclidean zones" (non-fractal) are defined. 118 images (59 cases, 25 malignant and 34 benign) obtained from a digital databank of mammograms with known radiologist diagnostics were analyzed to determine which cases would be plotted in the fractal zone and which cases would fall in the Euclidean zones. 92% of malignant breast lesions studied (23 out of 25 cases) were in the fractal zone while 88% of the benign lesions were in the Euclidean zones (30 out of 34 cases). Furthermore, a Bayesian statistical analysis shows that, with 95% credibility, the probability that fractal breast lesions are malignant is between 74% and 98%. Alternatively, with 95% credibility, the probability that Euclidean breast lesions are benign is between 76% and 96%. These results support the notion that the fractal structure of malignant tumors is more likely to be associated with an invasive behavior into the surrounding tissue compared to the less invasive, Euclidean structure of benign tumors. Finally, based on indirect 3D reconstructions from the 2D views, we conjecture that all breast tumors considered in this study, benign and malignant, fractal or Euclidean, restrict their growth to 2-dimensional manifolds within the breast tissue.

  9. Towards autonomic computing in machine vision applications: techniques and strategies for in-line 3D reconstruction in harsh industrial environments

    Science.gov (United States)

    Molleda, Julio; Usamentiaga, Rubén; García, Daniel F.; Bulnes, Francisco G.

    2011-03-01

    Nowadays machine vision applications require skilled users to configure, tune, and maintain. Because such users are scarce, the robustness and reliability of applications are usually significantly affected. Autonomic computing offers a set of principles such as self-monitoring, self-regulation, and self-repair which can be used to partially overcome those problems. Systems which include self-monitoring observe their internal states, and extract features about them. Systems with self-regulation are capable of regulating their internal parameters to provide the best quality of service depending on the operational conditions and environment. Finally, self-repairing systems are able to detect anomalous working behavior and to provide strategies to deal with such conditions. Machine vision applications are the perfect field to apply autonomic computing techniques. This type of application has strong constraints on reliability and robustness, especially when working in industrial environments, and must provide accurate results even under changing conditions such as luminance, or noise. In order to exploit the autonomic approach of a machine vision application, we believe the architecture of the system must be designed using a set of orthogonal modules. In this paper, we describe how autonomic computing techniques can be applied to machine vision systems, using as an example a real application: 3D reconstruction in harsh industrial environments based on laser range finding. The application is based on modules with different responsibilities at three layers: image acquisition and processing (low level), monitoring (middle level) and supervision (high level). High level modules supervise the execution of low-level modules. Based on the information gathered by mid-level modules, they regulate low-level modules in order to optimize the global quality of service, and tune the module parameters based on operational conditions and on the environment. Regulation actions involve

  10. The Virtual 3D Reconstruction of the East Pediment of the Temple of Zeus at Olympia – Presentation of an Interactive CD-ROM

    Directory of Open Access Journals (Sweden)

    András PATAY-HORVÁTH Patay-Horváth

    2011-12-01

    Full Text Available The paper gives an overview of a two-years project concerning a major monument of ancient Greek art and presents the interactive, bilingual (English/Hungarian CD-ROM, which is intended to summarize and visualize its final results. The presented project approaches a century-old controversy in a new way by producing a virtual 3D reconstruction of a monumental marble group. Digital models of the statues were produced by scanning the original fragments and by reconstructing them virtually. The virtual model of the pediment surrounding the sculptures was prepared on the basis of the latest architectural studies and afterwards the reconstructed models were inserted in this frame, in order to test the technical feasibility and aesthetic effects the four possible arrangements. The resulting models enable easy and very instructive experimentation, which would be otherwise impossible with the originals and/or very expensive and not very practicable with traditional tools (e.g. real-size plaster models. The complete model can effectively be used to verify the results of earlier or more recent reconstructions presented only in simple drawings. In addition, the 3D models of the individual fragments can be used for further research and for visualization.  The documentary CD-ROM presenting the full background, the methods and the conclusions of the project contains beside a comprehensive text various kinds of supporting documents (images, 3D models, papers, broadcasts, audiovisual material. It is addressed to a mixed audience: a picture gallery, a short documentary movie some other attachments including a selected bibliography is intended for the general public, but scholarly publications, presentations on related problems are also included for specialists interested in certain details.

  11. 3D reconstruction of VZV infected cell nuclei and PML nuclear cages by serial section array scanning electron microscopy and electron tomography.

    Directory of Open Access Journals (Sweden)

    Mike Reichelt

    Full Text Available Varicella-zoster virus (VZV is a human alphaherpesvirus that causes varicella (chickenpox and herpes zoster (shingles. Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity, what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the

  12. Wavelet-Based 3D Reconstruction of Microcalcification Clusters from Two Mammographic Views: New Evidence That Fractal Tumors Are Malignant and Euclidean Tumors Are Benign

    Science.gov (United States)

    Batchelder, Kendra A.; Tanenbaum, Aaron B.; Albert, Seth; Guimond, Lyne; Kestener, Pierre; Arneodo, Alain; Khalil, Andre

    2014-01-01

    The 2D Wavelet-Transform Modulus Maxima (WTMM) method was used to detect microcalcifications (MC) in human breast tissue seen in mammograms and to characterize the fractal geometry of benign and malignant MC clusters. This was done in the context of a preliminary analysis of a small dataset, via a novel way to partition the wavelet-transform space-scale skeleton. For the first time, the estimated 3D fractal structure of a breast lesion was inferred by pairing the information from two separate 2D projected mammographic views of the same breast, i.e. the cranial-caudal (CC) and mediolateral-oblique (MLO) views. As a novelty, we define the “CC-MLO fractal dimension plot”, where a “fractal zone” and “Euclidean zones” (non-fractal) are defined. 118 images (59 cases, 25 malignant and 34 benign) obtained from a digital databank of mammograms with known radiologist diagnostics were analyzed to determine which cases would be plotted in the fractal zone and which cases would fall in the Euclidean zones. 92% of malignant breast lesions studied (23 out of 25 cases) were in the fractal zone while 88% of the benign lesions were in the Euclidean zones (30 out of 34 cases). Furthermore, a Bayesian statistical analysis shows that, with 95% credibility, the probability that fractal breast lesions are malignant is between 74% and 98%. Alternatively, with 95% credibility, the probability that Euclidean breast lesions are benign is between 76% and 96%. These results support the notion that the fractal structure of malignant tumors is more likely to be associated with an invasive behavior into the surrounding tissue compared to the less invasive, Euclidean structure of benign tumors. Finally, based on indirect 3D reconstructions from the 2D views, we conjecture that all breast tumors considered in this study, benign and malignant, fractal or Euclidean, restrict their growth to 2-dimensional manifolds within the breast tissue. PMID:25222610

  13. Video tracking in the extreme: video analysis for nocturnal underwater animal movement.

    Science.gov (United States)

    Patullo, B W; Jolley-Rogers, G; Macmillan, D L

    2007-11-01

    Computer analysis of video footage is one option for recording locomotor behavior for a range of neurophysiological and behavioral studies. This technique is reasonably well established and accepted, but its use for some behavioral analyses remains a challenge. For example, filming through water can lead to reflection, and filming nocturnal activity can reduce resolution and clarity of filmed images. The aim of this study was to develop a noninvasive method for recording nocturnal activity in aquatic decapods and test the accuracy of analysis by video tracking software. We selected crayfish, Cherax destructor, because they are often active at night, they live underwater, and data on their locomotion is important for answering biological and physiological questions such as how they explore and navigate. We constructed recording arenas and filmed animals in infrared light. Wethen compared human observer data and software-acquired values. In this article, we outline important apparatus and software issues to obtain reliable computer tracking.

  14. 3D Reconstruction of the Digestive System in Octopus vulgaris Cuvier, 1797 Embryos and Paralarvae during the First Month of Life

    Directory of Open Access Journals (Sweden)

    Raquel Fernández-Gago

    2017-07-01

    length. 3D reconstruction represents a new tool to study the morphology and functionality of the cephalopod digestive system during the first days of life.

  15. 3D Reconstruction of the Digestive System in Octopus vulgaris Cuvier, 1797 Embryos and Paralarvae during the First Month of Life

    Science.gov (United States)

    Fernández-Gago, Raquel; Heß, Martin; Gensler, Heidemarie; Rocha, Francisco

    2017-01-01

    Octopus vulgaris aquaculture is limited due to poor biological knowledge of the paralarval stages (e.g., digestive system functionality), their nutritional requirements (e.g., adequate live diet) and standardization of rearing techniques. These factors are important in explaining the high mortality rate observed in this developmental stage under culture conditions. For a better understanding of nutrition biology of this species, we investigated the 3D microanatomy of the digestive tract of the embryo and paralarvae during the first month of life. O. vulgaris paralarvae digestive system is similar to that in the adult. The “descending branch” has a dorsal position and is formed by the buccal mass, oesophagus and crop. Ventrally, the “ascending branch” is formed by the intestine and the anus. The digestive gland, the posterior salivary glands and the inner yolk sac (in the case of the embryo and hatched paralarvae) are located between the “ascending” and “descending” branches. In the curve of the U-shaped digestive tract, a caecum and the stomach can be found. The reconstructions reveal that anatomically the digestive system is already complete when the paralarvae hatch. The reconstruction of the buccal mass at different post-hatching days has demonstrated that all the necessary structures for food intake are present. However, the radula surface in contact with the pharynx is very small on the first day of life. Although the digestive system has all the structures to feed, the digestive gland and radula take longer to reach full functionality. We have established four development periods: embryonic, early post-hatching, late post-hatching and juvenile-adult. The differentiation between these periods was done by type of feeding (endogenous or exogenous), the state of maturation and hence functionality of the digestive gland, type of growth (linear, no net, or exponential), and measurement of the arm lengths with respect to the mantle length. 3D

  16. 3D Reconstruction of a Fluvial Sediment Slug from Source to Sink: reach-scale modeling of the Dart River, NZ

    Science.gov (United States)

    Brasington, J.; Cook, S.; Cox, S.; James, J.; Lehane, N.; McColl, S. T.; Quincey, D. J.; Williams, R. D.

    2014-12-01

    Following heavy rainfall on 4/1/14, a debris flow at Slip Stream (44.59 S 168.34 E) introduced >106 m3 of sediment to the Dart River valley floor in NZ Southern Alps. Runout over an existing fan dammed the Dart River causing a sudden drop in discharge downstream. This broad dam was breached quickly; however the temporary loss of conveyance impounded a 3 km lake with a volume of 6 x 106 m3 and depths that exceed 10 m. Quantifying the impact of this large sediment pulse on the Dart River is urgently needed to assess potential sedimentation downstream and will also provide an ideal vehicle to test theories of bed wave migration in large, extensively braided rivers. Recent advances in geomatics offer the opportunity to study these impacts directly through the production of high-resolution DEMs. These 3D snapshots can then be compared through time to quantify the morphodynamic response of the channel as it adjusts to the change in sediment supply. In this study we describe the methods and results of a novel survey strategy designed to capture of the complex morphology of the Dart River along a remote 40 km reach, from the upstream landslide source to its distal sediment sink in Lake Wakatipu. The scale of this system presents major logistical and methodological challenges, and hitherto would have conventionally be addressed with airborne laser scanning, bringing with it significant deployment constraints and costs. By contrast, we present sub-metre 3D reconstructions of the system (Figure 1), derived from highly redundant aerial photography shot with a non-metric camera from a helicopter survey that extended over an 80 km2 area. Structure-from-Motion photogrammetry was used to solve simultaneously camera position, pose and derive a 3D point cloud based on over 4000 images. Reconstructions were found to exhibit significant systematic error resulting from the implicit estimation of the internal camera orientation parameters, and we show how these effects can be minimized

  17. 3D Reconstruction of historical wind erosion concerning an inland dune development of the Lower Geest of Schleswig-Holstein (Northern Central Europe)

    Science.gov (United States)

    Lungershausen, Uta

    2010-05-01

    Rainer Duttmann, Department of Geography, University of Kiel Hans-Rudolf Bork, Ecology Centre, University of Kiel 3D Reconstruction of historical wind erosion concerning an inland dune development of the Lower Geest of Schleswig-Holstein (Northern Central Europe) PhD project "Geoarchaeological reconstruction and 3D visualization of an inland dune development in Northern Germany" Wind erosion and the occurrence of sand drifts has been a distinctive phenomenon of the Weichselian outwash plain in northern Germany since the very beginning of deforestation and agricultural land use. Although the main periods of aeolian activity are broadly constrained, estimations of the frequency of wind erosion events during these periods remain elusive. The aim of this investigation is to provide a 3-dimensional reconstruction of historical wind erosion of a dune complex in high spatial and temporal resolution, using a small inland dune complex in the vicinity of Joldelund (Germany, Northern Frisia) as a study area. The dune complex,Kuhharder hill, covers an area of around 2 ha and forms the westernmost part of a larger inland dune field approximately 80 ha in size. During forestation in the 1950s, several archaeological sites were discovered which which formed the basis for further archaeological investigations during the 20th century. The reconstruction of man-nature interactions against the background of dune development on Kuhharder hill is achieved via a multi-disciplinary approach interlinking the study of soil-sediment-sequences, ancient dune surfaces as well as archaeological and historical records, pollen and anthracological analysis. On the basis of a dated, process-based stratigraphy different phases of dune activity (sediment deposition) and dune stability (soil formation) can be interpreted. The early aeolian relief developed during the Wechselian Late Glacial (Younger Dryas) and was followed by a longer period of dune stabilisation and soil formation due to natural

  18. 3D Reconstruction of the Digestive System in Octopus vulgaris Cuvier, 1797 Embryos and Paralarvae during the First Month of Life.

    Science.gov (United States)

    Fernández-Gago, Raquel; Heß, Martin; Gensler, Heidemarie; Rocha, Francisco

    2017-01-01

    Octopus vulgaris aquaculture is limited due to poor biological knowledge of the paralarval stages (e.g., digestive system functionality), their nutritional requirements (e.g., adequate live diet) and standardization of rearing techniques. These factors are important in explaining the high mortality rate observed in this developmental stage under culture conditions. For a better understanding of nutrition biology of this species, we investigated the 3D microanatomy of the digestive tract of the embryo and paralarvae during the first month of life. O. vulgaris paralarvae digestive system is similar to that in the adult. The "descending branch" has a dorsal position and is formed by the buccal mass, oesophagus and crop. Ventrally, the "ascending branch" is formed by the intestine and the anus. The digestive gland, the posterior salivary glands and the inner yolk sac (in the case of the embryo and hatched paralarvae) are located between the "ascending" and "descending" branches. In the curve of the U-shaped digestive tract, a caecum and the stomach can be found. The reconstructions reveal that anatomically the digestive system is already complete when the paralarvae hatch. The reconstruction of the buccal mass at different post-hatching days has demonstrated that all the necessary structures for food intake are present. However, the radula surface in contact with the pharynx is very small on the first day of life. Although the digestive system has all the structures to feed, the digestive gland and radula take longer to reach full functionality. We have established four development periods: embryonic, early post-hatching, late post-hatching and juvenile-adult. The differentiation between these periods was done by type of feeding (endogenous or exogenous), the state of maturation and hence functionality of the digestive gland, type of growth (linear, no net, or exponential), and measurement of the arm lengths with respect to the mantle length. 3D reconstruction

  19. A novel video tracking method to evaluate the effect of influenza infection and antiviral treatment on ferret activity.

    Science.gov (United States)

    Oh, Ding Yuan; Barr, Ian G; Hurt, Aeron C

    2015-01-01

    Ferrets are the preferred animal model to assess influenza virus infection, virulence and transmission as they display similar clinical symptoms and pathogenesis to those of humans. Measures of disease severity in the ferret include weight loss, temperature rise, sneezing, viral shedding and reduced activity. To date, the only available method for activity measurement has been the assignment of an arbitrary score by a 'blind' observer based on pre-defined responsiveness scale. This manual scoring method is subjective and can be prone to bias. In this study, we described a novel video-tracking methodology for determining activity changes in a ferret model of influenza infection. This method eliminates the various limitations of manual scoring, which include the need for a sole 'blind' observer and the requirement to recognise the 'normal' activity of ferrets in order to assign relative activity scores. In ferrets infected with an A(H1N1)pdm09 virus, video-tracking was more sensitive than manual scoring in detecting ferret activity changes. Using this video-tracking method, oseltamivir treatment was found to ameliorate the effect of influenza infection on activity in ferret. Oseltamivir treatment of animals was associated with an improvement in clinical symptoms, including reduced inflammatory responses in the upper respiratory tract, lower body weight loss and a smaller rise in body temperature, despite there being no significant reduction in viral shedding. In summary, this novel video-tracking is an easy-to-use, objective and sensitive methodology for measuring ferret activity.

  20. Contour interpolated radial basis functions with spline boundary correction for fast 3D reconstruction of the human articular cartilage from MR images

    Energy Technology Data Exchange (ETDEWEB)

    Javaid, Zarrar; Unsworth, Charles P., E-mail: c.unsworth@auckland.ac.nz [Department of Engineering Science, The University of Auckland, Auckland 1010 (New Zealand); Boocock, Mark G.; McNair, Peter J. [Health and Rehabilitation Research Center, Auckland University of Technology, Auckland 1142 (New Zealand)

    2016-03-15

    Purpose: The aim of this work is to demonstrate a new image processing technique that can provide a “near real-time” 3D reconstruction of the articular cartilage of the human knee from MR images which is user friendly. This would serve as a point-of-care 3D visualization tool which would benefit a consultant radiologist in the visualization of the human articular cartilage. Methods: The authors introduce a novel fusion of an adaptation of the contour method known as “contour interpolation (CI)” with radial basis functions (RBFs) which they describe as “CI-RBFs.” The authors also present a spline boundary correction which further enhances volume estimation of the method. A subject cohort consisting of 17 right nonpathological knees (ten female and seven male) is assessed to validate the quality of the proposed method. The authors demonstrate how the CI-RBF method dramatically reduces the number of data points required for fitting an implicit surface to the entire cartilage, thus, significantly improving the speed of reconstruction over the comparable RBF reconstruction method of Carr. The authors compare the CI-RBF method volume estimation to a typical commercial package (3D DOCTOR), Carr’s RBF method, and a benchmark manual method for the reconstruction of the femoral, tibial, and patellar cartilages. Results: The authors demonstrate how the CI-RBF method significantly reduces the number of data points (p-value < 0.0001) required for fitting an implicit surface to the cartilage, by 48%, 31%, and 44% for the patellar, tibial, and femoral cartilages, respectively. Thus, significantly improving the speed of reconstruction (p-value < 0.0001) by 39%, 40%, and 44% for the patellar, tibial, and femoral cartilages over the comparable RBF model of Carr providing a near real-time reconstruction of 6.49, 8.88, and 9.43 min for the patellar, tibial, and femoral cartilages, respectively. In addition, it is demonstrated how the CI-RBF method matches the volume

  1. Newton’s Cradle Experiment Using Video Tracking Analysis with Multiple Representation Approach

    Science.gov (United States)

    Anissofira, A.; Latief, F. D. E.; Kholida, L.; Sinaga, P.

    2017-09-01

    This paper reports a Physics lesson using video tracking analysis applied in Newton’s Cradle experiment to train student’s multiple representation skill. This study involved 30 science high school students from class XI. In this case, Tracker software was used to verify energy conservation law, with help from data result such as graphs and tables. Newton’s Cradle is commonly used to demonstrate the law of energy and momentum conservation. It consists of swinging spherical bobs which transfers energy from one to another by means of elastic collisions. From the video analysis, it is found that there is a difference in the velocity of the two bobs of opposite ends. Furthermore, investigation of what might cause it to happen can be done by observing and analysing the recorded video. This paper discusses students’ response and teacher’s reflection after using Tracker video analysis software in the Physics lesson. Since Tracker has the ability to provide us with multiple means of data representation way, we conclude that this method could be a good alternative solution and might also be considered better than performing a hands-on experiment activity in which not every school have suitable laboratory equipment.

  2. The Habituation/Cross-Habituation Test Revisited: Guidance from Sniffing and Video Tracking

    Directory of Open Access Journals (Sweden)

    G. Coronas-Samano

    2016-01-01

    Full Text Available The habituation/cross-habituation test (HaXha is a spontaneous odor discrimination task that has been used for many decades to evaluate olfactory function in animals. Animals are presented repeatedly with the same odorant after which a new odorant is introduced. The time the animal explores the odor object is measured. An animal is considered to cross-habituate during the novel stimulus trial when the exploration time is higher than the prior trial and indicates the degree of olfactory patency. On the other hand, habituation across the repeated trials involves decreased exploration time and is related to memory patency, especially at long intervals. Classically exploration is timed using a stopwatch when the animal is within 2 cm of the object and aimed toward it. These criteria are intuitive, but it is unclear how they relate to olfactory exploration, that is, sniffing. We used video tracking combined with plethysmography to improve accuracy, avoid observer bias, and propose more robust criteria for exploratory scoring when sniff measures are not available. We also demonstrate that sniff rate combined with proximity is the most direct measure of odorant exploration and provide a robust and sensitive criterion.

  3. Novel approach to automatically classify rat social behavior using a video tracking system.

    Science.gov (United States)

    Peters, Suzanne M; Pinter, Ilona J; Pothuizen, Helen H J; de Heer, Raymond C; van der Harst, Johanneke E; Spruijt, Berry M

    2016-08-01

    In the past, studies in behavioral neuroscience and drug development have relied on simple and quick readout parameters of animal behavior to assess treatment efficacy or to understand underlying brain mechanisms. The predominant use of classical behavioral tests has been repeatedly criticized during the last decades because of their poor reproducibility, poor translational value and the limited explanatory power in functional terms. We present a new method to monitor social behavior of rats using automated video tracking. The velocity of moving and the distance between two rats were plotted in frequency distributions. In addition, behavior was manually annotated and related to the automatically obtained parameters for a validated interpretation. Inter-individual distance in combination with velocity of movement provided specific behavioral classes, such as moving with high velocity when "in contact" or "in proximity". Human observations showed that these classes coincide with following (chasing) behavior. In addition, when animals are "in contact", but at low velocity, behaviors such as allogrooming and social investigation were observed. Also, low dose treatment with morphine and short isolation increased the time animals spent in contact or in proximity at high velocity. Current methods that involve the investigation of social rat behavior are mostly limited to short and relatively simple manual observations. A new and automated method for analyzing social behavior in a social interaction test is presented here and shows to be sensitive to drug treatment and housing conditions known to influence social behavior in rats. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Compression of Video Tracking and Bandwidth Balancing Routing in Wireless Multimedia Sensor Networks

    Directory of Open Access Journals (Sweden)

    Yin Wang

    2015-12-01

    Full Text Available There has been a tremendous growth in multimedia applications over wireless networks. Wireless Multimedia Sensor Networks(WMSNs have become the premier choice in many research communities and industry. Many state-of-art applications, such as surveillance, traffic monitoring, and remote heath care are essentially video tracking and transmission in WMSNs. The transmission speed is constrained by the big file size of video data and fixed bandwidth allocation in constant routing paths. In this paper, we present a CamShift based algorithm to compress the tracking of videos. Then we propose a bandwidth balancing strategy in which each sensor node is able to dynamically select the node for the next hop with the highest potential bandwidth capacity to resume communication. Key to this strategy is that each node merely maintains two parameters that contain its historical bandwidth varying trend and then predict its near future bandwidth capacity. Then, the forwarding node selects the next hop with the highest potential bandwidth capacity. Simulations demonstrate that our approach significantly increases the data received by the sink node and decreases the delay on video transmission in Wireless Multimedia Sensor Network environments.

  5. A bioinformatics-based overview of protein Lys-Ne-acetylation

    Science.gov (United States)

    Among posttranslational modifications, there are some conceptual similarities between Lys-N'-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. T...

  6. 3-D reconstructions of active stars

    DEFF Research Database (Denmark)

    Korhonen, Heidi Helena

    2012-01-01

    Stars are usually faint point sources and investigating their surfaces and interiors observationally is very demanding. Here I give a review on the state-of-the-art observing techniques and recent results on studying interiors and surface features of active stars.......Stars are usually faint point sources and investigating their surfaces and interiors observationally is very demanding. Here I give a review on the state-of-the-art observing techniques and recent results on studying interiors and surface features of active stars....

  7. 3D reconstruction of tensors and vectors

    Energy Technology Data Exchange (ETDEWEB)

    Defrise, Michel; Gullberg, Grant T.

    2005-02-17

    Here we have developed formulations for the reconstruction of 3D tensor fields from planar (Radon) and line-integral (X-ray) projections of 3D vector and tensor fields. Much of the motivation for this work is the potential application of MRI to perform diffusion tensor tomography. The goal is to develop a theory for the reconstruction of both Radon planar and X-ray or line-integral projections because of the flexibility of MRI to obtain both of these type of projections in 3D. The development presented here for the linear tensor tomography problem provides insight into the structure of the nonlinear MRI diffusion tensor inverse problem. A particular application of tensor imaging in MRI is the potential application of cardiac diffusion tensor tomography for determining in vivo cardiac fiber structure. One difficulty in the cardiac application is the motion of the heart. This presents a need for developing future theory for tensor tomography in a motion field. This means developing a better understanding of the MRI signal for diffusion processes in a deforming media. The techniques developed may allow the application of MRI tensor tomography for the study of structure of fiber tracts in the brain, atherosclerotic plaque, and spine in addition to fiber structure in the heart. However, the relations presented are also applicable to other fields in medical imaging such as diffraction tomography using ultrasound. The mathematics presented can also be extended to exponential Radon transform of tensor fields and to other geometric acquisitions such as cone beam tomography of tensor fields.

  8. A Multi-Data Source and Multi-Sensor Approach for the 3D Reconstruction and Web Visualization of a Complex Archaelogical Site: The Case Study of “Tolmo De Minateda”

    Directory of Open Access Journals (Sweden)

    Jose Alberto Torres-Martínez

    2016-06-01

    Full Text Available The complexity of archaeological sites hinders creation of an integral model using the current Geomatic techniques (i.e., aerial, close-range photogrammetry and terrestrial laser scanner individually. A multi-sensor approach is therefore proposed as the optimal solution to provide a 3D reconstruction and visualization of these complex sites. Sensor registration represents a riveting milestone when automation is required and when aerial and terrestrial datasets must be integrated. To this end, several problems must be solved: coordinate system definition, geo-referencing, co-registration of point clouds, geometric and radiometric homogeneity, etc. The proposed multi-data source and multi-sensor approach is applied to the study case of the “Tolmo de Minateda” archaeological site. A total extension of 9 ha is reconstructed, with an adapted level of detail, by an ultralight aerial platform (paratrike, an unmanned aerial vehicle, a terrestrial laser scanner and terrestrial photogrammetry. Finally, a mobile device (e.g., tablet or smartphone has been used to integrate, optimize and visualize all this information, providing added value to archaeologists and heritage managers who want to use an efficient tool for their works at the site, and even for non-expert users who just want to know more about the archaeological settlement.

  9. Frecuencia y tipo de fracturas en traumatismos maxilofaciales: Evaluación con Tomografía Multislice con reconstrucciones multiplanares y tridimensionales Frequency and types of fractures in maxillofacial traumas: Assessment using MDCT with multiplanar and 3D reconstructions

    Directory of Open Access Journals (Sweden)

    Gabriela Tomich

    2011-12-01

    multiplanar imaging techniques for a proper evaluation. Objectives. To describe frequency and types of fractures in a series of patients with MFT evaluated by multi-slice computed tomography (MDCT with multiplanar and 3D reconstructions. Materials and Methods. Facial bone CTs ordered for MFT by the Emergency Department from June 2008 to December 2009 were retrospectively reviewed. The following data were obtained: age, gender, cause of trauma, presence and type of fractures. Patients were evaluated with an 8-channel MDCT. Multiplanar reconstructions were performed in all cases using high resolution bone window and soft tissue window, as well as 3D reconstructions. Results. One-hundred and thirty-seven CTs were performed for MFT: 78 (57% showed 131 fractures. Of these 78 patients, 52 (66% were males and 26 (34% were females; mean age 33 years old (range: 14-90 yrs.. Causes: 58 % were injuries from traffic accidents; 24% were injuries from fights; 13% were sport injuries; and 7% were due to miscellaneous etiologies. Type and frequency of fractures: 18.3% were orbital floor fractures, 16% were maxillary sinus fractures, 15.3% were nasal fractures, 13% were jaw fractures, 9.2% were orbital fractures, and 12.3% were fractures of the zygomatic-malar complex; two cases of Le Fort II-III fractures were also observed. Conclusions. Fractures were more common in males, in the age range from 15 to 35 years old. Most fractures, and the most complex ones, were caused by traffic accidents. The most common fracture, either isolated or associated with other fractures, was the orbital floor fracture.

  10. a Multi-Data Source and Multi-Sensor Approach for the 3d Reconstruction and Visualization of a Complex Archaelogical Site: the Case Study of Tolmo de Minateda

    Science.gov (United States)

    Torres-Martínez, J. A.; Seddaiu, M.; Rodríguez-Gonzálvez, P.; Hernández-López, D.; González-Aguilera, D.

    2015-02-01

    The complexity of archaeological sites hinders to get an integral modelling using the actual Geomatic techniques (i.e. aerial, closerange photogrammetry and terrestrial laser scanner) individually, so a multi-sensor approach is proposed as the best solution to provide a 3D reconstruction and visualization of these complex sites. Sensor registration represents a riveting milestone when automation is required and when aerial and terrestrial dataset must be integrated. To this end, several problems must be solved: coordinate system definition, geo-referencing, co-registration of point clouds, geometric and radiometric homogeneity, etc. Last but not least, safeguarding of tangible archaeological heritage and its associated intangible expressions entails a multi-source data approach in which heterogeneous material (historical documents, drawings, archaeological techniques, habit of living, etc.) should be collected and combined with the resulting hybrid 3D of "Tolmo de Minateda" located models. The proposed multi-data source and multi-sensor approach is applied to the study case of "Tolmo de Minateda" archaeological site. A total extension of 9 ha is reconstructed, with an adapted level of detail, by an ultralight aerial platform (paratrike), an unmanned aerial vehicle, a terrestrial laser scanner and terrestrial photogrammetry. In addition, the own defensive nature of the site (i.e. with the presence of three different defensive walls) together with the considerable stratification of the archaeological site (i.e. with different archaeological surfaces and constructive typologies) require that tangible and intangible archaeological heritage expressions can be integrated with the hybrid 3D models obtained, to analyse, understand and exploit the archaeological site by different experts and heritage stakeholders.

  11. Evaluating sub-lethal effects of orchard-applied pyrethroids using video-tracking software to quantify honey bee behaviors.

    Science.gov (United States)

    Ingram, Erin M; Augustin, Julie; Ellis, Marion D; Siegfried, Blair D

    2015-09-01

    Managed honey bee, Apis mellifera L., colonies are contracted to pollinate fruit and nut orchards improving crop quality and yield. Colonies placed in orchards are potentially exposed to pyrethroid insecticides used for broad-spectrum pest control. Pyrethroids have been reported to pose minimal risk to bees due to their low application rates in the field and putative repellent properties. This repellency is believed to alter foraging behavior with the benefit of preventing bees from encountering a lethal dose in the field. However, sub-lethal exposure to pyrethroids may adversely impact bee behavior potentially resulting in social dysfunction or disruption of foraging. This study quantified behaviors associated with sub-lethal exposure to orchard-applied pyrethroids including, lambda-cyhalothrin, esfenvalerate, and permethrin, using video tracking software, Ethovision XT (Noldus Information Technologies). Bee locomotion, social interaction, and time spent near a food source were measured over a 24-h period. Bees treated with a pyrethroid traveled 30-71% less than control bees. Social interaction time decreased by 43% for bees treated with a high sub-lethal dose of esfenvalerate. Bees exposed to a high sub-lethal dose of permethrin spent 67% less time in social interaction and spent more than 5 times as long in the food zone compared to control bees. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Assessment of acute sublethal effects of clothianidin on motor function of honeybee workers using video-tracking analysis.

    Science.gov (United States)

    Alkassab, Abdulrahim T; Kirchner, Wolfgang H

    2018-01-01

    Sublethal impacts of pesticides on the locomotor activity might occur to different degrees and could escape visual observation. Therefore, our objective is the utilization of video-tracking to quantify how the acute oral exposure to different doses (0.1-2ng/bee) of the neonicotinoid "clothianidin" influences the locomotor activity of honeybees in a time course experiment. The total distance moved, resting time as well as the duration and frequency of bouts of laying upside down are measured. Our results show that bees exposed to acute sublethal doses of clothianidin exhibit a significant increase in the total distance moved after 30 and 60min of the treatment at the highest dose (2ng/bee). Nevertheless, a reduction of the total distance is observed at this dose 90min post-treatment compared to the distance of the same group after 30min, where the treated bees show an arched abdomen and start to lose their postural control. The treated bees with 1ng clothianidin show a significant increase in total distance moved over the experimental period. Moreover, a reduction in the resting time and increase of the duration and frequency of bouts of laying upside down at these doses are found. Furthermore, significant effects on the tested parameters are observed at the dose (0.5ng/bee) first at 60min post-treatment compared to untreated bees. The lowest dose (0.1ng/bee) has non-significant effects on the motor activity of honeybees compared to untreated bees over the experimental period. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Effects of the pyrethroid insecticide Cypermethrin on the locomotor activity of the wolf spider Pardosa amentata: quantitative analysis employing computer-automated video tracking

    DEFF Research Database (Denmark)

    Baatrup, E; Bayley, M

    1993-01-01

    Pardosa amentata was quantified in an open field setup, using computer-automated video tracking. Each spider was recorded for 24 hr prior to pesticide exposure. After topical application of 4.6 ng of Cypermethrin, the animal was recorded for a further 48 hr. Finally, after 9 days of recovery, the spider...... was tracked for 24 hr. Initially, Cypermethrin induced an almost instant paralysis of the hind legs and a lack of coordination in movement seen in the jagged and circular track appearance. This phase culminated in total quiescence, lasting approximately 12 hr in males and 24-48 hr in females. Following...

  14. Quantifying sublethal effects of glyphosate and Roundup® to Daphnia magna using a fluorescence based enzyme activity assay and video tracking

    DEFF Research Database (Denmark)

    Roslev, Peter; R. Hansen, Lone; Ørsted, Michael

    Glyphosate (N-(phosphonomethyl)glycine) is the active ingredient in a range of popular broad-spectrum, non-selective herbicide formulations. The toxicity of this herbicide to non-target aquatic organisms such as Daphnia magna is often evaluated using conventional toxicity assays that focus...... on endpoints such as immobility and mortality. In this study, we investigated sublethal effects of glyphosate and Roundup® to D. magna using video tracking for quantifying behavioral changes, and a novel fluorescence based assay for measuring in vivo hydrolytic enzyme activity (FLEA assay). Roundup® exposure...... resulted in concentration-dependent inhibition of alkaline phosphatase activity in D. magna. The inhibition of alkaline phosphatase by Roundup® was temperature-dependent with lowest inhibition at 14 °C and greater inhibition at 20 and 26 °C. Exposure of D. magna to sublethal concentrations of glyphosate...

  15. Manual versus Automated Rodent Behavioral Assessment: Comparing Efficacy and Ease of Bederson and Garcia Neurological Deficit Scores to an Open Field Video-Tracking System

    Directory of Open Access Journals (Sweden)

    Fiona A. Desland

    2014-01-01

    Full Text Available Animal models of stroke have been crucial in advancing our understanding of the pathophysiology of cerebral ischemia. Currently, the standards for determining neurological deficit in rodents are the Bederson and Garcia scales, manual assessments scoring animals based on parameters ranked on a narrow scale of severity. Automated open field analysis of a live-video tracking system that analyzes animal behavior may provide a more sensitive test. Results obtained from the manual Bederson and Garcia scales did not show significant differences between pre- and post-stroke animals in a small cohort. When using the same cohort, however, post-stroke data obtained from automated open field analysis showed significant differences in several parameters. Furthermore, large cohort analysis also demonstrated increased sensitivity with automated open field analysis versus the Bederson and Garcia scales. These early data indicate use of automated open field analysis software may provide a more sensitive assessment when compared to traditional Bederson and Garcia scales.

  16. Accuracy of spiral CT and 3D reconstruction in the detection of acute pulmonary embolism - development of an animal model using porcine lungs and technical specimens. Development of an animal model using porcine lungs and technical specimens; Diagnostik der akuten Lungenembolie mittels Spiral-CT und 3D-Rekonstruktion. Entwicklung eines Tiermodells und technischer Probekoerper im Ex-vivo-Experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ries, B.G. [Klinik und Poliklinik fuer Radiologie, Univ. Mainz (Germany); Klinik fuer Radiologische Diagnostik, RWTH Aachen (Germany); Kauczor, H.U.; Thelen, M. [Klinik und Poliklinik fuer Radiologie, Univ. Mainz (Germany); Konerding, M.A. [Anatomisches Inst., Mainz Univ (Germany)

    2001-02-01

    Purpose: To develop a model for simulation the CT morphologic situation of acute pulmonary embolism, to evaluate the accuracy of spiral CT and 3D reconstruction in the detection of artificial emboli and to investigate the influence of the orientation of emboli depending on z-axis orientation. Materials and Methods: Standardized artificial emboli made of wax and of defined size and shape were positioned into the pulmonary arteries of porcine lungs. Castings of the embolized pulmonary arterial trees were made by injection of a special opaque resin. After performance of spiral CT the data sets of the emboli and the pulmonary arteries were post-processed. The 3D segmentations were compared with the anatomic preparation to evaluate the accuracy of spiral CT/3D reconstruction-technique. Technical specimens simulating CT-morphology of acute embolized vessels underwent spiral CT in six different positions with respect to the z-axis. The CT data were reconstructed using a standardized and a contrastadapted method with interactive correction. The 3D emboli were analysed under qualitative aspects, and measurements of their extent were done. Results: In nearly 91%, there was complete agreement between CT and the corresponding findings at the anatomical preparation. Measurements of the 3D reconstructed technical specimens showed discrepancies of shape and size in dependence of the size of the original preparation, orientation and reconstruction technique. Overestimation up to 4 mm and underestimation to 2,2 mm were observed. Measurements of preparations with heights from 14 to 26 mm showed variances of {+-}1,5 mm ({proportional_to}6-11%). Conclusion: The presented models are suitable to simulate CT morphology of acute pulmonary embolism under ex-vivo conditions. Accuracy in the detection of artificial emboli using spiral CT/3D reconstruction is affected by localization, size and orientation of the emboli and the reconstruction technique. (orig.) [German] Ziel: Die Entwicklung

  17. Can fractal methods applied to video tracking detect the effects of deltamethrin pesticide or mercury on the locomotion behavior of shrimps?

    Science.gov (United States)

    Tenorio, Bruno Mendes; da Silva Filho, Eurípedes Alves; Neiva, Gentileza Santos Martins; da Silva, Valdemiro Amaro; Tenorio, Fernanda das Chagas Angelo Mendes; da Silva, Themis de Jesus; Silva, Emerson Carlos Soares E; Nogueira, Romildo de Albuquerque

    2017-08-01

    Shrimps can accumulate environmental toxicants and suffer behavioral changes. However, methods to quantitatively detect changes in the behavior of these shrimps are still needed. The present study aims to verify whether mathematical and fractal methods applied to video tracking can adequately describe changes in the locomotion behavior of shrimps exposed to low concentrations of toxic chemicals, such as 0.15µgL-1 deltamethrin pesticide or 10µgL-1 mercuric chloride. Results showed no change after 1min, 4, 24, and 48h of treatment. However, after 72 and 96h of treatment, both the linear methods describing the track length, mean speed, mean distance from the current to the previous track point, as well as the non-linear methods of fractal dimension (box counting or information entropy) and multifractal analysis were able to detect changes in the locomotion behavior of shrimps exposed to deltamethrin. Analysis of angular parameters of the track points vectors and lacunarity were not sensitive to those changes. None of the methods showed adverse effects to mercury exposure. These mathematical and fractal methods applicable to software represent low cost useful tools in the toxicological analyses of shrimps for quality of food, water and biomonitoring of ecosystems. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. 3D reconstruction of microminiature objects based on contour line

    Science.gov (United States)

    Li, Cailin; Wang, Qiang; Guo, Baoyun

    2009-10-01

    A new 3D automatic reconstruction method of micro solid of revolution is presented in this paper. In the implementation procedure of this method, image sequence of the solid of revolution of 360° is obtained, which rotation speed is controlled by motor precisely, in the rotate photographic mode of back light. Firstly, we need calibrate the height of turntable, the size of pixel and rotation axis of turntable. Then according to the calibration result of rotation axis, the height of turntable, rotation angle and the pixel size, the contour points of each image can be transformed into 3D points in the reference coordinate system to generate the point cloud model. Finally, the surface geometrical model of solid of revolution is obtained by using the relationship of two adjacent contours. Experimental results on real images are presented, which demonstrate the effectiveness of the Approach.

  19. Autonomous Planetary 3-D Reconstruction From Satellite Images

    DEFF Research Database (Denmark)

    Denver, Troelz

    1999-01-01

    operator detects an interesting object or feature on a, say, asteroid, to a command is issued to aim a science instrument at the feature. This delay may be in the range of hours for all except the objects closest to the Earth. Because the transit time of a typical interesting feature is in the range...

  20. 3D Reconstruction of human bones based on dictionary learning.

    Science.gov (United States)

    Zhang, Binkai; Wang, Xiang; Liang, Xiao; Zheng, Jinjin

    2017-11-01

    An effective method for reconstructing a 3D model of human bones from computed tomography (CT) image data based on dictionary learning is proposed. In this study, the dictionary comprises the vertices of triangular meshes, and the sparse coefficient matrix indicates the connectivity information. For better reconstruction performance, we proposed a balance coefficient between the approximation and regularisation terms and a method for optimisation. Moreover, we applied a local updating strategy and a mesh-optimisation method to update the dictionary and the sparse matrix, respectively. The two updating steps are iterated alternately until the objective function converges. Thus, a reconstructed mesh could be obtained with high accuracy and regularisation. The experimental results show that the proposed method has the potential to obtain high precision and high-quality triangular meshes for rapid prototyping, medical diagnosis, and tissue engineering. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

  1. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells.

    Science.gov (United States)

    Luo, Tong; Chen, Huan; Kassab, Ghassan S

    2016-01-01

    The 3D geometry of individual vascular smooth muscle cells (VSMCs), which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI) selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell's initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations) was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9 μm, 4.6±0.6 μm and 6.2±1.8 μm (mean±SD). In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle) was found to be 8±7.6° with median as 5.7°. A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function.

  2. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells

    OpenAIRE

    Tong Luo; Huan Chen; Kassab, Ghassan S.

    2016-01-01

    Aims The 3D geometry of individual vascular smooth muscle cells (VSMCs), which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation. Methods and Results A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well a...

  3. 3D reconstruction of pelvic floor for numerical simulation purpose

    OpenAIRE

    Fatima Alexandre; Rania F El Sayed; Teresa Mascarenhas; Natal M N Jorge; Parente, MP; Fernandes,AA; Tavares, Joao Manuel R.S.

    2008-01-01

    Female pelvic floor disorders (stress urinary incontinence, fecal incontinence, pelvic organ prolapse) affect approximately 60% of woman over 60 years old [1]. The real geometry and architecture of female pelvic floor and connective tissues are complex and difficult to visualize from two-dimensional (21)) images. To facilitate the understanding of pelvic floor geometry, in this work 31) models were building. A 3D helpful model of pelvic floor could aid the understanding of the anatomy and phy...

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

    Science.gov (United States)

    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/.

  5. Underwater Photogrammetry and 3d Reconstruction of Marble Cargos Shipwreck

    Science.gov (United States)

    Balletti, C.; Beltrame, C.; Costa, E.; Guerra, F.; Vernier, P.

    2015-04-01

    Nowadays archaeological and architectural surveys are based on the acquisition and processing of point clouds, allowing a high metric precision, essential prerequisite for a good documentation. Digital image processing and laser scanner have changed the archaeological survey campaign, from manual and direct survey to a digital one and, actually, multi-image photogrammetry is a good solution for the underwater archaeology. This technical documentation cannot operate alone, but it has to be supported by a topographical survey to georeference all the finds in the same reference system. In the last years the Ca' Foscari and IUAV University of Venice are conducting a research on integrated survey techniques to support underwater metric documentation. The paper will explain all the phases regarding the survey's design, images acquisition, topographic measure and the data processing of two Roman shipwrecks in south Sicily. The cargos of the shipwrecks are composed by huge marble blocks, but they are different for morphological characteristic of the sites, for the depth and for their distribution on the seabed. Photogrammetrical and topographical surveys were organized in two distinct methods, especially for the second one, due to the depth that have allowed an experimentation of GPS RTK's measurements on one shipwreck. Moreover, this kind of three-dimensional documentation is useful for educational and dissemination aspect, for the ease of understanding by wide public.

  6. 3-D reconstruction of the human skeleton during motion

    OpenAIRE

    Donati, Marco

    2007-01-01

    L’analisi del movimento umano ha come obiettivo la descrizione del movimento assoluto e relativo dei segmenti ossei del soggetto e, ove richiesto, dei relativi tessuti molli durante l’esecuzione di esercizi fisici. La bioingegneria mette a disposizione dell’analisi del movimento gli strumenti ed i metodi necessari per una valutazione quantitativa di efficacia, funzione e/o qualità del movimento umano, consentendo al clinico l’analisi di aspetti non individuabili con gli esam...

  7. Neurofunctional systems. 3D reconstructions with correlated neuroimaging

    Energy Technology Data Exchange (ETDEWEB)

    Kretschmann, H.J.; Fiekert, W.; Gerke, M.; Vogt, H.; Weirich, D.; Wesemann, M. [Medizinische Hochschule Hannover (Germany). Abt. Neuroanatomie; Weinrich, W. [Staedtisches Krankenhaus Nordstadt, Hannover (Germany). Abt. fuer Neurologie

    1998-12-31

    This book introduces, for the first time, computer-generated images of the neurofunctional systems of the human brain. These images are more accurate than drawings. The main views presented are of the medial lemniscus system, auditory system, visual system, basal ganglia, corticospinal system, and the limbic system. The arteries and sulci of the cerebral hemispheres are also illustrated by computer. These images provide a three-dimensional orientation of the intracranial space and help, for example, to assess vascular functional disturbance of the brain. Clinicians will find these images valuable for the spatial interpretation of magnetic resonance (MR), computed tomography (CT), and positron emission tomography (PET) images since many neurofunctional systems cannot be visualized as isolated structures in neuroimaging. Computer-assisted surface reconstructions of the neurofunctional systems and the cerebral arteries serve as a basis for constructing these computer-generated images. The surface reconstructions are anatomically realistic having been created from brain sections with minimal deformations. The method of computer graphics, known as ray tracing, produces digital images form these reconstructions. The computer-generated methods are explained. The computer-generated images are accompanied by illustrations and texts on neuroanatomy and clinical practice. The neurofunctional systems of the human brain are also shown in sections so that the reader can mentally reconstruct the neurofunctional systems, thus facilitating the transformation of information into textbooks and atlantes of MR and CT imaging. The aim of this book is acquaint the reader with the three-dimensional aspects of the neurofunctional systems and the cerebral arteries of the human brain using methods of computer graphics. Computer scientists and those interested in this technique are provided with basic neuroanatomic and neurofunctional information. Physicians will have a clearer understanding of the limitations and possibilities of computer graphics in the field of medicine. The three-dimensional aspects of these neurofunctional systems should serve as a tool for clinicians and will appeal to neurologists, neurosurgeons, neuroradiologists, nuclear physicians, neurophysiologists, traumatologists and oncologists. Physicians and students with an interest in neurobiology will also find this an instructive and practical handbook. (orig.)

  8. The New Approach to Sport Medicine: 3-D Reconstruction

    Science.gov (United States)

    Ince, Alparslan

    2015-01-01

    The aim of this study is to present a new approach to sport medicine. Comparative analysis of the Vertebrae Lumbales was done in sedentary group and Muay Thai athletes. It was done by acquiring three dimensional (3-D) data and models through photogrammetric methods from the Multi-detector Computerized Tomography (MDCT) images of the Vertebrae…

  9. Deep monocular 3D reconstruction for assisted navigation in bronchoscopy.

    Science.gov (United States)

    Visentini-Scarzanella, Marco; Sugiura, Takamasa; Kaneko, Toshimitsu; Koto, Shinichiro

    2017-07-01

    In bronchoschopy, computer vision systems for navigation assistance are an attractive low-cost solution to guide the endoscopist to target peripheral lesions for biopsy and histological analysis. We propose a decoupled deep learning architecture that projects input frames onto the domain of CT renderings, thus allowing offline training from patient-specific CT data. A fully convolutional network architecture is implemented on GPU and tested on a phantom dataset involving 32 video sequences and [Formula: see text]60k frames with aligned ground truth and renderings, which is made available as the first public dataset for bronchoscopy navigation. An average estimated depth accuracy of 1.5 mm was obtained, outperforming conventional direct depth estimation from input frames by 60%, and with a computational time of [Formula: see text]30 ms on modern GPUs. Qualitatively, the estimated depth and renderings closely resemble the ground truth. The proposed method shows a novel architecture to perform real-time monocular depth estimation without losing patient specificity in bronchoscopy. Future work will include integration within SLAM systems and collection of in vivo datasets.

  10. 3D Reconstruction for Exploration of Indoor Environments

    Science.gov (United States)

    Wettach, Jens; Berns, Karsten

    Autonomous exploration of arbitrary indoor environments with a mobile robot depends on a reliable self-localization strategy. Existing approaches that use only 2D distance information from e.g. planar laser scanners may fail in highly cluttered areas due to the lack of stable landmark detection. This paper presents an approach for extracting room and furniture primitives from a 3D point cloud by matching shape primitives to the data samples. These basic building blocks can serve as landmarks for relocalization and give hints for interesting places during environmental exploration. Input data is acquired by a tiltable 2D laser scanner in reality and a realistic virtual sensor simulation. In the paper the complete process from sensor data acquisition, data filtering, RANSAC1 based plane extraction and smoothing is described and tested in simulation and reality.

  11. A new algorithm for 3D reconstruction from support functions

    DEFF Research Database (Denmark)

    Gardner, Richard; Kiderlen, Markus

    2009-01-01

    We introduce a new algorithm for reconstructing an unknown shape from a finite number of noisy measurements of its support function. The algorithm, based on a least squares procedure, is very easy to program in standard software such as Matlab and allows, for the first time, good 3D reconstructio...

  12. 3D reconstruction of the final PHILAE landing site: Abydos

    Science.gov (United States)

    Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquière, Gilles; Delmas, Cédric; Durand, Joëlle; Gaudon, Philippe; Jurado, Eric

    2015-11-01

    The Abydos region is the region of the final landing site of the PHILAE lander. The landing site has been potentially identified on images of this region acquired by the OSIRIS imaging system aboard the orbiter before (Oct 22, 2014) and after (Dec 6-13, 2014) the landing of PHILAE (Lamy et al., in prep.). Assuming that this identification is correct, we reconstructed the topography of Abydos in 3D using a method called ``multiresolution photoclinometry by deformation'' (MPCD, Capanna et al., The Visual Computer, 29(6-8): 825-835, 2013). The method works in two steps: (a) a DTM of this region is extracted from the global MPCD shape model, (b) the resulting triangular mesh is progressively deformed at increasing spatial resolution in order to match a set of 14 images of Abydos at pixel resolutions between 1 and 8 m. The method used to perform the image matching is the L-BFGS-b non-linear optimization (Morales et al., ACM Trans. Math. Softw., 38(1): 1-4, 2011).In spite of the very unfavourable illumination conditions, we achieve a vertical accuracy of about 3 m, while the horizontal sampling is 0.5 m. The accuracy is limited by high incidence angles on the images (about 60 deg on average) combined with a complex topography including numerous cliffs and a few overhangs. We also check the compatibility of the local DTM with the images obtained by the CIVA-P instrument aboard PHILAE. If the Lamy et al. identification is correct, our DTM shows that PHILAE landed in a cavity at the bottom of a small cliff of 8 m height.

  13. 3D reconstruction software comparison for short sequences

    Science.gov (United States)

    Strupczewski, Adam; Czupryński, BłaŻej

    2014-11-01

    Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

  14. 3D Reconstruction of Coronary Artery Vascular Smooth Muscle Cells.

    Directory of Open Access Journals (Sweden)

    Tong Luo

    Full Text Available The 3D geometry of individual vascular smooth muscle cells (VSMCs, which are essential for understanding the mechanical function of blood vessels, are currently not available. This paper introduces a new 3D segmentation algorithm to determine VSMC morphology and orientation.A total of 112 VSMCs from six porcine coronary arteries were used in the analysis. A 3D semi-automatic segmentation method was developed to reconstruct individual VSMCs from cell clumps as well as to extract the 3D geometry of VSMCs. A new edge blocking model was introduced to recognize cell boundary while an edge growing was developed for optimal interpolation and edge verification. The proposed methods were designed based on Region of Interest (ROI selected by user and interactive responses of limited key edges. Enhanced cell boundary features were used to construct the cell's initial boundary for further edge growing. A unified framework of morphological parameters (dimensions and orientations was proposed for the 3D volume data. Virtual phantom was designed to validate the tilt angle measurements, while other parameters extracted from 3D segmentations were compared with manual measurements to assess the accuracy of the algorithm. The length, width and thickness of VSMCs were 62.9±14.9 μm, 4.6±0.6 μm and 6.2±1.8 μm (mean±SD. In longitudinal-circumferential plane of blood vessel, VSMCs align off the circumferential direction with two mean angles of -19.4±9.3° and 10.9±4.7°, while an out-of-plane angle (i.e., radial tilt angle was found to be 8±7.6° with median as 5.7°.A 3D segmentation algorithm was developed to reconstruct individual VSMCs of blood vessel walls based on optical image stacks. The results were validated by a virtual phantom and manual measurement. The obtained 3D geometries can be utilized in mathematical models and leads a better understanding of vascular mechanical properties and function.

  15. Electrical Impedance Tomography: 3D Reconstructions using Scattering Transforms

    DEFF Research Database (Denmark)

    Delbary, Fabrice; Hansen, Per Christian; Knudsen, Kim

    2012-01-01

    In three dimensions the Calderon problem was addressed and solved in theory in the 1980s. The main ingredients in the solution of the problem are complex geometrical optics solutions to the conductivity equation and a (non-physical) scattering transform. The resulting reconstruction algorithm is ...

  16. Improved biocytin labeling and neuronal 3D reconstruction.

    Science.gov (United States)

    Marx, Manuel; Günter, Robert H; Hucko, Werner; Radnikow, Gabriele; Feldmeyer, Dirk

    2012-02-02

    In this report, we describe a reliable protocol for biocytin labeling of neuronal tissue and diaminobenzidine (DAB)-based processing of brain slices. We describe how to embed tissues in different media and how to subsequently histochemically label the tissues for light or electron microscopic examination. We provide a detailed dehydration and embedding protocol using Eukitt that avoids the common problem of tissue distortion and therefore prevents fading of cytoarchitectural features (in particular, lamination) of brain tissue; as a result, additional labeling methods (such as cytochrome oxidase staining) become unnecessary. In addition, we provide correction factors for tissue shrinkage in all spatial dimensions so that a realistic neuronal morphology can be obtained from slice preparations. Such corrections were hitherto difficult to calculate because embedding in viscous media resulted in highly nonlinear tissue deformation. Fixation, immunocytochemistry and embedding procedures for light microscopy (LM) can be completed within 42-48 h. Subsequent reconstructions and morphological analyses take an additional 24 h or more.

  17. Image-Based 3d Reconstruction and Analysis for Orthodontia

    Science.gov (United States)

    Knyaz, V. A.

    2012-08-01

    Among the main tasks of orthodontia are analysis of teeth arches and treatment planning for providing correct position for every tooth. The treatment plan is based on measurement of teeth parameters and designing perfect teeth arch curve which teeth are to create after treatment. The most common technique for teeth moving uses standard brackets which put on teeth and a wire of given shape which is clamped by these brackets for producing necessary forces to every tooth for moving it in given direction. The disadvantages of standard bracket technique are low accuracy of tooth dimensions measurements and problems with applying standard approach for wide variety of complex orthodontic cases. The image-based technique for orthodontic planning, treatment and documenting aimed at overcoming these disadvantages is proposed. The proposed approach provides performing accurate measurements of teeth parameters needed for adequate planning, designing correct teeth position and monitoring treatment process. The developed technique applies photogrammetric means for teeth arch 3D model generation, brackets position determination and teeth shifting analysis.

  18. A Bioinformatics-Based Alternative mRNA Splicing Code that May Explain Some Disease Mutations Is Conserved in Animals.

    Science.gov (United States)

    Qu, Wen; Cingolani, Pablo; Zeeberg, Barry R; Ruden, Douglas M

    2017-01-01

    Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns. In humans, we identified 42 different consensus sequences that are each present in at least 100 human introns. 37 of the 42 top consensus sequences are significantly enriched or depleted in at least one of the 36 types of introns. We further supported our hypothesis by showing that 96 out of 96 analyzed human disease mutations that affect RNA splicing, and change alternative splicing from one class to another, can be partially explained by a mutation altering a consensus sequence from one type of intron to that of another type of intron. Some of the alternative splicing consensus sequences, and presumably their small-RNA or protein targets, are evolutionarily conserved from 50 plant to animal species. We also noticed the set of introns within a gene usually share the same splicing codes, thus arguing that one sub-type of splicesosome might process all (or most) of the introns in a given gene. Our work sheds new light on a possible mechanism for generating the tremendous diversity in protein structure by alternative splicing of pre-mRNAs.

  19. Non destructive testing of industrial pieces by radiography: quantitative characterization and 3 D reconstruction by the way of a limited number of images; Controle non destructif de pieces industrielles par radiographie: caracterisation quantitative et reconstruction 3D a partir d`un nombre limite de vues

    Energy Technology Data Exchange (ETDEWEB)

    Retraint, F

    1998-12-31

    The non destructive testing of industrial pieces is evaluated on the basis of numerical radiographies.The context of the study is the online control of the fuel rods production. A direct model of a numerical radiography formation is proposed and detailed for an acquisition system consisting of a CCD video connected to a converter screen by an optical system. As this approach does not allow the determination of the measured matter thickness from the X-ray photograph, an approximate model based on realistic approximations of the industrial non destructive testing, has been developed. For the specific cases it is possible to inverse the model and to reach the quantitative information present in the x-ray photograph, in other words, the map of the X-rays measured matter thickness. It becomes then possible to access to the quantitative parameters of the possible defects present in the measured specimen, such as the surface and the bulk. To reach the 3 D information on the defects a 3 D reconstruction method, from 3 X-rays photographs, is proposed.The inverse problem is solved by the non convex energy minimization. (A.L.B.) 109 refs.

  20. GPS-Aided Video Tracking

    Directory of Open Access Journals (Sweden)

    Udo Feuerhake

    2015-08-01

    Full Text Available Tracking moving objects is both challenging and important for a large variety of applications. Different technologies based on the global positioning system (GPS and video or radio data are used to obtain the trajectories of the observed objects. However, in some use cases, they fail to provide sufficiently accurate, complete and correct data at the same time. In this work we present an approach for fusing GPS- and video-based tracking in order to exploit their individual advantages. In this way we aim to combine the reliability of GPS tracking with the high geometric accuracy of camera detection. For the fusion of the movement data provided by the different devices we use a hidden Markov model (HMM formulation and the Viterbi algorithm to extract the most probable trajectories. In three experiments, we show that our approach is able to deal with challenging situations like occlusions or objects which are temporarily outside the monitored area. The results show the desired increase in terms of accuracy, completeness and correctness.

  1. Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 & Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein

    Science.gov (United States)

    El-Assaad, Atlal; Dawy, Zaher; Nemer, Georges; Kobeissy, Firas

    2017-01-01

    The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios. Advanced proteomic techniques have shown a remarkable progress in identifying these BDPs experimentally. In this work, we present a bioinformatics-based prediction method that identifies protease-associated BDPs with high precision and efficiency. The method utilizes state-of-the-art sequence matching and alignment algorithms. It starts by locating consensus sequence occurrences and their variants in any set of protein substrates, generating all fragments resulting from cleavage. The complexity exists in space O(mn) as well as in O(Nmn) time, where N, m, and n are the number of protein sequences, length of the consensus sequence, and length per protein sequence, respectively. Finally, the proposed methodology is validated against βII-spectrin protein, a brain injury validated biomarker.

  2. INLINING 3D RECONSTRUCTION, MULTI-SOURCE TEXTURE MAPPING AND SEMANTIC ANALYSIS USING OBLIQUE AERIAL IMAGERY

    Directory of Open Access Journals (Sweden)

    D. Frommholz

    2016-06-01

    Full Text Available This paper proposes an in-line method for the simplified reconstruction of city buildings from nadir and oblique aerial images that at the same time are being used for multi-source texture mapping with minimal resampling. Further, the resulting unrectified texture atlases are analyzed for fac¸ade elements like windows to be reintegrated into the original 3D models. Tests on real-world data of Heligoland/ Germany comprising more than 800 buildings exposed a median positional deviation of 0.31 m at the fac¸ades compared to the cadastral map, a correctness of 67% for the detected windows and good visual quality when being rendered with GPU-based perspective correction. As part of the process building reconstruction takes the oriented input images and transforms them into dense point clouds by semi-global matching (SGM. The point sets undergo local RANSAC-based regression and topology analysis to detect adjacent planar surfaces and determine their semantics. Based on this information the roof, wall and ground surfaces found get intersected and limited in their extension to form a closed 3D building hull. For texture mapping the hull polygons are projected into each possible input bitmap to find suitable color sources regarding the coverage and resolution. Occlusions are detected by ray-casting a full-scale digital surface model (DSM of the scene and stored in pixel-precise visibility maps. These maps are used to derive overlap statistics and radiometric adjustment coefficients to be applied when the visible image parts for each building polygon are being copied into a compact texture atlas without resampling whenever possible. The atlas bitmap is passed to a commercial object-based image analysis (OBIA tool running a custom rule set to identify windows on the contained fac¸ade patches. Following multi-resolution segmentation and classification based on brightness and contrast differences potential window objects are evaluated against geometric constraints and conditionally grown, fused and filtered morphologically. The output polygons are vectorized and reintegrated into the previously reconstructed buildings by sparsely ray-tracing their vertices. Finally the enhanced 3D models get stored as textured geometry for visualization and semantically annotated ”LOD-2.5” CityGML objects for GIS applications.

  3. Ground truth evaluation of computer vision based 3D reconstruction of synthesized and real plant images

    DEFF Research Database (Denmark)

    Nielsen, Michael; Andersen, Hans Jørgen; Slaughter, David

    2007-01-01

    There is an increasing interest in using 3D computer vision in precision agriculture. This calls for better quantitative evaluation and understanding of computer vision methods. This paper proposes a test framework using ray traced crop scenes that allows in-depth analysis of algorithm performance...

  4. 2D and 3D reconstructions in acousto-electric tomography

    KAUST Repository

    Kuchment, Peter

    2011-04-18

    We propose and test stable algorithms for the reconstruction of the internal conductivity of a biological object using acousto-electric measurements. Namely, the conventional impedance tomography scheme is supplemented by scanning the object with acoustic waves that slightly perturb the conductivity and cause the change in the electric potential measured on the boundary of the object. These perturbations of the potential are then used as the data for the reconstruction of the conductivity. The present method does not rely on \\'perfectly focused\\' acoustic beams. Instead, more realistic propagating spherical fronts are utilized, and then the measurements that would correspond to perfect focusing are synthesized. In other words, we use synthetic focusing. Numerical experiments with simulated data show that our techniques produce high-quality images, both in 2D and 3D, and that they remain accurate in the presence of high-level noise in the data. Local uniqueness and stability for the problem also hold. © 2011 IOP Publishing Ltd.

  5. Streaming video-based 3D reconstruction method compatible with existing monoscopic and stereoscopic endoscopy systems

    NARCIS (Netherlands)

    Bouma, H.; Mark, W. van der; Eendebak, P.T.; Landsmeer, S.; Eekeren, A.W.M. van der; Haar, F.B. ter; Wieringa, F.P.; Basten, J.P. van

    2012-01-01

    Compared to open surgery, minimal invasive surgery offers reduced trauma and faster recovery. However, lack of direct view limits space perception. Stereo-endoscopy improves depth perception, but is still restricted to the direct endoscopic field-of-view. We describe a novel technology that

  6. 3D reconstruction optimization using imagery captured by unmanned aerial vehicles

    Science.gov (United States)

    Bassie, Abby L.; Meacham, Sean; Young, David; Turnage, Gray; Moorhead, Robert J.

    2017-05-01

    Because unmanned air vehicles (UAVs) are emerging as an indispensable image acquisition platform in precision agriculture, it is vitally important that researchers understand how to optimize UAV camera payloads for analysis of surveyed areas. In this study, imagery captured by a Nikon RGB camera attached to a Precision Hawk Lancaster was used to survey an agricultural field from six different altitudes ranging from 45.72 m (150 ft.) to 121.92 m (400 ft.). After collecting imagery, two different software packages (MeshLab and AgiSoft) were used to measure predetermined reference objects within six three-dimensional (3-D) point clouds (one per altitude scenario). In-silico measurements were then compared to actual reference object measurements, as recorded with a tape measure. Deviations of in-silico measurements from actual measurements were recorded as Δx, Δy, and Δz. The average measurement deviation in each coordinate direction was then calculated for each of the six flight scenarios. Results from MeshLab vs. AgiSoft offered insight into the effectiveness of GPS-defined point cloud scaling in comparison to user-defined point cloud scaling. In three of the six flight scenarios flown, MeshLab's 3D imaging software (user-defined scale) was able to measure object dimensions from 50.8 to 76.2 cm (20-30 inches) with greater than 93% accuracy. The largest average deviation in any flight scenario from actual measurements was 14.77 cm (5.82 in.). Analysis of the point clouds in AgiSoft (GPS-defined scale) yielded even smaller Δx, Δy, and Δz than the MeshLab measurements in over 75% of the flight scenarios. The precisions of these results are satisfactory in a wide variety of precision agriculture applications focused on differentiating and identifying objects using remote imagery.

  7. Comparative myoanatomy of Echinoderes (Kinorhyncha): a comprehensive investigation by CLSM and 3D reconstruction

    Science.gov (United States)

    2014-01-01

    Introduction Kinorhyncha is a clade of marine invertebrate meiofauna. Their body plan includes a retractable introvert bearing rings of cuticular spines, and a limbless trunk with distinct segmentation of nervous, muscular and epidermal organ systems. As derived members within the basal branch of Ecdysozoa, kinorhynchs may provide an important example of convergence on the evolution of segmentation within one of three bilaterian superclades. We describe the myoanatomy of Echinoderes, the most specious kinorhynch genus, and build upon historical studies of kinorhynch ultrastructure and gross morphology. This is the first multi-species comparison of a complete organ system by confocal microscopy and three-dimensional reconstruction within Kinorhyncha. Results Myoanatomy of adult Echinoderes is composed of the following: Head with two mouth cone circular muscles, nine pairs of oral style muscles, ten introvert retractors, one introvert circular muscle, and fourteen introvert circular muscle retractors; Neck with one circular muscle; Trunk showing distinct pairs of ventral and dorsal muscles within segments 1–10, dorsoventral muscles within segments 3–10, diagonal muscles within segments 1–8, longitudinal fibers spanning segments 1–9, three pairs of terminal spine muscles, and one pair of male penile spine muscles; Gut showing a pharynx with ten alternating rings of radial and circular muscle fibers enclosed in a complex sheath of protractors and retractors, an orthogonal grid of longitudinal and circular fibers surrounding the intestine, and paired hindgut dilators. Conclusions Myoanatomy is highly conserved between species of Echinoderes. Interspecific variation is observed in the arrangement and number of introvert fibers and the composition of pharyngeal muscles. Segmented trunk musculature facilitates the movements of articulated cuticular plates along the anterior-posterior axis. Intersegmental muscle fibers assist with dorsoventral and lateral trunk movements. Protractors, retractors and circular muscles coordinate eversion and retraction of the introvert and mouth cone, and relocation of the pharynx during locomotion and feeding behaviors. Pairs of posterior fibers suggest independent movements of terminal spines, and male penile spines. Within Scalidophora, myoanatomy is more similar between Kinorhyncha and Loricifera, than either group is to Priapulida. Kinorhynch myoanatomy may reflect a convergent transition from vermiform to segmented body plans during the early radiation of Ecdysozoa. PMID:24708877

  8. 3D Reconstruction of the Glycocalyx Structure in Mammalian Capillaries using Electron Tomography

    DEFF Research Database (Denmark)

    Arkill, Kp; Neal, Cr; Mantell, Jm

    2012-01-01

    of the proteoglycan components of the glycocalyx layer (fundamental spacing about 20 nm), but require a large sample number. Attempts to visualise the glycocalyx face-on (i.e. in a direction perpendicular to the endothelial cell layer in the lumen and directly applicable for permeability modelling) has had limited...... the endothelial cell layer. One preparation uses the novel staining technique using Lanthanum Dysprosium Glycosamino Glycan adhesion (the LaDy GAGa method). © 2012 John Wiley & Sons Ltd....

  9. Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration

    Directory of Open Access Journals (Sweden)

    Young-Gyu Yoon

    2017-10-01

    Full Text Available We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies—expansion microscopy (ExM and in-situ molecular barcoding. We utilize a convolutional neural network to detect neuronal boundaries from protein-tagged plasma membrane images obtained via ExM, as well as a subsequent supervoxel-merging pipeline guided by optical readout of information-rich, cell-specific nucleic acid barcodes. We attempt to use conservative imaging and labeling parameters, with the goal of establishing a baseline case that points to the potential feasibility of optical circuit reconstruction, leaving open the possibility of higher-performance labeling technologies and algorithms. We find that, even with these conservative assumptions, an all-optical approach to dense neural morphology reconstruction may be possible via the proposed algorithmic framework. Future work should explore both the design-space of chemical labels and barcodes, as well as algorithms, to ultimately enable routine, high-performance optical circuit reconstruction.

  10. Feasibility of 3D Reconstruction of Neural Morphology Using Expansion Microscopy and Barcode-Guided Agglomeration.

    Science.gov (United States)

    Yoon, Young-Gyu; Dai, Peilun; Wohlwend, Jeremy; Chang, Jae-Byum; Marblestone, Adam H; Boyden, Edward S

    2017-01-01

    We here introduce and study the properties, via computer simulation, of a candidate automated approach to algorithmic reconstruction of dense neural morphology, based on simulated data of the kind that would be obtained via two emerging molecular technologies-expansion microscopy (ExM) and in-situ molecular barcoding. We utilize a convolutional neural network to detect neuronal boundaries from protein-tagged plasma membrane images obtained via ExM, as well as a subsequent supervoxel-merging pipeline guided by optical readout of information-rich, cell-specific nucleic acid barcodes. We attempt to use conservative imaging and labeling parameters, with the goal of establishing a baseline case that points to the potential feasibility of optical circuit reconstruction, leaving open the possibility of higher-performance labeling technologies and algorithms. We find that, even with these conservative assumptions, an all-optical approach to dense neural morphology reconstruction may be possible via the proposed algorithmic framework. Future work should explore both the design-space of chemical labels and barcodes, as well as algorithms, to ultimately enable routine, high-performance optical circuit reconstruction.

  11. Diffuse mirrors: 3D reconstruction from diffuse indirect illumination using inexpensive time-of-flight sensors

    KAUST Repository

    Heide, Felix

    2014-06-01

    The functional difference between a diffuse wall and a mirror is well understood: one scatters back into all directions, and the other one preserves the directionality of reflected light. The temporal structure of the light, however, is left intact by both: assuming simple surface reflection, photons that arrive first are reflected first. In this paper, we exploit this insight to recover objects outside the line of sight from second-order diffuse reflections, effectively turning walls into mirrors. We formulate the reconstruction task as a linear inverse problem on the transient response of a scene, which we acquire using an affordable setup consisting of a modulated light source and a time-of-flight image sensor. By exploiting sparsity in the reconstruction domain, we achieve resolutions in the order of a few centimeters for object shape (depth and laterally) and albedo. Our method is robust to ambient light and works for large room-sized scenes. It is drastically faster and less expensive than previous approaches using femtosecond lasers and streak cameras, and does not require any moving parts.

  12. 3D reconstruction and analysis of wing deformation in free-flying dragonflies.

    Science.gov (United States)

    Koehler, Christopher; Liang, Zongxian; Gaston, Zachary; Wan, Hui; Dong, Haibo

    2012-09-01

    Insect wings demonstrate elaborate three-dimensional deformations and kinematics. These deformations are key to understanding many aspects of insect flight including aerodynamics, structural dynamics and control. In this paper, we propose a template-based subdivision surface reconstruction method that is capable of reconstructing the wing deformations and kinematics of free-flying insects based on the output of a high-speed camera system. The reconstruction method makes no rigid wing assumptions and allows for an arbitrary arrangement of marker points on the interior and edges of each wing. The resulting wing surfaces are projected back into image space and compared with expert segmentations to validate reconstruction accuracy. A least squares plane is then proposed as a universal reference to aid in making repeatable measurements of the reconstructed wing deformations. Using an Eastern pondhawk (Erythimus simplicicollis) dragonfly for demonstration, we quantify and visualize the wing twist and camber in both the chord-wise and span-wise directions, and discuss the implications of the results. In particular, a detailed analysis of the subtle deformation in the dragonfly's right hindwing suggests that the muscles near the wing root could be used to induce chord-wise camber in the portion of the wing nearest the specimen's body. We conclude by proposing a novel technique for modeling wing corrugation in the reconstructed flapping wings. In this method, displacement mapping is used to combine wing surface details measured from static wings with the reconstructed flapping wings, while not requiring any additional information be tracked in the high speed camera output.

  13. The first complete 3D reconstruction of a Spanish fly primary larva (Lytta vesicatoria, Meloidae, Coleoptera.

    Directory of Open Access Journals (Sweden)

    Si-Qin Ge

    Full Text Available The first detailed anatomical study of a primary larva of Meloidae is presented. Thereby techniques such as three-dimensional reconstructions, microtome sections, SEM (scanning electronic microscopy and CLSM (confocal laser scanning microscopy are applied. The structural features are discussed in the context of phylogeny, but also possible correlations with parasitism, phoresy and miniaturisation. The triungulin first instar larva is likely an apomorphy of Meloidae excl. Eleticinae and linked with a specialisation on acridoid eggs or larvae and provisions of bees. The campodeid body shape of Lytta and Meloinae is a groundplan feature of Meloidae, whereas a navicular body is an autapomorphy of the generally phoretic larvae of Nemognathinae. Head structures of Lytta and features of the postcephalic body are largely plesiomorphic. The musculature of the head is only moderately simplified while the one of the postcephalic body is well developed. Its thorax is largely characterised by plesiomorphies. The characteristics of the legs suggest phoretic habits, even though this does not apply to larvae of Lytta. It is conceivable that a phoretic behaviour is secondarily lost, together with some but not all morphological modifications related to it. Derived features of the abdomen of Meloidae are the complete loss of the fixed urogomphi (also missing in Rhipiphoridae and other related groups and the presence of one or two conspicuous caudal bristles. Only few features of Lytta are shared with the parasitic larvae of Rhipiphoridae and Strepsiptera. These characteristics, which are possibly linked with specialised life habits, have obviously evolved independently. Miniaturisation effects are minimal in the larvae of Lytta.

  14. 3D Reconstruction of End-Effector in Autonomous Positioning Process Using Depth Imaging Device

    National Research Council Canada - National Science Library

    Hu, Yanzhu; Li, Leiyuan

    2016-01-01

    .... In order to solve this problem, a simple depth imaging equipment (Kinect) is used and Kalman filtering method based on three-frame subtraction to capture the end-effector motion is proposed in this paper...

  15. On the 3-D reconstruction of Coronal Mass Ejections using coronagraph data

    Directory of Open Access Journals (Sweden)

    M. Mierla

    2010-01-01

    Full Text Available Coronal Mass ejections (CMEs are enormous eruptions of magnetized plasma expelled from the Sun into the interplanetary space, over the course of hours to days. They can create major disturbances in the interplanetary medium and trigger severe magnetic storms when they collide with the Earth's magnetosphere. It is important to know their real speed, propagation direction and 3-D configuration in order to accurately predict their arrival time at the Earth. Using data from the SECCHI coronagraphs onboard the STEREO mission, which was launched in October 2006, we can infer the propagation direction and the 3-D structure of such events. In this review, we first describe different techniques that were used to model the 3-D configuration of CMEs in the coronagraph field of view (up to 15 R⊙. Then, we apply these techniques to different CMEs observed by various coronagraphs. A comparison of results obtained from the application of different reconstruction algorithms is presented and discussed.

  16. AX-PET A novel PET detector concept with full 3D reconstruction

    CERN Document Server

    Braem, A; Séguinot, J; Dissertori, G; Djambazov, L; Lustermann, W; Nessi-Tedaldi, F; Pauss, F; Schinzel, D; Solevi, P; Lacasta, C; Oliver, J F; Rafecas, M; De Leo, R; Nappi, E; Vilardi, I; Chesi, E; Cochran, E; Honscheid, K; Kagan, H; Rudge, A; Smith, S; Weilhammer, P; Johnson, I; Renker, D; Clinthorne, N; Huh, S; Bolle, E; Stapnes, S; Meddi, F

    2009-01-01

    We describe the concept and first experimental tests of a novel 3D axial Positron Emission Tomography (PET) geometry. It allows for a new way of measuring the interaction point in the detector with very high precision. It is based on a matrix of long Lutetium-Yttrium OxyorthoSilicate (LYSO) crystals oriented in the axial direction, each coupled to one Geiger Mode Avalanche Photodiode (G-APD) array. To derive the axial coordinate, Wave Length Shifter (WLS) strips are mounted orthogonally and interleaved between the crystals. The light from the WLS strips is read by custom-made G-APDs. The weighted mean of the signals in the WLS strips has proven to give very precise axial resolution. The achievable resolution along the three axes is mainly driven by the dimensions of the LYSO crystals and WLS strips. This concept is inherently free of parallax errors. Furthermore, it will allow identification of Compton interactions in the detector and for reconstruction of a fraction of them, which is expected to enhance imag...

  17. a Photogrammetric Pipeline for the 3d Reconstruction of Cassis Images on Board Exomars Tgo

    Science.gov (United States)

    Simioni, E.; Re, C.; Mudric, T.; Pommerol, A.; Thomas, N.; Cremonese, G.

    2017-07-01

    CaSSIS (Colour and Stereo Surface Imaging System) is the stereo imaging system onboard the European Space Agency and ROSCOSMOS ExoMars Trace Gas Orbiter (TGO) that has been launched on 14 March 2016 and entered a Mars elliptical orbit on 19 October 2016. During the first bounded orbits, CaSSIS returned its first multiband images taken on 22 and 26 November 2016. The telescope acquired 11 images, each composed by 30 framelets, of the Martian surface near Hebes Chasma and Noctis Labyrithus regions reaching at closest approach at a distance of 250 km from the surface. Despite of the eccentricity of this first orbit, CaSSIS has provided one stereo pair with a mean ground resolution of 6 m from a mean distance of 520 km. The team at the Astronomical Observatory of Padova (OAPD-INAF) is involved into different stereo oriented missions and it is realizing a software for the generation of Digital Terrain Models from the CaSSIS images. The SW will be then adapted also for other projects involving stereo camera systems. To compute accurate 3D models, several sequential methods and tools have been developed. The preliminary pipeline provides: the generation of rectified images from the CaSSIS framelets, a matching core and post-processing methods. The software includes in particular: an automatic tie points detection by the Speeded Up Robust Features (SURF) operator, an initial search for the correspondences through Normalize Cross Correlation (NCC) algorithm and the Adaptive Least Square Matching (LSM) algorithm in a hierarchical approach. This work will show a preliminary DTM generated by the first CaSSIS stereo images.

  18. Further development of the EpiDerm 3D reconstructed human skin micronucleus (RSMN) assay.

    Science.gov (United States)

    Mun, Greg C; Aardema, Marilyn J; Hu, Ting; Barnett, Brenda; Kaluzhny, Yulia; Klausner, Mitchell; Karetsky, Viktor; Dahl, Erica L; Curren, Rodger D

    2009-03-17

    The upcoming ban on testing of cosmetics in animals by the European Union's 7th Amendment to the Cosmetics Directive will require genotoxicity safety assessments of cosmetics ingredients and final formulations to be based primarily on in vitro genotoxicity tests. The current in vitro test battery produces an unacceptably high rate of false positives, and used by itself would effectively prevent the use and development of many ingredients that are actually safe for human use. To address the need for an in vitro test that is more predictive of genotoxicity in vivo, we have developed an in vitro micronucleus assay using a three-dimensional human reconstructed skin model (EpiDerm) that more closely mimics the normal dermal exposure route of chemicals. We have refined this model and assessed its ability to predict genotoxicity of a battery of chemicals that have been previously classified as genotoxins or non-genotoxins based on in vivo rodent skin tests. Our reconstructed skin micronucleus assay correctly identified 7 genotoxins and 5 non-genotoxins, demonstrating its potential to have a higher predictive value than currently available in vitro genotoxicity tests, and its utility as part of a comprehensive in vitro genotoxicity testing strategy.

  19. The Avignon Bridge: a 3d Reconstruction Project Integrating Archaeological, Historical and Gemorphological Issues

    Science.gov (United States)

    Berthelot, M.; Nony, N.; Gugi, L.; Bishop, A.; De Luca, L.

    2015-02-01

    The history and identity of the Avignon's bridge is inseparable from that of the Rhône river. Therefore, in order to share the history and memory of the Rhône, it is essential to get to know this bridge and especially to identify and make visible the traces of its past, its construction, its interaction with the river dynamics, which greatly influenced his life. These are the objectives of the PAVAGE project that focuses on digitally surveying, modelling and re-visiting a heritage site of primary importance with the aim of virtually restoring the link between the two sides which, after the disappearance of the Roman bridge of Arles, constituted for a long time the only connection between Lyon or Vienna and the sea. Therefore, this project has an important geo-historical dimension for which geo-morphological and paleoenvironmental studies were implemented in connection with the latest digital simulation methods exploiting geographic information systems. By integrating knowledge and reflections of archaeologists, historians, geomorphologists, environmentalists, architects, engineers and computer scientists, the result of this project (which involved 5 laboratories during 4 years) is a 3D digital model covering an extension of 50 km2 achieved by integrating satellite imagery, UAV-based acquisitions, terrestrial laser scanning and photogrammetry, etc. Beyond the actions of scientific valorisation concerning the historical and geomorphological dimensions of the project, the results of this work of this interdisciplinary investigation and interpretation of this site are today integrated within a location-based augmented reality application allowing tourists to exploring the virtual reconstruction of the bridge and its environment through tablets inside the portion of territory covered by this project (between Avignon and Villeneuve-lez-Avignon). This paper presents the main aspects of the 3D virtual reconstruction approach.

  20. Evaluation of Low-Cost Terrestrial Photogrammetry for 3d Reconstruction of Complex Buildings

    Science.gov (United States)

    Altman, S.; Xiao, W.; Grayson, B.

    2017-09-01

    Terrestrial photogrammetry is an accessible method of 3D digital modelling, and can be done with low-cost consumer grade equipment. Globally there are many undocumented buildings, particularly in the developing world, that could benefit from 3D modelling for documentation, redesign or restoration. Areas with buildings at risk of destruction by natural disaster or war could especially benefit. This study considers a range of variables that affect the quality of photogrammetric results. Different point clouds of the same building are produced with different variables, and they are systematically tested to see how the output was affected. This is done by geometrically comparing them to a laser scanned point cloud of the same building. It finally considers how best results can be achieved for different applications, how to mitigate negative effects, and the limits of this technique.

  1. Fusion of ALS Point Cloud and Optical Imagery for 3D Reconstruction of Building's Roof

    Directory of Open Access Journals (Sweden)

    B. Hujebri

    2013-09-01

    Full Text Available Three-dimensional building models are important in various applications such as disaster management and urban planning. In this paper a method based on fusion of LiDAR point cloud and aerial image data sources has been proposed. Firstly using 2D map, the point set relevant to each building separated from the overall LiDAR point cloud. In the next step, the mean shift clustering algorithm applied to the points of different buildings in the feature space. Finally the segmentation stage ended with the separation of parallel and coplanar segments. Then using the adjacency matrix, adjacent segments are intersected and inner vertices are determined. In the other space, the area of any building cropped in the image space and the mean shift algorithm applied to it. Then, the lines of roof’s outline edge extracted by the Hough transform algorithm and the points obtained from the intersection of these lines transformed to the ground space. Finally, by integration of structural points of intersected adjacent facets and the transformed points from image space, reconstruction performed. In order to evaluate the efficiency of proposed method, buildings with different shapes and different level of complexity selected and the results of the 3D model reconstruction evaluated. The results showed credible efficiency of method for different buildings.

  2. Metric 3D reconstruction and texture acquisition of surfaces of revolution from a single uncalibrated view.

    Science.gov (United States)

    Colombo, Carlo; Del Bimbo, Alberto; Pernici, Federico

    2005-01-01

    Image analysis and computer vision can be effectively employed to recover the three-dimensional structure of imaged objects, together with their surface properties. In this paper, we address the problem of metric reconstruction and texture acquisition from a single uncalibrated view of a surface of revolution (SOR). Geometric constraints induced in the image by the symmetry properties of the SOR structure are exploited to perform self-calibration of a natural camera, 3D metric reconstruction, and texture acquisition. By exploiting the analogy with the geometry of single axis motion, we demonstrate that the imaged apparent contour and the visible segments of two imaged cross sections in a single SOR view provide enough information for these tasks. Original contributions of the paper are: single view self-calibration and reconstruction based on planar rectification, previously developed for planar surfaces, has been extended to deal also with the SOR class of curved surfaces; self-calibration is obtained by estimating both camera focal length (one parameter) and principal point (two parameters) from three independent linear constraints for the SOR fixed entities; the invariant-based description of the SOR scaling function has been extended from affine to perspective projection. The solution proposed exploits both the geometric and topological properties of the transformation that relates the apparent contour to the SOR scaling function. Therefore, with this method, a metric localization of the SOR occluded parts can be made, so as to cope with them correctly. For the reconstruction of textured SORs, texture acquisition is performed without requiring the estimation of external camera calibration parameters, but only using internal camera parameters obtained from self-calibration.

  3. Hybrid 3D reconstruction and image-based rendering techniques for reality modeling

    Science.gov (United States)

    Sequeira, Vitor; Wolfart, Erik; Bovisio, Emanuele; Biotti, Ester; Goncalves, Joao G. M.

    2000-12-01

    This paper presents a component approach that combines in a seamless way the strong features of laser range acquisition with the visual quality of purely photographic approaches. The relevant components of the system are: (i) Panoramic images for distant background scenery where parallax is insignificant; (ii) Photogrammetry for background buildings and (iii) High detailed laser based models for the primary environment, structure of exteriors of buildings and interiors of rooms. These techniques have a wide range of applications in visualization, virtual reality, cost effective as-built analysis of architectural and industrial environments, building facilities management, real-estate, E-commerce, remote inspection of hazardous environments, TV production and many others.

  4. EVALUATION OF LOW-COST TERRESTRIAL PHOTOGRAMMETRY FOR 3D RECONSTRUCTION OF COMPLEX BUILDINGS

    Directory of Open Access Journals (Sweden)

    S. Altman

    2017-09-01

    Full Text Available Terrestrial photogrammetry is an accessible method of 3D digital modelling, and can be done with low-cost consumer grade equipment. Globally there are many undocumented buildings, particularly in the developing world, that could benefit from 3D modelling for documentation, redesign or restoration. Areas with buildings at risk of destruction by natural disaster or war could especially benefit. This study considers a range of variables that affect the quality of photogrammetric results. Different point clouds of the same building are produced with different variables, and they are systematically tested to see how the output was affected. This is done by geometrically comparing them to a laser scanned point cloud of the same building. It finally considers how best results can be achieved for different applications, how to mitigate negative effects, and the limits of this technique.

  5. Assessments for 3d Reconstructions of Cultural Heritage Using Digital Technologies

    Science.gov (United States)

    Manferdini, A. M.; Galassi, M.

    2013-02-01

    The aim of this contribution is to show the results of evaluations on 3D digitizations performed using different methodologies and technologies. In particular, for surveys conducted at the architectural and urban scale, the recent reduction of costs related to Time of Flight and phase shift laser scanners is actually enhancing the replacement of traditional topographic instruments (i.e. total stations) with range-based technologies for the acquisition of 3D data related to built heritage. If compared to surveys performed using traditional topographic technologies, range-based ones offer a wide range of advantages, but they also require different skills, procedures and times. The present contribution shows the results of a practical application of both approaches on the same case study. Another application was suggested by the recent developments in the photogrammetric field that enhance the improvement of software able to automatically orient uncalibrated cameras and derive dense and accurate 3D point clouds, with evident benefits in reduction of costs required for survey equipment. Therefore, the presented case study constituted the occasion to compare a rangebased survey with a fast 3D acquisition and modelling using a Structure from Motion solution. These survey procedures were adopted at an architectural scale, on a single building, that was surveyed both on the outside and on the inside. Assessments on the quality of the rebuilt information is reported, as far as metric accuracy and reliability is concerned, as well as on time consuming and on skills required during each step of the adopted pipelines. For all approaches, these analysis highlighted advantages and disadvantages that allow to conduct evaluations on the possible convenience of adopting range-based technologies instead of a traditional topographic approach or a photogrammetric one instead of a range based one in case of surveys conducted at an architectural/urban scale.

  6. On the 3-D reconstruction of Coronal Mass Ejections using coronagraph data

    Directory of Open Access Journals (Sweden)

    M. Mierla

    2010-01-01

    Full Text Available Coronal Mass ejections (CMEs are enormous eruptions of magnetized plasma expelled from the Sun into the interplanetary space, over the course of hours to days. They can create major disturbances in the interplanetary medium and trigger severe magnetic storms when they collide with the Earth's magnetosphere. It is important to know their real speed, propagation direction and 3-D configuration in order to accurately predict their arrival time at the Earth. Using data from the SECCHI coronagraphs onboard the STEREO mission, which was launched in October 2006, we can infer the propagation direction and the 3-D structure of such events. In this review, we first describe different techniques that were used to model the 3-D configuration of CMEs in the coronagraph field of view (up to 15 R⊙. Then, we apply these techniques to different CMEs observed by various coronagraphs. A comparison of results obtained from the application of different reconstruction algorithms is presented and discussed.

  7. 3D reconstruction of carotid atherosclerotic plaque: comparison between spatial compound ultrasound models and anatomical models

    DEFF Research Database (Denmark)

    Lind, Bo L.; Fagertun, Jens; Wilhjelm, Jens E.

    2007-01-01

    This study deals with the creation of 3D models that can work as a tool for discriminating between tissue and background in the development of tissue classification methods. Ten formalin-fixed atherosclerotic carotid plaques removed by endarterectomy were scanned with 3D multi-angle spatial...

  8. 3D reconstruction and characterization of laser induced craters by in situ optical microscopy

    Science.gov (United States)

    Casal, A.; Cerrato, R.; Mateo, M. P.; Nicolas, G.

    2016-06-01

    A low-cost optical microscope was developed and coupled to an irradiation system in order to study the induced effects on material during a multipulse regime by an in situ visual inspection of the surface, in particular of the spot generated at different pulses. In the case of laser ablation, a reconstruction of the crater in 3D was made from the images of the sample surface taken during the irradiation process, and the subsequent profiles of ablated material were extracted. The implementation of this homemade optical device gives an added value to the irradiation system, providing information about morphology evolution of irradiated area when successive pulses are applied. In particular, the determination of ablation rates in real time can be especially useful for a better understanding and controlling of the ablation process in applications where removal of material is involved, such as laser cleaning and in-depth characterization of multilayered samples and diffusion processes. The validation of the developed microscope was made by a comparison with a commercial confocal microscope configured for the characterization of materials where similar results of crater depth and diameter were obtained for both systems.

  9. Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction

    NARCIS (Netherlands)

    Mollink, J.; Baarsen, K. van; Dederen, P.J.W.C.; Foxley, S.; Miller, K.L.; Jbabdi, S.; Slump, C.H.; Grotenhuis, J.A.; Kleinnijenhuis, M.; Cappellen van Walsum, A.M. van

    2016-01-01

    Diffusion-weighted imaging (DWI) tractography is a technique with great potential to characterize the in vivo anatomical position and integrity of white matter tracts. Tractography, however, remains an estimation of white matter tracts, and false-positive and false-negative rates are not available.

  10. Dentatorubrothalamic tract localization with postmortem MR diffusion tractography compared to histological 3D reconstruction

    OpenAIRE

    Mollink, J.; van Baarsen, K. M.; Dederen, P. J. W. C.; Foxley, S.; Miller, K. L.; Jbabdi, S.; Slump, C. H.; Grotenhuis, J. A.; Kleinnijenhuis, M.; van Cappellen van Walsum, A. M.

    2015-01-01

    Diffusion-weighted imaging (DWI) tractography is a technique with great potential to characterize the in vivo anatomical position and integrity of white matter tracts. Tractography, however, remains an estimation of white matter tracts, and false-positive and false-negative rates are not available. The goal of the present study was to compare postmortem tractography of the dentatorubrothalamic tract (DRTT) by its 3D histological reconstruction, to estimate the reliability of the tractography ...

  11. Inlining 3d Reconstruction, Multi-Source Texture Mapping and Semantic Analysis Using Oblique Aerial Imagery

    Science.gov (United States)

    Frommholz, D.; Linkiewicz, M.; Poznanska, A. M.

    2016-06-01

    This paper proposes an in-line method for the simplified reconstruction of city buildings from nadir and oblique aerial images that at the same time are being used for multi-source texture mapping with minimal resampling. Further, the resulting unrectified texture atlases are analyzed for façade elements like windows to be reintegrated into the original 3D models. Tests on real-world data of Heligoland/ Germany comprising more than 800 buildings exposed a median positional deviation of 0.31 m at the façades compared to the cadastral map, a correctness of 67% for the detected windows and good visual quality when being rendered with GPU-based perspective correction. As part of the process building reconstruction takes the oriented input images and transforms them into dense point clouds by semi-global matching (SGM). The point sets undergo local RANSAC-based regression and topology analysis to detect adjacent planar surfaces and determine their semantics. Based on this information the roof, wall and ground surfaces found get intersected and limited in their extension to form a closed 3D building hull. For texture mapping the hull polygons are projected into each possible input bitmap to find suitable color sources regarding the coverage and resolution. Occlusions are detected by ray-casting a full-scale digital surface model (DSM) of the scene and stored in pixel-precise visibility maps. These maps are used to derive overlap statistics and radiometric adjustment coefficients to be applied when the visible image parts for each building polygon are being copied into a compact texture atlas without resampling whenever possible. The atlas bitmap is passed to a commercial object-based image analysis (OBIA) tool running a custom rule set to identify windows on the contained façade patches. Following multi-resolution segmentation and classification based on brightness and contrast differences potential window objects are evaluated against geometric constraints and conditionally grown, fused and filtered morphologically. The output polygons are vectorized and reintegrated into the previously reconstructed buildings by sparsely ray-tracing their vertices. Finally the enhanced 3D models get stored as textured geometry for visualization and semantically annotated "LOD-2.5" CityGML objects for GIS applications.

  12. 3D RECONSTRUCTION AND ANALYSIS OF THE FRAGMENTED GRAINS IN A COMPOSITE MATERIAL

    Directory of Open Access Journals (Sweden)

    Luc Gillibert

    2013-06-01

    Full Text Available X-ray microtomography from solid propellant allows studying the microstructure of fragmented grains in damaged samples. A new reconstruction algorithm of fragmented grains for 3D images is introduced. Based on a watershed transform of a morphological closing of the input image, the algorithm can be used  with different sets of markers. Two of them are compared. After the grain reconstruction, a multiscale segmentation  algorithm is used to extract each fragment of the damaged grains. This allows an original quantitative study of the  fragmentation of each grain in 3D. Experimental results on X-ray microtomographic images of a solid propellant fragmented under compression are presented and validated.

  13. Tools to Perform Local Dense 3D Reconstruction of Shallow Water Seabed

    Directory of Open Access Journals (Sweden)

    Loïca Avanthey

    2016-05-01

    Full Text Available Tasks such as distinguishing or identifying individual objects of interest require the production of dense local clouds at the scale of these individual objects of interest. Due to the physical and dynamic properties of an underwater environment, the usual dense matching algorithms must be rethought in order to be adaptive. These properties also imply that the scene must be observed at close range. Classic robotized acquisition systems are oversized for local studies in shallow water while the systematic acquisition of data is not guaranteed with divers. We address these two major issues through a multidisciplinary approach. To efficiently acquire on-demand stereoscopic pairs using simple logistics in small areas of shallow water, we devised an agile light-weight dedicated system which is easy to reproduce. To densely match two views in a reliable way, we devised a reconstruction algorithm that automatically accounts for the dynamics, variability and light absorption of the underwater environment. Field experiments in the Mediterranean Sea were used to assess the results.

  14. A Method towards Automated Thrombolysis in Myocardial Infarction (TIMI) Frame Counting Using 3D Reconstruction

    NARCIS (Netherlands)

    ten Brinke, G.A.; Slump, Cornelis H.; Storm, C.J.; Stoel, M.G.

    2009-01-01

    Coronary stenosis is often assessed using planar X-ray angiography while injecting contrast agent. The data obtained during the intervention can be used to assess coronary flow velocity by tracking the contrast agent. The contrast flow can be used to estimate the functional behavior of the coronary

  15. Usefulness of 3D Reconstructed Computed Tomography Imaging for Double Outlet Right Ventricle

    Directory of Open Access Journals (Sweden)

    Shyh-Jye Chen

    2008-05-01

    Conclusion: 3D constructed CT imaging is a good modality for differentiating VSD type in DORV. It allowed us to directly evaluate the inside of cardiac chambers for the right ventricular outlet, great arterial root, and determine the VSD relationships.

  16. A Smartphone Interface for a Wireless EEG Headset with Real-Time 3D Reconstruction

    DEFF Research Database (Denmark)

    Stopczynski, Arkadiusz; Larsen, Jakob Eg; Stahlhut, Carsten

    2011-01-01

    We demonstrate a fully functional handheld brain scanner consisting of a low-cost 14-channel EEG headset with a wireless connec- tion to a smartphone, enabling minimally invasive EEG monitoring in naturalistic settings. The smartphone provides a touch-based interface with real-time brain state...

  17. PHOTOGRAMMETRIC 3D RECONSTRUCTION IN MATLAB: DEVELOPMENT OF A FREE TOOL

    Directory of Open Access Journals (Sweden)

    A. Masiero

    2017-11-01

    Full Text Available This paper presents the current state of development of a free Matlab tool for photogrammetric reconstruction developed at the University of Padova, Italy. The goal of this software is mostly educational, i.e. allowing students to have a close look to the specific steps which lead to the computation of a dense point cloud. As most of recently developed photogrammetric softwares, it is based on a Structure from Motion approach. Despite being mainly motivated by educational purposes, certain implementation details are clearly inspired by recent research works, e.g. limiting the computational burden of the feature matching by determining a suboptimal set of features to be considered, using information provided by external sensors to ease the matching process.

  18. A PHOTOGRAMMETRIC PIPELINE FOR THE 3D RECONSTRUCTION OF CASSIS IMAGES ON BOARD EXOMARS TGO

    Directory of Open Access Journals (Sweden)

    E. Simioni

    2017-07-01

    Full Text Available CaSSIS (Colour and Stereo Surface Imaging System is the stereo imaging system onboard the European Space Agency and ROSCOSMOS ExoMars Trace Gas Orbiter (TGO that has been launched on 14 March 2016 and entered a Mars elliptical orbit on 19 October 2016. During the first bounded orbits, CaSSIS returned its first multiband images taken on 22 and 26 November 2016. The telescope acquired 11 images, each composed by 30 framelets, of the Martian surface near Hebes Chasma and Noctis Labyrithus regions reaching at closest approach at a distance of 250 km from the surface. Despite of the eccentricity of this first orbit, CaSSIS has provided one stereo pair with a mean ground resolution of 6 m from a mean distance of 520 km. The team at the Astronomical Observatory of Padova (OAPD-INAF is involved into different stereo oriented missions and it is realizing a software for the generation of Digital Terrain Models from the CaSSIS images. The SW will be then adapted also for other projects involving stereo camera systems. To compute accurate 3D models, several sequential methods and tools have been developed. The preliminary pipeline provides: the generation of rectified images from the CaSSIS framelets, a matching core and post-processing methods. The software includes in particular: an automatic tie points detection by the Speeded Up Robust Features (SURF operator, an initial search for the correspondences through Normalize Cross Correlation (NCC algorithm and the Adaptive Least Square Matching (LSM algorithm in a hierarchical approach. This work will show a preliminary DTM generated by the first CaSSIS stereo images.

  19. Motion corrected 3D reconstruction of the fetal thorax from prenatal MRI.

    Science.gov (United States)

    Kainz, Bernhard; Malamateniou, Christina; Murgasova, Maria; Keraudren, Kevin; Rutherford, Mary; Hajnal, Joseph V; Rueckert, Daniel

    2014-01-01

    In this paper we present a semi-automatic method for analysis of the fetal thorax in genuine three-dimensional volumes. After one initial click we localize the spine and accurately determine the volume of the fetal lung from high resolution volumetric images reconstructed from motion corrupted prenatal Magnetic Resonance Imaging (MRI). We compare the current state-of-the-art method of segmenting the lung in a slice-by-slice manner with the most recent multi-scan reconstruction methods. We use fast rotation invariant spherical harmonics image descriptors with Classification Forest ensemble learning methods to extract the spinal cord and show an efficient way to generate a segmentation prior for the fetal lung from this information for two different MRI field strengths. The spinal cord can be segmented with a DICE coefficient of 0.89 and the automatic lung segmentation has been evaluated with a DICE coefficient of 0.87. We evaluate our method on 29 fetuses with a gestational age (GA) between 20 and 38 weeks and show that our computed segmentations and the manual ground truth correlate well with the recorded values in literature.

  20. 3D reconstruction from non-uniform point clouds via local hierarchical clustering

    Science.gov (United States)

    Yang, Jiaqi; Li, Ruibo; Xiao, Yang; Cao, Zhiguo

    2017-07-01

    Raw scanned 3D point clouds are usually irregularly distributed due to the essential shortcomings of laser sensors, which therefore poses a great challenge for high-quality 3D surface reconstruction. This paper tackles this problem by proposing a local hierarchical clustering (LHC) method to improve the consistency of point distribution. Specifically, LHC consists of two steps: 1) adaptive octree-based decomposition of 3D space, and 2) hierarchical clustering. The former aims at reducing the computational complexity and the latter transforms the non-uniform point set into uniform one. Experimental results on real-world scanned point clouds validate the effectiveness of our method from both qualitative and quantitative aspects.

  1. 3-D Reconstruction From 2-D Radiographic Images and Its Application to Clinical Veterinary Medicine

    Science.gov (United States)

    Hamamoto, Kazuhiko; Sato, Motoyoshi

    3D imaging technique is very important and indispensable in diagnosis. The main stream of the technique is one in which 3D image is reconstructed from a set of slice images, such as X-ray CT and MRI. However, these systems require large space and high costs. On the other hand, a low cost and small size 3D imaging system is needed in clinical veterinary medicine, for example, in the case of diagnosis in X-ray car or pasture area. We propose a novel 3D imaging technique using 2-D X-ray radiographic images. This system can be realized by cheaper system than X-ray CT and enables to get 3D image in X-ray car or portable X-ray equipment. In this paper, a 3D visualization technique from 2-D radiographic images is proposed and several reconstructions are shown. These reconstructions are evaluated by veterinarians.

  2. Monocular 3D Reconstruction and Augmentation of Elastic Surfaces with Self-Occlusion Handling.

    Science.gov (United States)

    Haouchine, Nazim; Dequidt, Jeremie; Berger, Marie-Odile; Cotin, Stephane

    2015-12-01

    This paper focuses on the 3D shape recovery and augmented reality on elastic objects with self-occlusions handling, using only single view images. Shape recovery from a monocular video sequence is an underconstrained problem and many approaches have been proposed to enforce constraints and resolve the ambiguities. State-of-the art solutions enforce smoothness or geometric constraints, consider specific deformation properties such as inextensibility or resort to shading constraints. However, few of them can handle properly large elastic deformations. We propose in this paper a real-time method that uses a mechanical model and able to handle highly elastic objects. The problem is formulated as an energy minimization problem accounting for a non-linear elastic model constrained by external image points acquired from a monocular camera. This method prevents us from formulating restrictive assumptions and specific constraint terms in the minimization. In addition, we propose to handle self-occluded regions thanks to the ability of mechanical models to provide appropriate predictions of the shape. Our method is compared to existing techniques with experiments conducted on computer-generated and real data that show the effectiveness of recovering and augmenting 3D elastic objects. Additionally, experiments in the context of minimally invasive liver surgery are also provided and results on deformations with the presence of self-occlusions are exposed.

  3. Photogrammetric 3d Reconstruction in Matlab: Development of a Free Tool

    Science.gov (United States)

    Masiero, A.

    2017-11-01

    This paper presents the current state of development of a free Matlab tool for photogrammetric reconstruction developed at the University of Padova, Italy. The goal of this software is mostly educational, i.e. allowing students to have a close look to the specific steps which lead to the computation of a dense point cloud. As most of recently developed photogrammetric softwares, it is based on a Structure from Motion approach. Despite being mainly motivated by educational purposes, certain implementation details are clearly inspired by recent research works, e.g. limiting the computational burden of the feature matching by determining a suboptimal set of features to be considered, using information provided by external sensors to ease the matching process.

  4. The CHT2 Project: Diachronic 3d Reconstruction of Historic Sites

    Science.gov (United States)

    Guidi, G.; Micoli, L.; Gonizzi Barsanti, S.; Malik, U.

    2017-08-01

    Digital modelling archaeological and architectural monuments in their current state and in their presumed past aspect has been recognized not only as a way for explaining to the public the genesis of a historical site, but also as an effective tool for research. The search for historical sources, their proper analysis and interdisciplinary relationship between technological disciplines and the humanities are fundamental for obtaining reliable hypothetical reconstructions. This paper presents an experimental activity defined by the project Cultural Heritage Through Time - CHT2 (http://cht2-project.eu), funded in the framework of the Joint Programming Initiative on Cultural Heritage (JPI-CH) of the European Commission. Its goal is to develop time-varying 3D products, from landscape to architectural scale, deals with the implementation of the methodology on one of the case studies: the late Roman circus of Milan, built in the era when the city was the capital of the Western Roman Empire (286-402 A.D). The work presented here covers one of the cases in which the physical evidences have now been almost entirely disappeared. The diachronic reconstruction is based on a proper mix of quantitative data originated by 3D surveys at present time, and historical sources like ancient maps, drawings, archaeological reports, archaeological restrictions decrees and old photographs. Such heterogeneous sources have been first georeferenced and then properly integrated according to the methodology defined in the framework of the CHT2 project, to hypothesize a reliable reconstruction of the area in different historical periods.

  5. Quantitative Analysis of 3D Reconstruction Parameters of Multi-Materialsin Soft Clay

    Directory of Open Access Journals (Sweden)

    Zhiqing Liu

    2018-03-01

    Full Text Available The results of the three-dimensional reconstruction of soil were derived from the X-ray absorption coefficient of the material itself. However, the absorption coefficient is not a fixed value, and is related to densities, chemical molecular weight, and the weight percentages of chemical components. How to accurately obtain the density of one component is a vital issue in multi-materials. In this study, the influence of the physical parameters of each component in the data-constrained modeling (DCM of the microstructure of soft clay was investigated. The results showed that density changes were more prominent. A reasonable multi-component density was calculated, and the density of organic matter had a significant effect on the volume percentage of three-dimensional soft clay. In the clay mineral montmorillonite, the density significantly affected the volume percentage data, which directly limited the accuracy of the material distribution analysis. Based on this, other physical parameters of each component in the data constraint model could be further explored. Based on the density value of the simple material, a reasonable multi-materials density was calculated, which provides a quantitative method for the evolution analysis of soil structure.

  6. Extreme 3D reconstruction of the final ROSETTA/PHILAE landing site

    Science.gov (United States)

    Capanna, Claire; Jorda, Laurent; Lamy, Philippe; Gesquiere, Gilles; Delmas, Cédric; Durand, Joelle; Garmier, Romain; Gaudon, Philippe; Jurado, Eric

    2016-04-01

    The Philae lander aboard the Rosetta spacecraft successfully landed at the surface of comet 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) after two rebounds on November 12, 2014. The final landing site, now known as « Abydos », has been identified on images acquired by the OSIRIS imaging system onboard the Rosetta orbiter[1]. The available images of Abydos are very limited in number and reveal a very extreme topography containing cliffs and overhangs. Furthermore, the surface is only observed under very high incidence angles of 60° on average, which implies that the images also exhibit lots of cast shadows. This makes it very difficult to reconstruct the 3D topography with standard methods such as photogrammetry or standard clinometry. We apply a new method called ''Multiresolution PhotoClinometry by Deformation'' (MPCD, [2]) to retrieve the 3D topography of the area around Abydos. The method works in two main steps: (i) a DTM of this region is extracted from a low resolution MPCD global shape model of comet 67P/C-G, and (ii) the resulting triangular mesh is progressively deformed at increasing spatial sampling down to 0.25 m in order to match a set of 14 images of Abydos with projected pixel scales between 1 and 8 m. The method used to perform the image matching is a quasi-Newton non-linear optimization method called L-BFGS-b[3] especially suited to large-scale problems. Finally, we also checked the compatibility of the final MPCD digital terrain model with a set of five panoramic images obtained by the CIVA-P instrument aboard Philae[4]. [1] Lamy et al., 2016, submitted. [2] Capanna et al., Three dimensional reconstruction using multiresoluton photoclinometry by deformation, The visual Computer, v. 29(6-8) pp. 825-835, 2013. [3] Morales et al., Remark on "Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound constrained optimization", v.38(1) pp.1-4, ACM Trans. Math. Softw., 2011 [4] Bibring et al., 67P/Churyumov-Gerasimenko surface properties as derived from CIVA panoramic images, Science, v. 349(6247), 2015

  7. DIRECT DETECTION OF THE HELICAL MAGNETIC FIELD GEOMETRY FROM 3D RECONSTRUCTION OF PROMINENCE KNOT TRAJECTORIES

    Energy Technology Data Exchange (ETDEWEB)

    Zapiór, Maciej; Martinez-Gómez, David, E-mail: zapior.maciek@gmail.com [Physics Department, University of the Balearic Islands, Cra. de Valldemossa, km 7.5. Palma (Illes Balears), E-07122 (Spain)

    2016-02-01

    Based on the data collected by the Vacuum Tower Telescope located in the Teide Observatory in the Canary Islands, we analyzed the three-dimensional (3D) motion of so-called knots in a solar prominence of 2014 June 9. Trajectories of seven knots were reconstructed, giving information of the 3D geometry of the magnetic field. Helical motion was detected. From the equipartition principle, we estimated the lower limit of the magnetic field in the prominence to ≈1–3 G and from the Ampère’s law the lower limit of the electric current to ≈1.2 × 10{sup 9} A.

  8. A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures

    Energy Technology Data Exchange (ETDEWEB)

    Mangipudi, K.R., E-mail: mangipudi@ump.gwdg.de [Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen (Germany); Radisch, V., E-mail: vradisch@ump.gwdg.de [Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen (Germany); Holzer, L., E-mail: holz@zhaw.ch [Züricher Hochschule für Angewandte Wissenschaften, Institute of Computational Physics, Wildbachstrasse 21, CH-8400 Winterthur (Switzerland); Volkert, C.A., E-mail: volkert@ump.gwdg.de [Institut für Materialphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen (Germany)

    2016-04-15

    We present an automated focused ion beam nanotomography method for nanoporous microstructures with open porosity, and apply it to reconstruct nanoporous gold (np-Au) structures with ligament sizes on the order of a few tens of nanometers. This method uses serial sectioning of a well-defined wedge-shaped geometry to determine the thickness of individual slices from the changes in the sample width in successive cross-sectional images. The pore space of a selected region of the np-Au is infiltrated with ion-beam-deposited Pt composite before serial sectioning. The cross-sectional images are binarized and stacked according to the individual slice thicknesses, and then processed using standard reconstruction methods. For the image conditions and sample geometry used here, we are able to determine the thickness of individual slices with an accuracy much smaller than a pixel. The accuracy of the new method based on actual slice thickness is assessed by comparing it with (i) a reconstruction using the same cross-sectional images but assuming a constant slice thickness, and (ii) a reconstruction using traditional FIB-tomography method employing constant slice thickness. The morphology and topology of the structures are characterized using ligament and pore size distributions, interface shape distribution functions, interface normal distributions, and genus. The results suggest that the morphology and topology of the final reconstructions are significantly influenced when a constant slice thickness is assumed. The study reveals grain-to-grain variations in the morphology and topology of np-Au. - Highlights: • FIB nanotomography of nanoporous structure with features sizes of ∼40 nm or less. • Accurate determination of individual slice thickness with subpixel precision. • The method preserves surface topography. • Quantitative 3D microstructural analysis of materials with open porosity.

  9. 3D RECONSTRUCTION OF BUILDINGS WITH GABLED AND HIPPED STRUCTURES USING LIDAR DATA

    Directory of Open Access Journals (Sweden)

    H. Amini

    2014-10-01

    Full Text Available Buildings are the most important objects in urban areas. Thus, building detection using photogrammetry and remote sensing data as well as 3D model of buildings are very useful for many applications such as mobile navigation, tourism, and disaster management. In this paper, an approach has been proposed for detecting buildings by LiDAR data and aerial images, as well as reconstructing 3D model of buildings. In this regard, firstly, building detection carried out by utilizing a Supper Vector Machine (SVM as a supervise method. The supervise methods need training data that could be collected from some features. Hence, LiDAR data and aerial images were utilized to produce some features. The features were selected by considering their abilities for separating buildings from other objects. The evaluation results of building detection showed high accuracy and precision of the utilized approach. The detected buildings were labeled in order to reconstruct buildings, individually. Then the planes of each building were separated and adjacent planes were recognized to reduce the calculation volume and to increase the accuracy. Subsequently, the bottom planes of each building were detected in order to compute the corners of hipped roofs using intersection of three adjacent planes. Also, the corners of gabled roofs were computed by both calculating the intersection line of the adjacent planes and finding the intersection between the planes intersection line and their detected parcel. Finally, the coordinates of some nodes in building floor were computed and 3D model reconstruction was carried out. In order to evaluate the proposed method, 3D model of some buildings with different complexity level were generated. The evaluation results showed that the proposed method has reached credible performance.

  10. Historic photos and TLS data fusion for the 3D reconstruction of a monastery altar ensemble

    Directory of Open Access Journals (Sweden)

    K. Hanke

    2015-08-01

    Full Text Available The basis of the photogrammetric reconstruction of the altar at the monastery / church are 2 historic photos from around 1920’s as well as a 3D documentation of the church from terrestrial laser scanning. The point cloud from the laser scan was the starting point for an approximate computation of the interior and exterior orientation of that image that also contains parts of the altar area that still do exist. Using a projection of the recent geometry into the image allowed the analysis of changes of the altar ensemble since the time of image acquisition. Those parts that are still in situ are the origin for further action. Whether fragments and parts should be used further or newly positioned was decided in the next phase of reconstruction process. The focus of the first step of the workflow was at the outlines of the parts in the center of the altar. Using a monoplotting approach and assuming that the profiles are vertical and parallel to each other these object could be definitely compiled. Theses outlines also allowed an approximate determination of the interior and exterior orientation of the second historic photograph in which otherwise the complete connection to the recent altar area was missing. The side parts of the altar showed to be more complicated for reconstruction. The difference in depth of the varying edges could not be distinguished any more in the images. Such, the sequence and form of the different edges was adopted, scaled and transferred from the central part of the altar to the peripheral ones. Using this geometric information it was possible to define the necessary projection planes for the monoplotting restitution of the visible outlines. A concluding rigorous control was accomplished by back projection of the geometry into both historical images.

  11. QUALITY ASSESSMENT OF 3D RECONSTRUCTION USING FISHEYE AND PERSPECTIVE SENSORS

    Directory of Open Access Journals (Sweden)

    C. Strecha

    2015-03-01

    Full Text Available Recent mathematical advances, growing alongside the use of unmanned aerial vehicles, have not only overcome the restriction of roll and pitch angles during flight but also enabled us to apply non-metric cameras in photogrammetric method, providing more flexibility for sensor selection. Fisheye cameras, for example, advantageously provide images with wide coverage; however, these images are extremely distorted and their non-uniform resolutions make them more difficult to use for mapping or terrestrial 3D modelling. In this paper, we compare the usability of different camera-lens combinations, using the complete workflow implemented in Pix4Dmapper to achieve the final terrestrial reconstruction result of a well-known historical site in Switzerland: the Chillon Castle. We assess the accuracy of the outcome acquired by consumer cameras with perspective and fisheye lenses, comparing the results to a laser scanner point cloud.

  12. Historic photos and TLS data fusion for the 3D reconstruction of a monastery altar ensemble

    Science.gov (United States)

    Hanke, K.; Moser, M.; Rampold, R.

    2015-08-01

    The basis of the photogrammetric reconstruction of the altar at the monastery / church are 2 historic photos from around 1920's as well as a 3D documentation of the church from terrestrial laser scanning. The point cloud from the laser scan was the starting point for an approximate computation of the interior and exterior orientation of that image that also contains parts of the altar area that still do exist. Using a projection of the recent geometry into the image allowed the analysis of changes of the altar ensemble since the time of image acquisition. Those parts that are still in situ are the origin for further action. Whether fragments and parts should be used further or newly positioned was decided in the next phase of reconstruction process. The focus of the first step of the workflow was at the outlines of the parts in the center of the altar. Using a monoplotting approach and assuming that the profiles are vertical and parallel to each other these object could be definitely compiled. Theses outlines also allowed an approximate determination of the interior and exterior orientation of the second historic photograph in which otherwise the complete connection to the recent altar area was missing. The side parts of the altar showed to be more complicated for reconstruction. The difference in depth of the varying edges could not be distinguished any more in the images. Such, the sequence and form of the different edges was adopted, scaled and transferred from the central part of the altar to the peripheral ones. Using this geometric information it was possible to define the necessary projection planes for the monoplotting restitution of the visible outlines. A concluding rigorous control was accomplished by back projection of the geometry into both historical images.

  13. Comparative myoanatomy of Echinoderes (Kinorhyncha): a comprehensive investigation by CLSM and 3D reconstruction

    National Research Council Canada - National Science Library

    Herranz, María; Boyle, Michael J; Pardos, Fernando; Neves, Ricardo C

    2014-01-01

    Kinorhyncha is a clade of marine invertebrate meiofauna. Their body plan includes a retractable introvert bearing rings of cuticular spines, and a limbless trunk with distinct segmentation of nervous, muscular and epidermal organ systems...

  14. Dental non-linear image registration and collection method with 3D reconstruction and change detection

    Science.gov (United States)

    Rahmes, Mark; Fagan, Dean; Lemieux, George

    2017-03-01

    The capability of a software algorithm to automatically align same-patient dental bitewing and panoramic x-rays over time is complicated by differences in collection perspectives. We successfully used image correlation with an affine transform for each pixel to discover common image borders, followed by a non-linear homography perspective adjustment to closely align the images. However, significant improvements in image registration could be realized if images were collected from the same perspective, thus facilitating change analysis. The perspective differences due to current dental image collection devices are so significant that straightforward change analysis is not possible. To address this, a new custom dental tray could be used to provide the standard reference needed for consistent positioning of a patient's mouth. Similar to sports mouth guards, the dental tray could be fabricated in standard sizes from plastic and use integrated electronics that have been miniaturized. In addition, the x-ray source needs to be consistently positioned in order to collect images with similar angles and scales. Solving this pose correction is similar to solving for collection angle in aerial imagery for change detection. A standard collection system would provide a method for consistent source positioning using real-time sensor position feedback from a digital x-ray image reference. Automated, robotic sensor positioning could replace manual adjustments. Given an image set from a standard collection, a disparity map between images can be created using parallax from overlapping viewpoints to enable change detection. This perspective data can be rectified and used to create a three-dimensional dental model reconstruction.

  15. 3D reconstruction for partial data electrical impedance tomography using a sparsity prior

    DEFF Research Database (Denmark)

    Garde, Henrik; Knudsen, Kim

    2015-01-01

    In electrical impedance tomography the electrical conductivity inside a physical body is computed from electro-static boundary measurements. The focus of this paper is to extend recent results for the 2D problem to 3D: prior information about the sparsity and spatial distribution of the conductiv...... regularization parameter. The optimization problem is solved numerically using a generalized conditional gradient method with soft thresholding. Numerical examples show the effectiveness of the suggested method even for the partial data problem with measurements affected by noise....

  16. Stereo Vision and 3D Reconstruction on a Distributed Memory System

    NARCIS (Netherlands)

    Kuijpers, N.H.L.; Paar, G.; Lukkien, J.J.

    1996-01-01

    An important research topic in image processing is stereo vision. The objective is to compute a 3-dimensional representation of some scenery from two 2-dimensional digital images. Constructing a 3-dimensional representation involves finding pairs of pixels from the two images which correspond to the

  17. Interstitial solute transport in 3D reconstructed neuropil occurs by diffusion rather than bulk flow.

    Science.gov (United States)

    Holter, Karl Erik; Kehlet, Benjamin; Devor, Anna; Sejnowski, Terrence J; Dale, Anders M; Omholt, Stig W; Ottersen, Ole Petter; Nagelhus, Erlend Arnulf; Mardal, Kent-André; Pettersen, Klas H

    2017-09-12

    The brain lacks lymph vessels and must rely on other mechanisms for clearance of waste products, including amyloid [Formula: see text] that may form pathological aggregates if not effectively cleared. It has been proposed that flow of interstitial fluid through the brain's interstitial space provides a mechanism for waste clearance. Here we compute the permeability and simulate pressure-mediated bulk flow through 3D electron microscope (EM) reconstructions of interstitial space. The space was divided into sheets (i.e., space between two parallel membranes) and tunnels (where three or more membranes meet). Simulation results indicate that even for larger extracellular volume fractions than what is reported for sleep and for geometries with a high tunnel volume fraction, the permeability was too low to allow for any substantial bulk flow at physiological hydrostatic pressure gradients. For two different geometries with the same extracellular volume fraction the geometry with the most tunnel volume had [Formula: see text] higher permeability, but the bulk flow was still insignificant. These simulation results suggest that even large molecule solutes would be more easily cleared from the brain interstitium by diffusion than by bulk flow. Thus, diffusion within the interstitial space combined with advection along vessels is likely to substitute for the lymphatic drainage system in other organs.

  18. A LOW-COST AND PORTABLE SYSTEM FOR 3D RECONSTRUCTION OF TEXTURE-LESS OBJECTS

    Directory of Open Access Journals (Sweden)

    A. Hosseininaveh

    2015-12-01

    Full Text Available The optical methods for 3D modelling of objects can be classified into two categories including image-based and range-based methods. Structure from Motion is one of the image-based methods implemented in commercial software. In this paper, a low-cost and portable system for 3D modelling of texture-less objects is proposed. This system includes a rotating table designed and developed by using a stepper motor and a very light rotation plate. The system also has eight laser light sources with very dense and strong beams which provide a relatively appropriate pattern on texture-less objects. In this system, regarding to the step of stepper motor, images are semi automatically taken by a camera. The images can be used in structure from motion procedures implemented in Agisoft software.To evaluate the performance of the system, two dark objects were used. The point clouds of these objects were obtained by spraying a light powders on the objects and exploiting a GOM laser scanner. Then these objects were placed on the proposed turntable. Several convergent images were taken from each object while the laser light sources were projecting the pattern on the objects. Afterward, the images were imported in VisualSFM as a fully automatic software package for generating an accurate and complete point cloud. Finally, the obtained point clouds were compared to the point clouds generated by the GOM laser scanner. The results showed the ability of the proposed system to produce a complete 3D model from texture-less objects.

  19. Visualization and 3D reconstruction of flame cells of Taenia solium (cestoda.

    Directory of Open Access Journals (Sweden)

    Laura E Valverde-Islas

    Full Text Available BACKGROUND: Flame cells are the terminal cells of protonephridial systems, which are part of the excretory systems of invertebrates. Although the knowledge of their biological role is incomplete, there is a consensus that these cells perform excretion/secretion activities. It has been suggested that the flame cells participate in the maintenance of the osmotic environment that the cestodes require to live inside their hosts. In live Platyhelminthes, by light microscopy, the cells appear beating their flames rapidly and, at the ultrastructural, the cells have a large body enclosing a tuft of cilia. Few studies have been performed to define the localization of the cytoskeletal proteins of these cells, and it is unclear how these proteins are involved in cell function. METHODOLOGY/PRINCIPAL FINDINGS: Parasites of two different developmental stages of T. solium were used: cysticerci recovered from naturally infected pigs and intestinal adults obtained from immunosuppressed and experimentally infected golden hamsters. Hamsters were fed viable cysticerci to recover adult parasites after one month of infection. In the present studies focusing on flame cells of cysticerci tissues was performed. Using several methods such as video, confocal and electron microscopy, in addition to computational analysis for reconstruction and modeling, we have provided a 3D visual rendition of the cytoskeletal architecture of Taenia solium flame cells. CONCLUSIONS/SIGNIFICANCE: We consider that visual representations of cells open a new way for understanding the role of these cells in the excretory systems of Platyhelminths. After reconstruction, the observation of high resolution 3D images allowed for virtual observation of the interior composition of cells. A combination of microscopic images, computational reconstructions and 3D modeling of cells appears to be useful for inferring the cellular dynamics of the flame cell cytoskeleton.

  20. A predictive model of asymmetric morphogenesis from 3D reconstructions of mouse heart looping dynamics

    OpenAIRE

    Le Garrec, Jean-François; Domínguez, Jorge N; Desgrange, Audrey; Ivanovitch, Kenzo D; Raphaël, Etienne; Bangham, J Andrew; Torres, Miguel; Coen, Enrico; Timothy J. Mohun; Meilhac, Sigolène M

    2017-01-01

    eLife digest The heart is an organ that pumps blood throughout the body to supply oxygen and to remove carbon dioxide and waste products. Its left and right side are shaped differently to circulate blood through two pathways: to the lungs and to all other organs. As the heart develops inside the embryo, it transforms from a simple, straight tube into a helix shape similar to the shell of a snail. During this process called looping, the helix coils anti-clockwise, which determines where the le...

  1. Geometrical Calibration of X-Ray Imaging With RGB Cameras for 3D Reconstruction.

    Science.gov (United States)

    Albiol, Francisco; Corbi, Alberto; Albiol, Alberto

    2016-08-01

    We present a methodology to recover the geometrical calibration of conventional X-ray settings with the help of an ordinary video camera and visible fiducials that are present in the scene. After calibration, equivalent points of interest can be easily identifiable with the help of the epipolar geometry. The same procedure also allows the measurement of real anatomic lengths and angles and obtains accurate 3D locations from image points. Our approach completely eliminates the need for X-ray-opaque reference marks (and necessary supporting frames) which can sometimes be invasive for the patient, occlude the radiographic picture, and end up projected outside the imaging sensor area in oblique protocols. Two possible frameworks are envisioned: a spatially shifting X-ray anode around the patient/object and a moving patient that moves/rotates while the imaging system remains fixed. As a proof of concept, experiences with a device under test (DUT), an anthropomorphic phantom and a real brachytherapy session have been carried out. The results show that it is possible to identify common points with a proper level of accuracy and retrieve three-dimensional locations, lengths and shapes with a millimetric level of precision. The presented approach is simple and compatible with both current and legacy widespread diagnostic X-ray imaging deployments and it can represent a good and inexpensive alternative to other radiological modalities like CT.

  2. Bayesian inversion method for the 3D reconstruction of settlements from metric SAR observations

    Science.gov (United States)

    Quartulli, Marco; Datcu, Mihai P.

    2002-02-01

    The reconstruction of urban structures from InSAR (Interferometric Synthetic Aperture Radar) observations is a complex task. Until now it has been tipically approached using the methods of radargrammetry and SAR interferometry, in a direct extension of what had been done in the past for the reconstruction of natural surfaces from generally much lower resolution data. In this work, we present a new concept aiming at the accurate and detailed reconstruction of the observed city scenes for metric SAR observations. We use a model-based approach for the synergetic analysis of the different sources of information in InSAR data. We define a hierarchical model of the InSAR observation that is both deterministic and stochastic. While the deterministic section describes the SAR imaging geometry and its effects and expresses the different scene structures, the stochastic part incapsulates instead prior knowledge about the signal and defines its attributes while also describing incertitude over the parameters of the geometrical model. Bayesian inference is used to couple the diffent levels of the model, and to further define parameter estimation algorithms.

  3. Organotypic and 3D reconstructed cultures of the human bladder and urinary tract.

    Science.gov (United States)

    Varley, Claire L; Southgate, Jennifer

    2011-01-01

    Three-dimensional organotypic cultures of human urinary tract tissue have been established as intact and reconstituted tissues, with the latter generated by combining cultured normal human urothelial (NHU) cells with an appropriate stroma. Organoids may be maintained at an air-liquid interface in static culture for periods of up to 20 weeks, with analysis by immunohistology for expression of urothelial differentiation-associated markers providing a qualitative, but objective assessment criterion. Where reconstructed using bladder cancer cell lines, the resultant organoids recapitulate the invasive characteristics of the originating tumour, but the need to use authenticated cell line stocks is emphasised. The organoid approach represents an important tool for investigating urothelial-stromal cell interactions during homeostasis and disease, and for testing bladder tissue engineering and reconstructive strategies. Potential future developments of the technique are discussed and include genetic manipulation of the urothelial cells to generate disease models and incorporation of biomaterial scaffolds to support artificial stroma development.

  4. High Resolution Electron Microbeam Examination and 3D Reconstruction of Alligator Gar Scale

    Science.gov (United States)

    2016-06-27

    Abstract and Presentation: Symposium: Biomineralization Abstract Title: Nanoscale Investigation of Hydroxylapatite Formation in Alligator Gar Fish Scale...zones within the collagen fibrils. The high calcium and oxygen bands that run horizontally in this image correspond to the gap zone of the collagen...while the high carbon bands correspond to the overlap zone. However, these bands do not correspond to collections of HAp crystals, but to regions of

  5. 3-D Reconstruction of Neurons from Multichannel Confocal Laser Scanning Image Series

    NARCIS (Netherlands)

    Wouterlood, F.G.

    2014-01-01

    A confocal laser scanning microscope (CLSM) collects information from a thin, focal plane and ignores out-of-focus information. Scanning of a specimen, with stepwise axial (Z-) movement of the stage in between each scan, produces Z-series of confocal images of a tissue volume, which then can be used

  6. A fast 3D reconstruction system with a low-cost camera accessory.

    Science.gov (United States)

    Zhang, Yiwei; Gibson, Graham M; Hay, Rebecca; Bowman, Richard W; Padgett, Miles J; Edgar, Matthew P

    2015-06-09

    Photometric stereo is a three dimensional (3D) imaging technique that uses multiple 2D images, obtained from a fixed camera perspective, with different illumination directions. Compared to other 3D imaging methods such as geometry modeling and 3D-scanning, it comes with a number of advantages, such as having a simple and efficient reconstruction routine. In this work, we describe a low-cost accessory to a commercial digital single-lens reflex (DSLR) camera system allowing fast reconstruction of 3D objects using photometric stereo. The accessory consists of four white LED lights fixed to the lens of a commercial DSLR camera and a USB programmable controller board to sequentially control the illumination. 3D images are derived for different objects with varying geometric complexity and results are presented, showing a typical height error of <3 mm for a 50 mm sized object.

  7. EVALUATION OF FRINGE PROJECTION AND LASER SCANNING FOR 3D RECONSTRUCTION OF DENTAL PIECES

    OpenAIRE

    NATALIA MÚNERA; GABRIEL J. LORA; JORGE GARCIA-SUCERQUIA

    2012-01-01

    La generación rápida de prototipos y la copia de objetos 3D reales desempeñan un papel clave en algunas industrias. Ambas aplicaciones se basan en la producción de archivos apropiados de fabricación asistida por computadora (CAM). Estos archivos representan un conjunto de coordenadas del objeto y que pueden ser entendidos por máquinas de control numérico (CNC). Técnicas de no contacto, como el escaneo láser y la proyección de franjas, se cuentan entre las posibilidades de generar los archivos...

  8. EVALUATION OF FRINGE PROJECTION AND LASER SCANNING FOR 3D RECONSTRUCTION OF DENTAL PIECES

    Directory of Open Access Journals (Sweden)

    NATALIA MÚNERA

    2012-01-01

    Full Text Available La generación rápida de prototipos y la copia de objetos 3D reales desempeñan un papel clave en algunas industrias. Ambas aplicaciones se basan en la producción de archivos apropiados de fabricación asistida por computadora (CAM. Estos archivos representan un conjunto de coordenadas del objeto y que pueden ser entendidos por máquinas de control numérico (CNC. Técnicas de no contacto, como el escaneo láser y la proyección de franjas, se cuentan entre las posibilidades de generar los archivos CAM. En este trabajo se presenta una comparación entre las dos mencionadas técnicas de no contacto, sobre la base de su desempeño como candidatos para la generación de archivos CAM de objetos con dimensiones laterales máximas del orden de 15 mm y alta reflectividad. Los parámetros de prueba son la calidad de la reconstrucción 3D, el tiempo de procesamiento, la posibilidad de ser aplicado en los escenarios industriales, entre otros. En el marco de aplicación de estos parámetros se concluye que el escaneo láser ofrece un rendimiento superior para el tipo de objetos aquí considerados. Las técnicas son evaluadas con piezas dentales para la validación de estas metodologías en la generación rápida de prototipos y copiado de dientes.

  9. Visualization and 3D Reconstruction of Flame Cells of Taenia solium (Cestoda)

    Science.gov (United States)

    Valverde-Islas, Laura E.; Arrangoiz, Esteban; Vega, Elio; Robert, Lilia; Villanueva, Rafael; Reynoso-Ducoing, Olivia; Willms, Kaethe; Zepeda-Rodríguez, Armando; Fortoul, Teresa I.; Ambrosio, Javier R.

    2011-01-01

    Background Flame cells are the terminal cells of protonephridial systems, which are part of the excretory systems of invertebrates. Although the knowledge of their biological role is incomplete, there is a consensus that these cells perform excretion/secretion activities. It has been suggested that the flame cells participate in the maintenance of the osmotic environment that the cestodes require to live inside their hosts. In live Platyhelminthes, by light microscopy, the cells appear beating their flames rapidly and, at the ultrastructural, the cells have a large body enclosing a tuft of cilia. Few studies have been performed to define the localization of the cytoskeletal proteins of these cells, and it is unclear how these proteins are involved in cell function. Methodology/Principal Findings Parasites of two different developmental stages of T. solium were used: cysticerci recovered from naturally infected pigs and intestinal adults obtained from immunosuppressed and experimentally infected golden hamsters. Hamsters were fed viable cysticerci to recover adult parasites after one month of infection. In the present studies focusing on flame cells of cysticerci tissues was performed. Using several methods such as video, confocal and electron microscopy, in addition to computational analysis for reconstruction and modeling, we have provided a 3D visual rendition of the cytoskeletal architecture of Taenia solium flame cells. Conclusions/Significance We consider that visual representations of cells open a new way for understanding the role of these cells in the excretory systems of Platyhelminths. After reconstruction, the observation of high resolution 3D images allowed for virtual observation of the interior composition of cells. A combination of microscopic images, computational reconstructions and 3D modeling of cells appears to be useful for inferring the cellular dynamics of the flame cell cytoskeleton. PMID:21412407

  10. Post-processing methods of rendering and visualizing 3-D reconstructed tomographic images

    Energy Technology Data Exchange (ETDEWEB)

    Wong, S.T.C. [Univ. of California, San Francisco, CA (United States)

    1997-02-01

    The purpose of this presentation is to discuss the computer processing techniques of tomographic images, after they have been generated by imaging scanners, for volume visualization. Volume visualization is concerned with the representation, manipulation, and rendering of volumetric data. Since the first digital images were produced from computed tomography (CT) scanners in the mid 1970s, applications of visualization in medicine have expanded dramatically. Today, three-dimensional (3D) medical visualization has expanded from using CT data, the first inherently digital source of 3D medical data, to using data from various medical imaging modalities, including magnetic resonance scanners, positron emission scanners, digital ultrasound, electronic and confocal microscopy, and other medical imaging modalities. We have advanced from rendering anatomy to aid diagnosis and visualize complex anatomic structures to planning and assisting surgery and radiation treatment. New, more accurate and cost-effective procedures for clinical services and biomedical research have become possible by integrating computer graphics technology with medical images. This trend is particularly noticeable in current market-driven health care environment. For example, interventional imaging, image-guided surgery, and stereotactic and visualization techniques are now stemming into surgical practice. In this presentation, we discuss only computer-display-based approaches of volumetric medical visualization. That is, we assume that the display device available is two-dimensional (2D) in nature and all analysis of multidimensional image data is to be carried out via the 2D screen of the device. There are technologies such as holography and virtual reality that do provide a {open_quotes}true 3D screen{close_quotes}. To confine the scope, this presentation will not discuss such approaches.

  11. Artifact reduction based on sinogram interpolation for the 3D reconstruction of nanoparticles using electron tomography

    NARCIS (Netherlands)

    K. Sentosun; I. Lobato (Ivan); E. Bladt; Y. Zhang (Yang); W.J. Palenstijn (Willem Jan); K.J. Batenburg (Joost); D. Van Dyck (Dirk); S. Bals (Sara)

    2017-01-01

    textabstractElectron tomography is a well-known technique providing a 3D characterization of the morphology and chemical composition of nanoparticles. However, several reasons hamper the acquisition of tilt series with a large number of projection images, which deteriorate the quality of the 3D

  12. High dynamic range (HDR) virtual bronchoscopy rendering for video tracking

    Science.gov (United States)

    Popa, Teo; Choi, Jae

    2007-03-01

    In this paper, we present the design and implementation of a new rendering method based on high dynamic range (HDR) lighting and exposure control. This rendering method is applied to create video images for a 3D virtual bronchoscopy system. One of the main optical parameters of a bronchoscope's camera is the sensor exposure. The exposure adjustment is needed since the dynamic range of most digital video cameras is narrower than the high dynamic range of real scenes. The dynamic range of a camera is defined as the ratio of the brightest point of an image to the darkest point of the same image where details are present. In a video camera exposure is controlled by shutter speed and the lens aperture. To create the virtual bronchoscopic images, we first rendered a raw image in absolute units (luminance); then, we simulated exposure by mapping the computed values to the values appropriate for video-acquired images using a tone mapping operator. We generated several images with HDR and others with low dynamic range (LDR), and then compared their quality by applying them to a 2D/3D video-based tracking system. We conclude that images with HDR are closer to real bronchoscopy images than those with LDR, and thus, that HDR lighting can improve the accuracy of image-based tracking.

  13. High-speed digital video tracking system for generic applications

    Science.gov (United States)

    Walton, James S.; Hallamasek, Karen G.

    2001-04-01

    The value of high-speed imaging for making subjective assessments is widely recognized, but the inability to acquire useful data from image sequences in a timely fashion has severely limited the use of the technology. 4DVideo has created a foundation for a generic instrument that can capture kinematic data from high-speed images. The new system has been designed to acquire (1) two-dimensional trajectories of points; (2) three-dimensional kinematics of structures or linked rigid-bodies; and (3) morphological reconstructions of boundaries. The system has been designed to work with an unlimited number of cameras configured as nodes in a network, with each camera able to acquire images at 1000 frames per second (fps) or better, with a spatial resolution of 512 X 512 or better, and an 8-bit gray scale. However, less demanding configurations are anticipated. The critical technology is contained in the custom hardware that services the cameras. This hardware optimizes the amount of information stored, and maximizes the available bandwidth. The system identifies targets using an algorithm implemented in hardware. When complete, the system software will provide all of the functionality required to capture and process video data from multiple perspectives. Thereafter it will extract, edit and analyze the motions of finite targets and boundaries.

  14. 3D reconstruction and standardization of the rat facial nucleus for precise mapping of vibrissal motor networks.

    Science.gov (United States)

    Guest, Jason M; Seetharama, Mythreya M; Wendel, Elizabeth S; Strick, Peter L; Oberlaender, Marcel

    2017-09-27

    The rodent facial nucleus (FN) comprises motoneurons (MNs) that control the facial musculature. In the lateral part of the FN, populations of vibrissal motoneurons (vMNs) innervate two groups of muscles that generate movements of the whiskers. Vibrissal MNs thus represent the terminal point of the neuronal networks that generate rhythmic whisking during exploratory behaviors and that modify whisker movements based on sensory-motor feedback during tactile-based perception. Here, we combined retrograde tracer injections into whisker-specific muscles, with large-scale immunohistochemistry and digital reconstructions to generate an average model of the rat FN. The model incorporates measurements of the FN geometry, its cellular organization and a whisker row-specific map formed by vMNs. Furthermore, the model provides a digital 3D reference frame that allows registering structural data - obtained across scales and animals - into a common coordinate system with a precision of ∼60 µm. We illustrate the registration method by injecting replication competent rabies virus into the muscle of a single whisker. Retrograde transport of the virus to vMNs enabled reconstruction of their dendrites. Subsequent trans-synaptic transport enabled mapping the presynaptic neurons of the reconstructed vMNs. Registration of these data to the FN reference frame provides a first account of the morphological and synaptic input variability within a population of vMNs that innervate the same muscle. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. A detailed description of the development of the hemichordate Saccoglossus kowalevskii using SEM, TEM, Histology and 3D-reconstructions

    OpenAIRE

    Kaul-Strehlow, Sabrina; Stach, Thomas

    2013-01-01

    Introduction Traditionally, the origin of the third germ layer and its special formation of coelomic cavities by enterocoely is regarded to be an informative character in phylogenetic analyses. In early deuterostomes such as sea urchins, the mesoderm forms through a single evagination pinching off from the apical end of the archenteron which then gives off mesocoela and metacoela on each side. This echinoid-type coelom formation has conventionally been assumed to be ancestral for Deuterostomi...

  16. The External Ligurian tectonic units in the Northern Apennines (Italy): 3D reconstruction and relationships with the foreland (Po Plain).

    Science.gov (United States)

    Toscani, G.; Fantoni, R.; Rogledi, S.; Seno, S.

    2003-04-01

    Field, seismic and well data have been merged in order to reconstruct in 3D the basal surface of the External Ligurian tectonic units in the Northern Apennine sector confined between the Bobbio window and the Po Plain. The stacking of the pile of nappes coming from different palaeogeographic domains is displayed in a well-known large antiformal structure, the Bobbio tectonic window. From bottom to top, the Tuscan units are overthrust by Subligurian units, and the structural sequence is closed upward by a group of units belonging to the External Ligurian domain. The evolution of this sector of the Northern Apennine front and the relationships with the foreland have been studied also by means of a cross section running from the exposed axial zone of the chain up to the external structures, buried under the central part of the Po Plain. The basal thrust of the External Ligurian units shows a great deepening moving from the window in all directions. In particular, moving westward, this surface reaches a maximum depth of thousand metres under the sea level less than 10 km away from the core of the window. In the frontal zone (moving northward, i.e. toward the foreland) Ligurian units' thickness appears to be progressively reduced and these units overlap younger rocks (from Serravallian to Messinian age) belonging to the Po Plain's autochthonous sequence.

  17. 3D-Reconstruction of recent volcanic activity from ROV-video, Charles Darwin Seamounts, Cape Verdes

    Science.gov (United States)

    Kwasnitschka, T.; Hansteen, T. H.; Kutterolf, S.; Freundt, A.; Devey, C. W.

    2011-12-01

    As well as providing well-localized samples, Remotely Operated Vehicles (ROVs) produce huge quantities of visual data whose potential for geological data mining has seldom if ever been fully realized. We present a new workflow to derive essential results of field geology such as quantitative stratigraphy and tectonic surveying from ROV-based photo and video material. We demonstrate the procedure on the Charles Darwin Seamounts, a field of small hot spot volcanoes recently identified at a depth of ca. 3500m southwest of the island of Santo Antao in the Cape Verdes. The Charles Darwin Seamounts feature a wide spectrum of volcanic edifices with forms suggestive of scoria cones, lava domes, tuff rings and maar-type depressions, all of comparable dimensions. These forms, coupled with the highly fragmented volcaniclastic samples recovered by dredging, motivated surveying parts of some edifices down to centimeter scale. ROV-based surveys yielded volcaniclastic samples of key structures linked by extensive coverage of stereoscopic photographs and high-resolution video. Based upon the latter, we present our workflow to derive three-dimensional models of outcrops from a single-camera video sequence, allowing quantitative measurements of fault orientation, bedding structure, grain size distribution and photo mosaicking within a geo-referenced framework. With this information we can identify episodes of repetitive eruptive activity at individual volcanic centers and see changes in eruptive style over time, which, despite their proximity to each other, is highly variable.

  18. Use of 3D reconstruction of emergency and postoperative craniocerebral CT images to explore craniocerebral trauma mechanism.

    Science.gov (United States)

    Li, Zhengdong; Zou, Donghua; Zhang, Jianhua; Shao, Yu; Huang, Ping; Chen, Yijiu

    2015-10-01

    We report a craniocerebral trauma case in which a man sustained severe skull fractures and cerebral contusions and it demanded elucidating the injury mechanism of being formed by strike or tumble. However, the initial features of skull fractures were mostly lost when the forensic pathologists involved in the case 5 months later because of injury healing and craniocerebral surgery. Therefore, we aimed to reconstruct the original skull fracture features by utilizing the digital reconstruction technologies in terms of CT (computed tomography) scanning, 3D (3-dimentional) reconstruction, and virtual surgical tools. The original fracture skull was assembled by using Mimics 13.0 based on the CT slices of postoperative head and the removed craniotomy skull flaps, which revealed fracture features of focal and overall skull deformation. Based on the assembly skull model and the contrecoup cerebral contusions, we conclude that the man suffered a tumble after being drunk and the serious craniocerebral trauma occurred. The case demonstrated that the digital reconstruction technologies can serve as effective approaches for forensic investigation in case of survived craniocerebral trauma patients without direct evidences interpreting the original trauma patterns, which could potentially be helpful in exploring the injury mechanisms. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. 3D RECONSTRUCTION AND MODELING OF SUBTERRANEAN LANDSCAPES IN COLLABORATIVE MINING ARCHEOLOGY PROJECTS: TECHNIQUES, APPLICATIONS AND EXPERIENCES

    Directory of Open Access Journals (Sweden)

    A. Arles

    2013-07-01

    Full Text Available Mining and underground archaeology are two domains of expertise where three-dimensional data take an important part in the associated researches. Up to now, archaeologists study mines and underground networks from line-plot surveys, cross-section of galleries, and from tool marks surveys. All this kind of information can be clearly recorded back from the field from threedimensional models with a more cautious and extensive approach. Besides, the volumes of the underground structures that are very important data to explain the mining activities are difficult to evaluate from "traditional" hand-made recordings. They can now be calculated more accurately from a 3D model. Finally, reconstructed scenes are a powerful tool as thinking aid to look back again to a structure in the office or in future times. And the recorded models, rendered photo-realistically, can also be used for cultural heritage documentation presenting inaccessible and sometimes dangerous places to the public. Nowadays, thanks to modern computer technologies and highly developed software tools paired with sophisticated digital camera equipment, complex photogrammetric processes are available for moderate costs for research teams. Recognizing these advantages the authors develop and utilize image-based workflows in order to document ancient mining monuments and underground sites as a basis for further historical and archaeological researches, performed in collaborative partnership during recent projects on medieval silver mines and preventive excavations of undergrounds in France.

  20. Total Variation-Based Reduction of Streak Artifacts, Ring Artifacts and Noise in 3D Reconstruction from Optical Projection Tomography

    Czech Academy of Sciences Publication Activity Database

    Michálek, Jan

    2015-01-01

    Roč. 21, č. 6 (2015), s. 1602-1615 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LH13028; GA ČR(CZ) GA13-12412S Institutional support: RVO:67985823 Keywords : optical projection tomography * microscopy * artifacts * total variation * data mismatch Subject RIV: EA - Cell Biology Impact factor: 1.730, year: 2015

  1. 3-D reconstruction of sub-wavelength scatterers from the measurement of scattered fields in elastic waveguides

    NARCIS (Netherlands)

    Moreau, L.; Hunter, A.J.; Velichko, A.; Wilcox, P.D.

    2014-01-01

    In nondestructive testing, being able to remotely locate and size defects with good accuracy is an important requirement in many industrial sectors, such as the petrochemical, nuclear, and aerospace industries. The potential of ultrasonic guided waves is well known for this type of problem, but

  2. 3D reconstruction of prior β grains in friction stir-processed Ti-6Al-4V.

    Science.gov (United States)

    Tiley, J S; Shiveley, A R; Pilchak, A L; Shade, P A; Groeber, M A

    2014-08-01

    The prior β grain structure and orientations in the central stir zone of friction stir-processed Ti-6Al-4V were reconstructed from measured α phase orientations obtained by three-dimensional serial sectioning in a dual-beam focused ion beam scanning electron microscope. The data were processed to obtain the α colony and β grain size distributions in the volume. Several β grains were individually analysed to determine the total number of unique α variants and the respective volume fractions of each. The analysis revealed that some grains experienced overwhelming variant selection (i.e. one variant dominated) whereas other β grains contained a more evenly distributed mixture of all 12 variants. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

  3. Simulation of signal flow in 3D reconstructions of an anatomically realistic neural network in rat vibrissal cortex.

    Science.gov (United States)

    Lang, Stefan; Dercksen, Vincent J; Sakmann, Bert; Oberlaender, Marcel

    2011-11-01

    The three-dimensional (3D) structure of neural circuits represents an essential constraint for information flow in the brain. Methods to directly monitor streams of excitation, at subcellular and millisecond resolution, are at present lacking. Here, we describe a pipeline of tools that allow investigating information flow by simulating electrical signals that propagate through anatomically realistic models of average neural networks. The pipeline comprises three blocks. First, we review tools that allow fast and automated acquisition of 3D anatomical data, such as neuron soma distributions or reconstructions of dendrites and axons from in vivo labeled cells. Second, we introduce NeuroNet, a tool for assembling the 3D structure and wiring of average neural networks. Finally, we introduce a simulation framework, NeuroDUNE, to investigate structure-function relationships within networks of full-compartmental neuron models at subcellular, cellular and network levels. We illustrate the pipeline by simulations of a reconstructed excitatory network formed between the thalamus and spiny stellate neurons in layer 4 (L4ss) of a cortical barrel column in rat vibrissal cortex. Exciting the ensemble of L4ss neurons with realistic input from an ensemble of thalamic neurons revealed that the location-specific thalamocortical connectivity may result in location-specific spiking of cortical cells. Specifically, a radial decay in spiking probability toward the column borders could be a general feature of signal flow in a barrel column. Our simulations provide insights of how anatomical parameters, such as the subcellular organization of synapses, may constrain spiking responses at the cellular and network levels. Copyright © 2011 Elsevier Ltd. All rights reserved.

  4. A comparative analysis between active and passive techniques for underwater 3D reconstruction of close-range objects.

    Science.gov (United States)

    Bianco, Gianfranco; Gallo, Alessandro; Bruno, Fabio; Muzzupappa, Maurizio

    2013-08-20

    In some application fields, such as underwater archaeology or marine biology, there is the need to collect three-dimensional, close-range data from objects that cannot be removed from their site. In particular, 3D imaging techniques are widely employed for close-range acquisitions in underwater environment. In this work we have compared in water two 3D imaging techniques based on active and passive approaches, respectively, and whole-field acquisition. The comparison is performed under poor visibility conditions, produced in the laboratory by suspending different quantities of clay in a water tank. For a fair comparison, a stereo configuration has been adopted for both the techniques, using the same setup, working distance, calibration, and objects. At the moment, the proposed setup is not suitable for real world applications, but it allowed us to conduct a preliminary analysis on the performances of the two techniques and to understand their capability to acquire 3D points in presence of turbidity. The performances have been evaluated in terms of accuracy and density of the acquired 3D points. Our results can be used as a reference for further comparisons in the analysis of other 3D techniques and algorithms.

  5. A Comparative Analysis between Active and Passive Techniques for Underwater 3D Reconstruction of Close-Range Objects

    Directory of Open Access Journals (Sweden)

    Maurizio Muzzupappa

    2013-08-01

    Full Text Available In some application fields, such as underwater archaeology or marine biology, there is the need to collect three-dimensional, close-range data from objects that cannot be removed from their site. In particular, 3D imaging techniques are widely employed for close-range acquisitions in underwater environment. In this work we have compared in water two 3D imaging techniques based on active and passive approaches, respectively, and whole-field acquisition. The comparison is performed under poor visibility conditions, produced in the laboratory by suspending different quantities of clay in a water tank. For a fair comparison, a stereo configuration has been adopted for both the techniques, using the same setup, working distance, calibration, and objects. At the moment, the proposed setup is not suitable for real world applications, but it allowed us to conduct a preliminary analysis on the performances of the two techniques and to understand their capability to acquire 3D points in presence of turbidity. The performances have been evaluated in terms of accuracy and density of the acquired 3D points. Our results can be used as a reference for further comparisons in the analysis of other 3D techniques and algorithms.

  6. Interaction and behaviour imaging: a novel method to measure mother-infant interaction using video 3D reconstruction.

    Science.gov (United States)

    Leclère, C; Avril, M; Viaux-Savelon, S; Bodeau, N; Achard, C; Missonnier, S; Keren, M; Feldman, R; Chetouani, M; Cohen, D

    2016-05-24

    Studying early interaction is essential for understanding development and psychopathology. Automatic computational methods offer the possibility to analyse social signals and behaviours of several partners simultaneously and dynamically. Here, 20 dyads of mothers and their 13-36-month-old infants were videotaped during mother-infant interaction including 10 extremely high-risk and 10 low-risk dyads using two-dimensional (2D) and three-dimensional (3D) sensors. From 2D+3D data and 3D space reconstruction, we extracted individual parameters (quantity of movement and motion activity ratio for each partner) and dyadic parameters related to the dynamics of partners heads distance (contribution to heads distance), to the focus of mutual engagement (percentage of time spent face to face or oriented to the task) and to the dynamics of motion activity (synchrony ratio, overlap ratio, pause ratio). Features are compared with blind global rating of the interaction using the coding interactive behavior (CIB). We found that individual and dyadic parameters of 2D+3D motion features perfectly correlates with rated CIB maternal and dyadic composite scores. Support Vector Machine classification using all 2D-3D motion features classified 100% of the dyads in their group meaning that motion behaviours are sufficient to distinguish high-risk from low-risk dyads. The proposed method may present a promising, low-cost methodology that can uniquely use artificial technology to detect meaningful features of human interactions and may have several implications for studying dyadic behaviours in psychiatry. Combining both global rating scales and computerized methods may enable a continuum of time scale from a summary of entire interactions to second-by-second dynamics.

  7. Current Constriction at Electrode/Electrolyte Interfaces in Solid Oxide Cell Electrochemical Devices Calculated Via 3D Reconstructions

    DEFF Research Database (Denmark)

    Nielsen, Jimmi; Jørgensen, Peter Stanley; Graves, Christopher R.

    2016-01-01

    Electrochemical devices such as batteries, fuel cells, electrolysers, electrochemical reactors and electrochemical sensors are important technologies for the present and the future society. For further improvement or maturing of the various technologies it is important to understand, characterize...

  8. Validation of plant part measurements using a 3D reconstruction method suitable for high-throughput seedling phenotyping

    NARCIS (Netherlands)

    Golbach, Franck; Kootstra, Gert; Damjanovic, Sanja; Otten, Gerwoud; Zedde, van de Rick

    2016-01-01

    In plant phenotyping, there is a demand for high-throughput, non-destructive systems that can accurately analyse various plant traits by measuring features such as plant volume, leaf area, and stem length. Existing vision-based systems either focus on speed using 2D imaging, which is consequently

  9. Three-dimensional (3D) reconstruction and quantitative analysis of the microvasculature in medulloblastoma and ependymoma subtypes.

    NARCIS (Netherlands)

    Gilhuis, H.J.; Laak, J.A.W.M. van der; Pomp, J.; Kappelle, A.C.; Gijtenbeek, J.M.M.; Wesseling, P.

    2006-01-01

    In the World Health Organisation (WHO) classification of tumours of the nervous system, four main histopathological subtypes of medulloblastomas (classic medulloblastoma, desmoplastic medulloblastoma, medulloblastoma with extensive nodularity and advanced neuronal differentiation and large

  10. A validated methodology for the 3D reconstruction of cochlea geometries using human microCT images

    Science.gov (United States)

    Sakellarios, A. I.; Tachos, N. S.; Rigas, G.; Bibas, T.; Ni, G.; Böhnke, F.; Fotiadis, D. I.

    2017-05-01

    Accurate reconstruction of the inner ear is a prerequisite for the modelling and understanding of the inner ear mechanics. In this study, we present a semi-automated methodology for accurate reconstruction of the major inner ear structures (scalae, basilar membrane, stapes and semicircular canals). For this purpose, high resolution microCT images of a human specimen were used. The segmentation methodology is based on an iterative level set algorithm which provides the borders of the structures of interest. An enhanced coupled level set method which allows the simultaneous multiple image labeling without any overlapping regions has been developed for this purpose. The marching cube algorithm was applied in order to extract the surface from the segmented volume. The reconstructed geometries are then post-processed to improve the basilar membrane geometry to realistically represent physiologic dimensions. The final reconstructed model is compared to the available data from the literature. The results show that our generated inner ear structures are in good agreement with the published ones, while our approach is the most realistic in terms of the basilar membrane thickness and width reconstruction.

  11. Tentorial mobility in centipedes (Chilopoda revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha

    Directory of Open Access Journals (Sweden)

    Markus Koch

    2015-06-01

    Full Text Available Mandibular mechanisms in Geophilomorpha are revised based on three-dimensional reconstructions of the mandibulo-tentorial complex and its muscular equipment in Dicellophilus carniolensis (Placodesmata and Hydroschendyla submarina (Adesmata. Tentorial structure compares closely in the two species and homologies can be proposed for the 14/17 muscles that attach to the tentorium. Both species retain homologues of muscles that in other Pleurostigmophora are traditionally thought to cause swinging movements of the tentorium that complement the mobility of the mandibles. Although the original set of tentorial muscles is simplified in Geophilomorpha, the arrangement of the preserved homologues conforms to a system of six degrees of freedom of movement, as in non-geophilomorph Pleurostigmophora. A simplification of the mandibular muscles is confirmed for Geophilomorpha, but our results reject absence of muscles that in other Pleurostigmophora primarily support see-saw movements of the mandibles. In the construction of the tentorium, paralabial sclerites seem to be involved in neither Placodesmata nor Adesmata, and we propose their loss in Geophilomorpha as a whole. Current insights on the tentorial skeleton and its musculature permit two alternative conclusions on their transformation in Geophilomorpha: either tentorial mobility is primarily maintained in both Placodesmata and Adesmata (contrary to Manton’s arguments for immobility, or the traditional assumption of the tentorium as being mobile is a misinterpretation for Pleurostigmophora as a whole.

  12. THE COMPLETE VIRTUAL 3D RECONSTRUCTION OF THE EAST PEDIMENT OF THE TEMPLE OF ZEUS AT OLYMPIA

    National Research Council Canada - National Science Library

    A. Patay-Horváth

    2012-01-01

    The arrangement of the five central figures of the east pediment of the temple of Zeus at Olympia has been the subject of scholarly debates since the discovery of the fragments more than a century ago...

  13. SCAN TO BIM FOR 3D RECONSTRUCTION OF THE PAPAL BASILICA OF SAINT FRANCIS IN ASSISI IN ITALY

    Directory of Open Access Journals (Sweden)

    M. G. Angelini

    2017-05-01

    Full Text Available The historical building heritage, present in the most of Italian cities centres, is, as part of the construction sector, a working potential, but unfortunately it requires planning of more complex and problematic interventions. However, policies to support on the existing interventions, together with a growing sensitivity for the recovery of assets, determine the need to implement specific studies and to analyse the specific problems of each site. The purpose of this paper is to illustrate the methodology and the results obtained from integrated laser scanning activity in order to have precious architectural information useful not only from the cultural heritage point of view but also to construct more operative and powerful tools, such as BIM (Building Information Modelling aimed to the management of this cultural heritage. The Papal Basilica and the Sacred Convent of Saint Francis in Assisi in Italy are, in fact, characterized by unique and complex peculiarities, which require a detailed knowledge of the sites themselves to ensure visitor’s security and safety. For such a project, we have to take in account all the people and personnel normally present in the site, visitors with disabilities and finally the needs for cultural heritage preservation and protection. This aim can be reached using integrated systems and new technologies, such as Internet of Everything (IoE, capable of connecting people, things (smart sensors, devices and actuators; mobile terminals; wearable devices; etc., data/information/knowledge and processes to reach the desired goals. The IoE system must implement and support an Integrated Multidisciplinary Model for Security and Safety Management (IMMSSM for the specific context, using a multidisciplinary approach.

  14. Digital 3D reconstruction of Agustin de Betancourt's historical heritage: the machine for cutting grass in waterways

    Directory of Open Access Journals (Sweden)

    José Ignacio Rojas-Sola

    2016-05-01

    Full Text Available Agustín de Betancourt y Molina was one of the most distinguished engineers of the eighteenth and nineteenth centuries with numerous contributions to various fields of engineering, including civil engineering. This research shows the process followed in the documentation of the cultural heritage of that Canary engineer, especially in the geometric documentation of a machine for cutting grass in waterways presented in England in 1795 after three years researching on theory of machines. The baseline information has been recovered from the Canary Orotava Foundation of History of Science who has spent years collecting information about the Project Betancourt, in particular, planimetric information as well as a small report on its operation and description of parts of machine. From this information, we have constructed a three dimensional (3D model using CAD techniques with the use of Solid Edge ST7 parametric software, which has enabled the team to create the 3D model as well as different detail plans and exploded views.

  15. Scan to Bim for 3d Reconstruction of the Papal Basilica of Saint Francis in Assisi in Italy

    Science.gov (United States)

    Angelini, M. G.; Baiocchi, V.; Costantino, D.; Garzia, F.

    2017-05-01

    The historical building heritage, present in the most of Italian cities centres, is, as part of the construction sector, a working potential, but unfortunately it requires planning of more complex and problematic interventions. However, policies to support on the existing interventions, together with a growing sensitivity for the recovery of assets, determine the need to implement specific studies and to analyse the specific problems of each site. The purpose of this paper is to illustrate the methodology and the results obtained from integrated laser scanning activity in order to have precious architectural information useful not only from the cultural heritage point of view but also to construct more operative and powerful tools, such as BIM (Building Information Modelling) aimed to the management of this cultural heritage. The Papal Basilica and the Sacred Convent of Saint Francis in Assisi in Italy are, in fact, characterized by unique and complex peculiarities, which require a detailed knowledge of the sites themselves to ensure visitor's security and safety. For such a project, we have to take in account all the people and personnel normally present in the site, visitors with disabilities and finally the needs for cultural heritage preservation and protection. This aim can be reached using integrated systems and new technologies, such as Internet of Everything (IoE), capable of connecting people, things (smart sensors, devices and actuators; mobile terminals; wearable devices; etc.), data/information/knowledge and processes to reach the desired goals. The IoE system must implement and support an Integrated Multidisciplinary Model for Security and Safety Management (IMMSSM) for the specific context, using a multidisciplinary approach.

  16. 3D Reconstruction of the Human Airway Mucosa In Vitro as an Experimental Model to Study NTHi Infections

    Science.gov (United States)

    Marrazzo, Pasquale; Maccari, Silvia; Taddei, Annarita; Bevan, Luke; Telford, John; Soriani, Marco; Pezzicoli, Alfredo

    2016-01-01

    We have established an in vitro 3D system which recapitulates the human tracheo-bronchial mucosa comprehensive of the pseudostratified epithelium and the underlying stromal tissue. In particular, we reported that the mature model, entirely constituted of primary cells of human origin, develops key markers proper of the native tissue such as the mucociliary differentiation of the epithelial sheet and the formation of the basement membrane. The infection of the pseudo-tissue with a strain of NonTypeable Haemophilus influenzae results in bacteria association and crossing of the mucus layer leading to an apparent targeting of the stromal space where they release large amounts of vesicles and form macro-structures. In summary, we propose our in vitro model as a reliable and potentially customizable system to study mid/long term host-pathogen processes. PMID:27101006

  17. 3D Reconstruction of the Human Airway Mucosa In Vitro as an Experimental Model to Study NTHi Infections.

    Directory of Open Access Journals (Sweden)

    Pasquale Marrazzo

    Full Text Available We have established an in vitro 3D system which recapitulates the human tracheo-bronchial mucosa comprehensive of the pseudostratified epithelium and the underlying stromal tissue. In particular, we reported that the mature model, entirely constituted of primary cells of human origin, develops key markers proper of the native tissue such as the mucociliary differentiation of the epithelial sheet and the formation of the basement membrane. The infection of the pseudo-tissue with a strain of NonTypeable Haemophilus influenzae results in bacteria association and crossing of the mucus layer leading to an apparent targeting of the stromal space where they release large amounts of vesicles and form macro-structures. In summary, we propose our in vitro model as a reliable and potentially customizable system to study mid/long term host-pathogen processes.

  18. The braincase of the basal sauropod dinosaur Spinophorosaurus and 3D reconstructions of the cranial endocast and inner ear.

    Directory of Open Access Journals (Sweden)

    Fabien Knoll

    Full Text Available BACKGROUND: Sauropod dinosaurs were the largest animals ever to walk on land, and, as a result, the evolution of their remarkable adaptations has been of great interest. The braincase is of particular interest because it houses the brain and inner ear. However, only a few studies of these structures in sauropods are available to date. Because of the phylogenetic position of Spinophorosaurus nigerensis as a basal eusauropod, the braincase has the potential to provide key evidence on the evolutionary transition relative to other dinosaurs. METHODOLOGY/PRINCIPAL FINDINGS: The only known braincase of Spinophorosaurus ('Argiles de l'Irhazer', Irhazer Group; Agadez region, Niger differs significantly from those of the Jurassic sauropods examined, except potentially for Atlasaurus imelakei (Tilougguit Formation, Morocco. The basisphenoids of Spinophorosaurus and Atlasaurus bear basipterygoid processes that are comparable in being directed strongly caudally. The Spinophorosaurus specimen was CT scanned, and 3D renderings of the cranial endocast and inner-ear system were generated. The endocast resembles that of most other sauropods in having well-marked pontine and cerebral flexures, a large and oblong pituitary fossa, and in having the brain structure obscured by the former existence of relatively thick meninges and dural venous sinuses. The labyrinth is characterized by long and proportionally slender semicircular canals. This condition recalls, in particular, that of the basal non-sauropod sauropodomorph Massospondylus and the basal titanosauriform Giraffatitan. CONCLUSIONS/SIGNIFICANCE: Spinophorosaurus has a moderately derived paleoneuroanatomical pattern. In contrast to what might be expected early within a lineage leading to plant-eating graviportal quadrupeds, Spinophorosaurus and other (but not all sauropodomorphs show no reduction of the vestibular apparatus of the inner ear. This character-state is possibly a primitive retention in Spinophorosaurus, but due the scarcity of data it remains unclear whether it is also the case in the various later sauropods in which it is present or whether it has developed homoplastically in these taxa. Any interpretations remain tentative pending the more comprehensive quantitative analysis underway, but the size and morphology of the labyrinth of sauropodomorphs may be related to neck length and mobility, among other factors.

  19. Microcirculation in the murine liver: a computational fluid dynamic model based on 3D reconstruction from in vivo microscopy.

    Science.gov (United States)

    Piergiovanni, Monica; Bianchi, Elena; Capitani, Giada; Li Piani, Irene; Ganzer, Lucia; Guidotti, Luca G; Iannacone, Matteo; Dubini, Gabriele

    2017-10-03

    The liver is organized in hexagonal functional units - termed lobules - characterized by a rather peculiar blood microcirculation, due to the presence of a tangled network of capillaries - termed sinusoids. A better understanding of the hemodynamics that governs liver microcirculation is relevant to clinical and biological studies aimed at improving our management of liver diseases and transplantation. Herein, we built a CFD model of a 3D sinusoidal network, based on in vivo images of a physiological mouse liver obtained with a 2-photon microscope. The CFD model was developed with Fluent 16.0 (ANSYS Inc., Canonsburg, PA), particular care was taken in imposing the correct boundary conditions representing a physiological state. To account for the remaining branches of the sinusoids, a lumped parameter model was used to prescribe the correct pressure at each outlet. The effect of an adhered cell on local hemodynamics is also investigated for different occlusion degrees. The model here proposed accurately reproduces the fluid dynamics in a portion of the sinusoidal network in mouse liver. Mean velocities and mass flow rates are in agreement with literature values from in vivo measurements. Our approach provides details on local phenomena, hardly described by other computational studies, either focused on the macroscopic hepatic vasculature or based on homogeneous porous medium model. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

    Science.gov (United States)

    Annese, Jacopo; Schenker-Ahmed, Natalie M.; Bartsch, Hauke; Maechler, Paul; Sheh, Colleen; Thomas, Natasha; Kayano, Junya; Ghatan, Alexander; Bresler, Noah; Frosch, Matthew P.; Klaming, Ruth; Corkin, Suzanne

    2014-01-01

    Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology.

  1. [A study on individual mandibular prostheses according to 3D reconstruction of CT images and CNC simulation method].

    Science.gov (United States)

    Pan, Liu-guo; Sun, Li-qun

    2007-03-01

    The new method of manufacturing individual mandibular prostheses, in combination with CT data and CNC technique, can duplicate bone tissues accurately, and can have the individual mandibular prosthesis made to order, and repair the mandibular defect (especially the lager mandibular segmental defect).

  2. 3D reconstruction based on compressed-sensing (CS)-based framework by using a dental panoramic detector.

    Science.gov (United States)

    Je, U K; Cho, H M; Hong, D K; Cho, H S; Park, Y O; Park, C K; Kim, K S; Lim, H W; Kim, G A; Park, S Y; Woo, T H; Cho, S I

    2016-01-01

    In this work, we propose a practical method that can combine the two functionalities of dental panoramic and cone-beam CT (CBCT) features in one by using a single panoramic detector. We implemented a CS-based reconstruction algorithm for the proposed method and performed a systematic simulation to demonstrate its viability for 3D dental X-ray imaging. We successfully reconstructed volumetric images of considerably high accuracy by using a panoramic detector having an active area of 198.4 mm × 6.4 mm and evaluated the reconstruction quality as a function of the pitch (p) and the angle step (Δθ). Our simulation results indicate that the CS-based reconstruction almost completely recovered the phantom structures, as in CBCT, for p≤2.0 and θ≤6°, indicating that it seems very promising for accurate image reconstruction even for large-pitch and few-view data. We expect the proposed method to be applicable to developing a cost-effective, volumetric dental X-ray imaging system. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  3. A Kullback-Leibler approach for 3D reconstruction of spectral CT data corrupted by Poisson noise

    Science.gov (United States)

    Hohweiller, Tom; Ducros, Nicolas; Peyrin, Françoise; Sixou, Bruno

    2017-09-01

    While standard computed tomography (CT) data do not depend on energy, spectral computed tomography (SPCT) acquire energy-resolved data, which allows material decomposition of the object of interest. Decompo- sitions in the projection domain allow creating projection mass density (PMD) per materials. From decomposed projections, a tomographic reconstruction creates 3D material density volume. The decomposition is made pos- sible by minimizing a cost function. The variational approach is preferred since this is an ill-posed non-linear inverse problem. Moreover, noise plays a critical role when decomposing data. That is why in this paper, a new data fidelity term is used to take into account of the photonic noise. In this work two data fidelity terms were investigated: a weighted least squares (WLS) term, adapted to Gaussian noise, and the Kullback-Leibler distance (KL), adapted to Poisson noise. A regularized Gauss-Newton algorithm minimizes the cost function iteratively. Both methods decompose materials from a numerical phantom of a mouse. Soft tissues and bones are decomposed in the projection domain; then a tomographic reconstruction creates a 3D material density volume for each material. Comparing relative errors, KL is shown to outperform WLS for low photon counts, in 2D and 3D. This new method could be of particular interest when low-dose acquisitions are performed.

  4. Histological analysis and 3D reconstruction of winter cereal crowns recovering from freezing: a unique response in oat (Avena sativa L.).

    Science.gov (United States)

    Livingston, David P; Henson, Cynthia A; Tuong, Tan D; Wise, Mitchell L; Tallury, Shyamalrau P; Duke, Stanley H

    2013-01-01

    The crown is the below ground portion of the stem of a grass which contains meristematic cells that give rise to new shoots and roots following winter. To better understand mechanisms of survival from freezing, a histological analysis was performed on rye, wheat, barley and oat plants that had been frozen, thawed and allowed to resume growth under controlled conditions. Extensive tissue disruption and abnormal cell structure was noticed in the center of the crown of all 4 species with relatively normal cells on the outside edge of the crown. A unique visual response was found in oat in the shape of a ring of cells that stained red with Safranin. A tetrazolium analysis indicated that tissues immediately inside this ring were dead and those outside were alive. Fluorescence microscopy revealed that the barrier fluoresced with excitation between 405 and 445 nm. Three dimensional reconstruction of a cross sectional series of images indicated that the red staining cells took on a somewhat spherical shape with regions of no staining where roots entered the crown. Characterizing changes in plants recovering from freezing will help determine the genetic basis for mechanisms involved in this important aspect of winter hardiness.

  5. Examining rhyolite lava flow dynamics through photo-based 3-D reconstructions of the 2011-2012 lava flow field at Cordón Caulle, Chile.

    Science.gov (United States)

    James, M. R.; Farquharson, J.; Tuffen, H.

    2014-12-01

    The 2011-2012 eruption at Cordón-Caulle, Chile, afforded the opportunity to observe and measure active rhyolitic lava for the first time. In 2012 and 2013, ~2500 photos were acquired on foot, parallel to flow fronts on the north and north-east of the flow field. Image suites were then processed into 3-D point clouds using Structure-from-Motion Multi-view Stereo (SfM-MVS) freeware. Interpolating these clouds into digital elevation models for dates in 2012-13 enabled analysis of the changing flow field dimensions [1], from which velocity, depth and rheological parameters, e.g.viscosity, could be estimated [see Fig. 1]. Viscosities ranged from 7.5 x109 to 1.1 x1011Pa s, allowing for uncertainties in slope, surface displacement and velocity. Temperatures were modeled using a 1D finite difference method; in concert with viscosities of flow units these values compared well with published non-Arrhenian viscosity models. Derived thermodynamic and force ratios confirmed flow characteristics inferred from the image analyses. SfM-MVS represents an effective method of quantifying and displaying variation in the flow field, indicating several parallels between rhyolite emplacement and that of low-silica lavas. Initially channelised lava spread laterally and stagnated due to topography and the influence of the surface crust. Continued effusion resulted in iterative emplacement of breakout lobes, promoting lateral extension of the flow field. Insulation of the flow core by the viscous crust allowed this process to continue after effusion had ceased, creating features comparable to low-silica lavas, despite high viscosity and low effusion rates. This suggests that compound flow emplacement may be described by universal, cross-compositional models encompassing rheological differences of many orders of magnitude. Tuffen et al. 2013, Nat. Comms., 4, 2709, doi:10.1038/ncomms3709

  6. Systematic approaches for targeting an atom-probe tomography sample fabricated in a thin TEM specimen: Correlative structural, chemical and 3-D reconstruction analyses.

    Science.gov (United States)

    Baik, Sung-Il; Isheim, Dieter; Seidman, David N

    2018-01-01

    Atom-probe tomography (APT) is a unique analysis tool that enables true three-dimensional (3-D) analyses with sub-nano scale spatial resolution. Recent implementations of the local-electrode atom-probe (LEAP) tomograph with ultraviolet laser pulsing have significantly expanded the research applications of APT. The small field-of-view of a needle-shaped specimen with a less than 100 nm diam. is, however, a major limitation for analyzing materials. The systematic approaches for site-specific targeting of an APT nanotip in a transmission electron microscope (TEM) of a thin sample are introduced to solve the geometrical limitations of a sharpened APT nanotip. In addition to "coupling APT to TEM", the technique presented here allows for targeting the preparation of an APT tip based on TEM observation of a much larger area than what is captured in the APT tip. The correlative methods have synergies for not only high-resolution structural analyses but also for obtaining chemical information. Chemical analyses in a TEM, both energy-dispersive X-ray spectroscopy (EDS) and electron energy-loss spectroscopy (EELS), are performed and compared with the APT chemical analyses of a carbide phase (M 7 C 3 ) precipitate at a grain boundary in a Ni-based alloy. Additionally, a TEM image of a sharpened APT nanotip is utilized for calculation of the detection area ratio of an APT nanotip by comparison with a TEM image for precise tomographic reconstructions. A grain-boundary/carbide precipitate triple junction is used to attain precise positioning of an APT nanotip in an analyzed TEM specimen. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. High-Resolution Imaged-Based 3D Reconstruction Combined with X-Ray CT Data Enables Comprehensive Non-Destructive Documentation and Targeted Research of Astromaterials

    Science.gov (United States)

    Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

    2014-01-01

    Providing web-based data of complex and sensitive astromaterials (including meteorites and lunar samples) in novel formats enhances existing preliminary examination data on these samples and supports targeted sample requests and analyses. We have developed and tested a rigorous protocol for collecting highly detailed imagery of meteorites and complex lunar samples in non-contaminating environments. These data are reduced to create interactive 3D models of the samples. We intend to provide these data as they are acquired on NASA's Astromaterials Acquisition and Curation website at http://curator.jsc.nasa.gov/.

  8. 3D reconstruction of bony elements of the knee joint and finite element analysis of total knee prosthesis obtained from the reconstructed model.

    Science.gov (United States)

    Djoudi, Farid

    2013-01-01

    Two separate themes are presented in this paper. The first theme is to present a graphical modeling approach of human anatomical structures namely, the femur and the tibia. The second theme involves making a finite element analysis of stresses, displacements and deformations in prosthetic implants (the femoral implant and the polyethylene insert). The graphical modeling approach comes in two parts. The first is the segmentation of MRI scanned images, retrieved in DICOM format for edge detection. In the second part, 3D-CAD models are generated from the results of the segmentation stage. The finite element analysis is done by first extracting the prosthetic implants from the reconstructed 3D-CAD model, then do a finite element analysis of these implants under objectively determined conditions such as; forces, allowed displacements, the materials composing implant, and the coefficient of friction. The objective of this work is to implement an interface for exchanging data between 2D MRI images obtained from a medical diagnosis of a patient and the 3D-CAD model used in various applications, such as; the extraction of the implants, stress analysis at the knee joint and can serve as an aid to surgery, also predict the behavior of the prosthetic implants vis-a-vis the forces acting on the knee joints.

  9. Histological Analysis and 3D Reconstruction of Winter Cereal Crowns Recovering from Freezing: A Unique Response in Oat (Avena sativa L.)

    Science.gov (United States)

    Livingston, David P.; Henson, Cynthia A.; Tuong, Tan D.; Wise, Mitchell L.; Tallury, Shyamalrau P.; Duke, Stanley H.

    2013-01-01

    The crown is the below ground portion of the stem of a grass which contains meristematic cells that give rise to new shoots and roots following winter. To better understand mechanisms of survival from freezing, a histological analysis was performed on rye, wheat, barley and oat plants that had been frozen, thawed and allowed to resume growth under controlled conditions. Extensive tissue disruption and abnormal cell structure was noticed in the center of the crown of all 4 species with relatively normal cells on the outside edge of the crown. A unique visual response was found in oat in the shape of a ring of cells that stained red with Safranin. A tetrazolium analysis indicated that tissues immediately inside this ring were dead and those outside were alive. Fluorescence microscopy revealed that the barrier fluoresced with excitation between 405 and 445 nm. Three dimensional reconstruction of a cross sectional series of images indicated that the red staining cells took on a somewhat spherical shape with regions of no staining where roots entered the crown. Characterizing changes in plants recovering from freezing will help determine the genetic basis for mechanisms involved in this important aspect of winter hardiness. PMID:23341944

  10. Careful Dissection of the Distal Ureter Is Highly Important in Nerve-sparing Radical Pelvic Surgery: A 3D Reconstruction and Immunohistochemical Characterization of the Vesical Plexus.

    Science.gov (United States)

    Kraima, Anne C; Derks, Marloes; Smit, Noeska N; van de Velde, Cornelis J H; Kenter, Gemma G; DeRuiter, Marco C

    2016-06-01

    Radical hysterectomy with pelvic lymphadenectomy (RHL) is the preferred treatment for early-stage cervical cancer. Although oncological outcome is good with regard to recurrence and survival rates, it is well known that RHL might result in postoperative bladder impairments due to autonomic nerve disruption. The pelvic autonomic network has been extensively studied, but the anatomy of nerve fibers branching off the inferior hypogastric plexus to innervate the bladder is less known. Besides, the pathogenesis of bladder dysfunction after RHL is multifactorial but remains unclear. We studied the 3-dimensional anatomy and neuroanatomical composition of the vesical plexus and describe implications for RHL. Six female adult cadaveric pelvises were macroscopically dissected. Additionally, a series of 10 female fetal pelvises (embryonic age, 10-22 weeks) was studied. Paraffin-embedded blocks were transversely sliced in 8-μm sections. (Immuno) histological analysis was performed with hematoxylin and eosin, azan, and antibodies against S-100 (Schwann cells), tyrosine hydroxylase (postganglionic sympathetic fibers), and vasoactive intestinal peptide (postganglionic parasympathetic fibers). The results were 3-dimensionally visualized. The vesical plexus formed a group of nerve fibers branching off the ventral part of the inferior hypogastric plexus to innervate the bladder. In all adult and fetal specimens, the vesical plexus was closely related to the distal ureter and located in both the superficial and deep layers of the vesicouterine ligament. Efferent nerve fibers belonging to the vesical plexus predominantly expressed tyrosine hydroxylase and little vasoactive intestinal peptide. The vesical plexus is located in both layers of the vesicouterine ligament and has a very close relationship with the distal ureter. Complete mobilization of the ureter in RHL might cause bladder dysfunction due to sympathetic and parasympathetic denervation. Hence, the distal ureter should be regarded as a risk zone in which the vesical plexus can be damaged.

  11. The nervous system of the basal mollusk Wirenia argentea (Solenogastres): a study employing immunocytochemical and 3D reconstruction techniques

    DEFF Research Database (Denmark)

    Todt, Christiane; Bchinger, Thomas; Wanninger, Andreas Wilhelm Georg

    2008-01-01

    is present in most compartments of the nervous system, while serotonergic immunoreactivity appears to be restricted to the longitudinal nerve cords, the cerebro-pedal commissure and part of the cerebral ganglion. The buccal system shows immunoreactivity against none of the neurotransmitters....

  12. Fusion and Visualization of HiRISE Super-Resolution, Shape-from-Shading DTM with MER Stereo 3D Reconstructions

    Science.gov (United States)

    Gupta, S.; Paar, G.; Muller, J. P.; Tao, Y.; Tyler, L.; Traxler, C.; Hesina, G.; Huber, B.; Nauschnegg, B.

    2014-12-01

    The FP7-SPACE project PRoViDE has assembled a major portion of the imaging data gathered so far from rover vehicles, landers and probes on extra-terrestrial planetary surfaces into a unique database, bringing them into a common planetary geospatial context and providing access to a complete set of 3D vision products. One major aim of PRoViDE is the fusion between orbiter and rover image products. To close the gap between HiRISE imaging resolution (down to 25cm for the OrthoRectified image (ORI), down to 1m for the DTM) and surface vision products, images from multiple HiRISE acquisitions are combined into a super resolution data set (Tao & Muller, 2014), increasing to 5cm resolution the Ortho images. Furthermore, shape-from-shading is applied to one of the ORIs at its original resolution for refinement of the HiRISE DTM, leading to DTM ground resolutions of up to 25 cm. After texture-based co-registration with these refined orbiter 3D products, MER PanCam and NavCam 3D image products can be smoothly pasted into a multi-resolution 3D data representation. Typical results from the MER mission are presented by a dedicated real-time rendering tool which is fed by a hierarchical 3D data structure that is able to cope with all involved scales from global planetary scale down to close-up reconstructions in the mm range. This allows us to explore and analyze the geological characteristics of rock outcrops, for example the detailed geometry and internal features of sedimentary rock layers, to aid paleoenvironmental interpretation. This integrated approach enables more efficient development of geological models of martian rock outcrops. The rendering tool also provides measurement tools to obtain geospatial data of surface points and distances between them. We report on novel scientific use cases and the added value potential of the resultant high-quality data set and presentation means to support further geologic investigations. The research leading to these results has received funding from the EC's 7th Framework Programme (FP7/2007-2013) under grant agreement n° 312377.

  13. Understanding the response of winter cereals to freezing stress through freeze-fixation and 3d reconstruction of ice formation in crowns

    Science.gov (United States)

    One of the most difficult aspects of understanding mechanisms involved in winterhardiness is knowing where ice is formed and how it interacts with tissues in the frozen state. Many tissues recover and change shape during thawing which prevents a clear picture of ice formation and how individual cel...

  14. First-order and subsidiary faults controlling the time-space evolution of the Central Italy 2016 seismic sequence - a multi-source data detailed 3D reconstruction

    Science.gov (United States)

    Lavecchia, Giusy; de nardis, Rita; Ferrarini, Federica; Cirillo, Daniele; Brozzetti, Francesco

    2017-04-01

    The Central Italy 2016 seismic sequence, with its three major events (24 August, Mw 6.0/6.2; 26 October Mw5.9/6.0; 30 October Mw6.5/6.6), activated a well-known active west-dipping extensional fault alignment of central Italy (Vettore-Gorzano faults, VEGO). Soon after the first event, based on geological, interferometric and at that moment available seismological data, a preliminary 3D fault model of VEGO was built. Such a model is here updated and improved at the light of a large amount of relocated earthquake data (time interval 24 August to 30 November 2016, 0.1≤ML ≤6.5, Chiaraluce at al., submitted to SRL) plus additional geological information. The 3D modeling was done using the software package MOVE from the Midland Valley. All the available data were taken into consideration (surface traces, fault-slip data, primary co-seismic surface fractures, geological maps and cross-sections, hypocentral locations and focal mechanisms of both background seismicity and seismic sequences). The VEGO geometric configuration did not substantially changed with respect to the previous model, but some additional structures involved in the sequence were reconstructed. In particular, four additional faults are well evident: a NE-dipping normal fault (dip-angle 50˚ ) antithetic to Vettore Fault, located at depths between 1 and 5 km; a WNW dipping plane (dip-angle 30˚ ) located at depth between 1 and 4 km within the Vettore footwall volume; this structure represents a splay of the late Miocene Sibillini thrust, which is evidently cross-cut and dislocated by the Vettore normal fault; a SW-dipping normal fault representing an unknown northward prosecution of the VEGO alignment, where since 26 October a relevant seismic activity was released; an unknown east-dipping low-angle detachment, where VEGO detaches at a depth of about 10-11 km. An uninterrupted microseismic activity has illuminated such a detachment not only during the overall sequence, but also in the previous months. At the light of the reconstructed geometric pattern integrated with the evidences of primary co-seismic fractures, it results evident that the Central Italy seismic sequence represents a "classic", although complex, intra-Apennine normal-faulting event, reactivating a long-term quiescent seismogenic alignment (e.g. VEGO). The reactivated and inverted compressional structures are confined at shallow depth within the Vettore footwall, and in no way control the major events of the sequence. Conversely, an important regional role is played by the east-dipping detachment. It represents the missing geometric link between the Altotiberina LANF of northern Umbria and the recently discovered LANF of Latium-Abruzzi.

  15. Structure from Motion Photogrammetry and Micro X-Ray Computed Tomography 3-D Reconstruction Data Fusion for Non-Destructive Conservation Documentation of Lunar Samples

    Science.gov (United States)

    Beaulieu, K. R.; Blumenfeld, E. H.; Liddle, D. A.; Oshel, E. R.; Evans, C. A.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

    2017-01-01

    Our team is developing a modern, cross-disciplinary approach to documentation and preservation of astromaterials, specifically lunar and meteorite samples stored at the Johnson Space Center (JSC) Lunar Sample Laboratory Facility. Apollo Lunar Sample 60639, collected as part of rake sample 60610 during the 3rd Extra-Vehicular Activity of the Apollo 16 mission in 1972, served as the first NASA-preserved lunar sample to be examined by our team in the development of a novel approach to internal and external sample visualization. Apollo Sample 60639 is classified as a breccia with a glass-coated side and pristine mare basalt and anorthosite clasts. The aim was to accurately register a 3-dimensional Micro X-Ray Computed Tomography (XCT)-derived internal composition data set and a Structure-From-Motion (SFM) Photogrammetry-derived high-fidelity, textured external polygonal model of Apollo Sample 60639. The developed process provided the means for accurate, comprehensive, non-destructive visualization of NASA's heritage lunar samples. The data products, to be ultimately served via an end-user web interface, will allow researchers and the public to interact with the unique heritage samples, providing a platform to "slice through" a photo-realistic rendering of a sample to analyze both its external visual and internal composition simultaneously.

  16. Photostable bipolar fluorescent probe for video tracking plasma membranes related cellular processes.

    Science.gov (United States)

    Zhang, Xinfu; Wang, Chao; Jin, Liji; Han, Zhuo; Xiao, Yi

    2014-08-13

    Plasma membranes can sense the stimulations and transmit the signals from extracellular environment and then make further responses through changes in locations, shapes or morphologies. Common fluorescent membrane markers are not well suited for long time tracking due to their shorter retention time inside plasma membranes and/or their lower photostability. To this end, we develop a new bipolar marker, Mem-SQAC, which can stably insert into plasma membranes of different cells and exhibits a long retention time over 30 min. Mem-SQAC also inherits excellent photostability from the BODIPY dye family. Large two-photon absorption cross sections and long wavelength fluorescence emissions further enhance the competitiveness of Mem-SQAC as a membrane marker. By using Mem-SQAC, significant morphological changes of plasma membranes have been monitored during heavy metal poisoning and drug induced apoptosis of MCF-7 cells; the change tendencies are so distinctly different from each other that they can be used as indicators to distinguish different cell injuries. Further on, the complete processes of endocytosis toward Staphylococcus aureus and Escherichia coli by RAW 264.7 cells have been dynamically tracked. It is discovered that plasma membranes take quite different actions in response to the two bacteria, information unavailable in previous research reports.

  17. The repellency of lemongrass oil against stable flies, tested using video tracking

    Science.gov (United States)

    Baldacchino, Frédéric; Tramut, Coline; Salem, Ali; Liénard, Emmanuel; Delétré, Emilie; Franc, Michel; Martin, Thibaud; Duvallet, Gérard; Jay-Robert, Pierre

    2013-01-01

    Lemongrass oil (Cymbopogon citratus) is an effective repellent against mosquitoes (Diptera: Culicidae) and house flies (Diptera: Muscidae). In this study, its effectiveness was assessed on stable flies (Diptera: Muscidae) in laboratory conditions. First, we demonstrated that lemongrass oil is an active substance for antennal olfactory receptor cells of Stomoxys calcitrans as indicated by a significant increase in the electroantennogram responses to increasing doses of lemongrass oil. Feeding-choice tests in a flight cage with stable flies having access to two blood-soaked sanitary pads, one of which was treated with lemongrass oil, showed that stable flies (n = 24) spent significantly more time in the untreated zone (median value = 218.4 s) than in the treated zone (median value = 63.7 s). No stable flies fed on the treated pad, whereas nine fed on the untreated pad. These results suggest that lemongrass oil could be used as an effective repellent against stable flies. Additional studies to confirm its spatial repellent and feeding deterrent effects are warranted. PMID:23759542

  18. A data set for evaluating the performance of multi-class multi-object video tracking

    Science.gov (United States)

    Chakraborty, Avishek; Stamatescu, Victor; Wong, Sebastien C.; Wigley, Grant; Kearney, David

    2017-05-01

    One of the challenges in evaluating multi-object video detection, tracking and classification systems is having publically available data sets with which to compare different systems. However, the measures of performance for tracking and classification are different. Data sets that are suitable for evaluating tracking systems may not be appropriate for classification. Tracking video data sets typically only have ground truth track IDs, while classification video data sets only have ground truth class-label IDs. The former identifies the same object over multiple frames, while the latter identifies the type of object in individual frames. This paper describes an advancement of the ground truth meta-data for the DARPA Neovision2 Tower data set to allow both the evaluation of tracking and classification. The ground truth data sets presented in this paper contain unique object IDs across 5 different classes of object (Car, Bus, Truck, Person, Cyclist) for 24 videos of 871 image frames each. In addition to the object IDs and class labels, the ground truth data also contains the original bounding box coordinates together with new bounding boxes in instances where un-annotated objects were present. The unique IDs are maintained during occlusions between multiple objects or when objects re-enter the field of view. This will provide: a solid foundation for evaluating the performance of multi-object tracking of different types of objects, a straightforward comparison of tracking system performance using the standard Multi Object Tracking (MOT) framework, and classification performance using the Neovision2 metrics. These data have been hosted publically.

  19. Novel approach to automatically classify rat social behavior using a video tracking system

    NARCIS (Netherlands)

    Peters, Suzanne M.; Pinter, Ilona J.; Pothuizen, Helen H J; de Heer, Raymond C.; van der Harst, Johanneke E.|info:eu-repo/dai/nl/255335911; Spruijt, Berry M.|info:eu-repo/dai/nl/07079202X

    2016-01-01

    Background In the past, studies in behavioral neuroscience and drug development have relied on simple and quick readout parameters of animal behavior to assess treatment efficacy or to understand underlying brain mechanisms. The predominant use of classical behavioral tests has been repeatedly

  20. A System to Generate SignWriting for Video Tracks Enhancing Accessibility of Deaf People

    Directory of Open Access Journals (Sweden)

    Elena Verdú

    2017-12-01

    Full Text Available Video content has increased much on the Internet during last years. In spite of the efforts of different organizations and governments to increase the accessibility of websites, most multimedia content on the Internet is not accessible. This paper describes a system that contributes to make multimedia content more accessible on the Web, by automatically translating subtitles in oral language to SignWriting, a way of writing Sign Language. This system extends the functionality of a general web platform that can provide accessible web content for different needs. This platform has a core component that automatically converts any web page to a web page compliant with level AA of WAI guidelines. Around this core component, different adapters complete the conversion according to the needs of specific users. One adapter is the Deaf People Accessibility Adapter, which provides accessible web content for the Deaf, based on SignWritting. Functionality of this adapter has been extended with the video subtitle translator system. A first prototype of this system has been tested through different methods including usability and accessibility tests and results show that this tool can enhance the accessibility of video content available on the Web for Deaf people.

  1. A hardware/software simulation for the video tracking system of the Kuiper Airborne Observatory telescope

    Science.gov (United States)

    Boozer, G. A.; Mckibbin, D. D.; Haas, M. R.; Erickson, E. F.

    1984-01-01

    This simulator was created so that C-141 Kuiper Airborne Observatory investigators could test their Airborne Data Acquisition and Management System software on a system which is generally more accessible than the ADAMS on the plane. An investigator can currently test most of his data acquisition program using the data computer simulator in the Cave. (The Cave refers to the ground-based computer facilities for the KAO and the associated support personnel.) The main Cave computer is interfaced to the data computer simulator in order to simulate the data-Exec computer communications. However until now, there has been no way to test the data computer interface to the tracker. The simulator described here simulates both the KAO Exec and tracker computers with software which runs on the same Hewlett-Packard (HP) computer as the investigator's data acquisition program. A simulator control box is hardwired to the computer to provide monitoring of tracker functions, to provide an operator panel similar to the real tracker, and to simulate the 180 deg phase shifting of the chopper squre-wave reference with beam switching. If run in the Cave, one can use their Exec simulator and this tracker simulator.

  2. A data set for evaluating the performance of multi-class multi-object video tracking

    OpenAIRE

    Chakraborty, Avishek; Stamatescu, Victor; Wong, Sebastien C.; Wigley, Grant; Kearney, David

    2017-01-01

    One of the challenges in evaluating multi-object video detection, tracking and classification systems is having publically available data sets with which to compare different systems. However, the measures of performance for tracking and classification are different. Data sets that are suitable for evaluating tracking systems may not be appropriate for classification. Tracking video data sets typically only have ground truth track IDs, while classification video data sets only have ground tru...

  3. Studying the movement behaviour of benthic macroinvertebrates with automated video tracking

    NARCIS (Netherlands)

    Augusiak, J.A.; Brink, van den P.J.

    2015-01-01

    Quantifying and understanding movement is critical for a wide range of questions in basic and applied ecology. Movement ecology is also fostered by technological advances that allow automated tracking for a wide range of animal species. However, for aquatic macroinvertebrates, such detailed methods

  4. Movement behaviour and video tracking of Milnesium tardigradum Doyère, 1840 (Eutardigrada, Apochela)

    NARCIS (Netherlands)

    Shcherbakov, D.; Schill, R.O.; Brümmer, F.; Blum, M.

    2010-01-01

    Tardigrades or ‘water-bears’ live in moist environments with a high degree of gaseous exchange. In tardigrades, locomotion is essential, e.g. for feeding, to find sexual partners and to adjust the level of hydration by moving to wetter or dryer environments. Here we report on the movement behaviour

  5. Straightforward multi-object video tracking for quantification of mosquito flight activity.

    Science.gov (United States)

    Wilkinson, David A; Lebon, Cyrille; Wood, Trevor; Rosser, Gabriel; Gouagna, Louis Clément

    2014-12-01

    Mosquito flight activity has been studied using a variety of different methodologies, and largely concentrates on female mosquito activity as vectors of disease. Video recording using standard commercially available hardware has limited accuracy for the measurement of flight activity due to the lack of depth-perception in two-dimensional images, but multi-camera observation for three dimensional trajectory reconstructions remain challenging and inaccessible to the majority of researchers. Here, in silico simulations were used to quantify the limitations of two-dimensional flight observation. We observed that, under the simulated conditions, two dimensional observation of flight was more than 90% accurate for the determination of population flight speeds and thus that two dimensional imaging can be used to provide accurate estimates of mosquito population flight speeds, and to measure flight activity over long periods of time. We optimized single camera video imaging to study male Aedes albopictus mosquitoes over a 30 h time period, and tested two different multi-object tracking algorithms for their efficiency in flight tracking. A. Albopictus males were observed to be most active at the start of the day period (06h00-08h00) with the longest period of activity in the evening (15h00-18h00) and that a single mosquito will fly more than 600 m over the course of 24 h. No activity was observed during the night period (18h00-06h00). Simplistic tracking methodologies, executable on standard computational hardware, are sufficient to produce reliable data when video imaging is optimized under laboratory conditions. As this methodology does not require overly-expensive equipment, complex calibration of equipment or extensive knowledge of computer programming, the technology should be accessible to the majority of computer-literate researchers. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. A real-time 3D video tracking system for monitoring primate groups.

    Science.gov (United States)

    Ballesta, S; Reymond, G; Pozzobon, M; Duhamel, J-R

    2014-08-30

    To date, assessing the solitary and social behaviors of laboratory primates' colonies relies on time-consuming manual scoring methods. Here, we describe a real-time multi-camera 3D tracking system developed to measure the behavior of socially-housed primates. Their positions are identified using non-invasive color markers such as plastic collars, thus allowing to also track colored objects and to measure their usage. Compared to traditional manual ethological scoring, we show that this system can reliably evaluate solitary behaviors (foraging, solitary resting, toy usage, locomotion) as well as spatial proximity with peers, which is considered as a good proxy of their social motivation. Compared to existing video-based commercial systems currently available to measure animal activity, this system offers many possibilities (real-time data, large volume coverage, multiple animal tracking) at a lower hardware cost. Quantitative behavioral data of animal groups can now be obtained automatically over very long periods of time, thus opening new perspectives in particular for studying the neuroethology of social behavior in primates. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Three-dimensional neurophenotyping of adult zebrafish behavior.

    Directory of Open Access Journals (Sweden)

    Jonathan Cachat

    Full Text Available The use of adult zebrafish (Danio rerio in neurobehavioral research is rapidly expanding. The present large-scale study applied the newest video-tracking and data-mining technologies to further examine zebrafish anxiety-like phenotypes. Here, we generated temporal and spatial three-dimensional (3D reconstructions of zebrafish locomotion, globally assessed behavioral profiles evoked by several anxiogenic and anxiolytic manipulations, mapped individual endpoints to 3D reconstructions, and performed cluster analysis to reconfirm behavioral correlates of high- and low-anxiety states. The application of 3D swim path reconstructions consolidates behavioral data (while increasing data density and provides a novel way to examine and represent zebrafish behavior. It also enables rapid optimization of video tracking settings to improve quantification of automated parameters, and suggests that spatiotemporal organization of zebrafish swimming activity can be affected by various experimental manipulations in a manner predicted by their anxiolytic or anxiogenic nature. Our approach markedly enhances the power of zebrafish behavioral analyses, providing innovative framework for high-throughput 3D phenotyping of adult zebrafish behavior.

  8. Bioinformatics-based selection of a model cell type for in vitro biomaterial testing.

    Science.gov (United States)

    Groen, Nathalie; van de Peppel, Jeroen; Yuan, Huipin; van Leeuwen, Johannes P T M; van Blitterswijk, Clemens A; de Boer, Jan

    2013-07-01

    Biomaterial properties can be tailored for specific applications via systematic and high-throughput screening of biomaterial-cell interactions. However, progress in material development is often hampered by the lack of adequate in vitro testing methods, frequently due to incomplete understanding of involved in vivo mechanisms. In line with drug discovery in pharmacology, a crucial step in assay development for biomaterial screening is the identification of a target to direct the screen against. Herein, the cell type to be used for screening is of essential importance and has to be carefully chosen. So far, few attention has been put on selecting a cell type specifically suitable for in vitro testing of materials for predefined applications. In this manuscript, we describe an approach to define a suitable cell type for screening assays, for which biomaterials for bone regeneration served as example. Using a bioinformatics methodology, different cell lines are compared on three well-characterized model materials. The transcriptional profiles of MG63, iMSC, SV-HFO, hPPCT, hBPCT and SW480 cells are assessed on 3 calcium phosphate-based materials to evaluate their potential application in a screening assay. We show that MG63 is the most suitable cell line to evaluate biomaterials for bone regeneration applications, evidenced by their robust gene expression differences between the 3 model materials. The gene expression differences between the cell lines were assessed based on the overall gene expression profiles and specific subsets of genes and pathways related to osteogenesis and bone homeostasis in response to the 3 materials tested. In the next phase, this cell line will be used to identify a target correlating with in vivo biomaterial performance and henceforth to develop an in vitro screening system. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. Brief communication: 3-D reconstruction of a collapsed rock pillar from Web-retrieved images and terrestrial lidar data - the 2005 event of the west face of the Drus (Mont Blanc massif)

    Science.gov (United States)

    Guerin, Antoine; Abellán, Antonio; Matasci, Battista; Jaboyedoff, Michel; Derron, Marc-Henri; Ravanel, Ludovic

    2017-07-01

    In June 2005, a series of major rockfall events completely wiped out the Bonatti Pillar located in the legendary Drus west face (Mont Blanc massif, France). Terrestrial lidar scans of the west face were acquired after this event, but no pre-event point cloud is available. Thus, in order to reconstruct the volume and the shape of the collapsed blocks, a 3-D model has been built using photogrammetry (structure-from-motion (SfM) algorithms) based on 30 pictures collected on the Web. All these pictures were taken between September 2003 and May 2005. We then reconstructed the shape and volume of the fallen compartment by comparing the SfM model with terrestrial lidar data acquired in October 2005 and November 2011. The volume is calculated to 292 680 m3 (±5.6 %). This result is close to the value previously assessed by Ravanel and Deline (2008) for this same rock avalanche (265 000 ± 10 000 m3). The difference between these two estimations can be explained by the rounded shape of the volume determined by photogrammetry, which may lead to a volume overestimation. However it is not excluded that the volume calculated by Ravanel and Deline (2008) is slightly underestimated, the thickness of the blocks having been assessed manually from historical photographs.

  10. Computer-based image analysis in radiological diagnostics and image-guided therapy 3D-Reconstruction, contrast medium dynamics, surface analysis, radiation therapy and multi-modal image fusion

    CERN Document Server

    Beier, J

    2001-01-01

    This book deals with substantial subjects of postprocessing and analysis of radiological image data, a particular emphasis was put on pulmonary themes. For a multitude of purposes the developed methods and procedures can directly be transferred to other non-pulmonary applications. The work presented here is structured in 14 chapters, each describing a selected complex of research. The chapter order reflects the sequence of the processing steps starting from artefact reduction, segmentation, visualization, analysis, therapy planning and image fusion up to multimedia archiving. In particular, this includes virtual endoscopy with three different scene viewers (Chap. 6), visualizations of the lung disease bronchiectasis (Chap. 7), surface structure analysis of pulmonary tumors (Chap. 8), quantification of contrast medium dynamics from temporal 2D and 3D image sequences (Chap. 9) as well as multimodality image fusion of arbitrary tomographical data using several visualization techniques (Chap. 12). Thus, the softw...

  11. The non-hierarchical, non-uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X-ray microtomography

    NARCIS (Netherlands)

    Hammel, J.U.; Filatov, M.V.; Herzen, J.; Beckmann, F.; Kaandorp, J.A.; Nickel, M.

    2012-01-01

    As sessile filter feeders, sponges rely on a highly efficient fluid transport system. Their physiology depends on efficient water exchange, which is performed by the aquiferous system. This prominent poriferan anatomical character represents a dense network of incurrent and excurrent canals on which

  12. Prediction of petrophysical properties by 3D reconstruction of porous media from image analysis; Estimativa de propriedades petrofisicas atraves da reconstrucao 3D do meio poroso a partir da analise de imagens

    Energy Technology Data Exchange (ETDEWEB)

    Gasperi, Patricia Martins Silva de

    1999-07-01

    The aim of this work is to investigate and apply a method for predicting petrophysical properties from bidimensional petrographic image data. Based on the assumption of statistical homogeneity, the method uses stochastic simulation to reconstruct the porous media tridimensional structure. The geometrical characterization of the simulated media allows the construction of a network model to simulate fluid flow and estimate permeability, formation factor, mercury capillary pressure curves and resistivity index as function of water saturation. This method is applied to four porous systems with different heterogeneity levels. The results demonstrate that good predictions depend on the appropriate image acquisition resolution, which identifies pores and throats that effectively control the flow properties of the system. The capillary pressure curves suggest the necessity of scale composition. The electrical properties are affected by samples porosity, with reliable estimates being restricted to water-wet systems. (author)

  13. A novel video-tracking system to quantify the behaviour of nocturnal mosquitoes attacking human hosts in the field.

    Science.gov (United States)

    Angarita-Jaimes, N C; Parker, J E A; Abe, M; Mashauri, F; Martine, J; Towers, C E; McCall, P J; Towers, D P

    2016-04-01

    Many vectors of malaria and other infections spend most of their adult life within human homes, the environment where they bloodfeed and rest, and where control has been most successful. Yet, knowledge of peri-domestic mosquito behaviour is limited, particularly how mosquitoes find and attack human hosts or how insecticides impact on behaviour. This is partly because technology for tracking mosquitoes in their natural habitats, traditional dwellings in disease-endemic countries, has never been available. We describe a sensing device that enables observation and recording of nocturnal mosquitoes attacking humans with or without a bed net, in the laboratory and in rural Africa. The device addresses requirements for sub-millimetre resolution over a 2.0 × 1.2 × 2.0 m volume while using minimum irradiance. Data processing strategies to extract individual mosquito trajectories and algorithms to describe behaviour during host/net interactions are introduced. Results from UK laboratory and Tanzanian field tests showed that Culex quinquefasciatus activity was higher and focused on the bed net roof when a human host was present, in colonized and wild populations. Both C. quinquefasciatus and Anopheles gambiae exhibited similar behavioural modes, with average flight velocities varying by less than 10%. The system offers considerable potential for investigations in vector biology and many other fields. © 2016 The Authors.

  14. A New Distance Measure Based on Generalized Image Normalized Cross-Correlation for Robust Video Tracking and Image Recognition.

    Science.gov (United States)

    Nakhmani, Arie; Tannenbaum, Allen

    2013-02-01

    We propose two novel distance measures, normalized between 0 and 1, and based on normalized cross-correlation for image matching. These distance measures explicitly utilize the fact that for natural images there is a high correlation between spatially close pixels. Image matching is used in various computer vision tasks, and the requirements to the distance measure are application dependent. Image recognition applications require more shift and rotation robust measures. In contrast, registration and tracking applications require better localization and noise tolerance. In this paper, we explore different advantages of our distance measures, and compare them to other popular measures, including Normalized Cross-Correlation (NCC) and Image Euclidean Distance (IMED). We show which of the proposed measures is more appropriate for tracking, and which is appropriate for image recognition tasks.

  15. Bioinformatics based structural characterization of glucose dehydrogenase (gdh gene and growth promoting activity of Leclercia sp. QAU-66

    Directory of Open Access Journals (Sweden)

    Muhammad Naveed

    2014-06-01

    Full Text Available Glucose dehydrogenase (GDH; EC 1.1. 5.2 is the member of quinoproteins group that use the redox cofactor pyrroloquinoline quinoine, calcium ions and glucose as substrate for its activity. In present study, Leclercia sp. QAU-66, isolated from rhizosphere of Vigna mungo, was characterized for phosphate solubilization and the role of GDH in plant growth promotion of Phaseolus vulgaris. The strain QAU-66 had ability to solubilize phosphorus and significantly (p < 0.05 promoted the shoot and root lengths of Phaseolus vulgaris. The structural determination of GDH protein was carried out using bioinformatics tools like Pfam, InterProScan, I-TASSER and COFACTOR. These tools predicted the structural based functional homology of pyrroloquinoline quinone domains in GDH. GDH of Leclercia sp. QAU-66 is one of the main factor that involved in plant growth promotion and provides a solid background for further research in plant growth promoting activities.

  16. A Study of Relationships among Technical, Tactical, Physical Parameters and Final Outcomes in Elite Soccer Matches as Analyzed by a Semiautomatic Video Tracking System.

    Science.gov (United States)

    Filetti, Cristoforo; Ruscello, Bruno; D'Ottavio, Stefano; Fanelli, Vito

    2017-06-01

    The performance of a soccer team depends on many factors such as decision-making, cognitive and physical skills, and dynamic ever-changing space-time interactions between teammate and opponents in relation to the ball. Seventy ( n = 70) matches of the Italian SERIE A season 2013-2014 were investigated to analyze the mean performance of 360 players in terms of physical (physical efficiency index; PEI) and technical-tactical (technical efficiency index; TEI) standpoints. Using a semiautomatic video analysis system that has incorporated new parameters able to measure technical-tactical and physical efficiency (Patent IB2010/002593, 2011-ISA), the correlation between these new variables and how much it relates to the likelihood of winning were verified. Correlations between TEI and PEI were significant ( n = 140, r = .60, p < .001), and TEI showed a higher likelihood of winning than PEI factors ( p < .0001 vs. .0001, CI 95% [1.64, 3.00] vs. [1.28, 2.07]). Higher TEI and TEI + PEI differences between the teams were associated with a greater likelihood of winning, but PEI differences were not. Key performance indicators and this performance assessment method might be useful to better understand what determines winning and to assist the overall training process and match management.

  17. Optimisation and validation of a 3D reconstruction algorithm for single photon emission computed tomography by means of GATE simulation platform; Optimisation et validation d'un algorithme de reconstruction 3D en Tomographie d'Emission Monophotonique a l'aide de la plate forme de simulation GATE

    Energy Technology Data Exchange (ETDEWEB)

    El Bitar, Ziad [Ecole Doctorale des Sciences Fondamentales, Universite Blaise Pascal, U.F.R de Recherches Scientifiques et Techniques, 34, avenue Carnot - BP 185, 63006 Clermont-Ferrand Cedex (France); Laboratoire de Physique Corpusculaire, CNRS/IN2P3, 63177 Aubiere (France)

    2006-12-15

    Although time consuming, Monte-Carlo simulations remain an efficient tool enabling to assess correction methods for degrading physical effects in medical imaging. We have optimized and validated a reconstruction method baptized F3DMC (Fully 3D Monte Carlo) in which the physical effects degrading the image formation process were modelled using Monte-Carlo methods and integrated within the system matrix. We used the Monte-Carlo simulation toolbox GATE. We validated GATE in SPECT by modelling the gamma-camera (Philips AXIS) used in clinical routine. Techniques of threshold, filtering by a principal component analysis and targeted reconstruction (functional regions, hybrid regions) were used in order to improve the precision of the system matrix and to reduce the number of simulated photons as well as the time consumption required. The EGEE Grid infrastructures were used to deploy the GATE simulations in order to reduce their computation time. Results obtained with F3DMC were compared with the reconstruction methods (FBP, ML-EM, MLEMC) for a simulated phantom and with the OSEM-C method for the real phantom. Results have shown that the F3DMC method and its variants improve the restoration of activity ratios and the signal to noise ratio. By the use of the grid EGEE, a significant speed-up factor of about 300 was obtained. These results should be confirmed by performing studies on complex phantoms and patients and open the door to a unified reconstruction method, which could be used in SPECT and also in PET. (author)

  18. Expansão rápida da maxila: avaliação de dois métodos de reconstrução 3D por meio de um modelo laboratorial Rapid maxillary expansion: evaluation of two methods of 3D reconstruction by means of a laboratorial model

    Directory of Open Access Journals (Sweden)

    Pollyana Marques de Moura

    2009-02-01

    Full Text Available OBJETIVO: a proposta deste artigo é apresentar um modelo laboratorial para aquisição de imagens tomográficas para avaliação tridimensional do procedimento de expansão rápida da maxila (ERM. MÉTODOS: o procedimento de expansão rápida da maxila foi realizado em crânio seco e os exames foram executados em tomógrafo de alta resolução e em tomógrafo de feixe cônico, antes e depois da ERM. RESULTADOS: as imagens obtidas a partir do crânio seco, tomografia computadorizada multislice (TC e tomografia volumétrica (CBCT produziram resultados semelhantes para avaliação da abertura da sutura palatina mediana. CONCLUSÃO: a utilização de cortes tomográficos, adquiridos tanto por meio de tomógrafo computadorizado de alta resolução quanto por meio da técnica cone beam, possibilitou a reconstrução 3D da maxila com objetivo de oferecer a real avaliação da abertura intermaxilar.OBJECTIVE: This paper proposes to present a laboratorial model for acquisition of tomographic images for three-dimensional evaluation of the rapid maxillary expansion procedure. METHODS: The procedure of rapid maxillary expansion was developed using a dry skull and the images were acquired from a multi-slice tomography and a volumetric tomography. The examinations were taken prior to and after the ERM. RESULTS: The images acquired from the skull, multislice computed tomography (CT and cone beam computed tomography (CBCT had produced similar results. CONCLUSION: The use of tomographic slices, acquired by means of high resolution computerized tomography, as well as the cone beam technique, make possible the three-dimensional reconstruction of the palatomaxillary region in order to offer the real evaluation of the sutural opening.

  19. Contribution to the tracking and the 3D reconstruction of scenes composed of torus from image sequences a acquired by a moving camera; Contribution au suivi et a la reconstruction de scenes constituees d`objet toriques a partir de sequences d`images acquises par une camera mobile

    Energy Technology Data Exchange (ETDEWEB)

    Naudet, S

    1997-01-31

    The three-dimensional perception of the environment is often necessary for a robot to correctly perform its tasks. One solution, based on the dynamic vision, consists in analysing time-varying monocular images to estimate the spatial geometry of the scene. This thesis deals with the reconstruction of torus by dynamic vision. Though this object class is restrictive, it enables to tackle the problem of reconstruction of bent pipes usually encountered in industrial environments. The proposed method is based on the evolution of apparent contours of objects in the sequence. Using the expression of torus limb boundaries, it is possible to recursively estimate the object three-dimensional parameters by minimising the error between the predicted projected contours and the image contours. This process, which is performed by a Kalman filter, does not need a precise knowledge of the camera displacement or any matching of the tow limbs belonging to the same object. To complete this work, temporal tracking of objects which deals with occlusion situations is proposed. The approach consists in modeling and interpreting the apparent motion of objects in the successive images. The motion interpretation, based on a simplified representation of the scene, allows to recover pertinent three-dimensional information which is used to manage occlusion situations. Experiments, on synthetic and real images, proves he validity of the tracking and the reconstruction processes. (author) 127 refs.

  20. Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach.

    Science.gov (United States)

    Zeng, Lingfei; Shin, Woong-Hee; Zhu, Xiaolei; Park, Sung Hoon; Park, Chiwook; Tao, W Andy; Kihara, Daisuke

    2017-02-03

    Protein-ligand interaction plays a critical role in regulating the biochemical functions of proteins. Discovering protein targets for ligands is vital to new drug development. Here, we present a strategy that combines experimental and computational approaches to identify ligand-binding proteins in a proteomic scale. For the experimental part, we coupled pulse proteolysis with filter-assisted sample preparation (FASP) and quantitative mass spectrometry. Under denaturing conditions, ligand binding affected protein stability, which resulted in altered protein abundance after pulse proteolysis. For the computational part, we used the software Patch-Surfer2.0. We applied the integrated approach to identify nicotinamide adenine dinucleotide (NAD)-binding proteins in the Escherichia coli proteome, which has over 4200 proteins. Pulse proteolysis and Patch-Surfer2.0 identified 78 and 36 potential NAD-binding proteins, respectively, including 12 proteins that were consistently detected by the two approaches. Interestingly, the 12 proteins included 8 that are not previously known as NAD binders. Further validation of these eight proteins showed that their binding affinities to NAD computed by AutoDock Vina are higher than their cognate ligands and also that their protein ratios in the pulse proteolysis are consistent with known NAD-binding proteins. These results strongly suggest that these eight proteins are indeed newly identified NAD binders.

  1. Characterization of behavioral and endocrine effects of LSD on zebrafish.

    Science.gov (United States)

    Grossman, Leah; Utterback, Eli; Stewart, Adam; Gaikwad, Siddharth; Chung, Kyung Min; Suciu, Christopher; Wong, Keith; Elegante, Marco; Elkhayat, Salem; Tan, Julia; Gilder, Thomas; Wu, Nadine; Dileo, John; Cachat, Jonathan; Kalueff, Allan V

    2010-12-25

    Lysergic acid diethylamide (LSD) is a potent hallucinogenic drug that strongly affects animal and human behavior. Although adult zebrafish (Danio rerio) are emerging as a promising neurobehavioral model, the effects of LSD on zebrafish have not been investigated previously. Several behavioral paradigms (the novel tank, observation cylinder, light-dark box, open field, T-maze, social preference and shoaling tests), as well as modern video-tracking tools and whole-body cortisol assay were used to characterize the effects of acute LSD in zebrafish. While lower doses (5-100 microg/L) did not affect zebrafish behavior, 250 microg/L LSD increased top dwelling and reduced freezing in the novel tank and observation cylinder tests, also affecting spatiotemporal patterns of activity (as assessed by 3D reconstruction of zebrafish traces and ethograms). LSD evoked mild thigmotaxis in the open field test, increased light behavior in the light-dark test, reduced the number of arm entries and freezing in the T-maze and social preference test, without affecting social preference. In contrast, LSD affected zebrafish shoaling (increasing the inter-fish distance in a group), and elevated whole-body cortisol levels. Overall, our findings show sensitivity of zebrafish to LSD action, and support the use of zebrafish models to study hallucinogenic drugs of abuse. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  2. Vision System of Mobile Robot Combining Binocular and Depth Cameras

    National Research Council Canada - National Science Library

    Yuxiang Yang; Xiang Meng; Mingyu Gao

    2017-01-01

    In order to optimize the three-dimensional (3D) reconstruction and obtain more precise actual distances of the object, a 3D reconstruction system combining binocular and depth cameras is proposed in this paper...

  3. Three-dimensional Evaluation of Nasal Surgery in Patients with Obstructive Sleep Apnea

    Directory of Open Access Journals (Sweden)

    Dan-Mo Cui

    2016-01-01

    Conclusions: Nasal surgery improved OSA severity as measured by PSG, subjective complaints, and 3D reconstructed CT scan. 3D assessment of upper airway can play an important role in the evaluation of treatment outcome.

  4. Exploring miniature insect brains using micro-CT scanning techniques

    National Research Council Canada - National Science Library

    Smith, Dylan B; Bernhardt, Galina; Raine, Nigel E; Abel, Richard L; Sykes, Dan; Ahmed, Farah; Pedroso, Inti; Gill, Richard J

    2016-01-01

    ...). Here we present a method for accurate imaging and exploration of insect brains that keeps brain tissue free from trauma and in its natural stereo-geometry, and showcase our 3D reconstructions...

  5. A new Gis-based map of villa Adriana, a multimedia guide for ancient paths

    National Research Council Canada - National Science Library

    M Canciani; F Chiappetta; E Pallottino; M Saccone

    2014-01-01

    .... The goal of this study is to create a cultural heritage evaluation. In order to achieve this aim, we have created a multimedia guide with text, drawings, 3D reconstructions and augmented reality...

  6. 3D heart reconstruction

    OpenAIRE

    Roxo, Diogo

    2011-01-01

    The purpose of this thesis was to achieve a 3D reconstruction of the four heart chambers using 2D echocardiographic images. A level set algorithm based on the phase symmetry approach and on a new logarithmic based stopping function was used to extract simultaneously the four heart cavities from these images in a fully automatic way. However to proceed to the 3D reconstruction using the segmented images, it was first necessary to satisfy clinical practise requirements. This means that the algo...

  7. Monocular Depth Perception and Robotic Grasping of Novel Objects

    Science.gov (United States)

    2009-06-01

    through vision. For stereo systems, 3D reconstruction is difficult for objects without texture, and even when stereopsis works well, it would typically...reconstruction. Most work on visual 3D reconstruction has focused on binocular vision ( stereopsis , i.e., methods using two images) [155] and on other... stereopsis , has used multiple image geometric cues to infer depth. In contrast, single-image cues offer a largely orthogonal source of information, one

  8. Three-dimensional reconstruction of tumor microvasculature: simultaneous visualization of multiple components in paraffin-embedded tissue.

    Science.gov (United States)

    Gijtenbeek, J M M; Wesseling, P; Maass, C; Burgers, L; van der Laak, J A W M

    2005-01-01

    Three-dimensional (3D) visualization of microscopic structures may provide useful information about the exact 3D configuration, and offers a useful tool to examine the spatial relationship between different components in tissues. A promising field for 3D investigation is the microvascular architecture in normal and pathological tissue, especially because pathological angiogenesis plays a key role in tumor growth and metastasis formation. This paper describes an improved method for 3D reconstruction of microvessels and other microscopic structures in transmitted light microscopy. Serial tissue sections were stained for the endothelial marker CD34 to highlight microvessels and corresponding images were selected and aligned. Alignment of stored images was further improved by automated non-rigid image registration, and automated segmentation of microvessels was performed. Using this technique, 3D reconstructions were produced of the vasculature of the normal brain. Also, to illustrate the complexity of tumor vasculature, 3D reconstructions of two brain tumors were performed: a hemangioblastoma and a glioblastoma multiforme. The possibility of multiple component visualization was shown in a 3D reconstruction of endothelium and pericytes of normal cerebellar cortex and a hemangioblastoma using alternate staining for CD34 and alpha-smooth muscle actin in serial sections, and of a GBM using immunohistochemical double staining. In conclusion, the described 3D reconstruction procedure provides a promising tool for simultaneous visualization of microscopic structures.

  9. [Three-D visualization study on the acupoint of Jianliao (TE 14) based on the operational platform of Voxel-man].

    Science.gov (United States)

    Wang, Hai-sheng; Shao, Shui-jin; Wang, Yitan-yuan; Qin, Yi-lin; Cheng, Zhuo; Yan, Zhen-guo; Zhuang, Tian-ge; Min, You-jiang

    2006-11-01

    To discuss the problem difficult to be presented for nerves and blood vessels in the 3D reconstruction of acupoints through studying 3D reconstruction of Jianliao (TE 14). Muscles and other tissues were segmented by applying cointeractive segmentation method based on chromatic characteristic space; the nerve and blood vessels can be reconstructed by establishing mathematics model, and the needle-inserting animation of Jianliao (TE 14) could be obtained by running script file. During the course of 3D needle-inserting animation of Jianliao (TE 14), the spatial location between all kinds of tissues including the nerve and blood vessels and the needle body could be systematically observed. The difficulty of presenting the nerve and blood vessels in the study on 3D reconstruction of acupoints can be resolved by establishing mathematics model. The generation of 3D animation for acupoints with the nerve and blood vessels is benefit to acupuncture teaching and study on the essence of acupoints and channels.

  10. Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy

    Directory of Open Access Journals (Sweden)

    Nina Jährling

    2010-02-01

    Full Text Available Genetic mutants are invaluable for understanding the development, physiology and behaviour of Drosophila. Modern molecular genetic techniques enable the rapid generation of large numbers of different mutants. To phenotype these mutants sophisticated microscopy techniques are required, ideally allowing the 3D-reconstruction of the anatomy of an adult fly from a single scan. Ultramicroscopy enables up to cm fields of view, whilst providing micron resolution. In this paper, we present ultramicroscopy reconstructions of the flight musculature, the nervous system, and the digestive tract of entire, chemically cleared, drosophila in autofluorescent light. The 3D-reconstructions thus obtained verify that the anatomy of a whole fly, including the filigree spatial organisation of the direct flight muscles, can be analyzed from a single ultramicroscopy reconstruction. The recording procedure, including 3D-reconstruction using standard software, takes no longer than 30 minutes. Additionally, image segmentation, which would allow for further quantitative analysis, was performed.

  11. Unmanned Aerial Vehicle-Based Photogrammetry Using Automatic Capture And Point Of Interest For Object Reconstruction Of Large Scale 3d Architecture

    Directory of Open Access Journals (Sweden)

    Andria K. Wahyudi

    2016-10-01

    Full Text Available Large-scale architecture object are a complicated target for 3D Reconstruction. UAV is a common choice to take RAW pictures from the air. Manual control for Unmanned Aerial Vehicle (UAV can be difficult to perform picture taking and filight control simultaneously. This Paper discusses the Use of UAV for 3D Reconstruction using photogrammetry techniques. This study shows a Point Of Interest (POI for object point to be reconstructed and shooting automatically. With an existing SDK, UAVs can be monitored using the Android smartphone. In this investigation it has been confirmed that the POI and auto-capture techniques can generate models with high precision, with good texture quality and taking a short flight time. This study also shows optimal results in 3D Reconstruction.

  12. Three Dimensional Reconstruction Workflows for Lost Cultural Heritage Monuments Exploiting Public Domain and Professional Photogrammetric Imagery

    Science.gov (United States)

    Wahbeh, W.; Nebiker, S.

    2017-08-01

    In our paper, we document experiments and results of image-based 3d reconstructions of famous heritage monuments which were recently damaged or completely destroyed by the so-called Islamic state in Syria and Iraq. The specific focus of our research is on the combined use of professional photogrammetric imagery and of publicly available imagery from the web for optimally 3d reconstructing those monuments. The investigated photogrammetric reconstruction techniques include automated bundle adjustment and dense multi-view 3d reconstruction using public domain and professional imagery on the one hand and an interactive polygonal modelling based on projected panoramas on the other. Our investigations show that the combination of these two image-based modelling techniques delivers better results in terms of model completeness, level of detail and appearance.

  13. 3D range-gated super-resolution imaging based on stereo matching for moving platforms and targets

    Science.gov (United States)

    Sun, Liang; Wang, Xinwei; Zhou, Yan

    2017-11-01

    3D range-gated superresolution imaging is a novel 3D reconstruction technique for target detection and recognition with good real-time performance. However, for moving targets or platforms such as airborne, shipborne, remote operated vehicle and autonomous vehicle, 3D reconstruction has a large error or failure. In order to overcome this drawback, we propose a method of stereo matching for 3D range-gated superresolution reconstruction algorithm. In experiment, the target is a doll of Mario with a height of 38cm at the location of 34m, and we obtain two successive frame images of the Mario. To confirm our method is effective, we transform the original images with translation, rotation, scale and perspective, respectively. The experimental result shows that our method has a good result of 3D reconstruction for moving targets or platforms.

  14. Surgery of the eloquent area using neuronavigation system

    Energy Technology Data Exchange (ETDEWEB)

    Nakai, Hirofumi; Tanaka, Tatsuya; Hashizume, Kiyotaka; Hodozuka, Akira [Asahikawa Medical Coll., Hokkaido (Japan)

    2001-09-01

    The efficacy of a neuronavigation system for surgery of lesions near Broca's area (6 patients), skull base (5 patients), or paracentral sulcus (10 patients) was evaluated in this study. Using the neuronavigation system, three-dimensional (3D) brain images were reconstructed by plotting cerebral sulcus obtained by MRI and CT. For paracentral sulcus lesions, patients underwent blood oxygen level-dependent fMRI while performing a finger-tapping motor paradigm. 3D reconstructed images were demonstrated to be useful for understanding the anatomical relationship between the lesions and the surrounding vital structures. The precentral gyri identified by 3D reconstructed brain images coincided well with that identified by fMRI. In lesions near Broca's area, skull base, and paracentral sulcus, 3D reconstructed brain images were very useful for both the preoperative surgical simulation and the intraoperative neuronavigation to preserve the postoperative neurological function and to perform less invasive surgery. (author)

  15. Stereo Cameras for Clouds (STEREOCAM) Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Romps, David [Univ. of California, Berkeley, CA (United States); Oktem, Rusen [Univ. of California, Berkeley, CA (United States)

    2017-10-31

    The three pairs of stereo camera setups aim to provide synchronized and stereo calibrated time series of images that can be used for 3D cloud mask reconstruction. Each camera pair is positioned at approximately 120 degrees from the other pair, with a 17o-19o pitch angle from the ground, and at 5-6 km distance from the U.S. Department of Energy (DOE) Central Facility at the Atmospheric Radiation Measurement (ARM) Climate Research Facility Southern Great Plains (SGP) observatory to cover the region from northeast, northwest, and southern views. Images from both cameras of the same stereo setup can be paired together to obtain 3D reconstruction by triangulation. 3D reconstructions from the ring of three stereo pairs can be combined together to generate a 3D mask from surrounding views. This handbook delivers all stereo reconstruction parameters of the cameras necessary to make 3D reconstructions from the stereo camera images.

  16. First 4D Reconstruction of an Eruptive Prominence Using Three Simultaneous View Directions

    Science.gov (United States)

    Chifu, I.; Inhester, B.; Mierla, M.; Chifu, V.; Wiegelmann, T.

    2012-11-01

    Data from the STEREO ( Solar Terrestrial Relations Observatory) mission are intensively used for 3D reconstruction of solar coronal structures. After the launch of the SDO ( Solar Dynamic Observatory) satellite, its additional observations give the possibility to have a third eye for more accurate 3D reconstruction in the very low corona (MBSR (Multi-view B-spline Stereoscopic Reconstruction), we use three view directions (STEREO A, B, and SDO) to perform the 3D reconstruction and evolution of a prominence which triggered a CME on 1 August 2010. In the paper we present the reconstruction of this prominence from the moment it starts to erupt until it leaves the field of view of the coronagraph. We also determine the evolution of the leading edge of the CME. Based on the temporal evolution, we analyze some of its properties, such as velocity, acceleration, opening and rotation angles and evolution of the cavity.

  17. Three-dimensional biplanar radiography as a new means of accessing femoral version: a comparitive study of EOS three-dimensional radiography versus computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Pomerantz, M.L. [University of California San Diego School of Medicine, Orthopaedic Surgery Department, San Diego, CA (United States); Glaser, Diana [Aurora Spine, Carlsbad, CA (United States); Doan, Josh [Orthopedic Biomechanics Research Center, San Diego, CA (United States); Kumar, Sita [University of California, San Diego, CA (United States); Edmonds, Eric W. [University of California San Diego School of Medicine, Orthopaedic Surgery Department, San Diego, CA (United States); Rady Children' s Hospital San Diego, Division of Orthopedic Surgery, San Diego, CA (United States)

    2014-10-17

    To validate femoral version measurements made from biplanar radiography (BR), three-dimensional (3D) reconstructions (EOS imaging, France) were made in differing rotational positions against the gold standard of computed tomography (CT). Two cadaveric femurs were scanned with CT and BR in five different femoral versions creating ten total phantoms. The native version was modified by rotating through a mid-diaphyseal hinge twice into increasing anteversion and twice into increased retroversion. For each biplanar scan, the phantom itself was rotated -10, -5, 0, +5 and +10 . Three-dimensional CT reconstructions were designated the true value for femoral version. Two independent observers measured the femoral version on CT axial slices and BR 3D reconstructions twice. The mean error (upper bound of the 95 % confidence interval), inter- and intraobserver reliability, and the error compared to the true version were determined for both imaging techniques. Interobserver intraclass correlation for CT axial images ranged from 0.981 to 0.991, and the intraobserver intraclass correlation ranged from 0.994 to 0.996. For the BR 3D reconstructions these values ranged from 0.983 to 0.998 and 0.982 to 0.998, respectively. For the CT measurements the upper bound of error from the true value was 5.4-7.5 , whereas for BR 3D reconstructions it was 4.0-10.1 . There was no statistical difference in the mean error from the true values for any of the measurements done with axial CT or BR 3D reconstructions. BR 3D reconstructions accurately and reliably provide clinical data on femoral version compared to CT even with rotation of the patient of up to 10 from neutral. (orig.)

  18. Three-dimensional modeling and simulation of asphalt concrete mixtures based on X-ray CT microstructure images

    Directory of Open Access Journals (Sweden)

    Hainian Wang

    2014-02-01

    Full Text Available X-ray CT (computed tomography was used to scan asphalt mixture specimen to obtain high resolution continuous cross-section images and the meso-structure. According to the theory of three-dimensional (3D reconstruction, the 3D reconstruction algorithm was investigated in this paper. The key to the reconstruction technique is the acquisition of the voxel positions and the relationship between the pixel element and node. Three-dimensional numerical model of asphalt mixture specimen was created by a self-developed program. A splitting test was conducted to predict the stress distributions of the asphalt mixture and verify the rationality of the 3D model.

  19. 3D Membrane Imaging and Porosity Visualization

    KAUST Repository

    Sundaramoorthi, Ganesh

    2016-03-03

    Ultrafiltration asymmetric porous membranes were imaged by two microscopy methods, which allow 3D reconstruction: Focused Ion Beam and Serial Block Face Scanning Electron Microscopy. A new algorithm was proposed to evaluate porosity and average pore size in different layers orthogonal and parallel to the membrane surface. The 3D-reconstruction enabled additionally the visualization of pore interconnectivity in different parts of the membrane. The method was demonstrated for a block copolymer porous membrane and can be extended to other membranes with application in ultrafiltration, supports for forward osmosis, etc, offering a complete view of the transport paths in the membrane.

  20. MEASUREMENT ERROR WITH DIFFERENT COMPUTER VISION TECHNIQUES

    Directory of Open Access Journals (Sweden)

    O. Icasio-Hernández

    2017-09-01

    Full Text Available The goal of this work is to offer a comparative of measurement error for different computer vision techniques for 3D reconstruction and allow a metrological discrimination based on our evaluation results. The present work implements four 3D reconstruction techniques: passive stereoscopy, active stereoscopy, shape from contour and fringe profilometry to find the measurement error and its uncertainty using different gauges. We measured several dimensional and geometric known standards. We compared the results for the techniques, average errors, standard deviations, and uncertainties obtaining a guide to identify the tolerances that each technique can achieve and choose the best.

  1. Three-dimensional Reconstruction Method Study Based on Interferometric Circular SAR

    Directory of Open Access Journals (Sweden)

    Hou Liying

    2016-10-01

    Full Text Available Circular Synthetic Aperture Radar (CSAR can acquire targets’ scattering information in all directions by a 360° observation, but a single-track CSAR cannot efficiently obtain height scattering information for a strong directive scatter. In this study, we examine the typical target of the three-dimensional circular SAR interferometry theoryand validate the theory in a darkroom experiment. We present a 3D reconstruction of the actual tank metal model of interferometric CSAR for the first time, verify the validity of the method, and demonstrate the important potential applications of combining 3D reconstruction with omnidirectional observation.

  2. Granulomatous reaction to a foreign body mimicking bronchogenic tumor. CT findings with virtual endoscopy; Granulome a corps etranger mimant une tumeur bronchique. Aspects en TDM avec vue par endoscopie virtuelle

    Energy Technology Data Exchange (ETDEWEB)

    Mignon, F.; Chambellan, A.; Duboucher, C.; Dangeard-Chikhani, S.; Leclerc, P.; Lemesle, J. [Centre Hospitalier, 78 - Saint-Germain-en-Laye (France); Mesurolle, B. [Hopital Ambroise-Pare, 92 - Boulogne (France)

    1997-11-01

    The aim of this study is to report the spiral CT findings of an endobronchial foreign body (chicken`s bone) unknown on the postero-anterior chest radiograph and on the first bronchoscopy. The double originality of this case is the association with endobronchial actinomycosis mimicking a bronchial neoplasm and the utilization of virtual endoscopy by endo-luminal 3D reconstruction in this context which has never been reported. The endo-luminal 3D reconstruction of the bronchial tree could help guide the endoscopic procedure by better localization of the lesions. (authors)

  3. Measurement Error with Different Computer Vision Techniques

    Science.gov (United States)

    Icasio-Hernández, O.; Curiel-Razo, Y. I.; Almaraz-Cabral, C. C.; Rojas-Ramirez, S. R.; González-Barbosa, J. J.

    2017-09-01

    The goal of this work is to offer a comparative of measurement error for different computer vision techniques for 3D reconstruction and allow a metrological discrimination based on our evaluation results. The present work implements four 3D reconstruction techniques: passive stereoscopy, active stereoscopy, shape from contour and fringe profilometry to find the measurement error and its uncertainty using different gauges. We measured several dimensional and geometric known standards. We compared the results for the techniques, average errors, standard deviations, and uncertainties obtaining a guide to identify the tolerances that each technique can achieve and choose the best.

  4. THE USE OF 3D SCANNING AND RAPID PROTOTYPING IN MEDICAL ENGINEERING

    Directory of Open Access Journals (Sweden)

    Octavian CIOBANU

    2013-05-01

    Full Text Available New cost effective scanning and modeling techniques are used today to process data acquisition and3D reconstruction in order to fabricate prostheses and orthoses by 3D printing. Paper approaches two scanningand 3D modeling techniques used in order to fabricate orthoses and prostheses. In this study, an artificialprosthetic ear was produced through 3D printing using two scanning techniques: structured light scanningtechnique and single camera stereo photogrammetric scanning technique. The processing phases are describedand discussed from data acquisition to 3D printing. The surface scanning and 3D reconstruction techniques willcontinue to increase the accessibility of prostheses and orthoses, making them more cost-effective and morecomfortable.

  5. Vision System of Mobile Robot Combining Binocular and Depth Cameras

    Directory of Open Access Journals (Sweden)

    Yuxiang Yang

    2017-01-01

    Full Text Available In order to optimize the three-dimensional (3D reconstruction and obtain more precise actual distances of the object, a 3D reconstruction system combining binocular and depth cameras is proposed in this paper. The whole system consists of two identical color cameras, a TOF depth camera, an image processing host, a mobile robot control host, and a mobile robot. Because of structural constraints, the resolution of TOF depth camera is very low, which difficultly meets the requirement of trajectory planning. The resolution of binocular stereo cameras can be very high, but the effect of stereo matching is not ideal for low-texture scenes. Hence binocular stereo cameras also difficultly meet the requirements of high accuracy. In this paper, the proposed system integrates depth camera and stereo matching to improve the precision of the 3D reconstruction. Moreover, a double threads processing method is applied to improve the efficiency of the system. The experimental results show that the system can effectively improve the accuracy of 3D reconstruction, identify the distance from the camera accurately, and achieve the strategy of trajectory planning.

  6. Combination of HAADF-STEM and ADF-STEM Tomography for Core–Shell Hybrid Materials

    NARCIS (Netherlands)

    K. Sentosun; M.N. Sanz Ortiz; K.J. Batenburg (Joost); L.M. Liz-Marzán; S. Bals (Sara)

    2015-01-01

    htmlabstractCharacterization of core–shell type nanoparticles in 3D by transmission electron microscopy (TEM) can be very challenging. Especially when both heavy and light elements coexist within the same nanostructure, artifacts in the 3D reconstruction are often present. A representative example

  7. TOF Imaging in Smart Room Environments towards Improved People Tracking

    DEFF Research Database (Denmark)

    Guðmundsson, Sigurjón Árni; Larsen, Rasmus; Aanæs, Henrik

    2008-01-01

    In this Paper we present the use of Time-of-Flight (TOF) cameras in Smart-rooms and how this leads to improved results in segmenting the people in the room from the background and consequently better 3D reconstruction of the people. A calibrated rig of one Swissranger SR3100 Time-of-flight range ...

  8. An Interactive Visualization of the Past using a Situated Simulation Approach

    DEFF Research Database (Denmark)

    Madsen, Jacob Boesen; Madsen, Claus B.

    2013-01-01

    This paper describes aspects of the development of an interactive installation for visualizing a 3D reconstruction of a historical church chapel in Kolding, Denmark. We focus on three aspects inherent to a mobile Augmented Reality development con- text; 1) A procedure for combating gyroscope drift...

  9. Diagnostics of the BIOMASS feed array prototype

    DEFF Research Database (Denmark)

    Cappellin, Cecilia; Pivnenko, Sergey; Pontoppidan, Kennie Nybo

    2013-01-01

    The 3D reconstruction algorithm is applied to the prototype feed array of the BIOMASS synthetic aperture radar, recently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility in Denmark. Careful analysis of the measured feed array data has shown that the test support structure...

  10. Detailed Diagnostics of the BIOMASS Feed Array Prototype

    DEFF Research Database (Denmark)

    Cappellin, C.; Pivnenko, Sergey; Pontoppidan, K.

    2013-01-01

    The 3D reconstruction algorithm of DIATOOL is applied to the prototype feed array of the BIOMASS synthetic aperture radar, recently measured at the DTU-ESA Spherical Near-Field Antenna Test Facility in Denmark. Careful analysis of the measured feed array data had shown that the test support frame...

  11. Wear of micro end mills

    DEFF Research Database (Denmark)

    Bissacco, Giuliano; Hansen, Hans Nørgaard; De Chiffre, Leonardo

    2005-01-01

    part. For this investigation 200 microns end mills are considered. Visual inspection of the micro tools requires high magnification and depth of focus. 3D reconstruction based on scanning electron microscope (SEM) images and stereo-pair technique is foreseen as a possible method for quantification...

  12. Linear accuracy and reliability of volume data sets acquired by two CBCT-devices and an MSCT using virtual models : A comparative in-vitro study

    NARCIS (Netherlands)

    Wikner, Johannes; Hanken, Henning; Eulenburg, Christine; Heiland, Max; Groebe, Alexander; Assaf, Alexandre Thomas; Riecke, Bjoern; Friedrich, Reinhard E.

    2016-01-01

    Objective. To discriminate clinically relevant aberrance, the accuracy of linear measurements in three-dimensional (3D) reconstructed datasets was investigated. Materials and methods. Three partly edentulous human skulls were examined. Landmarks were defined prior to acquisition. Two CBCT-scanners

  13. Borgring

    DEFF Research Database (Denmark)

    2014-01-01

    3D reconstruction of the Viking fortress Borgring, Denmark. The reconstruction is produced by Archaeological IT for the Borgring project. The reconstruction is based on excavations and surveys conducted by Aarhus University and The Museum of South East Denmark in 2014. Some parts...

  14. Performance of computed tomography of the head to evaluate for skull fractures in infants with suspected non-accidental trauma

    Energy Technology Data Exchange (ETDEWEB)

    Culotta, Paige A.; Tran, Quynh-Anh; Donaruma-Kwoh, Marcella [Texas Children' s Hospital, Section of Public Health Pediatrics, Baylor College of Medicine, Houston, TX (United States); Crowe, James E.; Jones, Jeremy Y.; Mehollin-Ray, Amy R.; Tran, H.B.; Dodge, Cristina T. [Texas Children' s Hospital, The Edward B. Singleton, MD, Department of Pediatric Radiology, Baylor College of Medicine, Houston, TX (United States); Camp, Elizabeth A. [Texas Children' s Hospital, Emergency Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX (United States); Cruz, Andrea T. [Texas Children' s Hospital, Emergency Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX (United States); Texas Children' s Hospital, Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX (United States)

    2017-01-15

    Young children with suspected abusive head trauma often receive skull radiographs to evaluate for fractures as well as computed tomography (CT) of the head to assess for intracranial injury. Using a CT as the primary modality to evaluate both fracture and intracranial injury could reduce exposure to radiation without sacrificing performance. To evaluate the sensitivity of CT head with (3-D) reconstruction compared to skull radiographs to identify skull fractures in children with suspected abusive head trauma. This was a retrospective (2013-2014) cross-sectional study of infants evaluated for abusive head trauma via both skull radiographs and CT with 3-D reconstruction. The reference standard was skull radiography. All studies were read by pediatric radiologists and neuroradiologists, with ten percent read by a second radiologist to evaluate for interobserver reliability. One hundred seventy-seven children (47% female; mean/median age: 5 months) were included. Sixty-two (35%) had skull fractures by radiography. CT with 3-D reconstruction was 97% sensitive (95% confidence interval [CI]: 89-100%) and 94% specific (CI: 87-97%) for skull fracture. There was no significant difference between plain radiographs and 3-D CT scan results (P-value = 0.18). Kappa was 1 (P-value <0.001) between radiologist readings of CTs and 0.77 (P = 0.001) for skull radiographs. CT with 3-D reconstruction is equivalent to skull radiographs in identifying skull fractures. When a head CT is indicated, skull radiographs add little diagnostic value. (orig.)

  15. Evaluation of feature detection algorithms for structure from motion

    CSIR Research Space (South Africa)

    Govender, N

    2009-11-01

    Full Text Available Structure from motion is a widely-used technique in computer vision to perform 3D reconstruction. The 3D structure is recovered by analysing the motion of an object, based on its features, over time. The typical steps involved in SFM are feature...

  16. Report of a Rare Case of an Odontogenic Myxoma of the Maxilla ...

    African Journals Online (AJOL)

    The lesion crossed the midline medially, extended superiorly to right infra-orbital margin and inferiorly to the right side palate [Figure 3]. CT 3-D reconstruction of paranasal sinus region revealed cortical destruction of the right side maxilla encroaching onto right maxillary antrum as well as the right side of the nasal cavity and ...

  17. Integrated visualization of multi-angle bioluminescence imaging and micro CT

    NARCIS (Netherlands)

    Kok, P.; Dijkstra, J.; Botha, C.P.; Post, F.H.; Kaijzel, E.; Que, I.; Löwik, C.W.G.M.; Reiber, J.H.C.; Lelieveldt, B.P.F.

    2007-01-01

    This paper explores new methods to visualize and fuse multi-2D bioluminescence imaging (BLI) data with structural imaging modalities such as micro CT and MR. A geometric, back-projection-based 3D reconstruction for superficial lesions from multi-2D BLI data is presented, enabling a coarse estimate

  18. An ISVD-based Euclidian structure from motion for smartphones

    Science.gov (United States)

    Masiero, A.; Guarnieri, A.; Vettore, A.; Pirotti, F.

    2014-06-01

    The development of Mobile Mapping systems over the last decades allowed to quickly collect georeferenced spatial measurements by means of sensors mounted on mobile vehicles. Despite the large number of applications that can potentially take advantage of such systems, because of their cost their use is currently typically limited to certain specialized organizations, companies, and Universities. However, the recent worldwide diffusion of powerful mobile devices typically embedded with GPS, Inertial Navigation System (INS), and imaging sensors is enabling the development of small and compact mobile mapping systems. More specifically, this paper considers the development of a 3D reconstruction system based on photogrammetry methods for smartphones (or other similar mobile devices). The limited computational resources available in such systems and the users' request for real time reconstructions impose very stringent requirements on the computational burden of the 3D reconstruction procedure. This work takes advantage of certain recently developed mathematical tools (incremental singular value decomposition) and of photogrammetry techniques (structure from motion, Tomasi-Kanade factorization) to access very computationally efficient Euclidian 3D reconstruction of the scene. Furthermore, thanks to the presence of instrumentation for localization embedded in the device, the obtained 3D reconstruction can be properly georeferenced.

  19. Automated Inspection of Power Line Corridors to Measure Vegetation Undercut Using Uav-Based Images

    Science.gov (United States)

    Maurer, M.; Hofer, M.; Fraundorfer, F.; Bischof, H.

    2017-08-01

    Power line corridor inspection is a time consuming task that is performed mostly manually. As the development of UAVs made huge progress in recent years, and photogrammetric computer vision systems became well established, it is time to further automate inspection tasks. In this paper we present an automated processing pipeline to inspect vegetation undercuts of power line corridors. For this, the area of inspection is reconstructed, geo-referenced, semantically segmented and inter class distance measurements are calculated. The presented pipeline performs an automated selection of the proper 3D reconstruction method for on the one hand wiry (power line), and on the other hand solid objects (surrounding). The automated selection is realized by performing pixel-wise semantic segmentation of the input images using a Fully Convolutional Neural Network. Due to the geo-referenced semantic 3D reconstructions a documentation of areas where maintenance work has to be performed is inherently included in the distance measurements and can be extracted easily. We evaluate the influence of the semantic segmentation according to the 3D reconstruction and show that the automated semantic separation in wiry and dense objects of the 3D reconstruction routine improves the quality of the vegetation undercut inspection. We show the generalization of the semantic segmentation to datasets acquired using different acquisition routines and to varied seasons in time.

  20. Appearance based Key-Shot Selection for a Hand Held Camera

    NARCIS (Netherlands)

    Alefs, B.G.; Dijk, J.

    2009-01-01

    Automatic selection of key-shots is an important step for video data processing. Depending on the purpose, key-shot selection provides user feed back on recorded data, storage reduction and viewpoint selection and it can be used for panoramic image stitching and 3D-reconstruction. In particular,

  1. Images in medicine

    African Journals Online (AJOL)

    ebutamanya

    sensory and motor function, and by 8 months there was sensation in the autonomous zones of both median and ulnar nerves and good return of muscle power. Figure 1: A) radiograph of the left shoulder demonstrating fracture of the lateral border of the scapula; B and C) tomography scan with 3D reconstruction confirmed ...

  2. Model-based wear measurements in total knee arthroplasty : development and validation of novel radiographic techniques

    NARCIS (Netherlands)

    IJsseldijk, van E.A.

    2016-01-01

    The primary aim of this work was to develop novel model-based mJSW measurement methods using a 3D reconstruction and compare the accuracy and precision of these methods to conventional mJSW measurement. This thesis contributed to the development, validation and clinical application of model-based

  3. Face reconstruction from image sequences for forensic face comparison

    NARCIS (Netherlands)

    van Dam, C.; Veldhuis, Raymond N.J.; Spreeuwers, Lieuwe Jan

    2016-01-01

    The authors explore the possibilities of a dense model-free three-dimensional (3D) face reconstruction method, based on image sequences from a single camera, to improve the current state of forensic face comparison. They propose a new model-free 3D reconstruction method for faces, based on the

  4. Complex bud architecture and cell-specific chemical patterns enable supercooling of Picea abies bud primordial

    Science.gov (United States)

    Bud primordia of Picea abies, despite a frozen shoot, stay ice free down to -50 °C by a mechanism termed supercooling whose biophysical and biochemical requirements are poorly understood. Bud architecture was assessed by 3D-reconstruction, supercooling and freezing patterns by infrared video thermog...

  5. Three-dimensional architecture of scar and conducting channels based on high resolution ce-CMR: insights for ventricular tachycardia ablation

    NARCIS (Netherlands)

    Fernandez-Armenta, J.; Berruezo, A.; Andreu, D.; Camara, O.; Silva, E.; Serra, L.; Barbarito, V.; Carotenutto, L.; Evertz, R.; Ortiz-Perez, J.T.; Caralt, T.M. De; Perea, R.J.; Sitges, M.; Mont, L.; Frangi, A.; Brugada, J.

    2013-01-01

    BACKGROUND: Conducting channels are the target for ventricular tachycardia (VT) ablation. Conducting channels could be identified with contrast enhanced-cardiac magnetic resonance (ce-CMR) as border zone (BZ) corridors. A 3-dimensional (3D) reconstruction of the ce-CMR could allow visualization of

  6. Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

    Science.gov (United States)

    2011-01-01

    Background The present knowledge of protein structures at atomic level derives from some 60,000 molecules. Yet the exponential ever growing set of hypothetical protein sequences comprises some 10 million chains and this makes the problem of protein structure prediction one of the challenging goals of bioinformatics. In this context, the protein representation with contact maps is an intermediate step of fold recognition and constitutes the input of contact map predictors. However contact map representations require fast and reliable methods to reconstruct the specific folding of the protein backbone. Methods In this paper, by adopting a GRID technology, our algorithm for 3D reconstruction FT-COMAR is benchmarked on a huge set of non redundant proteins (1716) taking random noise into consideration and this makes our computation the largest ever performed for the task at hand. Results We can observe the effects of introducing random noise on 3D reconstruction and derive some considerations useful for future implementations. The dimension of the protein set allows also statistical considerations after grouping per SCOP structural classes. Conclusions All together our data indicate that the quality of 3D reconstruction is unaffected by deleting up to an average 75% of the real contacts while only few percentage of randomly generated contacts in place of non-contacts are sufficient to hamper 3D reconstruction. PMID:21232136

  7. The Art of Reconstruction. Documenting the process of 3D modeling: some preliminary results

    NARCIS (Netherlands)

    Lulof, P.S.; Opgenhaffen, L.; Sepers, M.H.; Addison, A.C.; Guidi, G.; De Luca, L.; Pescarin, S.

    2013-01-01

    The project `The Art of Reconstruction' explores the usage of digital three-dimensional (3D) reconstructions to support research into historical and archaeological architectural settings. More specifically, the aim is to enhance the research on buildings that are nowadays partly or entirely lost,

  8. Markerless motion capture can provide reliable 3D gait kinematics in the sagittal and frontal plane

    DEFF Research Database (Denmark)

    Sandau, Martin; Koblauch, Henrik; Moeslund, Thomas B.

    2014-01-01

    Estimating 3D joint rotations in the lower extremities accurately and reliably remains unresolved in markerless motion capture, despite extensive studies in the past decades. The main problems have been ascribed to the limited accuracy of the 3D reconstructions. Accordingly, the purpose of the pr...

  9. Melanopsin expressing human retinal ganglion cells

    DEFF Research Database (Denmark)

    Hannibal, Jens; Christensen, Anders Tolstrup; Heegaard, Steffen

    2017-01-01

    microscopy and 3D reconstruction of melanopsin immunoreactive (-ir) RGCs, we applied the criteria used in mouse on human melanopsin-ir RGCs. We identified M1, displaced M1, M2 and M4 cells. We found two other subtypes of melanopsin-ir RGCs, which were named "gigantic M1 (GM1)" and "gigantic displaced M1 (GDM...

  10. Advances and perspectives in tissue clearing using CLARITY

    DEFF Research Database (Denmark)

    Reveles Jensen, Kristian; Berg, Rune W.

    2017-01-01

    CLARITY is a tissue clearing method, which enables immunostaining and imaging of large volumes for 3D-reconstruction. The method was initially time-consuming, expensive and relied on electrophoresis to remove lipids to make the tissue transparent. Since then several improvements and simplifications...

  11. AUTOMATED INSPECTION OF POWER LINE CORRIDORS TO MEASURE VEGETATION UNDERCUT USING UAV-BASED IMAGES

    Directory of Open Access Journals (Sweden)

    M. Maurer

    2017-08-01

    Full Text Available Power line corridor inspection is a time consuming task that is performed mostly manually. As the development of UAVs made huge progress in recent years, and photogrammetric computer vision systems became well established, it is time to further automate inspection tasks. In this paper we present an automated processing pipeline to inspect vegetation undercuts of power line corridors. For this, the area of inspection is reconstructed, geo-referenced, semantically segmented and inter class distance measurements are calculated. The presented pipeline performs an automated selection of the proper 3D reconstruction method for on the one hand wiry (power line, and on the other hand solid objects (surrounding. The automated selection is realized by performing pixel-wise semantic segmentation of the input images using a Fully Convolutional Neural Network. Due to the geo-referenced semantic 3D reconstructions a documentation of areas where maintenance work has to be performed is inherently included in the distance measurements and can be extracted easily. We evaluate the influence of the semantic segmentation according to the 3D reconstruction and show that the automated semantic separation in wiry and dense objects of the 3D reconstruction routine improves the quality of the vegetation undercut inspection. We show the generalization of the semantic segmentation to datasets acquired using different acquisition routines and to varied seasons in time.

  12. Overview of the MPEG Activity on Point Cloud Compression

    NARCIS (Netherlands)

    R.N. Mekuria (Rufael); L. Bivolarsky (Lazar)

    2016-01-01

    textabstractWe present an overview of the MPEG activity on Point Cloud Compression (PCC). This activity aims to satisfy the growing need for lossless and lossy PCC in industry. It follows recent advances in consumer electronics in 3D reconstruction and capturing. We present the preliminary

  13. Field reconstruction and estimation of the antenna support structure effect on the measurement uncertainty of the BTS1940 antenna

    DEFF Research Database (Denmark)

    Cappellin, Cecilia; Pivnenko, Sergey

    2014-01-01

    the effect of the support structure on the measured field, by reconstructing the currents induced on the support frame with DIATOOL. The field obtained by filtering these currents is presented. Moreover, the spatial resolution obtained by the 3D reconstruction is discussed and compared with the one obtained...

  14. A> L1-TV algorithm for robust perspective photometric stereo with spatially-varying lightings

    DEFF Research Database (Denmark)

    Quéau, Yvain; Lauze, Francois Bernard; Durou, Jean-Denis

    2015-01-01

    We tackle the problem of perspective 3D-reconstruction of Lambertian surfaces through photometric stereo, in the presence of outliers to Lambert's law, depth discontinuities, and unknown spatially-varying lightings. To this purpose, we introduce a robust $L^1$-TV variational formulation of the re...

  15. Reconstruction 3D des structures adjacentes de l'articulation de la hanche par une segmentation multi-structures a l'aide des maillages surfaciques triangulaires

    Science.gov (United States)

    Meghoufel, Brahim

    A new 3D reconstruction technique of the two adjacent structures forming the hip joint from the 3D CT-scans images has been developed. The femoral head and the acetabulum are reconstructed using a 3D multi-structure segmentation method for the adjacent surfaces which is based on the use of a 3D triangular surface meshes. This method begins with a preliminary hierarchical segmentation of the two structures, using one triangular mesh for each structure. The two resulting 3D meshes of the hierarchical segmentation are deployed into two planar 2D surfaces. We have used the umbrella deployment to deploy the femoral head mesh, and the parameterization 3D/2D to deploy the acetabulum mesh. The two planar generated surfaces are used to deploy the CT-scan volume around each structure. The surface of each structure is nearly planar in the corresponding deployed volume. The iterative method of minimal surfaces ensures the optimal identification of both sought surfaces from the deployed volumes. The last step of the 3D reconstruction method aims at detecting and correcting the overlap between the two structures. This 3D reconstruction method has been validated using a data base of 10 3D CT-scan images. The results of the 3D reconstructions seem satisfactory. The precision errors of these 3D reconstructions have been quantified by comparing the 3D reconstructions with an available manual gold standard. The errors resulting from the quantification are better than those available in the literature; the mean of those errors is 0,83 +/- 0,25 mm for acetabulum and 0,70 +/- 0,17 mm for the femoral head. The mean execution time of the 3D reconstruction of the two structures forming the hip joint has been estimated at approximately 3,0 +/- 0,3 min . The proposed method shows the potential of the solution which the image processing can provide to the surgeons in order to achieve their routine tasks. Such a method can be applied to every imaging modality.

  16. Photogrammetry in 3d Modelling of Human Bone Structures from Radiographs

    Science.gov (United States)

    Hosseinian, S.; Arefi, H.

    2017-05-01

    Photogrammetry can have great impact on the success of medical processes for diagnosis, treatment and surgeries. Precise 3D models which can be achieved by photogrammetry improve considerably the results of orthopedic surgeries and processes. Usual 3D imaging techniques, computed tomography (CT) and magnetic resonance imaging (MRI), have some limitations such as being used only in non-weight-bearing positions, costs and high radiation dose(for CT) and limitations of MRI for patients with ferromagnetic implants or objects in their bodies. 3D reconstruction of bony structures from biplanar X-ray images is a reliable and accepted alternative for achieving accurate 3D information with low dose radiation in weight-bearing positions. The information can be obtained from multi-view radiographs by using photogrammetry. The primary step for 3D reconstruction of human bone structure from medical X-ray images is calibration which is done by applying principles of photogrammetry. After the calibration step, 3D reconstruction can be done using efficient methods with different levels of automation. Because of the different nature of X-ray images from optical images, there are distinct challenges in medical applications for calibration step of stereoradiography. In this paper, after demonstrating the general steps and principles of 3D reconstruction from X-ray images, a comparison will be done on calibration methods for 3D reconstruction from radiographs and they are assessed from photogrammetry point of view by considering various metrics such as their camera models, calibration objects, accuracy, availability, patient-friendly and cost.

  17. Digital forensic osteology--possibilities in cooperation with the Virtopsy project.

    Science.gov (United States)

    Verhoff, Marcel A; Ramsthaler, Frank; Krähahn, Jonathan; Deml, Ulf; Gille, Ralf J; Grabherr, Silke; Thali, Michael J; Kreutz, Kerstin

    2008-01-30

    The present study was carried out to check whether classic osteometric parameters can be determined from the 3D reconstructions of MSCT (multislice computed tomography) scans acquired in the context of the Virtopsy project. To this end, four isolated and macerated skulls were examined by six examiners. First the skulls were conventionally (manually) measured using 32 internationally accepted linear measurements. Then the skulls were scanned by the use of MSCT with slice thicknesses of 1.25 mm and 0.63 mm, and the 33 measurements were virtually determined on the digital 3D reconstructions of the skulls. The results of the traditional and the digital measurements were compared for each examiner to figure out variations. Furthermore, several parameters were measured on the cranium and postcranium during an autopsy and compared to the values that had been measured on a 3D reconstruction from a previously acquired postmortem MSCT scan. The results indicate that equivalent osteometric values can be obtained from digital 3D reconstructions from MSCT scans using a slice thickness of 1.25 mm, and from conventional manual examinations. The measurements taken from a corpse during an autopsy could also be validated with the methods used for the digital 3D reconstructions in the context of the Virtopsy project. Future aims are the assessment and biostatistical evaluation in respect to sex, age and stature of all data sets stored in the Virtopsy project so far, as well as of future data sets. Furthermore, a definition of new parameters, only measurable with the aid of MSCT data would be conceivable.

  18. Correction for Patient Sway in Radiographic Biplanar Imaging for Three-Dimensional Reconstruction of the Spine: In Vitro Study of a New Method

    Energy Technology Data Exchange (ETDEWEB)

    Legaye, J. (Dept. of Orthopedic Surgery, Univ. of Louvain - Mont-Godinne, Yvoir (Belgium)); Saunier, P.; Dumas, R. (Univ. of Lyon 1 - INRETS, Villeurbanne (France)); Vallee, C. (Radiology Dept., Hpital Raymond Poincare, Garches (France))

    2009-08-15

    Background: Three-dimensional (3D) reconstructions of the spine in the upright position are classically obtained using two-dimensional, non-simultaneous radiographic imaging. However, a subject's sway between exposures induces inaccuracy in the 3D reconstructions. Purpose: To evaluate the impact of patient sway between successive radiographic exposures, and to test if 3D reconstruction accuracy can be improved by a corrective method with simultaneous Moire-X-ray imaging. Material and Methods: Using a calibrated deformable phantom perceptible by both techniques (Moire and X-ray), the 3D positional and rotational vertebral data from 3D reconstructions with and without the corrective procedure were compared to the corresponding data of computed tomography (CT) scans, considered as a reference. All were expressed in the global axis system, as defined by the Scoliosis Research Society. Results: When a sagittal sway of 10 deg occurred between successive biplanar X-rays, the accuracy of the 3D reconstruction without correction was 8.8 mm for the anteroposterior vertebral locations and 6.4 deg for the sagittal orientations. When the corrective method was applied, the accuracy was improved to 1.3 mm and 1.5 deg, respectively. Conclusion: 3D accuracy improved significantly by using the corrective method, whatever the subject's sway. This technique is reliable for clinical appraisal of the spine, if the subject's sway does not exceed 10 deg. For greater sway, improvement persists, but a risk of lack of accuracy exists

  19. Combining Information Sources for Video Retrieval

    NARCIS (Netherlands)

    Westerveld, T.H.W.; Ianeva, T.; Boldareva, L.; de Vries, A.P.; Hiemstra, Djoerd

    The previous video track results demonstrated that it is far from trivial to take advantage of multiple modalities for the video retrieval search task. For almost any query, results based on ASR transcripts have been better than any other run. This year’s main success in our runs is that a

  20. Simultaneous recordings of human microsaccades and drifts with a contemporary video eye tracker and the search coil technique.

    Directory of Open Access Journals (Sweden)

    Michael B McCamy

    Full Text Available Human eyes move continuously, even during visual fixation. These "fixational eye movements" (FEMs include microsaccades, intersaccadic drift and oculomotor tremor. Research in human FEMs has grown considerably in the last decade, facilitated by the manufacture of noninvasive, high-resolution/speed video-oculography eye trackers. Due to the small magnitude of FEMs, obtaining reliable data can be challenging, however, and depends critically on the sensitivity and precision of the eye tracking system. Yet, no study has conducted an in-depth comparison of human FEM recordings obtained with the search coil (considered the gold standard for measuring microsaccades and drift and with contemporary, state-of-the art video trackers. Here we measured human microsaccades and drift simultaneously with the search coil and a popular state-of-the-art video tracker. We found that 95% of microsaccades detected with the search coil were also detected with the video tracker, and 95% of microsaccades detected with video tracking were also detected with the search coil, indicating substantial agreement between the two systems. Peak/mean velocities and main sequence slopes of microsaccades detected with video tracking were significantly higher than those of the same microsaccades detected with the search coil, however. Ocular drift was significantly correlated between the two systems, but drift speeds were higher with video tracking than with the search coil. Overall, our combined results suggest that contemporary video tracking now approaches the search coil for measuring FEMs.

  1. Extending Track Analysis from Animals in the Lab to Moving Objects Anywhere

    NARCIS (Netherlands)

    Dommelen, W. van; Laar, P.J.L.J. van de; Noldus, L.P.J.J.

    2013-01-01

    In this chapter we compare two application domains in which the tracking of objects and the analysis of their movements are core activities, viz. animal tracking and vessel tracking. More specifically, we investigate whether EthoVision XT, a research tool for video tracking and analysis of the

  2. Harmonic radar: assessing the impact of tag weight on walking behavior of Colorado potato beetle, plum curculio and corn rootworm

    Science.gov (United States)

    The impact of electronic dipole tags on the walking behavior of three insects was determined using video tracking software. Results varied within and between the three species studied. The mean horizontal speed of the Colorado potato beetle, Leptinotarsa decemlineata (Say), was reduced by 8 percen...

  3. Efficient Visual Tracking with Spatial Constraints

    NARCIS (Netherlands)

    Zhang, L.

    2015-01-01

    Object tracking is an important component in computer vision, which is the field that aims to replicate the abilities of human vision by automatically analyzing and understanding the content of digital images or videos. Tracking has applications in a wide range of domains. For instance, tracking

  4. Neuroprotective effect of paeonol against isoflurane- induced ...

    African Journals Online (AJOL)

    period of 10 min was noted and this was considered as anxiety index. The responses of the rats were recorded using the computerized video tracking system (SMART, Barcelona,. Spain). Y-maze test. The Y-maze test was performed to evaluate the spatial working memory. The apparatus consisted of a symmetrical Y-maze ...

  5. AMULET: A MUlti-cLuE Approach to Image Forensics

    Science.gov (United States)

    2014-12-31

    observables may refer to the audio and video tracks and so on. Even if the original target of our analysis was giving a theoretical background to... steganography and steganalysis, network intrusion detection, traffic monitoring, cognitive radio and many others. In the next subsections, we first give a...scenarios, including multimedia forensics, biometrics, digital watermarking, steganography and steganalysis, network intrusion detection, traffic

  6. Computer Reconstruction of Plant Growth and Chlorophyll Fluorescence Emission in Three Spatial Dimensions

    Directory of Open Access Journals (Sweden)

    Ladislav Nedbal

    2012-01-01

    Full Text Available Plant leaves grow and change their orientation as well their emission of chlorophyll fluorescence in time. All these dynamic plant properties can be semi-automatically monitored by a 3D imaging system that generates plant models by the method of coded light illumination, fluorescence imaging and computer 3D reconstruction. Here, we describe the essentials of the method, as well as the system hardware. We show that the technique can reconstruct, with a high fidelity, the leaf size, the leaf angle and the plant height. The method fails with wilted plants when leaves overlap obscuring their true area. This effect, naturally, also interferes when the method is applied to measure plant growth under water stress. The method is, however, very potent in capturing the plant dynamics under mild stress and without stress. The 3D reconstruction is also highly effective in correcting geometrical factors that distort measurements of chlorophyll fluorescence emission of naturally positioned plant leaves.

  7. Cone Beam Computed Tomography Evaluation of Inverted Mesiodentes.

    Science.gov (United States)

    Al-Sehaibany, Fares S; Marzouk, Hazem M; Salama, Fouad S

    2016-01-01

    A mesiodens is the most common type of supernumerary teeth. The purpose of this report is to present a rare occurrence of non-syndromic impacted inverted mesiodentes in an 8.5-year-old boy who presented with a chief complaint of delayed eruption of his permanent maxillary left central incisor. Occlusal and panoramic radiographs, as well as cone beam computed tomography (CBCT) with a three-dimensional (3-D) reconstruction image, confirmed that one supernumerary tooth had perforated the nasal fossa floor and the other was in close approximation to the to the same site. Surgical removal of both mesiodentes was indicated. Radiographic evidence of complete healing was observed 12 months following surgical removal. The use of CBCT with a 3-D reconstruction image as a tool in diagnosis and evaluation of healing after surgical removal is recommended.

  8. Preliminary development of augmented reality systems for spinal surgery

    Science.gov (United States)

    Nguyen, Nhu Q.; Ramjist, Joel M.; Jivraj, Jamil; Jakubovic, Raphael; Deorajh, Ryan; Yang, Victor X. D.

    2017-02-01

    Surgical navigation has been more actively deployed in open spinal surgeries due to the need for improved precision during procedures. This is increasingly difficult in minimally invasive surgeries due to the lack of visual cues caused by smaller exposure sites, and increases a surgeon's dependence on their knowledge of anatomical landmarks as well as the CT or MRI images. The use of augmented reality (AR) systems and registration technologies in spinal surgeries could allow for improvements to techniques by overlaying a 3D reconstruction of patient anatomy in the surgeon's field of view, creating a mixed reality visualization. The AR system will be capable of projecting the 3D reconstruction onto a field and preliminary object tracking on a phantom. Dimensional accuracy of the mixed media will also be quantified to account for distortions in tracking.

  9. PRIMAS: a real-time 3D motion-analysis system

    Science.gov (United States)

    Sabel, Jan C.; van Veenendaal, Hans L. J.; Furnee, E. Hans

    1994-03-01

    The paper describes a CCD TV-camera-based system for real-time multicamera 2D detection of retro-reflective targets and software for accurate and fast 3D reconstruction. Applications of this system can be found in the fields of sports, biomechanics, rehabilitation research, and various other areas of science and industry. The new feature of real-time 3D opens an even broader perspective of application areas; animations in virtual reality are an interesting example. After presenting an overview of the hardware and the camera calibration method, the paper focuses on the real-time algorithms used for matching of the images and subsequent 3D reconstruction of marker positions. When using a calibrated setup of two cameras, it is now possible to track at least ten markers at 100 Hz. Limitations in the performance are determined by the visibility of the markers, which could be improved by adding a third camera.

  10. Effect of Gas Pores on Mechanical Properties of High-Pressure Die-Casting AM50 Magnesium Alloy.

    Science.gov (United States)

    Jiang, Wei; Cao, Zhanyi; Liu, Liping; Jiang, Bo

    2016-08-01

    High-pressure die-casting (HPDC) AM50 tensile specimens were used to investigate characteristics of gas pores and its effect on mechanical properties of HPDC AM50 magnesium alloy. Combining microstructure morphology gained from optical microscopy, scanning electron microscopy (SEM), and three-dimensional (3D) reconstruction with the experimental data from uniaxial tensile testing, we pursued the relationship between gas pores and the mechanical properties of HPDC AM50 Mg alloy. Results indicate that comparing with 3D reconstruction models, 2D images like optical metallography images and SEM images have one-sidedness. Furthermore, the size and maximum areal fraction of gas pores have negative effects on the mechanical properties of HPDC AM50 Mg alloy. With increase of the maximum size of gas pores in the specimen, the ultimate tensile strength (UTS) and elongation decrease. In addition, with the maximum areal fraction becoming larger, both the UTS and elongation decrease linearly.

  11. Critical factors in SEM 3D stereo microscopy

    DEFF Research Database (Denmark)

    Marinello, F.; Bariano, P.; Savio, E.

    2008-01-01

    This work addresses dimensional measurements performed with the scanning electron microscope (SEM) using 3D reconstruction of surface topography through stereo-photogrammetry. The paper presents both theoretical and experimental investigations, on the effects of instrumental variables and measure......This work addresses dimensional measurements performed with the scanning electron microscope (SEM) using 3D reconstruction of surface topography through stereo-photogrammetry. The paper presents both theoretical and experimental investigations, on the effects of instrumental variables...... and measurement parameters on reconstruction accuracy. Investigations were performed on a novel sample, specifically developed and implemented for the tests. The description is based on the model function introduced by Piazzesi and adapted for eucentrically tilted stereopairs. Two main classes of influencing...... factors are recognized: the first one is related to the measurement operation and the instrument set-up; the second concerns the quality of scanned images and represents the major criticality in the application of SEMs for 3D characterizations....

  12. [The use of open source software in graphic anatomic reconstructions and in biomechanic simulations].

    Science.gov (United States)

    Ciobanu, O

    2009-01-01

    The objective of this study was to obtain three-dimensional (3D) images and to perform biomechanical simulations starting from DICOM images obtained by computed tomography (CT). Open source software were used to prepare digitized 2D images of tissue sections and to create 3D reconstruction from the segmented structures. Finally, 3D images were used in open source software in order to perform biomechanic simulations. This study demonstrates the applicability and feasibility of open source software developed in our days for the 3D reconstruction and biomechanic simulation. The use of open source software may improve the efficiency of investments in imaging technologies and in CAD/CAM technologies for implants and prosthesis fabrication which need expensive specialized software.

  13. The human myotendinous junction

    DEFF Research Database (Denmark)

    Knudsen, A B; Larsen, M; Mackey, Abigail

    2015-01-01

    been described in three dimensions (3D). The aim of this study was to describe the ultrastructure of the human MTJ and render 3D reconstructions. Fourteen subjects (age 25 ± 3 years) with isolated injury of the anterior cruciate ligament (ACL), scheduled for reconstruction with a semitendinosus....../gracilis graft were included. Semitendinosus and gracilis tendons were stripped as grafts for the ACL reconstruction. The MTJ was isolated from the grafts and prepared for transmission electron microscopy (TEM) and focused ion beam/scanning electron microscopy. It was possible to isolate recognizable MTJ tissue...... tissue. The 3D reconstruction revealed that tendon made ridge-like protrusions, which interdigitiated with groove-like indentations in the muscle cell....

  14. D Reconstruction with a Collaborative Approach Based on Smartphones and a Cloud-Based Server

    Science.gov (United States)

    Nocerino, E.; Poiesi, F.; Locher, A.; Tefera, Y. T.; Remondino, F.; Chippendale, P.; Van Gool, L.

    2017-11-01

    The paper presents a collaborative image-based 3D reconstruction pipeline to perform image acquisition with a smartphone and geometric 3D reconstruction on a server during concurrent or disjoint acquisition sessions. Images are selected from the video feed of the smartphone's camera based on their quality and novelty. The smartphone's app provides on-the-fly reconstruction feedback to users co-involved in the acquisitions. The server is composed of an incremental SfM algorithm that processes the received images by seamlessly merging them into a single sparse point cloud using bundle adjustment. Dense image matching algorithm can be lunched to derive denser point clouds. The reconstruction details, experiments and performance evaluation are presented and discussed.

  15. 3D building reconstruction in a remote sensing workflow

    Science.gov (United States)

    Becker, Merlin; Espinosa, Nayeli S.; Middelmann, Wolfgang; Runkel, Irmgard

    2017-10-01

    3D reconstruction and recognition of buildings and urban scenes is crucial for urban planning, disaster evaluation, historical, architectural and/or urban research and other photogrammetric tasks. The purpose of this research work is to evaluate 3D reconstruction of urban scenes by using the simplest workflow given by the optional IMAGINE UAV module for the ERDAS IMAGINE 2016 software. Digital elevation models and point clouds were extracted from RGB aerial images, which were captured by two SVS-Vistek nadir cameras with a resolution of 16 megapixel. The cameras were synchronized with a GPS/INS module for a direct georeferencing of the images. Additionally, the generated 3D models were imported to the Agiosoft PhotoScan application for a better visualization and to verify the focal length of the camera. The tridicon BuildingFinder software was used to improve the quality of the produced point clouds and for building recognition as well.

  16. 3D shape reconstruction of bone from two x-ray images using 2D/3D non-rigid registration based on moving least-squares deformation

    Science.gov (United States)

    Cresson, T.; Branchaud, D.; Chav, R.; Godbout, B.; de Guise, J. A.

    2010-03-01

    Several studies based on biplanar radiography technologies are foreseen as great systems for 3D-reconstruction applications for medical diagnoses. This paper proposes a non-rigid registration method to estimate a 3D personalized shape of bone models from two planar x-ray images using an as-rigid-as-possible deformation approach based on a moving least-squares optimization method. Based on interactive deformation methods, the proposed technique has the ability to let a user improve readily and with simplicity a 3D reconstruction which is an important step in clinical applications. Experimental evaluations of six anatomical femur specimens demonstrate good performances of the proposed approach in terms of accuracy and robustness when compared to CT-scan.

  17. Analysis of information for cerebrovascular disorders obtained by 3D MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Kohki [Tokyo Univ. (Japan). Inst. of Medical Science; Yoshioka, Naoki; Watanabe, Fumio; Shiono, Takahiro; Sugishita, Morihiro; Umino, Kazunori

    1995-12-01

    Recently, it becomes easy to analyze information obtained by 3D MR imaging due to remarkable progress of fast MR imaging technique and analysis tool. Six patients suffered from aphasia (4 cerebral infarctions and 2 bleedings) were performed 3D MR imaging (3D FLASH-TR/TE/flip angle; 20-50 msec/6-10 msec/20-30 degrees) and their volume information were analyzed by multiple projection reconstruction (MPR), surface rendering 3D reconstruction, and volume rendering 3D reconstruction using Volume Design PRO (Medical Design Co., Ltd.). Four of them were diagnosed as Broca`s aphasia clinically and their lesions could be detected around the cortices of the left inferior frontal gyrus. Another 2 patients were diagnosed as Wernicke`s aphasia and the lesions could be detected around the cortices of the left supramarginal gyrus. This technique for 3D volume analyses would provide quite exact locational information about cerebral cortical lesions. (author).

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

    Science.gov (United States)

    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.

  19. Digital holographic metrology based on multi-angle interferometry.

    Science.gov (United States)

    Dong, Jun; Jiang, Chao; Jia, Shuhai

    2016-09-15

    We propose a multi-angle interferometry method for digital holographic metrology. In an application of three-dimensional (3D) reconstruction, the hologram corresponding to a different illumination angle is recorded as the illumination angle with a single wavelength tilted at regular intervals by an electronically controlled rotating stage. A Fourier-transform-based axial depth scanning algorithm formed by the reconstructed phase is used to obtain the height point by point over the whole field of view. Hence, the 3D reconstruction can be obtained effectively; even the object has large depth discontinuities resulting from the difficulty of the phase unwrapping. Due to a monochrome source only being used, the method is available for objects with wavelength-dependent reflectivity and those that are free of chromatic aberration caused by the different wavelengths.

  20. [The ultrasound diagnosis of regional recurrent cancer of the thyroid gland].

    Science.gov (United States)

    Bochkareva, O V; Siniukova, G T; Matiakin, E G; Kostiakova, L A; Titova, I A; Tsiklauri, V T

    2012-01-01

    Examination of 220 patients was performed using ultrasound investigation (USI) in B-regimen, color and energy Doppler encoding, 3D-reconstruction of image and sonoelastography. There were 49 recurrences in the regional lymph nodes. Main semiotic signs of regional recurrences were identified. USI with the application of the methods described is highly informative: sensitivity--94.2%, specificity--92.5%, accuracy--91.7%.

  1. A L1-TV Algorithm for Robust Perspective Photometric Stereo with Spatially-Varying Lightings

    OpenAIRE

    Quéau, Yvain; Lauze, François; Durou, Jean-Denis

    2015-01-01

    We tackle the problem of perspective 3D-reconstruction of Lambertian surfaces through photometric stereo, in the presence of outliers to Lambert’s law, depth discontinuities, and unknown spatially-varying lightings. To this purpose, we introduce a robust L1-TV variational formulation of the recovery problem where the shape itself is the main unknown, which naturally enforces integrability and permits to avoid integrating the normal field.

  2. An anencephalus foetus petrified by Gerolamo Segato (1792-1836).

    Science.gov (United States)

    Ciranni, Rosalba; Fornaciari, Gino; Nardini, Vincenzo; Caramella, Davide

    2008-01-01

    We report the case of an anencephalic foetus petrified by Gerolamo Segato in the course of his experiments on body conservation. The specimen has been studied applying non-invasive methods. Digital radiography and computed tomography (CT) alogside more advanced techniques such as three-dimensional (3-D) reconstruction and virtual endoscopy (VE) have been used to investigate anatomic morphology and to perform hypotheses about Segato's method of petrification which is still unknown.

  3. Contribution à l'estimation de la similarité dans un ensemble de projections tomographiques non-orientées

    OpenAIRE

    Phan, Minh-Son

    2016-01-01

    Cryo-electron microscopy is a tomographic technique allowing to reconstruct a 3D model of complex structure in biology from a set of acquired images. These images are known as the tomographic projections and are taken at unknown directions. The advantage of the cryo-electron microscopy is the 3D reconstruction at very high resolution. The reconstruction procedure consists of many steps such as projection alignment, projection classification, orientation estimation and projection refinement. D...

  4. Computer Reconstruction of Plant Growth and Chlorophyll Fluorescence Emission in Three Spatial Dimensions

    Czech Academy of Sciences Publication Activity Database

    Bellasio, Ch.; Olejníčková, Julie; Tesař, R.; Šebela, David; Nedbal, Ladislav

    2012-01-01

    Roč. 12, č. 1 (2012), s. 1052-1071 ISSN 1424-8220 R&D Projects: GA ČR GA522/09/1565; GA MŠk(CZ) ED1.1.00/02.0073 Institutional support: RVO:67179843 Keywords : 3D reconstruction * chlorophyll fluorescence imaging * leaf area * leaf angle * plant growth * coded light Subject RIV: EH - Ecology, Behaviour Impact factor: 1.953, year: 2012

  5. Mechanisms of Precipitation of Different Generations of Gamma-Prime Precipitates During Continuous Cooling of a Nickel Base Superalloy (PREPRINT)

    Science.gov (United States)

    2012-08-01

    respectively. A better visual representation of the same 3D reconstruction is shown in Fig. 5(b), where an iso -concentration surface (or isosurface...80 1.66 1.68 1.7 1.72 D 2-Theta 16000 0 14000 12000 .£10000 ~ c .. - 8000 c - 6000 4000 2000 0 2.88 2.9 2.92 2.94 2.96 2-Tbeta Cooling

  6. Bilateral impacted inverted mesiodens associated with dentigerous cyst.

    Science.gov (United States)

    Byatnal, Aditi Amit; Byatnal, Amit; Singh, Ankur; Narayanaswamy, Venkadasalapathi; Radhakrishnan, Raghu

    2013-10-01

    Mesiodens, the most common type of supernumerary tooth, usually results in malocclusion, poor esthetics and cyst formation. The occurrence of a dentigerous cyst around the crown of an unerupted supernumerary tooth is infrequent. We present a case of a dentigerous cyst associated with a nonsyndromic bilateral impacted inverted supernumerary tooth in a 13-year-old boy. A thorough clinical workup, including 3-D reconstruction image and histological examination confirming the features of a dentigerous cyst is presented in this report.

  7. Calculating the axes of rotation for the subtalar and talocrural joints using 3D bone reconstructions

    OpenAIRE

    Parr, W. C. H.; Chatterjee, H. J.; Soligo, C.

    2012-01-01

    Orientation of the subtalar joint axis dictates inversion and eversion movements of the foot and has been the focus of evolutionary and clinical studies for a number of years. Previous studies have measured the subtalar joint axis against the axis of the whole foot, the talocrural joint axis and, recently, the principal axes of the talus. The present study introduces a new method for estimating average joint axes from 3D reconstructions of bones and applies the method to the talus to calculat...

  8. Nonlinear 3D foot FEA modeling from CT scan medical images

    OpenAIRE

    Antunes, P. J.; Dias, Gustavo R.; Coelho, A. T.; Rebelo, F.; Pereira, Tiago

    2011-01-01

    A 3D anatomically detailed non-linear finite element analysis human foot model is the final result of density segmentation 3D reconstruction techniques applied in Computed Tomography (CT) scan DICOM standard images in conjunction with 3D Computer Aided Design operations and finite element analysis (FEA) modelling. Density segmentation techniques were used to geometrically define the foot bone structure and the encapsulated soft tissues configuration. The monitoring of the contact ...

  9. Targeting Neuronal-like Metabolism of Metastatic Tumor Cells as a Novel Therapy for Breast Cancer Brain Metastasis

    Science.gov (United States)

    2016-03-01

    to reconstruct the brain metastasis landscape in 3D, but also provides new, exceptionally accurate perspectives on phenotypic heterogeneity of... Heterogeneous Metastasis Landscapes ”. This award is acknowledged. 7. Participants & Other Collaborating Organizations…………… What individuals have worked...brain astrocytes, tumor cell, proliferating cell (Edu) and blood vessel. We have conducted 3D reconstruction of brain metastasis landscape . We will

  10. An Interdisciplinary Method for the Visualization of Novel High-Resolution Precision Photography and Micro-XCT Data Sets of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Create Combined Research-Grade 3D Virtual Samples for the Benefit of Astromaterials Collections Conservation, Curation, Scientific Research and Education

    Science.gov (United States)

    Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Hanna, R. D.; Ketcham, R. A.

    2016-01-01

    New technologies make possible the advancement of documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. With increasing demands for accessibility to updated comprehensive data, and with new sample return missions on the horizon, it is of primary importance to develop new standards for contemporary documentation and visualization methodologies. Our interdisciplinary team has expertise in the fields of heritage conservation practices, professional photography, photogrammetry, imaging science, application engineering, data curation, geoscience, and astromaterials curation. Our objective is to create virtual 3D reconstructions of Apollo Lunar and Antarctic Meteorite samples that are a fusion of two state-of-the-art data sets: the interior view of the sample by collecting Micro-XCT data and the exterior view of the sample by collecting high-resolution precision photography data. These new data provide researchers an information-rich visualization of both compositional and textural information prior to any physical sub-sampling. Since January 2013 we have developed a process that resulted in the successful creation of the first image-based 3D reconstruction of an Apollo Lunar Sample correlated to a 3D reconstruction of the same sample's Micro- XCT data, illustrating that this technique is both operationally possible and functionally beneficial. In May of 2016 we began a 3-year research period during which we aim to produce Virtual Astromaterials Samples for 60 high-priority Apollo Lunar and Antarctic Meteorite samples and serve them on NASA's Astromaterials Acquisition and Curation website. Our research demonstrates that research-grade Virtual Astromaterials Samples are beneficial in preserving for posterity a precise 3D reconstruction of the sample prior to sub-sampling, which greatly improves documentation practices, provides unique and novel visualization of the sample's interior and

  11. Computational modeling of objects presented in images fundamentals, methods and applications

    CERN Document Server

    Iacoviello, Daniela; Jorge, Renato; Tavares, João

    2014-01-01

    This book contains extended versions of selected papers from the 3rd edition of the International Symposium CompIMAGE. These contributions include cover methods of signal and image processing and analysis to tackle problems found in medicine, material science, surveillance, biometric, robotics, defence, satellite data, traffic analysis and architecture, image segmentation, 2D and 3D reconstruction, data acquisition, interpolation and registration, data visualization, motion and deformation analysis, and 3D vision

  12. Clinical Application of an Open-Source 3D Volume Rendering Software to Neurosurgical Approaches.

    Science.gov (United States)

    Fernandes de Oliveira Santos, Bruno; Silva da Costa, Marcos Devanir; Centeno, Ricardo Silva; Cavalheiro, Sergio; Antônio de Paiva Neto, Manoel; Lawton, Michael T; Chaddad-Neto, Feres

    2018-02-01

    Preoperative recognition of the anatomic individualities of each patient can help to achieve more precise and less invasive approaches. It also may help to anticipate potential complications and intraoperative difficulties. Here we describe the use, accuracy, and precision of a free tool for planning microsurgical approaches using 3-dimensional (3D) reconstructions from magnetic resonance imaging (MRI). We used the 3D volume rendering tool of a free open-source software program for 3D reconstruction of images of surgical sites obtained by MRI volumetric acquisition. We recorded anatomic reference points, such as the sulcus and gyrus, and vascularization patterns for intraoperative localization of lesions. Lesion locations were confirmed during surgery by intraoperative ultrasound and/or electrocorticography and later by postoperative MRI. Between August 2015 and September 2016, a total of 23 surgeries were performed using this technique for 9 low-grade gliomas, 7 high-grade gliomas, 4 cortical dysplasias, and 3 arteriovenous malformations. The technique helped delineate lesions with an overall accuracy of 2.6 ± 1.0 mm. 3D reconstructions were successfully performed in all patients, and images showed sulcus, gyrus, and venous patterns corresponding to the intraoperative images. All lesion areas were confirmed both intraoperatively and at the postoperative evaluation. With the technique described herein, it was possible to successfully perform 3D reconstruction of the cortical surface. This reconstruction tool may serve as an adjunct to neuronavigation systems or may be used alone when such a system is unavailable. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Improved vision in forensic documentation: forensic 3D/CAD-supported photogrammetry of bodily injury external surfaces combined with volumetric radiologic scanning of bodily injury internal structures provides more investigative leads and stronger forensic evidence

    Science.gov (United States)

    Thali, Michael J.; Braun, Marcel; Kneubuehl, Beat P.; Brueschweiler, Walter; Vock, Peter; Dirnhofer, Richard

    2000-05-01

    In the field of the documentation of forensics-relevant injuries, from the reconstructive point of view, the Forensic, 3D/CAD-supported Photometry plays an important role; particularly so when a detailed 3D reconstruction is vital. This was demonstrated with an experimentally-produced 'injury' to a head model, the 'skin-skull-brain model'. The injury-causing instrument, drawn from a real forensic case, was a specifically formed weapon.

  14. Three-dimensional functional unit analysis of hemifacial microsomia mandible—a preliminary report

    OpenAIRE

    Choi, Ji Wook; Kim, Byung Hoon; Kim, Hyung Soo; Yu, Tae Hoon; Kim, Bong Chul; Lee, Sang-Hwy

    2015-01-01

    Background The aim of this study was to present three-dimensional (3D) structural characteristics of the mandible in the hemifacial microsomia. The mandible has six distinct functional units, and its architecture is the sum of balanced growth of each functional unit and surrounding matrix. Methods In order to characterize the mandibular 3D architecture of hemifacial microsomia, we analyzed the mandibular functional units of four hemifacial microsomia patients using the 3D reconstructed comput...

  15. Heterogeneous Sensor Webs for Automated Target Recognition and Tracking in Urban Terrain

    Science.gov (United States)

    2012-04-09

    2009 best paper award for IEEE Transactions on Multimedia for a 2006 paper. 11. A. Gu and A. Zakhor received a Best Paper Award from IEEE...training images (middle) plus sparse errors (right). [115], including in image super -resolution, object recognition, human activity recognition, speech...features in the environment such as circular corridors . Prior approaches often require unreliable 3D reconstructions, detailed calibration procedures, or

  16. Etude de L’endommagement en fluage de cuivre par tomographie à rayons X et polissages successifs

    OpenAIRE

    Abbasi, Kévin

    2013-01-01

    Power law creep damage is one of the most intriguing unsolved phenomena of materials science. Models based on continuum mechanics generally predict a much higher strain to failure, as well as a much longer creep lifetime than experimentally observed values. This thesis highlights two aspects of this problematic by analyzing creep damage in copper using in situ synchrotron tomography and 3D reconstruction of the damaged polycrystal structure by serial sectioning.Damage in terms of the area fra...

  17. An Interdisciplinary Method for the Visualization of Novel High-Resolution Precision Photography and Micro-XCT Data Sets of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Create Combined Research-Grade 3D Virtual Samples for the Benefit of Astromaterials Collections Conservation, Curation, Scientific Research and Education

    Science.gov (United States)

    Blumenfeld, E. H.; Evans, C. A.; Zeigler, R. A.; Righter, K.; Beaulieu, K. R.; Oshel, E. R.; Liddle, D. A.; Hanna, R.; Ketcham, R. A.; Todd, N. S.

    2016-12-01

    New technologies make possible the advancement of documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. With increasing demands for accessibility to updated comprehensive data, and with new sample return missions on the horizon, it is of primary importance to develop new standards for contemporary documentation and visualization methodologies. Our interdisciplinary team has expertise in the fields of heritage conservation practices, professional photography, photogrammetry, imaging science, application engineering, data curation, geoscience, and astromaterials curation. Our objective is to create virtual 3D reconstructions of Apollo Lunar and Antarctic Meteorite samples that are a fusion of two state-of-the-art data sets: the interior view of the sample by collecting Micro-XCT data and the exterior view of the sample by collecting high-resolution precision photography data. These new data provide researchers an information-rich visualization of both compositional and textural information prior to any physical sub-sampling. Since January 2013 we have developed a process that resulted in the successful creation of the first image-based 3D reconstruction of an Apollo Lunar Sample correlated to a 3D reconstruction of the same sample's Micro-XCT data, illustrating that this technique is both operationally possible and functionally beneficial. In May of 2016 we began a 3-year research period during which we aim to produce Virtual Astromaterials Samples for 60 high-priority Apollo Lunar and Antarctic Meteorite samples and serve them on NASA's Astromaterials Acquisition and Curation website. Our research demonstrates that research-grade Virtual Astromaterials Samples are beneficial in preserving for posterity a precise 3D reconstruction of the sample prior to sub-sampling, which greatly improves documentation practices, provides unique and novel visualization of the sample's interior and

  18. X-ray testing for short-time dynamic applications; Roentgenuntersuchungen fuer kurzzeitdynamische Anwendungen

    Energy Technology Data Exchange (ETDEWEB)

    Kurfiss, Malte; Moser, Stefan; Popko, Gregor; Nau, Siegfried [Fraunhofer-Institut fuer Kurzzeitdynamik, Efringen-Kirchen (Germany). Ernst-Mach-Inst. (EMI)

    2017-08-01

    For nondestructive testing purposes new challenges are short-time dynamic processes. The application of x-ray flash tubes and modern high-speed cameras allows the observation of the opening of air-bags or the energy absorption of compressed tubes as occurring during a vehicle crash. Special algorithms designed for computerized tomography analyses allow the 3D reconstruction at individual time points of the dynamic process. Possibilities and limitations of the actual techniques are discussed.

  19. A new imaging 2D and 3D for musculo-skeletal physiology and pathology with low radiation dose and standing position: the EOS system; Une nouvelle imagerie osteo-articulaire basse dose en position debout: le systeme EOS

    Energy Technology Data Exchange (ETDEWEB)

    Dubousset, J. [Academie Nationale de Medecine, et Hopital Saint Vincent de Paul, Service de Chirurgie Orthopedique, 75 - Paris (France); Charpak, G.; Dorion, I. [Biospace, Instruments, 75 - Paris (France); Skalli, W.; Lavaste, F. [Ecole Nationale Superieure des Arts et Metiers, 75 - Paris (France); Deguise, J. [Laboratoire de Recherche en Imagerie Orthopedique, Montreal (Canada); Kalifa, G.; Ferey, S. [Hopital Saint Vincent de Paul, Service de Radiologie, 75 - Paris (France)

    2005-06-01

    Very precise combined work between multidisciplinary partners (radiation engineers in physics, engineers in bio-mechanics, medical radiologists and orthopedic pediatric surgeons) lead to the concept and development of a new low dose radiation device named EOS. This device allows 3 main advantages: (1) thanks to the invention of Georges Charpak (Nobel Price 1992) who designed gaseous detectors for X-rays, the reduction of dose necessary to obtain a good image of skeletal system was 8 to 10 times less for 2D imaging, compared to the dose necessary to obtain a 3D reconstruction from CT scan cuts the reduction factor was 800 to 1000. (2) The accuracy of 3D reconstruction obtained is as good as a 3D reconstruction from CT scan cuts. (3) The patient in addition get its imaging in standing functional position thank to the X-rays obtained from head to feet simultaneously AP and lateral. This is a big advantage compared to CT scan used only in lying position. From this simultaneous AP and lateral X-rays of the whole body thanks to the 3D bone external envelop technique, the engineers in bio-mechanics allowed to obtain 3D reconstruction of every level of osteo-articular system in standing position with an acceptable period of time (15 to 30 minutes). This (in spite of the evolution of standing MRI) allows more precise bone reconstruction in orthopedics especially at the level of spine, lower limbs, etc. In addition the fact to study the entire skeleton in standing functional position instead of small segmented studies given by CT scan in lying position produce a real improvement as well for physiology as for pathology of bone and joints disorders and especially for spinal pathology. (author)

  20. Photogrammetric Processing of Rover Images by example of NASAs MER Mission Data

    OpenAIRE

    Peters, O.; Scholten, F.; Oberst, J.

    2011-01-01

    We have developed a photogrammetric processing scheme for planetary rover image data which involves several main steps: dense image matching, improvement of orientation, and 3d-reconstruction. The first step uses DLR matching software which originally was built for matching orbital imagery [1]. The main problem with close range imagery is the wide range of disparities caused by the varying distances to the surface in the foreground and in the background. If not specifically dealt with, th...

  1. A New In Vitro Model of Breast Cancer Metastasis to Bone

    Science.gov (United States)

    2010-04-01

    Figure 3: Progression in cell morphology monitored by confocal microscopy of Alexa Fluor 568 phalloidin stained MC3T3E-1 within the...with confocal microscopy. Shown are 3D reconstructed confocal images of z-stacks. Osteoblasts were fixed and stained with Alexa Fluor 568. The...for dental /orthopedic biomaterials. J Biomed Mater Res 2002;60:466–71. [74] Hendrich C, Noth U, Stahl U, Merklein F, Rader CP, Schiitze N, et al

  2. A comparison of manual neuronal reconstruction from biocytin histology or 2-photon imaging: morphometry and computer modeling

    OpenAIRE

    Blackman, Arne V.; Grabuschnig, Stefan; Legenstein, Robert; Sjöström, P. Jesper

    2014-01-01

    Accurate 3D reconstruction of neurons is vital for applications linking anatomy and physiology. Reconstructions are typically created using Neurolucida after biocytin histology (BH). An alternative inexpensive and fast method is to use freeware such as Neuromantic to reconstruct from fluorescence imaging (FI) stacks acquired using 2-photon laser-scanning microscopy during physiological recording. We compare these two methods with respect to morphometry, cell classification, and multicompartme...

  3. Towards using spectral domain optical coherence tomography for dental wear monitoring

    Science.gov (United States)

    Mǎrcǎuteanu, Corina; Bradu, Adrian; Sinescu, Cosmin; Topalǎ, Florin I.; Negrutiu, Meda Lavinia; Podoleanu, Adrian G.

    2014-03-01

    In this paper we demonstrate that fast spectral domain optical coherence tomography imaging systems have the potential to monitor the evolution of pathological dental wear. On 10 caries free teeth, four levels of artificially defects similar to those observed in the clinic were created. After every level of induced defect, OCT scanning was performed. B-scans were acquired and 3D reconstructions were generated.

  4. A 3D environment for surgical planning and simulation

    OpenAIRE

    Chiarelli, Tommaso

    2011-01-01

    The use of Computed Tomography (CT) images and their three-dimensional (3D) reconstruction has spread in the last decade for implantology and surgery. A common use of acquired CT datasets is to be handled by dedicated software that provide a work context to accomplish preoperative planning upon. These software are able to exploit image processing techniques and computer graphics to provide fundamental information needed to work in safety, in order to minimize the surgeon possible error during...

  5. 3D fast reconstruction in positron emission tomography; Reconstrucao 3D rapida em tomografia por emissao de positrons

    Energy Technology Data Exchange (ETDEWEB)

    Egger, M.L. [Sao Paulo Univ., SP (Brazil). Instituto do Coracao. Div. de Informatica; Scheurer, A. Hermann; Joseph, C. [Lausanne Univ. (Switzerland). Inst. de Physique Nucleaire; Morel, C. [Geneva Univ. (Switzerland). Hospital. Div. of Nuclear Medicine

    1996-12-31

    The issue of long reconstruction times in positron emission tomography (PET) has been addressed from several points of view, resulting in an affordable dedicated system capable of handling routine 3D reconstructions in a few minutes per frame : on the hardware side using fast processors and a parallel architecture, and on the software side, using efficient implementation of computationally less intensive algorithms 6 refs., 2 figs., 1 tab.

  6. Three-Dimensional Reconstruction of the S885A Mutant of Human Mitochondrial Lon Protease

    Czech Academy of Sciences Publication Activity Database

    Kereiche, S.; Kováčik, L.; Pevala, V.; Ambro, L.; Bellová, J.; Kutejová, Eva; Raška, I.

    2014-01-01

    Roč. 60, č. 2014 (2014), s. 62-65 ISSN 0015-5632 R&D Projects: GA MŠk(CZ) EE2.3.30.0030; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : transmission electron microscopy * 3D reconstruction * AAA plus protease Subject RIV: CE - Biochemistry Impact factor: 1.000, year: 2014

  7. Clinical Application of Solid Model Based on Trabecular Tibia Bone CT Images Created by 3D Printer

    OpenAIRE

    Cho, Jaemo; Park, Chan-Soo; Kim, Yeoun-Jae; Kim, Kwang Gi

    2015-01-01

    Objectives The aim of this work is to use a 3D solid model to predict the mechanical loads of human bone fracture risk associated with bone disease conditions according to biomechanical engineering parameters. Methods We used special image processing tools for image segmentation and three-dimensional (3D) reconstruction to generate meshes, which are necessary for the production of a solid model with a 3D printer from computed tomography (CT) images of the human tibia's trabecular and cortical...

  8. High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs.

    Science.gov (United States)

    Wan, Xiaohua; Zhang, Fa; Chu, Qi; Liu, Zhiyong

    2012-06-25

    Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs. In this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration. Experimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.

  9. Three dimensional reconstruction by electron microscopy in the life sciences: An introduction for cell and tissue biologists.

    Science.gov (United States)

    Miranda, Kildare; Girard-Dias, Wendell; Attias, Marcia; de Souza, Wanderley; Ramos, Isabela

    2015-01-01

    Early applications of transmission electron microscopy (TEM) in the life sciences have contributed tremendously to our current understanding at the subcellular level. Initially limited to two-dimensional representations of three-dimensional (3D) objects, this approach has revolutionized the fields of cellular and structural biology-being instrumental for determining the fine morpho-functional characterization of most cellular structures. Electron microscopy has progressively evolved towards the development of tools that allow for the 3D characterization of different structures. This was done with the aid of a wide variety of techniques, which have become increasingly diverse and highly sophisticated. We start this review by examining the principles of 3D reconstruction of cells and tissues using classical approaches in TEM, and follow with a discussion of the modern approaches utilizing TEM as well as on new scanning electron microscopy-based techniques. 3D reconstruction techniques from serial sections and (cryo) electron-tomography are examined, and the recent applications of focused ion beam-scanning microscopes and serial-block-face techniques for the 3D reconstruction of large volumes are discussed. Alternative low-cost techniques and more accessible approaches using basic transmission or field emission scanning electron microscopes are also examined. © 2014 Wiley Periodicals, Inc.

  10. Application of two segmentation protocols during the processing of virtual images in rapid prototyping: ex vivo study with human dry mandibles.

    Science.gov (United States)

    Ferraz, Eduardo Gomes; Andrade, Lucio Costa Safira; dos Santos, Aline Rode; Torregrossa, Vinicius Rabelo; Rubira-Bullen, Izabel Regina Fischer; Sarmento, Viviane Almeida

    2013-12-01

    The aim of this study was to evaluate the accuracy of virtual three-dimensional (3D) reconstructions of human dry mandibles, produced from two segmentation protocols ("outline only" and "all-boundary lines"). Twenty virtual three-dimensional (3D) images were built from computed tomography exam (CT) of 10 dry mandibles, in which linear measurements between anatomical landmarks were obtained and compared to an error probability of 5 %. The results showed no statistically significant difference among the dry mandibles and the virtual 3D reconstructions produced from segmentation protocols tested (p = 0,24). During the designing of a virtual 3D reconstruction, both "outline only" and "all-boundary lines" segmentation protocols can be used. Virtual processing of CT images is the most complex stage during the manufacture of the biomodel. Establishing a better protocol during this phase allows the construction of a biomodel with characteristics that are closer to the original anatomical structures. This is essential to ensure a correct preoperative planning and a suitable treatment.

  11. Mitotic spindle asymmetry in rodents and primates:2D versus 3D measurement methodologies

    Directory of Open Access Journals (Sweden)

    Delphine eDelaunay

    2015-02-01

    Full Text Available Recent data have uncovered that spindle size asymmetry (SSA is a key component of asymmetric cell division in the mouse cerebral cortex (Delaunay et al., 2014. In the present study we show that SSA also occurs during cortical progenitor divisions in the ventricular zone of the macaque cerebral cortex, pointing to a conserved mechanism in the mammalian lineage. Because SSA magnitude is smaller in cortical precursors than in invertebrate neuroblasts, the unambiguous demonstration of volume differences between the two half spindles is considered to require 3D reconstruction of the mitotic spindle (Delaunay et al., 2014. Although straightforward, the 3D analysis of SSA is time consuming, which is likely to hinder SSA identification and prevent further explorations of SSA related mechanisms in generating asymmetric cell division. We therefore set out to develop an alternative method for accurately measuring spindle asymmetry. Based on the mathematically demonstrated linear relationship between 2D and 3D analysis, we show that 2D assessment of spindle size in metaphase cells is as accurate and reliable as 3D reconstruction provided a specific procedure is applied. We have examined the experimental accuracy of the two methods by applying them to different sets of in vivo and in vitro biological data, including mouse and primate cortical precursors. Linear regression analysis demonstrates that the results from 2D and 3D reconstructions are equally powerful. We therefore provide a reliable and efficient technique to measure SSA in mammalian cells.

  12. Three-dimensional analysis of the early development of the dentition.

    Science.gov (United States)

    Peterkova, R; Hovorakova, M; Peterka, M; Lesot, H

    2014-06-01

    Tooth development has attracted the attention of researchers since the 19th century. It became obvious even then that morphogenesis could not fully be appreciated from two-dimensional histological sections. Therefore, methods of three-dimensional (3D) reconstructions were employed to visualize the surface morphology of developing structures and to help appreciate the complexity of early tooth morphogenesis. The present review surveys the data provided by computer-aided 3D analyses to update classical knowledge of early odontogenesis in the laboratory mouse and in humans. 3D reconstructions have demonstrated that odontogenesis in the early stages is a complex process which also includes the development of rudimentary odontogenic structures with different fates. Their developmental, evolutionary, and pathological aspects are discussed. The combination of in situ hybridization and 3D reconstruction have demonstrated the temporo-spatial dynamics of the signalling centres that reflect transient existence of rudimentary tooth primordia at loci where teeth were present in ancestors. The rudiments can rescue their suppressed development and revitalize, and then their subsequent autonomous development can give rise to oral pathologies. This shows that tooth-forming potential in mammals can be greater than that observed from their functional dentitions. From this perspective, the mouse rudimentary tooth primordia represent a natural model to test possibilities of tooth regeneration. © 2014 Australian Dental Association.

  13. [Application of dynamic contrast enhancement MRI and post-processing technique for diagnosis of breast cancer].

    Science.gov (United States)

    Peng, Kang-Qiang; Huang, Zi-Lin; Xie, Chuan-Miao; Chen, Lin; Ouyang, Yi; Zheng, Qing-Sheng; Zhang, Yan; He, Hao-Qiang; Wu, Pei-Hong

    2009-05-01

    Magnetic resonance imaging (MRI), an advanced non-invasive technique, is regarded as one of the potential modalities in the diagnosis of breast cancer. This study was to investigate the application of dynamic contrast enhancement MRI and 3D reconstruction images in diagnosing breast tumors. From May 2006 to September 2007, 30 patients with breast diseases were scanned with MRI in Sun Yat-sen University Cancer Center. MR plain scans, dynamic contrast enhancement scans were performed, and 3D reconstruction images were obtained. The normal breast tissue was used as control, and the maximum slope ratio was calculated. Forty-nine lesions were found in 30 patients, with an accuracy rate of 93.3%. MRI scan is an effective and specific modality for the diagnosis of breast diseases with high sensitivity and accuracy. Dynamic contrast enhancement MRI, image subtraction, time-signal intensity curve, 3D reconstruction images and the maximum slope ratio are helpful to make the correct diagnosis of breast lesions.

  14. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    Science.gov (United States)

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  15. Reconstruction Accuracy Assessment of Surface and Underwater 3D Motion Analysis: A New Approach

    Directory of Open Access Journals (Sweden)

    Kelly de Jesus

    2015-01-01

    Full Text Available This study assessed accuracy of surface and underwater 3D reconstruction of a calibration volume with and without homography. A calibration volume (6000 × 2000 × 2500 mm with 236 markers (64 above and 88 underwater control points—with 8 common points at water surface—and 92 validation points was positioned on a 25 m swimming pool and recorded with two surface and four underwater cameras. Planar homography estimation for each calibration plane was computed to perform image rectification. Direct linear transformation algorithm for 3D reconstruction was applied, using 1600000 different combinations of 32 and 44 points out of the 64 and 88 control points for surface and underwater markers (resp.. Root Mean Square (RMS error with homography of control and validations points was lower than without it for surface and underwater cameras (P≤0.03. With homography, RMS errors of control and validation points were similar between surface and underwater cameras (P≥0.47. Without homography, RMS error of control points was greater for underwater than surface cameras (P≤0.04 and the opposite was observed for validation points (P≤0.04. It is recommended that future studies using 3D reconstruction should include homography to improve swimming movement analysis accuracy.

  16. Computerized tomography with 3-dimensional reconstruction for the evaluation of renal size and arterial anatomy in the living kidney donor.

    Science.gov (United States)

    Janoff, Daniel M; Davol, Patrick; Hazzard, James; Lemmers, Michael J; Paduch, Darius A; Barry, John M

    2004-01-01

    Computerized tomography (CT) with 3-dimensional (3-D) reconstruction has gained acceptance as an imaging study to evaluate living renal donors. We report our experience with this technique in 199 consecutive patients to validate its predictions of arterial anatomy and kidney volumes. Between January 1997 and March 2002, 199 living donor nephrectomies were performed at our institution using an open technique. During the operation arterial anatomy was recorded as well as kidney weight in 98 patients and displacement volume in 27. Each donor had been evaluated preoperatively by CT angiography with 3-D reconstruction. Arterial anatomy described by a staff radiologist was compared with intraoperative findings. CT estimated volumes were reported. Linear correlation graphs were generated to assess the reliability of CT volume predictions. The accuracy of CT angiography for predicting arterial anatomy was 90.5%. However, as the number of renal arteries increased, predictive accuracy decreased. The ability of CT to predict multiple arteries remained high with a positive predictive value of 95.2%. Calculated CT volume and kidney weight significantly correlated (0.654). However, the coefficient of variation index (how much average CT volume differed from measured intraoperative volume) was 17.8%. CT angiography with 3-D reconstruction accurately predicts arterial vasculature in more than 90% of patients and it can be used to compare renal volumes. However, accuracy decreases with multiple renal arteries and volume comparisons may be inaccurate when the difference in kidney volumes is within 17.8%.

  17. Pediatric craniofacial surgery: comparison of milling and stereolithography for 3D model manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Klein, H.M.; Schneider, W.; Alzen, G.; Guenther, R.W. (Univ. of Technology Medical Center, Aachen (Germany). Dept. of Diagnostic Radiology); Voy, E.D. (Evangelisches Krankenhaus, Hattingen (Germany). Dept. of Maxillofacial and Plastic Surgery)

    1992-10-01

    To improve the planning for pediatric craniofacial surger, 3D reconstructions of CT image series were performed on a personal computer. For construction of true models of the surgical site, two concepts were pursued. CT image data of six patients were used for model manufacturing by a conventional 2 1/2 axis milling system. The material used was polyurethane foam. Alternatively, in one patient a stereolithography was produced on the basis of the 3D reconstructed CT data. This new manufacturing device uses a photocurable monomer, hardened by a UV-laser. The spatial resolution of the system is about 0.1 mm. 3D-reconstructions were performed on a personal computer. Data were then transferred into a surface oriented structure to control a stereolithographic modeling device. Time for transfer was 70 min. The production of the modelled cranium took a total time of 59 h. Accuracy was found to be much higher in sterolithography than in milled models. The model served for surgical planning. The long time for production was caused by inadequate computer capacities, which are configured for much less complex objects in computer aided design. Furthermore the programs for the machine control are optimized for technical purposes. If theses conditions are improved, stereolithography could be an attractive alternative to milling of medical models. (orig.).

  18. Markerless motion capture can provide reliable 3D gait kinematics in the sagittal and frontal plane.

    Science.gov (United States)

    Sandau, Martin; Koblauch, Henrik; Moeslund, Thomas B; Aanæs, Henrik; Alkjær, Tine; Simonsen, Erik B

    2014-09-01

    Estimating 3D joint rotations in the lower extremities accurately and reliably remains unresolved in markerless motion capture, despite extensive studies in the past decades. The main problems have been ascribed to the limited accuracy of the 3D reconstructions. Accordingly, the purpose of the present study was to develop a new approach based on highly detailed 3D reconstructions in combination with a translational and rotational unconstrained articulated model. The highly detailed 3D reconstructions were synthesized from an eight camera setup using a stereo vision approach. The subject specific articulated model was generated with three rotational and three translational degrees of freedom for each limb segment and without any constraints to the range of motion. This approach was tested on 3D gait analysis and compared to a marker based method. The experiment included ten healthy subjects in whom hip, knee and ankle joint were analysed. Flexion/extension angles as well as hip abduction/adduction closely resembled those obtained from the marker based system. However, the internal/external rotations, knee abduction/adduction and ankle inversion/eversion were less reliable. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

  19. Calibration of a dedicated software for 3D rendering

    Energy Technology Data Exchange (ETDEWEB)

    Abrantes, Marcos E.S.; Felix, Warley F.; Veloso, Maria Auxiliadora F., E-mail: marcos.nuclear@yahoo.com.br, E-mail: warleyferreirafelix@gmail.com, E-mail: mdora@nuclear.ufmg.br [Faculdade Ciencias Medicas de Minas Gerais (FCMMG), Belo Horizonte, MG (Brazil); Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Nuclear

    2017-11-01

    With the increasing use of 3D reconstruction techniques, to assist in diagnosis, dedicated programs are being widely used. For this they must be calibrated in order to encounter the values of the real volumes of the human tissues. The purpose of this work is to indicate correction and calibration values for true volumes, read in a 3D reconstruction system dedicated, using DICOM images of Computed Tomography. This work utilized a PMMA thorax phantom associated with the DICOM image and the volume found by a program of a tomograph. The physical volume of the PMMA phantom found was 10359.0 cm³. For the volumes found according to the structures of interest, the values are 11005.5 cm³, 10249.3 cm³ and 10205.1 cm³ and the correction values are -6.2%, +1.1% e +1.5% respectively for tissues: pulmonary, bony and soft tissues. The procedure performed can be used for calibration in other 3D reconstruction programs, observing the necessary corrections and the methodology used. (author)

  20. 3D shape reconstruction from relief calculation: application to human body

    Directory of Open Access Journals (Sweden)

    Valle V.

    2010-06-01

    Full Text Available In experimental mechanics especially in experimental biomechanics, evaluating a volume object is a major research axe. In mechanics, 3D reconstruction is made from different optical methods like stereovision [1] or structured light methods. In biomechanics, it is achieved from tomography techniques or from models which divide human body into 15, 16 and 17 polyarticulated solids [2][3]. Those solids are simple volumes (cylinders, spheres. In this review, a method of 3D reconstruction from two calculated relief is proposed. Then, the geometric parameters are extracted using an algorithm and compared to the real dimension of various objects. The first test consist in studying the feasibility of the 3D reconstruction using a real upper arm and a mannequin. In a second test an analysis of a sphere and two cylinders which have different dimensions is performed. The aim of those last tests is to evaluate the performances of the proposed method, to show distortion volume problems and to propose solutions.

  1. Three-Dimensional Reconstruction of Oral Tongue Squamous Cell Carcinoma at Invasion Front

    Directory of Open Access Journals (Sweden)

    Tomoo Kudo

    2013-01-01

    Full Text Available We conducted three-dimensional (3D reconstruction of oral tongue squamous cell carcinoma (OTSCC using serial histological sections to visualize the architecture of invasive tumors. Fourteen OTSCC cases were collected from archival paraffin-embedded specimens. Based on a pathodiagnostic survey of whole cancer lesions, a core tissue specimen (3 mm in diameter was dissected out from the deep invasion front using a paraffin tissue microarray. Serial sections (4 μm thick were double immunostained with pan-cytokeratin and Ki67 antibodies and digitized images were acquired using virtual microscopy. For 3D reconstruction, image registration and RGB color segmentation were automated using ImageJ software to avoid operator-dependent subjective errors. Based on the 3D tumor architecture, we classified the mode of invasion into four types: pushing and bulky architecture; trabecular architecture; diffuse spreading; and special forms. Direct visualization and quantitative assessment of the parenchymal-stromal border provide a new dimension in our understanding of OTSCC architecture. These 3D morphometric analyses also ascertained that cell invasion (individually and collectively occurs at the deep invasive front of the OTSCC. These results demonstrate the advantages of histology-based 3D reconstruction for evaluating tumor architecture and its potential for a wide range of applications.

  2. Three-dimensional reconstruction of oral tongue squamous cell carcinoma at invasion front.

    Science.gov (United States)

    Kudo, Tomoo; Shimazu, Yoshihito; Yagishita, Hisao; Izumo, Toshiyuki; Soeno, Yuuichi; Sato, Kaori; Taya, Yuji; Aoba, Takaaki

    2013-01-01

    We conducted three-dimensional (3D) reconstruction of oral tongue squamous cell carcinoma (OTSCC) using serial histological sections to visualize the architecture of invasive tumors. Fourteen OTSCC cases were collected from archival paraffin-embedded specimens. Based on a pathodiagnostic survey of whole cancer lesions, a core tissue specimen (3 mm in diameter) was dissected out from the deep invasion front using a paraffin tissue microarray. Serial sections (4  μ m thick) were double immunostained with pan-cytokeratin and Ki67 antibodies and digitized images were acquired using virtual microscopy. For 3D reconstruction, image registration and RGB color segmentation were automated using ImageJ software to avoid operator-dependent subjective errors. Based on the 3D tumor architecture, we classified the mode of invasion into four types: pushing and bulky architecture; trabecular architecture; diffuse spreading; and special forms. Direct visualization and quantitative assessment of the parenchymal-stromal border provide a new dimension in our understanding of OTSCC architecture. These 3D morphometric analyses also ascertained that cell invasion (individually and collectively) occurs at the deep invasive front of the OTSCC. These results demonstrate the advantages of histology-based 3D reconstruction for evaluating tumor architecture and its potential for a wide range of applications.

  3. Estimation of pretraumatic femoral antetorsion in bilateral femoral shaft fractures

    Energy Technology Data Exchange (ETDEWEB)

    Citak, Musa; Jagodzinski, Michael; Krettek, Christian; Huefner, Tobias [Hannover Medical School, Trauma Department, Hannover (Germany); Citak, Mustafa [BG-University Hospital Bergmannsheil, Department of Surgery, Bochum (Germany); Kendoff, Daniel; O' Loughlin, Padhraig F. [Hospital for Special Surgery, Orthopaedic Department, New York, NY (United States); Tavassol, Frank [Hannover Medical School, Department of Oral and Maxillofacial Surgery, Hannover (Germany)

    2009-12-15

    To describe a system for measurement of the pretraumatic femoral antetorsion angle post-bilateral femoral shaft fracture with the use of new imaging software which allows segmentation and three dimensional (3D) reconstruction of DICOM (digital imaging and communications in medicine) images. This case involved a 20-year-old patient with bilateral femoral shaft fractures. Following initial clinical examination, CT scans of both femurs were performed. Subsequently, the DICOM datasets were uploaded to the new software tool. Following segmentation and 3D reconstruction, pretraumatic femoral antetorsion angles were determined. Femoral antetorsion was described and assessed in two ways by referring to the intersection of the posterior condylar plane and (1) a line drawn between the center of the femoral head and femoral neck, (2) a line drawn between the centers of the femoral head and greater trochanter. Using these definitions, values for femoral antetorsion were found to be, respectively, 20 at the right fracture site and 19 on the left site, and 33 bilaterally. The investigators describe in this current technical report the use of new imaging software which enables the calculation of femoral AV following reduction of virtual fracture fragments which are created from standard DICOM images. We believe that this 3D reconstruction method of measuring the antetorsion angle can be integrated into a regular treatment algorithm and may potentially optimize clinical outcomes. (orig.)

  4. Positron Emission Tomography with Three-Dimensional Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Erlandsson, K.

    1996-10-01

    The development of two different low-cost scanners for positron emission tomography (PET) based on 3D acquisition are presented. The first scanner consists of two rotating scintillation cameras, and produces quantitative images, which have shown to be clinically useful. The second one is a system with two opposed sets of detectors, based on the limited angle tomography principle, dedicated for mammographic studies. The development of low-cost PET scanners can increase the clinical impact of PET, which is an expensive modality, only available at a few centres world-wide and mainly used as a research tool. A 3D reconstruction method was developed that utilizes all the available data. The size of the data-sets is considerably reduced, using the single-slice rebinning approximation. The 3D reconstruction is divided into 1D axial deconvolution and 2D transaxial reconstruction, which makes it relatively fast. This method was developed for the rotating scanner, but was also implemented for multi-ring scanners with and without inter plane septa. An iterative 3D reconstruction method was developed for the limited angle scanner, based on the new concept of `mobile pixels`, which reduces the finite pixel errors and leads to an improved signal to noise ratio. 100 refs.

  5. THREE-DIMENSIONAL BUILDING RECONSTRUCTION USING IMAGES OBTAINED BY UNMANNED AERIAL VEHICLES

    Directory of Open Access Journals (Sweden)

    C. Wefelscheid

    2012-09-01

    Full Text Available Unmanned Aerial Vehicles (UAVs offer several new possibilities in a wide range of applications. One example is the 3D reconstruction of buildings. In former times this was either restricted by earthbound vehicles to the reconstruction of facades or by air-borne sensors to generate only very coarse building models. This paper describes an approach for fully automatic image-based 3D reconstruction of buildings using UAVs. UAVs are able to observe the whole 3D scene and to capture images of the object of interest from completely different perspectives. The platform used by this work is a Falcon 8 octocopter from Ascending Technologies. A slightly modified high-resolution consumer camera serves as sensor for data acquisition. The final 3D reconstruction is computed offline after image acquisition and follows a reconstruction process originally developed for image sequences obtained by earthbound vehicles. The per- formance of the described method is evaluated on benchmark datasets showing that the achieved accuracy is high and even comparable with Light Detection and Ranging (LIDAR. Additionally, the results of the application of the complete processing-chain starting at image acquisition and ending in a dense surface-mesh are presented and discussed.

  6. Three-dimensional analysis of the early development of the dentition

    Science.gov (United States)

    Peterkova, R; Hovorakova, M; Peterka, M; Lesot, H

    2014-01-01

    Tooth development has attracted the attention of researchers since the 19th century. It became obvious even then that morphogenesis could not fully be appreciated from two-dimensional histological sections. Therefore, methods of three-dimensional (3D) reconstructions were employed to visualize the surface morphology of developing structures and to help appreciate the complexity of early tooth morphogenesis. The present review surveys the data provided by computer-aided 3D analyses to update classical knowledge of early odontogenesis in the laboratory mouse and in humans. 3D reconstructions have demonstrated that odontogenesis in the early stages is a complex process which also includes the development of rudimentary odontogenic structures with different fates. Their developmental, evolutionary, and pathological aspects are discussed. The combination of in situ hybridization and 3D reconstruction have demonstrated the temporo-spatial dynamics of the signalling centres that reflect transient existence of rudimentary tooth primordia at loci where teeth were present in ancestors. The rudiments can rescue their suppressed development and revitalize, and then their subsequent autonomous development can give rise to oral pathologies. This shows that tooth-forming potential in mammals can be greater than that observed from their functional dentitions. From this perspective, the mouse rudimentary tooth primordia represent a natural model to test possibilities of tooth regeneration. PMID:24495023

  7. Nerves of Steel: a Low-Cost Method for 3D Printing the Cranial Nerves.

    Science.gov (United States)

    Javan, Ramin; Davidson, Duncan; Javan, Afshin

    2017-02-21

    Steady-state free precession (SSFP) magnetic resonance imaging (MRI) can demonstrate details down to the cranial nerve (CN) level. High-resolution three-dimensional (3D) visualization can now quickly be performed at the workstation. However, we are still limited by visualization on flat screens. The emerging technologies in rapid prototyping or 3D printing overcome this limitation. It comprises a variety of automated manufacturing techniques, which use virtual 3D data sets to fabricate solid forms in a layer-by-layer technique. The complex neuroanatomy of the CNs may be better understood and depicted by the use of highly customizable advanced 3D printed models. In this technical note, after manually perfecting the segmentation of each CN and brain stem on each SSFP-MRI image, initial 3D reconstruction was performed. The bony skull base was also reconstructed from computed tomography (CT) data. Autodesk 3D Studio Max, available through freeware student/educator license, was used to three-dimensionally trace the 3D reconstructed CNs in order to create smooth graphically designed CNs and to assure proper fitting of the CNs into their respective neural foramina and fissures. This model was then 3D printed with polyamide through a commercial online service. Two different methods are discussed for the key segmentation and 3D reconstruction steps, by either using professional commercial software, i.e., Materialise Mimics, or utilizing a combination of the widely available software Adobe Photoshop, as well as a freeware software, OsiriX Lite.

  8. Comparison between Simple Radiographic and Computed Tomographic Three-Dimensional Reconstruction for Evaluation of the Distal Metatarsal Articular Angle.

    Science.gov (United States)

    Cruz, Eduardo Pedrini; Wagner, Felipe Victora; Henning, Carlo; Sanhudo, José Antônio Veiga; Pagnussato, Fernando; Galia, Carlos Roberto

    The hallux valgus is a pathologic condition in the forefoot that often causes pain and functional limitations. Assessing all deformity components, such as the distal metatarsal articular angle (DMAA) is essential to hallux valgus treatment. Nevertheless, interobserver agreement of DMAA is poor on plain radiographs. The present study compared computed tomographic (CT) 3-dimensional (3D) reconstruction with plain radiographic measurements for measuring the DMAA. We included 43 consecutive patients (77 feet), diagnosed with hallux valgus at the orthopedic outpatient clinic at Hospital de Clínicas de Porto Alegre (Porto Alegre, Brazil) from April 2014 to June 2015 in our prospective study. The DMAAs were measured by 2 observers using CT 3D reconstruction. The results were compared between observers and with the plain radiographic measurements using the concordance correlation coefficient and the Bland-Altman plot to determine the agreement between the 2 methods. The interobserver agreement of the CT 3D measurements was high (concordance correlation coefficient 0.90; p DMAA values were associated with the presence of metatarsal rotation. The interobserver agreement of DMAA measurements was greater on CT 3D reconstruction than on plain radiography. The poor interobserver agreement of the radiographic DMAA might have resulted from metatarsal rotation. Copyright © 2017 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  9. Three-dimensional visualization and quantification for the growth and invasion of oral squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Yoshihito Shimazu

    2010-02-01

    Full Text Available Recent advance in three-dimensional (3D imaging technology allows us to inspect visually and quantitatively the architecture of complex biological tissues and pathological lesions. We initiated histology-based 3D reconstruction of oral squamous cell carcinoma (SCC in order to collect quantitative information of diagnostic value regarding cancer invasion and prognosis. The basic procedures for 3D reconstruction are: preparation of serial histological sections in combination with immunostaining of cell/tissue constituents of interest, alignment and superposition of digitized images, computer-assisted color segmentation of labeled targets, and finally viewing and morphometric analysis of the reconstruct. Our past experience showed that cytokeratin-positive tumor parenchyma can be segmented readily from the surrounding stroma with the aid of Image-J and RATOC TRI-SRF2 software. Cytoplasm/nucleus segmentation of individual SCC cells was also feasible at higher magnifications, leading to quantitative analysis of several histological parameters in tissue space, e.g., parenchyma and stroma volume, nuclear numbers and nuclear/cytoplasm volume ratio, as well as proliferation activity of cancer cells by counting separately the number of Ki-67 positive and negative nuclei in the parenchyma. The results support the wide potential usage and advantage of histology-based 3D reconstruction in cancer biology understanding and pathological diagnosis.

  10. High-quality three-dimensional reconstruction and noise reduction of multifocal images from oversized samples

    Science.gov (United States)

    Martišek, Dalibor; Procházková, Jana; Ficker, Tomáš

    2015-09-01

    Three-dimensional (3-D) reconstruction is an indispensable tool in areas such as biology, chemistry, medicine, material sciences, etc. The sample can be reconstructed using confocal or nonconfocal mode of a microscope. The limitation of the confocal approach is the sample size. Currently used devices work mostly with sample surface area up to 1 cm2. We suggest a three-step method that creates 3-D reconstruction from multifocal images in nonconfocal mode that is qualitatively comparable to the confocal results. Our method, thus, takes advantage of both microscope modes-high-quality results without sample size limitation. The preprocessing step eliminates the additive noise with Linderberg-Lévi theorem. The main focus criterion is based on adjusted Fourier transform. In the final step, we eliminate the defective clusters using the adaptive pixel neighborhood algorithm. We proved the effectiveness of our noise reduction and 3-D reconstruction method by the statistical comparisons; the correlation coefficients average 0.987 for all types of Fourier transforms.

  11. Three dimensional reconstruction of the pancreas based on the virtual Chinese human—female number 1

    Science.gov (United States)

    Zhou, Z M; Fang, C H; Huang, L W; Zhong, S Z; Wang, B L; Zhou, W Y

    2006-01-01

    Objective To study the three dimensional (3D) reconstruction and 3D visualisation of the pancreas and create anatomy of the digitalised visual pancreas so as to construct a concrete basis for virtual operation and surgical operation on pancreas. Methods The digital imaging data of pancreas, duodenum, common bile duct, arteries, and veins were obtained from the virtual Chinese human—female 1 (VCH‐F1). The image data were investigated and 380 images ascertained of pancreas picked up from images numbers 2617 to 2996. Finally, the images from number 2574 to 3017 were adopted to segment and processed using ACDSee and Photoshop so as to reconstruct 3D pancreas digitally. The data of pancreatic surfaces were transformed into Visualization Toolkit (VTK). The GUI program written with VC+ was used to display this VTK file and realise 3D visualisation of the pancreas. Results 3D reconstruction and visualisation of the pancreas and the peri‐pancreatic structures (the duodenum, the common bile duct,the inferior vena cava, the portal vein vessels, the aorta, the coeliac trunk vessels) was successful. The 3D and visualised pancreas manifested itself with its complete structure as well as its adjacency to other tissues. Conclusion The 3D reconstruction and 3D visualisation of the pancreas based on the digital data of VCH‐F1 produces a digitally visualised pancreas, which promises a novel method for virtual operation on the pancreas, clinical operation on the pancreas, and anatomy of 3D visualised pancreas. PMID:16754708

  12. Analysis of acetabular orientation and femoral anteversion using images of three-dimensional reconstructed bone models.

    Science.gov (United States)

    Park, Jaeyeong; Kim, Jun-Young; Kim, Hyun Deok; Kim, Young Cheol; Seo, Anna; Je, Minkyu; Mun, Jong Uk; Kim, Bia; Park, Il Hyung; Kim, Shin-Yoon

    2017-05-01

    Radiographic measurements using two-dimensional (2D) plain radiographs or planes from computed tomography (CT) scans have several drawbacks, while measurements using images of three-dimensional (3D) reconstructed bone models can provide more consistent anthropometric information. We compared the consistency of results using measurements based on images of 3D reconstructed bone models (3D measurements) with those using planes from CT scans (measurements using 2D slice images). Ninety-six of 561 patients who had undergone deep vein thrombosis-CT between January 2013 and November 2014 were randomly selected. We evaluated measurements using 2D slice images and 3D measurements. The images used for 3D reconstruction of bone models were obtained and measured using [Formula: see text] and [Formula: see text] (Materialize, Leuven, Belgium). The mean acetabular inclination, acetabular anteversion and femoral anteversion values on 2D slice images were 42.01[Formula: see text], 18.64[Formula: see text] and 14.44[Formula: see text], respectively, while those using images of 3D reconstructed bone models were 52.80[Formula: see text], 14.98[Formula: see text] and 17.26[Formula: see text]. Intra-rater reliabilities for acetabular inclination, acetabular anteversion, and femoral anteversion on 2D slice images were 0.55, 0.81, and 0.85, respectively, while those for 3D measurements were 0.98, 0.99, and 0.98. Inter-rater reliabilities for acetabular inclination, acetabular anteversion and femoral anteversion on 2D slice images were 0.48, 0.86, and 0.84, respectively, while those for 3D measurements were 0.97, 0.99, and 0.97. The differences between the two measurements are explained by the use of different tools. However, more consistent measurements were possible using the images of 3D reconstructed bone models. Therefore, 3D measurement can be a good alternative to measurement using 2D slice images.

  13. A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes

    Directory of Open Access Journals (Sweden)

    Agurto Carla

    2011-01-01

    Full Text Available Abstract Background A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes. Methods We present a low-cost and flexible ultrasound imaging system that integrates several image processing components to allow for 3D reconstructions from limited numbers of 2D image planes and multiple acoustic views. Our approach is based on a 3D freehand ultrasound system that allows users to control the 2D acquisition imaging using conventional 2D probes. For reliable performance, we develop new methods for image segmentation and robust multi-view registration. We first present a new hybrid geometric level-set approach that provides reliable segmentation performance with relatively simple initializations and minimum edge leakage. Optimization of the segmentation model parameters and its effect on performance is carefully discussed. Second, using the segmented images, a new coarse to fine automatic multi-view registration method is introduced. The approach uses a 3D Hotelling transform to initialize an optimization search. Then, the fine scale feature-based registration is performed using a robust, non-linear least squares algorithm. The robustness of the multi-view registration system allows for accurate 3D reconstructions from sparse 2D image planes. Results Volume measurements from multi-view 3D reconstructions are found to be consistently and significantly more accurate than measurements from single view reconstructions. The volume error of multi-view reconstruction is measured to be less than 5% of the true volume. We show that volume reconstruction accuracy is a function of the total number of 2D image planes and the number of views for calibrated phantom. In clinical in-vivo cardiac experiments, we show that volume estimates of the left ventricle from multi-view reconstructions

  14. Mitigating the Effects of Atmospheric Turbulence: Towards More Useful Micro Air Vehicles

    Science.gov (United States)

    2010-07-18

    pressures and forces on aerofoils in order to examine the possibility of “feeling” through turbulent air and to also understanding the influence on...10 Adjunct Experiments 11 Dynamic Pressure Measurements on Thin Aerofoils 11 Low Cost Video Tracking Investigation 17 Dynamic...investigating the influence of large scale (> 1m) turbulence of the performance of Low Reynolds number thin aerofoils . Interim results are given

  15. Enhancing data from commercial space flights (Conference Presentation)

    Science.gov (United States)

    Sherman, Ariel; Paolini, Aaron; Kozacik, Stephen; Kelmelis, Eric J.

    2017-05-01

    Video tracking of rocket launches inherently must be done from long range. Due to the high temperatures produced, cameras are often placed far from launch sites and their distance to the rocket increases as it is tracked through the flight. Consequently, the imagery collected is generally severely degraded by atmospheric turbulence. In this talk, we present our experience in enhancing commercial space flight videos. We will present the mission objectives, the unique challenges faced, and the solutions to overcome them.

  16. Long-range eye tracking: A feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Jayaweera, S.K.; Lu, Shin-yee

    1994-08-24

    The design considerations for a long-range Purkinje effects based video tracking system using current technology is presented. Past work, current experiments, and future directions are thoroughly discussed, with an emphasis on digital signal processing techniques and obstacles. It has been determined that while a robust, efficient, long-range, and non-invasive eye tracking system will be difficult to develop, such as a project is indeed feasible.

  17. Digital Video Stabilization with Inertial Fusion

    OpenAIRE

    Freeman, William John

    2013-01-01

    As computing power becomes more and more available, robotic systems are moving away from active sensors for environmental awareness and transitioning into passive vision sensors.  With the advent of teleoperation and real-time video tracking of dynamic environments, the need to stabilize video onboard mobile robots has become more prevalent. This thesis presents a digital stabilization method that incorporates inertial fusion with a Kalman filter.  The camera motion is derived visually by tra...

  18. Performance Evaluation of Random Set Based Pedestrian Tracking Algorithms

    OpenAIRE

    Ristic, Branko; Sherrah, Jamie; García-Fernández, Ángel F.

    2012-01-01

    The paper evaluates the error performance of three random finite set based multi-object trackers in the context of pedestrian video tracking. The evaluation is carried out using a publicly available video dataset of 4500 frames (town centre street) for which the ground truth is available. The input to all pedestrian tracking algorithms is an identical set of head and body detections, obtained using the Histogram of Oriented Gradients (HOG) detector. The tracking error is measured using the re...

  19. Register indicators of physical endurance of biological objects when running a treadmill and swimming with weights using computer video markerless tracking

    Directory of Open Access Journals (Sweden)

    Datsenko A.V.

    2014-12-01

    Full Text Available Purpose: to study the use of video tracking to assess physical endurance and indicators of biological objects fatigue when running on a treadmill and swimming with the load. Material and methods. Physical endurance evaluated by test facilities for running on a treadmill and swimming with the load. As the object of the studies used laboratory rats. Results. For indicators of physical endurance biological objects isolated areas running track of treadmill and electrical stimulation site, when swimming on the total area of the container isolated subarea near the water surface. With video tracking performed computer timing of finding biological object in different zones of the treadmill and containers for swimming. On the basis of data on the time location rats in a given zone apparatus for running and swimming, obtained in the dynamics of the test of physical endurance, build a "fatigue curves", quantified changes in the indices of hard work, depending on the duration of its execution. Conclusion. Video tracking allows to define the execution of physical work to overflowing with loads of aerobic and mixed aerobic-anaerobic power, establish quantitative indicators of changes in the dynamics of biological objects operability testing with the construction of "fatigue curve" and objectively determine the times of occurrence in experimental animals exhaustion when fails to perform physical work.

  20. Surgery of the eloquent area using neuronavigation system

    Energy Technology Data Exchange (ETDEWEB)

    Nakai, Hirofumi; Tanaka, Tatsuya; Hashizume, Kiyotaka; Hodozuka, Akira; Ono, Hidetoshi; Goto, Takumi; Aburano, Tamio [Asahikawa Medical Coll., Hokkaido (Japan)

    2001-03-01

    The purpose of this minimally invasive study was to evaluate the efficacy of a neuronavigation system for surgery of lesions near Broca's area, skull base, or paracentral sulcus. With regards to paracentral sulcus lesions, precise localization of the precentral gyrus was evaluated not only with preoperative 3D images of the brain but also confirmed by the combination of fMRI and intraoperative SEP. Using the neuronavigation system, Viewing Wand (ISG Technologies), three-dimensional (3D) brain images were reconstructed by plotting cerebral sulcus and skull representations obtained by MRI and CT. Six patients with lesions near Broca's area, 5 patients with skull base lesions, and 9 patients with lesions near the central sulcus were analyzed. For paracentral sulcus lesions, patients underwent blood oxygen level-dependent fMRI while performing a finger-tapping motor paradigm, which was composed of repetition of rest-task every in 30 seconds for 150 seconds, in a 1.5-tesla echo-speed MR imager (Signa Horizon; General Electric Medical Systems, Milwaukee, WI). Statistical cross-correlation functional maps were generated and overlaid onto high-resolution anatomical MR images. Presurgical assessment of 3D reconstructed brain images were performed in all cases. They were analyzed in Broca's lesions, skull base lesions and paracentral sulcus lesions and were demonstrated to be useful for understanding the anatomical relationship between the lesions and the surrounding vital structures. In fMRI, motor activation sites were obtained on both ipsilateral and contralateral hemispheres in all patients except for one patient with a hemorrhagic cyst. Locations of precentral gyri were predicted preoperatively. In all patients except for one case, fMRI was obtained even in tumor patient in whom intraoperative SEP was technically not feasible due to severe cortical brain damage from the paracentral tumor. The precentral gyri identified by 3D reconstructed brain images

  1. 3D Equilibrium Reconstructions in DIII-D

    Science.gov (United States)

    Lao, L. L.; Ferraro, N. W.; Strait, E. J.; Turnbull, A. D.; King, J. D.; Hirshman, H. P.; Lazarus, E. A.; Sontag, A. C.; Hanson, J.; Trevisan, G.

    2013-10-01

    Accurate and efficient 3D equilibrium reconstruction is needed in tokamaks for study of 3D magnetic field effects on experimentally reconstructed equilibrium and for analysis of MHD stability experiments with externally imposed magnetic perturbations. A large number of new magnetic probes have been recently installed in DIII-D to improve 3D equilibrium measurements and to facilitate 3D reconstructions. The V3FIT code has been in use in DIII-D to support 3D reconstruction and the new magnetic diagnostic design. V3FIT is based on the 3D equilibrium code VMEC that assumes nested magnetic surfaces. V3FIT uses a pseudo-Newton least-square algorithm to search for the solution vector. In parallel, the EFIT equilibrium reconstruction code is being extended to allow for 3D effects using a perturbation approach based on an expansion of the MHD equations. EFIT uses the cylindrical coordinate system and can include the magnetic island and stochastic effects. Algorithms are being developed to allow EFIT to reconstruct 3D perturbed equilibria directly making use of plasma response to 3D perturbations from the GATO, MARS-F, or M3D-C1 MHD codes. DIII-D 3D reconstruction examples using EFIT and V3FIT and the new 3D magnetic data will be presented. Work supported in part by US DOE under DE-FC02-04ER54698, DE-FG02-95ER54309 and DE-AC05-06OR23100.

  2. Improving Visibility of Stereo-Radiographic Spine Reconstruction with Geometric Inferences.

    Science.gov (United States)

    Kumar, Sampath; Nayak, K Prabhakar; Hareesha, K S

    2016-04-01

    Complex deformities of the spine, like scoliosis, are evaluated more precisely using stereo-radiographic 3D reconstruction techniques. Primarily, it uses six stereo-corresponding points available on the vertebral body for the 3D reconstruction of each vertebra. The wireframe structure obtained in this process has poor visualization, hence difficult to diagnose. In this paper, a novel method is proposed to improve the visibility of this wireframe structure using a deformation of a generic spine model in accordance with the 3D-reconstructed corresponding points. Then, the geometric inferences like vertebral orientations are automatically extracted from the radiographs to improve the visibility of the 3D model. Biplanar radiographs are acquired from five scoliotic subjects on a specifically designed calibration bench. The stereo-corresponding point reconstruction method is used to build six-point wireframe vertebral structures and thus the entire spine model. Using the 3D spine midline and automatically extracted vertebral orientation features, a more realistic 3D spine model is generated. To validate the method, the 3D spine model is back-projected on biplanar radiographs and the error difference is computed. Though, this difference is within the error limits available in the literature, the proposed work is simple and economical. The proposed method does not require more corresponding points and image features to improve the visibility of the model. Hence, it reduces the computational complexity. Expensive 3D digitizer and vertebral CT scan models are also excluded from this study. Thus, the visibility of stereo-corresponding point reconstruction is improved to obtain a low-cost spine model for a better diagnosis of spinal deformities.

  3. Three-dimensional Evaluation of Nasal Surgery in Patients with Obstructive Sleep Apnea.

    Science.gov (United States)

    Cui, Dan-Mo; Han, De-Min; Nicolas, Busaba; Hu, Chang-Long; Wu, Jun; Su, Min-Min

    2016-03-20

    Obstructive sleep apnea (OSA) is a common sleep disorder and is characterized by airway collapse at multiple levels of upper airway. The effectiveness of nasal surgery has been discussed in several studies and shows a promising growing interest. In this study, we intended to evaluate the effects of nasal surgery on the upper airway dimensions in patients with OSA using three-dimensional (3D) reconstruction of cone-beam computed tomography (CT). Twelve patients with moderate to severe OSA who underwent nasal surgery were included in this study. All patients were diagnosed with OSA using polysomnography (PSG) in multi sleep health centers associated with Massachusetts General Hospital, Massachusetts Eye and Ear Infirmary and the Partners Health Care from May 31, 2011 to December 14, 2013. The effect of nasal surgery was evaluated by the examination of PSG, subjective complains, and 3D reconstructed CT scan. Cross-sectional area was measured in eleven coronal levels, and nasal cavity volume was evaluated from anterior nasal spine to posterior nasal spine. The thickness of soft tissue in oral pharynx region was also measured. Five out of the 12 patients were successfully treated by nasal surgery, with more than 50% drop of apnea-hypopnea index. All the 12 patients showed significant increase of cross-sectional area and volume postoperatively. The thickness of soft tissue in oral pharynx region revealed significant decrease postoperatively, which decreased from 19.14 ± 2.40 cm 2 and 6.11 ± 1.76 cm 2 to 17.13 ± 1.91 cm 2 and 5.22 ± 1.20 cm 2 . Nasal surgery improved OSA severity as measured by PSG, subjective complaints, and 3D reconstructed CT scan. 3D assessment of upper airway can play an important role in the evaluation of treatment outcome.

  4. The caudal complex of Giardia lamblia and its relation to motility.

    Science.gov (United States)

    Carvalho, Karina Penedo; Monteiro-Leal, Luiz Henrique

    2004-01-01

    This paper presents a detailed study of the caudal complex of Giardia lamblia and its relation to movements observed in this region. The caudal complex of Giardia, composed of axonemes from the caudal flagella plus associated microtubular sheets, was investigated by light, electron microscopy, and 3D reconstruction tools. By the use of video-microscopy and digital image processing techniques, we were able to visualize in detail the caudal movements. A non-ionic detergent, Triton X-100, was used to isolate the complex that was afterwards analyzed by video-microscopy and transmission electron microscopy (TEM). We showed for the first time, using video-microscopy, that the intracellular portion of the caudal flagella axonemes presented motility, even after the disrupture of the cell membrane, contrasting with the caudal flagella themselves, that do not show active beating pattern. To check if actin filaments play a role in the above described movements, as previously supposed, we incubated the cells with jasplakinolide, a drug that induces the disruption of actin filaments in living cells. The experiments demonstrated that the drug did not affect the caudal motility. The analysis of the caudal complex by transmission electron microscopy (TEM) revealed that, even after the exposure to higher detergent concentrations, the connections between their components remained intact. The information obtained by TEM and 3D reconstruction tools showed that the region between both nuclei marks the intracellular end of the caudal complex, which proceeds toward the caudal portion of the cell following its longitudinal axis, where the axonemes emerge as the caudal flagella. The results obtained from video-microscopy assays of the isolated beating complex together with the 3D reconstruction data indicated that the internal portion of the caudal flagella is the force-generator of the movements in this region.

  5. The effect of virtual reality and training on liver operation planning.

    Science.gov (United States)

    Herfarth, C; Lamadé, W; Fischer, L; Chiu, P; Cardenas, C; Thorn, M; Vetter, M; Grenacher, L; Meinzer, H P

    2002-01-01

    The three-dimensional relation of a liver tumour to the intrahepatic vascular trees is basis of operation planning in liver surgery. Yet it has not been proven whether 3D reconstruction and further computerised processing will enhance precision of operation planning in liver surgery which has been based on the liver segment classification of Couinaud up to now. Our interdisciplinary group (department of Surgery, German Cancer Research Center and Department of Radiology) has developed a new interactive computer-based quantitative 3D operation planning system for liver surgery which is being introduced into the clinical routine. The system quantifies the organ structures semiautomatically, defines resection planes depending on safety margins and the vascular trees, and presents the data in digital movies as well as in quantitative reports. We conducted a clinical trial to evaluate whether 3D reconstruction will lead to an improved operation planning. Data of 7 virtual patients were presented to a total of 81 surgeons in different levels of training. The tumours had to be assigned to a liver segment and subsequently drawn together with the operation proposals into a liver model. The precision of both was measured quantitatively for each surgeon and stratified concerning 2D and different types of 3D presentations. The 3D anatomy can be visualised in high quality which results in good perception of the third dimension (depth). Tumour assignment to liver segments was significantly correlated to the level of training (p classification of the liver segments compared to the true vascular anatomy of up to 40% were found. The impact of individual 3D-reconstruction on surgical planning has been proven to be significant and increases precision quantitatively. The merit of Couinaud's classification may be enhanced by individualisation of the segment borders in future.

  6. Single-image-based Modelling Architecture from a Historical Photograph

    Science.gov (United States)

    Dzwierzynska, Jolanta

    2017-10-01

    Historical photographs are proved to be very useful to provide a dimensional and geometrical analysis of buildings as well as to generate 3D reconstruction of the whole structure. The paper addresses the problem of single historical photograph analysis and modelling of an architectural object from it. Especially, it focuses on reconstruction of the original look of New-Town synagogue from the single historic photograph, when camera calibration is completely unknown. Due to the fact that the photograph faithfully followed the geometric rules of perspective, it was possible to develop and apply the method to obtain a correct 3D reconstruction of the building. The modelling process consisted of a series of familiar steps: feature extraction, determination of base elements of perspective, dimensional analyses and 3D reconstruction. Simple formulas were proposed in order to estimate location of characteristic points of the building in 3D Cartesian system of axes on the base of their location in 2D Cartesian system of axes. The reconstruction process proceeded well, although slight corrections were necessary. It was possible to reconstruct the shape of the building in general, and two of its facades in detail. The reconstruction of the other two facades requires some additional information or the additional picture. The success of the presented reconstruction method depends on the geometrical content of the photograph as well as quality of the picture, which ensures the legibility of building edges. The presented method of reconstruction is a combination of the descriptive method of reconstruction and computer aid; therefore, it seems to be universal. It can prove useful for single-image-based modelling architecture.

  7. Self-adapting denoising, alignment and reconstruction in electron tomography in materials science

    Energy Technology Data Exchange (ETDEWEB)

    Printemps, Tony, E-mail: tony.printemps@cea.fr [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Mula, Guido [Dipartimento di Fisica, Università di Cagliari, Cittadella Universitaria, S.P. 8km 0.700, 09042 Monserrato (Italy); Sette, Daniele; Bleuet, Pierre; Delaye, Vincent; Bernier, Nicolas; Grenier, Adeline; Audoit, Guillaume; Gambacorti, Narciso; Hervé, Lionel [Université Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France)

    2016-01-15

    An automatic procedure for electron tomography is presented. This procedure is adapted for specimens that can be fashioned into a needle-shaped sample and has been evaluated on inorganic samples. It consists of self-adapting denoising, automatic and accurate alignment including detection and correction of tilt axis, and 3D reconstruction. We propose the exploitation of a large amount of information of an electron tomography acquisition to achieve robust and automatic mixed Poisson–Gaussian noise parameter estimation and denoising using undecimated wavelet transforms. The alignment is made by mixing three techniques, namely (i) cross-correlations between neighboring projections, (ii) common line algorithm to get a precise shift correction in the direction of the tilt axis and (iii) intermediate reconstructions to precisely determine the tilt axis and shift correction in the direction perpendicular to that axis. Mixing alignment techniques turns out to be very efficient and fast. Significant improvements are highlighted in both simulations and real data reconstructions of porous silicon in high angle annular dark field mode and agglomerated silver nanoparticles in incoherent bright field mode. 3D reconstructions obtained with minimal user-intervention present fewer artefacts and less noise, which permits easier and more reliable segmentation and quantitative analysis. After careful sample preparation and data acquisition, the denoising procedure, alignment and reconstruction can be achieved within an hour for a 3D volume of about a hundred million voxels, which is a step toward a more routine use of electron tomography. - Highlights: • Goal: perform a reliable and user-independent 3D electron tomography reconstruction. • Proposed method: self-adapting denoising and alignment prior to 3D reconstruction. • Noise estimation and denoising are performed using wavelet transform. • Tilt axis determination is done automatically as well as projection alignment.

  8. Determination of a new uniform thorax density representative of the living population from 3D external body shape modeling.

    Science.gov (United States)

    Amabile, Celia; Choisne, Julie; Nérot, Agathe; Pillet, Hélène; Skalli, Wafa

    2016-05-03

    Body segment parameters (BSP) for each body׳s segment are needed for biomechanical analysis. To provide population-specific BSP, precise estimation of body׳s segments volume and density are needed. Widely used uniform densities, provided by cadavers׳ studies, did not consider the air present in the lungs when determining the thorax density. The purpose of this study was to propose a new uniform thorax density representative of the living population from 3D external body shape modeling. Bi-planar X-ray radiographies were acquired on 58 participants allowing 3D reconstructions of the spine, rib cage and human body shape. Three methods of computing the thorax mass were compared for 48 subjects: (1) the Dempster Uniform Density Method, currently in use for BSPs calculation, using Dempster density data, (2) the Personalized Method using full-description of the thorax based on 3D reconstruction of the rib cage and spine and (3) the Improved Uniform Density Method using a uniform thorax density resulting from the Personalized Method. For 10 participants, comparison was made between the body mass obtained from a force-plate and the body mass computed with each of the three methods. The Dempster Uniform Density Method presented a mean error of 4.8% in the total body mass compared to the force-plate vs 0.2% for the Personalized Method and 0.4% for the Improved Uniform Density Method. The adjusted thorax density found from the 3D reconstruction was 0.74g/cm(3) for men and 0.73g/cm(3) for women instead of the one provided by Dempster (0.92g/cm(3)), leading to a better estimate of the thorax mass and body mass. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity.

    Science.gov (United States)

    Tolkach, Yuri; Thomann, Stefan; Kristiansen, Glen

    2018-01-11

    Conventional morphology of prostate cancer considers only the two-dimensional (2D) architecture of the tumour. Our aim was to examine the feasibility of three-dimensional (3D) reconstruction of tumour morphology based on multiple consecutive histological sections and to decipher relevant features of prostate cancer architecture. Seventy-five consecutive histological sections (5 μm) of a typical prostate adenocarcinoma (Gleason score of 3 + 4 = 7) were immunostained (pan-cytokeratin) and scanned for further 3D reconstructions with fiji/imagej software. The main findings related to the prostate cancer architecture in this case were: (i) continuity of all glands, with the tumour being an integrated system, even in Gleason pattern 4 with poorly formed glands-no short-range migration of cells by Gleason pattern 4 (poorly formed glands); (ii) no repeated interconnections between the glands, with a tumour building a tree-like branched structure with very 'plastic' branches (maximal depth of investigation 375 μm); (iii) very stark compartmentalisation of the tumour related to extensive branching, the coexistence of independent terminal units of such branches in one 2D slice explaining intratumoral heterogeneity; (iv) evidence of a craniocaudal growth direction in interglandular regions of the prostate and for a lateromedial growth direction in subcapsular posterolateral regions; and (v) a 3D architecture-based description of Gleason pattern 4 with poorly formed glands, and its continuum with Gleason pattern 3. Consecutive histological sections provide high-quality material for 3D reconstructions of the tumour architecture, with excellent resolution. The reconstruction of multiple regions in this typical case of a Gleason score 3 + 4 = 7 tumour provides insights into relevant aspects of tumour growth, the continuity of Gleason patterns 3 and 4, and tumour heterogeneity. © 2018 John Wiley & Sons Ltd.

  10. A simple, fast, and repeatable survey method for underwater visual 3D benthic mapping and monitoring.

    Science.gov (United States)

    Pizarro, Oscar; Friedman, Ariell; Bryson, Mitch; Williams, Stefan B; Madin, Joshua

    2017-03-01

    Visual 3D reconstruction techniques provide rich ecological and habitat structural information from underwater imagery. However, an unaided swimmer or diver struggles to navigate precisely over larger extents with consistent image overlap needed for visual reconstruction. While underwater robots have demonstrated systematic coverage of areas much larger than the footprint of a single image, access to suitable robotic systems is limited and requires specialized operators. Furthermore, robots are poor at navigating hydrodynamic habitats such as shallow coral reefs. We present a simple approach that constrains the motion of a swimmer using a line unwinding from a fixed central drum. The resulting motion is the involute of a circle, a spiral-like path with constant spacing between revolutions. We test this survey method at a broad range of habitats and hydrodynamic conditions encircling Lizard Island in the Great Barrier Reef, Australia. The approach generates fast, structured, repeatable, and large-extent surveys (~110 m2 in 15 min) that can be performed with two people and are superior to the commonly used "mow the lawn" method. The amount of image overlap is a design parameter, allowing for surveys that can then be reliably used in an automated processing pipeline to generate 3D reconstructions, orthographically projected mosaics, and structural complexity indices. The individual images or full mosaics can also be labeled for benthic diversity and cover estimates. The survey method we present can serve as a standard approach to repeatedly collecting underwater imagery for high-resolution 2D mosaics and 3D reconstructions covering spatial extents much larger than a single image footprint without requiring sophisticated robotic systems or lengthy deployment of visual guides. As such, it opens up cost-effective novel observations to inform studies relating habitat structure to ecological processes and biodiversity at scales and spatial resolutions not readily

  11. Automated UAV-based video exploitation using service oriented architecture framework

    Science.gov (United States)

    Se, Stephen; Nadeau, Christian; Wood, Scott

    2011-05-01

    Airborne surveillance and reconnaissance are essential for successful military missions. Such capabilities are critical for troop protection, situational awareness, mission planning, damage assessment, and others. Unmanned Aerial Vehicles (UAVs) gather huge amounts of video data but it is extremely labour-intensive for operators to analyze hours and hours of received data. At MDA, we have developed a suite of tools that can process the UAV video data automatically, including mosaicking, change detection and 3D reconstruction, which have been integrated within a standard GIS framework. In addition, the mosaicking and 3D reconstruction tools have also been integrated in a Service Oriented Architecture (SOA) framework. The Visualization and Exploitation Workstation (VIEW) integrates 2D and 3D visualization, processing, and analysis capabilities developed for UAV video exploitation. Visualization capabilities are supported through a thick-client Graphical User Interface (GUI), which allows visualization of 2D imagery, video, and 3D models. The GUI interacts with the VIEW server, which provides video mosaicking and 3D reconstruction exploitation services through the SOA framework. The SOA framework allows multiple users to perform video exploitation by running a GUI client on the operator's computer and invoking the video exploitation functionalities residing on the server. This allows the exploitation services to be upgraded easily and allows the intensive video processing to run on powerful workstations. MDA provides UAV services to the Canadian and Australian forces in Afghanistan with the Heron, a Medium Altitude Long Endurance (MALE) UAV system. On-going flight operations service provides important intelligence, surveillance, and reconnaissance information to commanders and front-line soldiers.

  12. Self-calibration of biplanar radiographic images through geometric spine shape descriptors.

    Science.gov (United States)

    Kadoury, Samuel; Cheriet, Farida; Labelle, Hubert

    2010-07-01

    This paper presents a novel self-calibration method of an X-ray scene applied for the 3-D reconstruction of the scoliotic spine. Current calibration techniques either use a cumbersome calibration apparatus or depend on manually identified landmarks to determine the geometric configuration, thus limiting routine clinical evaluation. The proposed approach uses high-level information automatically extracted from biplanar X-rays to solve the radiographic scene parameters. We first present a segmentation method that takes into account the variable appearance and geometry of a scoliotic spine in order to isolate and extract the silhouettes of the anterior vertebral body. By incorporating prior anatomical information through a Bayesian formulation of the morphological distribution, a multiscale spine segmentation framework is proposed for scoliotic patients. An iterative nonlinear optimization procedure, integrating a 3-D visual hull reconstruction and geometrical torsion properties of the spine, is then applied to globally refine the geometrical parameters of the 3-D viewing scene and obtain the optimal 3-D reconstruction. An experimental comparison with data provided from reference synthetic models yields similar accuracy on the retroprojection of low-level primitives such as anatomical landmarks identified on each vertebra (2.2 mm). Results obtained from a clinical validation on 60 pairs of uncalibrated digitized X-rays of adolescents with scoliosis show that the 3-D reconstructions from the new system offer geometrically accurate models with insignificant differences for 3-D clinical indexes commonly used in the evaluation of spinal deformities. The reported experiments demonstrate a viable and accurate alternative to previous reconstruction techniques, offering the first automatic approach for routine 3-D clinical assessment in radiographic suites.

  13. Wavelets filtering for classification of very noisy electron microscopic single particles images- application on structure determination of VP5-VP19C recombinant

    Directory of Open Access Journals (Sweden)

    Saad Ali

    2003-12-01

    Full Text Available Abstract Background Images of frozen hydrated [vitrified] virus particles were taken close-to-focus in an electron microscope containing structural signals at high spatial frequencies. These images had very low contrast due to the high levels of noise present in the image. The low contrast made particle selection, classification and orientation determination very difficult. The final purpose of the classification is to improve the signal-to-noise ratio of the particle representing the class, which is usually the average. In this paper, the proposed method is based on wavelet filtering and multi-resolution processing for the classification and reconstruction of this very noisy data. A multivariate statistical analysis (MSA is used for this classification. Results The MSA classification method is noise dependant. A set of 2600 projections from a 3D map of a herpes simplex virus -to which noise was added- was classified by MSA. The classification shows the power of wavelet filtering in enhancing the quality of class averages (used in 3D reconstruction compared to Fourier band pass filtering. A 3D reconstruction of a recombinant virus (VP5-VP19C is presented as an application of multi-resolution processing for classification and reconstruction. Conclusion The wavelet filtering and multi-resolution processing method proposed in this paper offers a new way for processing very noisy images obtained from electron cryo-microscopes. The multi-resolution and filtering improves the speed and accuracy of classification, which is vital for the 3D reconstruction of biological objects. The VP5-VP19C recombinant virus reconstruction presented here is an example, which demonstrates the power of this method. Without this processing, it is not possible to get the correct 3D map of this virus.

  14. WASS: An open-source pipeline for 3D stereo reconstruction of ocean waves

    Science.gov (United States)

    Bergamasco, Filippo; Torsello, Andrea; Sclavo, Mauro; Barbariol, Francesco; Benetazzo, Alvise

    2017-10-01

    Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community and industry. Indeed, recent advances of both computer vision algorithms and computer processing power now allow the study of the spatio-temporal wave field with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner, so that the implementation of a sea-waves 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well tested software package that automates the reconstruction process from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS (http://www.dais.unive.it/wass), an Open-Source stereo processing pipeline for sea waves 3D reconstruction. Our tool completely automates all the steps required to estimate dense point clouds from stereo images. Namely, it computes the extrinsic parameters of the stereo rig so that no delicate calibration has to be performed on the field. It implements a fast 3D dense stereo reconstruction procedure based on the consolidated OpenCV library and, lastly, it includes set of filtering techniques both on the disparity map and the produced point cloud to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface. In this paper, we describe the architecture of WASS and the internal algorithms involved. The pipeline workflow is shown step-by-step and demonstrated on real datasets acquired at sea.

  15. Measuring stone volume - three-dimensional software reconstruction or an ellipsoid algebra formula?

    Science.gov (United States)

    Finch, William; Johnston, Richard; Shaida, Nadeem; Winterbottom, Andrew; Wiseman, Oliver

    2014-04-01

    To determine the optimal method for assessing stone volume, and thus stone burden, by comparing the accuracy of scalene, oblate, and prolate ellipsoid volume equations with three-dimensional (3D)-reconstructed stone volume. Kidney stone volume may be helpful in predicting treatment outcome for renal stones. While the precise measurement of stone volume by 3D reconstruction can be accomplished using modern computer tomography (CT) scanning software, this technique is not available in all hospitals or with routine acute colic scanning protocols. Therefore, maximum diameters as measured by either X-ray or CT are used in the calculation of stone volume based on a scalene ellipsoid formula, as recommended by the European Association of Urology. In all, 100 stones with both X-ray and CT (1-2-mm slices) were reviewed. Complete and partial staghorn stones were excluded. Stone volume was calculated using software designed to measure tissue density of a certain range within a specified region of interest. Correlation coefficients among all measured outcomes were compared. Stone volumes were analysed to determine the average 'shape' of the stones. The maximum stone diameter on X-ray was 3-25 mm and on CT was 3-36 mm, with a reasonable correlation (r = 0.77). Smaller stones (15 mm towards scalene ellipsoids. There was no difference in stone shape by location within the kidney. As the average shape of renal stones changes with diameter, no single equation for estimating stone volume can be recommended. As the maximum diameter increases, calculated stone volume becomes less accurate, suggesting that larger stones have more asymmetric shapes. We recommend that research looking at stone clearance rates should use 3D-reconstructed stone volumes when available, followed by prolate, oblate, or scalene ellipsoid formulas depending on the maximum stone diameter. © 2013 The Authors. BJU International © 2013 BJU International.

  16. Development of a 3D optical scanner for evaluating patient-specific dose distributions.

    Science.gov (United States)

    Chang, Kyung Hwan; Lee, Suk; Jung, Hong; Choo, Yeon-Wook; Cao, Yuan Jie; Shim, Jang Bo; Kim, Kwang Hyeon; Lee, Nam Kwon; Park, Young Je; Kim, Chul Yong; Cho, Sam Ju; Lee, Sang Hoon; Min, Chul Kee; Kim, Woo Chul; Cho, Kwang Hwan; Huh, Hyun Do; Lim, Sangwook

    2015-07-01

    This paper describes the hardware and software characteristics of a 3D optical scanner (P3DS) developed in-house. The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software. We performed optical simulation, 2D and 3D reconstruction image testing, and pre-clinical testing for the P3DS. We developed the optical scanner with three key characteristics in mind. First, we developed a continuous scanning method to expand possible clinical applications. Second, we manufactured a collimator to improve image quality by reducing scattering from the light source. Third, we developed an optical scanner with changeable camera positioning to enable acquisition of optimal images according to the size of the gel dosimeter. We confirmed ray-tracing in P3DS with optic simulation and found that 2D projection and 3D reconstructed images were qualitatively similar to the phantom images. For pre-clinical tests, the dose distribution and profile showed good agreement among RTP, optical CT, and external beam radiotherapy film data for the axial and coronal views. The P3DS has shown that it can scan and reconstruct for evaluation of the gel dosimeter within 1 min. We confirmed that the P3DS system is a useful tool for the measurement of 3D dose distributions for 3D radiation therapy QA. Further experiments are needed to investigate quantitative analysis for 3D dose distribution. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  17. Lower-limb lengths and angles in children older than six years: Reliability and reference values by EOS®stereoradiography.

    Science.gov (United States)

    Rampal, V; Rohan, P-Y; Assi, A; Ghanem, I; Rosello, O; Simon, A-L; Gaumetou, E; Merzoug, V; Skalli, W; Wicart, P

    2017-11-07

    Lower-limb alignment in children is classically assessed clinically or based on conventional radiography, which is associated with projection bias. Low-dose biplanar radiography was described recently as an alternative to conventional imaging. The primary objective of this study was to assess the reliability of length and angle values inferred from 3D reconstructions in children seen in everyday practice. The secondary objective was to obtain reference values for goniometry parameters in children. 3D reconstructions can be used to assess the lower limbs in children. The paediatric reliability study was done in 18 volunteers who were divided into three groups based on whether they were typically developing (TD) children, had skeletal development abnormalities, or had cerebral palsy. The reference data were obtained in 129 TD children. Each study participant underwent biplanar radiography with 3D reconstruction performed by experts and radiology technicians. Goniometry parameters were computed automatically. Reproducibility was assessed based on the intra-class coefficient (ICC) and the ISO 5725 standard (standard deviation of reproducibility, SDR). For length parameters, the ICCs ranged from 0.94 to 1.00 and the SDR from 2.1 to 3.5mm. For angle parameters, the ICC and SDR ranges were 0.60-0.95 and 0.9°-4.6°, respectively. No significant differences were found across experts or radiology technicians. Age-specific reference data are reported. These findings confirm the reliability of low-dose biplanar radiography for assessing lower-limb parameters in children seen in clinical practice. In addition, the study provides reference data for commonly measured parameters. IV. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  18. Close-range photogrametry and three-dimensional visualization of LeShan Grand Buddha

    Science.gov (United States)

    Zhu, Yixuan; Ning, Xiaogang; Li, Deren; Li, Jingliang

    2003-01-01

    Based on Leshan Grand Buddha"s isoline images gained from conventional close-range photogrammetry work many years ago, a simple digitized method is suggested in this paper for 3D reconstruction of such famous buddhas, which is very important for these buddhas" reparation, research and reproduction. The whole work of 3D Buddha reconstruction includes digitization of buddha"s contour line map, generation of digital buddha model, texture mapping using close-range imagery as well as 3D simulation and animation. The experiment shows that the GIS software package GeoStar can be directly used for 3D generation and visualization of Chinese buddhas.

  19. ENT aspects of the mummification of the head in ancient Egypt: an imaging study.

    Science.gov (United States)

    Motamed, M; Alusi, G; Campos, J; East, C

    1998-01-01

    This study of a mummified head from the British museum by high resolution computer tomography and 3D reconstruction illustrates, without mutilation of the specimen, some aspects of mummification of the head; namely the extraction of the brain through the nose and filling the cranium with linen like material, packing of the oral cavity and the presence of false eyes. These findings alone allow one to date the mummy to no sooner than the 20th dynasty, a time when this custom was at its peak. ENT aspects of the mummification of the head are discussed.

  20. Small Particle Impact Damage on Different Glass Substrates

    Science.gov (United States)

    Waxman, R.; Guven, I.; Gray, P.

    2017-01-01

    Impact experiments using sand particles were performed on four distinct glass substrates. The sand particles were characterized using the X-Ray micro-CT technique; 3-D reconstruction of the particles was followed by further size and shape analyses. High-speed video footage from impact tests was used to calculate the incoming and rebound velocities of the individual sand impact events, as well as particle volume. Further, video analysis was used in conjunction with optical and scanning electron microscopy to relate the incoming velocity and shape of the particles to subsequent fractures, including both radial and lateral cracks. Analysis was performed using peridynamic simulations.