WorldWideScience

Sample records for image analysis software

  1. Image processing and analysis software development

    International Nuclear Information System (INIS)

    Shahnaz, R.

    1999-01-01

    The work presented in this project is aimed at developing a software 'IMAGE GALLERY' to investigate various image processing and analysis techniques. The work was divided into two parts namely the image processing techniques and pattern recognition, which further comprised of character and face recognition. Various image enhancement techniques including negative imaging, contrast stretching, compression of dynamic, neon, diffuse, emboss etc. have been studied. Segmentation techniques including point detection, line detection, edge detection have been studied. Also some of the smoothing and sharpening filters have been investigated. All these imaging techniques have been implemented in a window based computer program written in Visual Basic Neural network techniques based on Perception model have been applied for face and character recognition. (author)

  2. Development of Image Analysis Software of MAXI

    Science.gov (United States)

    Eguchi, S.; Ueda, Y.; Hiroi, K.; Isobe, N.; Sugizaki, M.; Suzuki, M.; Tomida, H.; Maxi Team

    2010-12-01

    Monitor of All-sky X-ray Image (MAXI) is an X-ray all-sky monitor, attached to the Japanese experiment module Kibo on the International Space Station. The main scientific goals of the MAXI mission include the discovery of X-ray novae followed by prompt alerts to the community (Negoro et al., in this conference), and production of X-ray all-sky maps and new source catalogs with unprecedented sensitivities. To extract the best capabilities of the MAXI mission, we are working on the development of detailed image analysis tools. We utilize maximum likelihood fitting to a projected sky image, where we take account of the complicated detector responses, such as the background and point spread functions (PSFs). The modeling of PSFs, which strongly depend on the orbit and attitude of MAXI, is a key element in the image analysis. In this paper, we present the status of our software development.

  3. Uses of software in digital image analysis: a forensic report

    Science.gov (United States)

    Sharma, Mukesh; Jha, Shailendra

    2010-02-01

    Forensic image analysis is required an expertise to interpret the content of an image or the image itself in legal matters. Major sub-disciplines of forensic image analysis with law enforcement applications include photo-grammetry, photographic comparison, content analysis and image authentication. It has wide applications in forensic science range from documenting crime scenes to enhancing faint or indistinct patterns such as partial fingerprints. The process of forensic image analysis can involve several different tasks, regardless of the type of image analysis performed. Through this paper authors have tried to explain these tasks, which are described in to three categories: Image Compression, Image Enhancement & Restoration and Measurement Extraction. With the help of examples like signature comparison, counterfeit currency comparison and foot-wear sole impression using the software Canvas and Corel Draw.

  4. A software package for biomedical image processing and analysis

    International Nuclear Information System (INIS)

    Goncalves, J.G.M.; Mealha, O.

    1988-01-01

    The decreasing cost of computing power and the introduction of low cost imaging boards justifies the increasing number of applications of digital image processing techniques in the area of biomedicine. There is however a large software gap to be fulfilled, between the application and the equipment. The requirements to bridge this gap are twofold: good knowledge of the hardware provided and its interface to the host computer, and expertise in digital image processing and analysis techniques. A software package incorporating these two requirements was developed using the C programming language, in order to create a user friendly image processing programming environment. The software package can be considered in two different ways: as a data structure adapted to image processing and analysis, which acts as the backbone and the standard of communication for all the software; and as a set of routines implementing the basic algorithms used in image processing and analysis. Hardware dependency is restricted to a single module upon which all hardware calls are based. The data structure that was built has four main features: hierchical, open, object oriented, and object dependent dimensions. Considering the vast amount of memory needed by imaging applications and the memory available in small imaging systems, an effective image memory management scheme was implemented. This software package is being used for more than one and a half years by users with different applications. It proved to be an excellent tool for helping people to get adapted into the system, and for standardizing and exchanging software, yet preserving flexibility allowing for users' specific implementations. The philosophy of the software package is discussed and the data structure that was built is described in detail

  5. A software platform for the analysis of dermatology images

    Science.gov (United States)

    Vlassi, Maria; Mavraganis, Vlasios; Asvestas, Panteleimon

    2017-11-01

    The purpose of this paper is to present a software platform developed in Python programming environment that can be used for the processing and analysis of dermatology images. The platform provides the capability for reading a file that contains a dermatology image. The platform supports image formats such as Windows bitmaps, JPEG, JPEG2000, portable network graphics, TIFF. Furthermore, it provides suitable tools for selecting, either manually or automatically, a region of interest (ROI) on the image. The automated selection of a ROI includes filtering for smoothing the image and thresholding. The proposed software platform has a friendly and clear graphical user interface and could be a useful second-opinion tool to a dermatologist. Furthermore, it could be used to classify images including from other anatomical parts such as breast or lung, after proper re-training of the classification algorithms.

  6. SIMA: Python software for analysis of dynamic fluorescence imaging data

    Directory of Open Access Journals (Sweden)

    Patrick eKaifosh

    2014-09-01

    Full Text Available Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs, and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

  7. Software for 3D diagnostic image reconstruction and analysis

    International Nuclear Information System (INIS)

    Taton, G.; Rokita, E.; Sierzega, M.; Klek, S.; Kulig, J.; Urbanik, A.

    2005-01-01

    Recent advances in computer technologies have opened new frontiers in medical diagnostics. Interesting possibilities are the use of three-dimensional (3D) imaging and the combination of images from different modalities. Software prepared in our laboratories devoted to 3D image reconstruction and analysis from computed tomography and ultrasonography is presented. In developing our software it was assumed that it should be applicable in standard medical practice, i.e. it should work effectively with a PC. An additional feature is the possibility of combining 3D images from different modalities. The reconstruction and data processing can be conducted using a standard PC, so low investment costs result in the introduction of advanced and useful diagnostic possibilities. The program was tested on a PC using DICOM data from computed tomography and TIFF files obtained from a 3D ultrasound system. The results of the anthropomorphic phantom and patient data were taken into consideration. A new approach was used to achieve spatial correlation of two independently obtained 3D images. The method relies on the use of four pairs of markers within the regions under consideration. The user selects the markers manually and the computer calculates the transformations necessary for coupling the images. The main software feature is the possibility of 3D image reconstruction from a series of two-dimensional (2D) images. The reconstructed 3D image can be: (1) viewed with the most popular methods of 3D image viewing, (2) filtered and processed to improve image quality, (3) analyzed quantitatively (geometrical measurements), and (4) coupled with another, independently acquired 3D image. The reconstructed and processed 3D image can be stored at every stage of image processing. The overall software performance was good considering the relatively low costs of the hardware used and the huge data sets processed. The program can be freely used and tested (source code and program available at

  8. An ion beam analysis software based on ImageJ

    International Nuclear Information System (INIS)

    Udalagama, C.; Chen, X.; Bettiol, A.A.; Watt, F.

    2013-01-01

    The suit of techniques (RBS, STIM, ERDS, PIXE, IL, IF,…) available in ion beam analysis yields a variety of rich information. Typically, after the initial challenge of acquiring data we are then faced with the task of having to extract relevant information or to present the data in a format with the greatest impact. This process sometimes requires developing new software tools. When faced with such situations the usual practice at the Centre for Ion Beam Applications (CIBA) in Singapore has been to use our computational expertise to develop ad hoc software tools as and when we need them. It then became apparent that the whole ion beam community can benefit from such tools; specifically from a common software toolset that can be developed and maintained by everyone with freedom to use and allowance to modify. In addition to the benefits of readymade tools and sharing the onus of development, this also opens up the possibility for collaborators to access and analyse ion beam data without having to depend on an ion beam lab. This has the virtue of making the ion beam techniques more accessible to a broader scientific community. We have identified ImageJ as an appropriate software base to develop such a common toolset. In addition to being in the public domain and been setup for collaborative tool development, ImageJ is accompanied by hundreds of modules (plugins) that allow great breadth in analysis. The present work is the first step towards integrating ion beam analysis into ImageJ. Some of the features of the current version of the ImageJ ‘ion beam’ plugin are: (1) reading list mode or event-by-event files, (2) energy gates/sorts, (3) sort stacks, (4) colour function, (5) real time map updating, (6) real time colour updating and (7) median and average map creation

  9. An ion beam analysis software based on ImageJ

    Energy Technology Data Exchange (ETDEWEB)

    Udalagama, C., E-mail: chammika@nus.edu.sg [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117 542 (Singapore); Chen, X.; Bettiol, A.A.; Watt, F. [Centre for Ion Beam Applications (CIBA), Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117 542 (Singapore)

    2013-07-01

    The suit of techniques (RBS, STIM, ERDS, PIXE, IL, IF,…) available in ion beam analysis yields a variety of rich information. Typically, after the initial challenge of acquiring data we are then faced with the task of having to extract relevant information or to present the data in a format with the greatest impact. This process sometimes requires developing new software tools. When faced with such situations the usual practice at the Centre for Ion Beam Applications (CIBA) in Singapore has been to use our computational expertise to develop ad hoc software tools as and when we need them. It then became apparent that the whole ion beam community can benefit from such tools; specifically from a common software toolset that can be developed and maintained by everyone with freedom to use and allowance to modify. In addition to the benefits of readymade tools and sharing the onus of development, this also opens up the possibility for collaborators to access and analyse ion beam data without having to depend on an ion beam lab. This has the virtue of making the ion beam techniques more accessible to a broader scientific community. We have identified ImageJ as an appropriate software base to develop such a common toolset. In addition to being in the public domain and been setup for collaborative tool development, ImageJ is accompanied by hundreds of modules (plugins) that allow great breadth in analysis. The present work is the first step towards integrating ion beam analysis into ImageJ. Some of the features of the current version of the ImageJ ‘ion beam’ plugin are: (1) reading list mode or event-by-event files, (2) energy gates/sorts, (3) sort stacks, (4) colour function, (5) real time map updating, (6) real time colour updating and (7) median and average map creation.

  10. Gamma camera image processing and graphical analysis mutual software system

    International Nuclear Information System (INIS)

    Wang Zhiqian; Chen Yongming; Ding Ailian; Ling Zhiye; Jin Yongjie

    1992-01-01

    GCCS gamma camera image processing and graphical analysis system is a special mutual software system. It is mainly used to analyse various patient data acquired from gamma camera. This system is used on IBM PC, PC/XT or PC/AT. It consists of several parts: system management, data management, device management, program package and user programs. The system provides two kinds of user interfaces: command menu and command characters. It is easy to change and enlarge this system because it is best modularized. The user programs include almost all the clinical protocols used now

  11. Software Graphical User Interface For Analysis Of Images

    Science.gov (United States)

    Leonard, Desiree M.; Nolf, Scott R.; Avis, Elizabeth L.; Stacy, Kathryn

    1992-01-01

    CAMTOOL software provides graphical interface between Sun Microsystems workstation and Eikonix Model 1412 digitizing camera system. Camera scans and digitizes images, halftones, reflectives, transmissives, rigid or flexible flat material, or three-dimensional objects. Users digitize images and select from three destinations: work-station display screen, magnetic-tape drive, or hard disk. Written in C.

  12. An online database for plant image analysis software tools

    OpenAIRE

    Lobet, Guillaume; Draye, Xavier; Périlleux, Claire

    2013-01-01

    Background: Recent years have seen an increase in methods for plant phenotyping using image analyses. These methods require new software solutions for data extraction and treatment. These solutions are instrumental in supporting various research pipelines, ranging from the localisation of cellular compounds to the quantification of tree canopies. However, due to the variety of existing tools and the lack of central repository, it is challenging for researchers to identify the software that is...

  13. Image analysis software versus direct anthropometry for breast measurements.

    Science.gov (United States)

    Quieregatto, Paulo Rogério; Hochman, Bernardo; Furtado, Fabianne; Machado, Aline Fernanda Perez; Sabino Neto, Miguel; Ferreira, Lydia Masako

    2014-10-01

    To compare breast measurements performed using the software packages ImageTool(r), AutoCAD(r) and Adobe Photoshop(r) with direct anthropometric measurements. Points were marked on the breasts and arms of 40 volunteer women aged between 18 and 60 years. When connecting the points, seven linear segments and one angular measurement on each half of the body, and one medial segment common to both body halves were defined. The volunteers were photographed in a standardized manner. Photogrammetric measurements were performed by three independent observers using the three software packages and compared to direct anthropometric measurements made with calipers and a protractor. Measurements obtained with AutoCAD(r) were the most reproducible and those made with ImageTool(r) were the most similar to direct anthropometry, while measurements with Adobe Photoshop(r) showed the largest differences. Except for angular measurements, significant differences were found between measurements of line segments made using the three software packages and those obtained by direct anthropometry. AutoCAD(r) provided the highest precision and intermediate accuracy; ImageTool(r) had the highest accuracy and lowest precision; and Adobe Photoshop(r) showed intermediate precision and the worst accuracy among the three software packages.

  14. AMIDE: A Free Software Tool for Multimodality Medical Image Analysis

    Directory of Open Access Journals (Sweden)

    Andreas Markus Loening

    2003-07-01

    Full Text Available Amide's a Medical Image Data Examiner (AMIDE has been developed as a user-friendly, open-source software tool for displaying and analyzing multimodality volumetric medical images. Central to the package's abilities to simultaneously display multiple data sets (e.g., PET, CT, MRI and regions of interest is the on-demand data reslicing implemented within the program. Data sets can be freely shifted, rotated, viewed, and analyzed with the program automatically handling interpolation as needed from the original data. Validation has been performed by comparing the output of AMIDE with that of several existing software packages. AMIDE runs on UNIX, Macintosh OS X, and Microsoft Windows platforms, and it is freely available with source code under the terms of the GNU General Public License.

  15. Design and validation of Segment - freely available software for cardiovascular image analysis

    International Nuclear Information System (INIS)

    Heiberg, Einar; Sjögren, Jane; Ugander, Martin; Carlsson, Marcus; Engblom, Henrik; Arheden, Håkan

    2010-01-01

    Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format. Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page (http://segment.heiberg.se). Segment

  16. An instructional guide for leaf color analysis using digital imaging software

    Science.gov (United States)

    Paula F. Murakami; Michelle R. Turner; Abby K. van den Berg; Paul G. Schaberg

    2005-01-01

    Digital color analysis has become an increasingly popular and cost-effective method utilized by resource managers and scientists for evaluating foliar nutrition and health in response to environmental stresses. We developed and tested a new method of digital image analysis that uses Scion Image or NIH image public domain software to quantify leaf color. This...

  17. Public-domain software for root image analysis

    Directory of Open Access Journals (Sweden)

    Mirian Cristina Gomes Costa

    2014-10-01

    Full Text Available In the search for high efficiency in root studies, computational systems have been developed to analyze digital images. ImageJ and Safira are public-domain systems that may be used for image analysis of washed roots. However, differences in root properties measured using ImageJ and Safira are supposed. This study compared values of root length and surface area obtained with public-domain systems with values obtained by a reference method. Root samples were collected in a banana plantation in an area of a shallower Typic Carbonatic Haplic Cambisol (CXk, and an area of a deeper Typic Haplic Ta Eutrophic Cambisol (CXve, at six depths in five replications. Root images were digitized and the systems ImageJ and Safira used to determine root length and surface area. The line-intersect method modified by Tennant was used as reference; values of root length and surface area measured with the different systems were analyzed by Pearson's correlation coefficient and compared by the confidence interval and t-test. Both systems ImageJ and Safira had positive correlation coefficients with the reference method for root length and surface area data in CXk and CXve. The correlation coefficient ranged from 0.54 to 0.80, with lowest value observed for ImageJ in the measurement of surface area of roots sampled in CXve. The IC (95 % revealed that root length measurements with Safira did not differ from that with the reference method in CXk (-77.3 to 244.0 mm. Regarding surface area measurements, Safira did not differ from the reference method for samples collected in CXk (-530.6 to 565.8 mm² as well as in CXve (-4231 to 612.1 mm². However, measurements with ImageJ were different from those obtained by the reference method, underestimating length and surface area in samples collected in CXk and CXve. Both ImageJ and Safira allow an identification of increases or decreases in root length and surface area. However, Safira results for root length and surface area are

  18. Image analysis software for following progression of peripheral neuropathy

    Science.gov (United States)

    Epplin-Zapf, Thomas; Miller, Clayton; Larkin, Sean; Hermesmeyer, Eduardo; Macy, Jenny; Pellegrini, Marco; Luccarelli, Saverio; Staurenghi, Giovanni; Holmes, Timothy

    2009-02-01

    A relationship has been reported by several research groups [1 - 4] between the density and shapes of nerve fibers in the cornea and the existence and severity of peripheral neuropathy. Peripheral neuropathy is a complication of several prevalent diseases or conditions, which include diabetes, HIV, prolonged alcohol overconsumption and aging. A common clinical technique for confirming the condition is intramuscular electromyography (EMG), which is invasive, so a noninvasive technique like the one proposed here carries important potential advantages for the physician and patient. A software program that automatically detects the nerve fibers, counts them and measures their shapes is being developed and tested. Tests were carried out with a database of subjects with levels of severity of diabetic neuropathy as determined by EMG testing. Results from this testing, that include a linear regression analysis are shown.

  19. Software phantom with realistic speckle modeling for validation of image analysis methods in echocardiography

    Science.gov (United States)

    Law, Yuen C.; Tenbrinck, Daniel; Jiang, Xiaoyi; Kuhlen, Torsten

    2014-03-01

    Computer-assisted processing and interpretation of medical ultrasound images is one of the most challenging tasks within image analysis. Physical phenomena in ultrasonographic images, e.g., the characteristic speckle noise and shadowing effects, make the majority of standard methods from image analysis non optimal. Furthermore, validation of adapted computer vision methods proves to be difficult due to missing ground truth information. There is no widely accepted software phantom in the community and existing software phantoms are not exible enough to support the use of specific speckle models for different tissue types, e.g., muscle and fat tissue. In this work we propose an anatomical software phantom with a realistic speckle pattern simulation to _ll this gap and provide a exible tool for validation purposes in medical ultrasound image analysis. We discuss the generation of speckle patterns and perform statistical analysis of the simulated textures to obtain quantitative measures of the realism and accuracy regarding the resulting textures.

  20. Development of image analysis software for quantification of viable cells in microchips.

    Science.gov (United States)

    Georg, Maximilian; Fernández-Cabada, Tamara; Bourguignon, Natalia; Karp, Paola; Peñaherrera, Ana B; Helguera, Gustavo; Lerner, Betiana; Pérez, Maximiliano S; Mertelsmann, Roland

    2018-01-01

    Over the past few years, image analysis has emerged as a powerful tool for analyzing various cell biology parameters in an unprecedented and highly specific manner. The amount of data that is generated requires automated methods for the processing and analysis of all the resulting information. The software available so far are suitable for the processing of fluorescence and phase contrast images, but often do not provide good results from transmission light microscopy images, due to the intrinsic variation of the acquisition of images technique itself (adjustment of brightness / contrast, for instance) and the variability between image acquisition introduced by operators / equipment. In this contribution, it has been presented an image processing software, Python based image analysis for cell growth (PIACG), that is able to calculate the total area of the well occupied by cells with fusiform and rounded morphology in response to different concentrations of fetal bovine serum in microfluidic chips, from microscopy images in transmission light, in a highly efficient way.

  1. JUPOS : Amateur analysis of Jupiter images with specialized measurement software

    Science.gov (United States)

    Jacquesson, M.; Mettig, H.-J.

    2008-09-01

    Introduction - Beginning of JUPOS in 1989, H.J. Mettig and Grischa Hahn in Dresden - 350.000 positional measures on electronic images of almost 180 observers have been gathered since 1998 - What do we mean by "electronic images": o digitized hi-res chemical photographs o traditional CCD technique o webcam images - 2002 started the implementation of WinJUPOS by Grischa, now finished - Cooperation with the Jupiter Section of the BAA for many years - At present, JUPOS has four active measurers: o Gianluigi Adamoli and Marco Vedovato (Italy) o H.J. Mettig (Germany) o Michel Jacquesson (France) How we work together - Each member of the team measures images of several observers (useful to detect and avoid systematic errors) - When necessary, exchange of problems and ideas by e-mail - During the period of visibility of Jupiter, team leader H.J. Mettig: o collects all recent measurements about once a month o produces drift charts - Once a year or two, the JUPOS team helds an informal meeting Criteria for image selection 1) Validity of time and date: Origins of time errors: 1. local zonal times are wrongly (or, not at all) converted to UT. This is still easy to find out: Either "only" the full hour is erroneous, or/and the date (problem of observers with UTC+10) 2. the computer clock has not been synchronised over a longer period 3. exposure of the final image exceeds the recommended two minutes or observers communicate begin or end of the total period of image recording instead of its middle How to test the validity of the time? - Position of a galilean satellite visible on or near Jupiter - Position of a satellite shadow - Measuring the longitude of permanent or long lived objects whose positions are known from former measurements 2) Avoid measuring the same object on different images taken at about the same time. One image every 1 ½ hours is sufficient 3) Duration of exposure: not more than 2-3 minutes because of the rapid rotation of Jupiter 4) Spectral range: Visual

  2. Software Analysis of Mining Images for Objects Detection

    Directory of Open Access Journals (Sweden)

    Jan Tomecek

    2013-11-01

    Full Text Available The contribution is dealing with the development of the new module of robust FOTOMNG system for editing images from a video or miningimage from measurements for subsequent improvement of detection of required objects in the 2D image. The generated module allows create a finalhigh-quality picture by combination of multiple images with the search objects. We can combine input data according to the parameters or basedon reference frames. Correction of detected 2D objects is also part of this module. The solution is implemented intoFOTOMNG system and finishedwork has been tested in appropriate frames, which were validated core functionality and usability. Tests confirmed the function of each part of themodule, its accuracy and implications of integration.

  3. Accuracy of 3D Imaging Software in Cephalometric Analysis

    Science.gov (United States)

    2013-06-21

    the accurate measurement of external apical root resorption (EARR). Lund, Grondahl and Grondahl (2010) reported that CBCT images of root length...H, Grondahl K, Grondahl HG. (2010). Cone beam computed tomography for assessment of root length and marginal bone level during orthodontic ... root angulation using panoramic and cone beam CT. Angle Orthodontics , 77(2), 206-213.   Periago DR, Scarge WC, Moshiri M, Scheetz JP, Silveira AM

  4. PyElph - a software tool for gel images analysis and phylogenetics

    Directory of Open Access Journals (Sweden)

    Pavel Ana Brânduşa

    2012-01-01

    Full Text Available Abstract Background This paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do. Results PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism, AFLP (Amplified Fragment Length Polymorphism, RAPD

  5. CEBAF beam viewer imaging software

    International Nuclear Information System (INIS)

    Bowling, B.A.; McDowell, C.

    1993-01-01

    This paper discusses the various software used in the analysis of beam viewer images at CEBAF. This software, developed at CEBAF, includes a three-dimensional viewscreen calibration code which takes into account such factors as multiple camera/viewscreen rotations and perspective imaging, and maintaining a calibration database for each unit. Additional software allows single-button beam spot detection, with determination of beam location, width, and quality, in less than three seconds. Software has also been implemented to assist in the determination of proper chopper RF control parameters from digitized chopper circles, providing excellent results

  6. CALIPSO: an interactive image analysis software package for desktop PACS workstations

    Science.gov (United States)

    Ratib, Osman M.; Huang, H. K.

    1990-07-01

    The purpose of this project is to develop a low cost workstation for quantitative analysis of multimodality images using a Macintosh II personal computer. In the current configuration the Macintosh operates as a stand alone workstation where images are imported either from a central PACS server through a standard Ethernet network or recorded through video digitizer board. The CALIPSO software developed contains a large variety ofbasic image display and manipulation tools. We focused our effort however on the design and implementation ofquantitative analysis methods that can be applied to images from different imaging modalities. Analysis modules currently implemented include geometric and densitometric volumes and ejection fraction calculation from radionuclide and cine-angiograms Fourier analysis ofcardiac wall motion vascular stenosis measurement color coded parametric display of regional flow distribution from dynamic coronary angiograms automatic analysis ofmyocardial distribution ofradiolabelled tracers from tomoscintigraphic images. Several of these analysis tools were selected because they use similar color coded andparametric display methods to communicate quantitative data extracted from the images. 1. Rationale and objectives of the project Developments of Picture Archiving and Communication Systems (PACS) in clinical environment allow physicians and radiologists to assess radiographic images directly through imaging workstations (''). This convenient access to the images is often limited by the number of workstations available due in part to their high cost. There is also an increasing need for quantitative analysis ofthe images. During thepast decade

  7. InterFace: A software package for face image warping, averaging, and principal components analysis.

    Science.gov (United States)

    Kramer, Robin S S; Jenkins, Rob; Burton, A Mike

    2017-12-01

    We describe InterFace, a software package for research in face recognition. The package supports image warping, reshaping, averaging of multiple face images, and morphing between faces. It also supports principal components analysis (PCA) of face images, along with tools for exploring the "face space" produced by PCA. The package uses a simple graphical user interface, allowing users to perform these sophisticated image manipulations without any need for programming knowledge. The program is available for download in the form of an app, which requires that users also have access to the (freely available) MATLAB Runtime environment.

  8. Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

    Science.gov (United States)

    Markiewicz, Tomasz

    2011-03-30

    The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server

  9. ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

    Science.gov (United States)

    Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

    2018-04-27

    This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

  10. Electrophoresis gel image processing and analysis using the KODAK 1D software.

    Science.gov (United States)

    Pizzonia, J

    2001-06-01

    The present article reports on the performance of the KODAK 1D Image Analysis Software for the acquisition of information from electrophoresis experiments and highlights the utility of several mathematical functions for subsequent image processing, analysis, and presentation. Digital images of Coomassie-stained polyacrylamide protein gels containing molecular weight standards and ethidium bromide stained agarose gels containing DNA mass standards are acquired using the KODAK Electrophoresis Documentation and Analysis System 290 (EDAS 290). The KODAK 1D software is used to optimize lane and band identification using features such as isomolecular weight lines. Mathematical functions for mass standard representation are presented, and two methods for estimation of unknown band mass are compared. Given the progressive transition of electrophoresis data acquisition and daily reporting in peer-reviewed journals to digital formats ranging from 8-bit systems such as EDAS 290 to more expensive 16-bit systems, the utility of algorithms such as Gaussian modeling, which can correct geometric aberrations such as clipping due to signal saturation common at lower bit depth levels, is discussed. Finally, image-processing tools that can facilitate image preparation for presentation are demonstrated.

  11. Quality control in dual head γ-cameras: comparison between methods and software s used for image analysis

    International Nuclear Information System (INIS)

    Nayl E, A.; Fornasier, M. R.; De Denaro, M.; Sulieman, A.; Alkhorayef, M.; Bradley, D.

    2017-10-01

    Patient radiation dose and image quality are the main issues in nuclear medicine (Nm) procedures. Currently, many protocols are used for image acquisition and analysis of quality control (Qc) tests. National Electrical Manufacturers Association (Nema) methods and protocols are widely accepted method used for providing accurate description, measurement and reporting of γ-camera performance parameters. However, no standard software is available for image analysis. The aim os this study was to compare between the vendor Qc software analysis and three software from different developers downloaded free from internet; NMQC, Nm Tool kit and ImageJ-Nm Tool kit software. The three software are used for image analysis of some Qc tests for γ-cameras based on Nema protocols including non-uniformity evaluation. Ten non-uniformity Qc images were taken from dual head γ-camera (Siemens Symbia) installed in Trieste general hospital (Italy), and analyzed. Excel analysis was used as baseline calculation of the non-uniformity test according Nema procedures. The results of the non-uniformity analysis showed good agreement between the three independent software and excel calculation (the average differences were 0.3%, 2.9%, 1.3% and 1.6% for UFOV integral, UFOV differential, CFOV integral and CFOV differential respectively), while significant difference was detected on the analysis of the company Qc software with compare to the excel analysis (the average differences were 14.6%, 20.7%, 25.7% and 31.9% for UFOV integral, UFOV differential, CFOV integral and CFOV differential respectively). NMQC software was the best in comparison with the excel calculations. The variation in the results is due to different pixel sizes used for analysis in the three software and the γ-camera Qc software. Therefore, is important to perform the tests by the vendor Qc software as well as by independent analysis to understand the differences between the values. Moreover, the medical physicist should know

  12. Quality control in dual head γ-cameras: comparison between methods and software s used for image analysis

    Energy Technology Data Exchange (ETDEWEB)

    Nayl E, A. [Sudan Atomic Energy Commission, Radiation Safety Institute, Khartoum (Sudan); Fornasier, M. R.; De Denaro, M. [Azienda Sanitaria Universitaria Integrata di Trieste, Medical Physics Department, Via Giovanni Sai 7, 34128 Trieste (Italy); Sulieman, A. [Prince Sattam bin Abdulaziz University, College of Applied Medical Sciences, Radiology and Medical Imaging Department, P. O. Box 422, 11942 Al-Kharj (Saudi Arabia); Alkhorayef, M.; Bradley, D., E-mail: abdwsh10@hotmail.com [University of Surrey, Department of Physics, GU2-7XH Guildford, Surrey (United Kingdom)

    2017-10-15

    Patient radiation dose and image quality are the main issues in nuclear medicine (Nm) procedures. Currently, many protocols are used for image acquisition and analysis of quality control (Qc) tests. National Electrical Manufacturers Association (Nema) methods and protocols are widely accepted method used for providing accurate description, measurement and reporting of γ-camera performance parameters. However, no standard software is available for image analysis. The aim os this study was to compare between the vendor Qc software analysis and three software from different developers downloaded free from internet; NMQC, Nm Tool kit and ImageJ-Nm Tool kit software. The three software are used for image analysis of some Qc tests for γ-cameras based on Nema protocols including non-uniformity evaluation. Ten non-uniformity Qc images were taken from dual head γ-camera (Siemens Symbia) installed in Trieste general hospital (Italy), and analyzed. Excel analysis was used as baseline calculation of the non-uniformity test according Nema procedures. The results of the non-uniformity analysis showed good agreement between the three independent software and excel calculation (the average differences were 0.3%, 2.9%, 1.3% and 1.6% for UFOV integral, UFOV differential, CFOV integral and CFOV differential respectively), while significant difference was detected on the analysis of the company Qc software with compare to the excel analysis (the average differences were 14.6%, 20.7%, 25.7% and 31.9% for UFOV integral, UFOV differential, CFOV integral and CFOV differential respectively). NMQC software was the best in comparison with the excel calculations. The variation in the results is due to different pixel sizes used for analysis in the three software and the γ-camera Qc software. Therefore, is important to perform the tests by the vendor Qc software as well as by independent analysis to understand the differences between the values. Moreover, the medical physicist should know

  13. PlantCV v2: Image analysis software for high-throughput plant phenotyping

    Directory of Open Access Journals (Sweden)

    Malia A. Gehan

    2017-12-01

    Full Text Available Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

  14. Open source software for the analysis of corneal deformation parameters on the images from the Corvis tonometer.

    Science.gov (United States)

    Koprowski, Robert

    2015-04-11

    The software supplied with the Corvis tonometer (which is designed to measure intraocular pressure with the use of the air-puff method) is limited to providing basic numerical data. These data relate to the values of the measured intraocular pressure and, for example, applanation amplitudes. However, on the basis of a sequence of images obtained from the Corvis tonometer, it is possible to obtain much more information which is not available in its original software. This will be presented in this paper. The proposed software has been tested on 1400 images from the Corvis tonometer. The number of analysed 2D images (with a resolution of 200 × 576 pixels) in a sequence is arbitrary. However, in typical cases there are 140 images. The proposed software has been written in Matlab (Version 7.11.0.584, R2010b). The methods of image analysis and processing and in particular edge detection and the fast Fourier transform have been applied. The software allows for fully automatic (1) acquisition of 12 new parameters previously unavailable in the original software of the Corvis tonometer. It also enables off-line (2) manual and (3) automatic browsing of images in a sequence; 3D graph visualization of: (4) the corneal deformation and (5) eyeball response; 6) change of the colour palette; (7) filtration and (8) visualization of selected measured values on individual 2D images. In addition, the proposed software enables (9) to save the obtained results for further analysis and processing. The dedicated software described in this paper enables to obtain additional new features of corneal deformations during intraocular pressure measurement. The software can be applied in the diagnosis of corneal deformation vibrations, glaucoma diagnosis, evaluation of measurement repeatability and others. The software has no licensing restrictions and can be used both commercially and non-commercially without any limitations.

  15. An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited.

    Science.gov (United States)

    Zöllner, Frank G; Daab, Markus; Sourbron, Steven P; Schad, Lothar R; Schoenberg, Stefan O; Weisser, Gerald

    2016-01-14

    Perfusion imaging has become an important image based tool to derive the physiological information in various applications, like tumor diagnostics and therapy, stroke, (cardio-) vascular diseases, or functional assessment of organs. However, even after 20 years of intense research in this field, perfusion imaging still remains a research tool without a broad clinical usage. One problem is the lack of standardization in technical aspects which have to be considered for successful quantitative evaluation; the second problem is a lack of tools that allow a direct integration into the diagnostic workflow in radiology. Five compartment models, namely, a one compartment model (1CP), a two compartment exchange (2CXM), a two compartment uptake model (2CUM), a two compartment filtration model (2FM) and eventually the extended Toft's model (ETM) were implemented as plugin for the DICOM workstation OsiriX. Moreover, the plugin has a clean graphical user interface and provides means for quality management during the perfusion data analysis. Based on reference test data, the implementation was validated against a reference implementation. No differences were found in the calculated parameters. We developed open source software to analyse DCE-MRI perfusion data. The software is designed as plugin for the DICOM Workstation OsiriX. It features a clean GUI and provides a simple workflow for data analysis while it could also be seen as a toolbox providing an implementation of several recent compartment models to be applied in research tasks. Integration into the infrastructure of a radiology department is given via OsiriX. Results can be saved automatically and reports generated automatically during data analysis ensure certain quality control.

  16. An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited

    International Nuclear Information System (INIS)

    Zöllner, Frank G.; Daab, Markus; Sourbron, Steven P.; Schad, Lothar R.; Schoenberg, Stefan O.; Weisser, Gerald

    2016-01-01

    Perfusion imaging has become an important image based tool to derive the physiological information in various applications, like tumor diagnostics and therapy, stroke, (cardio-) vascular diseases, or functional assessment of organs. However, even after 20 years of intense research in this field, perfusion imaging still remains a research tool without a broad clinical usage. One problem is the lack of standardization in technical aspects which have to be considered for successful quantitative evaluation; the second problem is a lack of tools that allow a direct integration into the diagnostic workflow in radiology. Five compartment models, namely, a one compartment model (1CP), a two compartment exchange (2CXM), a two compartment uptake model (2CUM), a two compartment filtration model (2FM) and eventually the extended Toft’s model (ETM) were implemented as plugin for the DICOM workstation OsiriX. Moreover, the plugin has a clean graphical user interface and provides means for quality management during the perfusion data analysis. Based on reference test data, the implementation was validated against a reference implementation. No differences were found in the calculated parameters. We developed open source software to analyse DCE-MRI perfusion data. The software is designed as plugin for the DICOM Workstation OsiriX. It features a clean GUI and provides a simple workflow for data analysis while it could also be seen as a toolbox providing an implementation of several recent compartment models to be applied in research tasks. Integration into the infrastructure of a radiology department is given via OsiriX. Results can be saved automatically and reports generated automatically during data analysis ensure certain quality control

  17. Imaging software accuracy for 3-dimensional analysis of the upper airway.

    Science.gov (United States)

    Weissheimer, André; Menezes, Luciane Macedo de; Sameshima, Glenn T; Enciso, Reyes; Pham, John; Grauer, Dan

    2012-12-01

    The aim of this study was to compare the precision and accuracy of 6 imaging software programs for measuring upper airway volumes in cone-beam computed tomography data. The sample consisted of 33 growing patients and an oropharynx acrylic phantom, scanned with an i-CAT scanner (Imaging Sciences International, Hatfield, Pa). The known oropharynx acrylic phantom volume was used as the gold standard. Semi-automatic segmentations with interactive and fixed threshold protocols of the patients' oropharynx and oropharynx acrylic phantom were performed by using Mimics (Materialise, Leuven, Belgium), ITK-Snap (www.itksnap.org), OsiriX (Pixmeo, Geneva, Switzerland), Dolphin3D (Dolphin Imaging & Management Solutions, Chatsworth, Calif), InVivo Dental (Anatomage, San Jose, Calif), and Ondemand3D (CyberMed, Seoul, Korea) software programs. The intraclass correlation coefficient was used for the reliability tests. A repeated measurements analysis of variance (ANOVA) test and post-hoc tests (Bonferroni) were used to compare the software programs. The reliability was high for all programs. With the interactive threshold protocol, the oropharynx acrylic phantom segmentations with Mimics, Dolphin3D, OsiriX, and ITK-Snap showed less than 2% errors in volumes compared with the gold standard. Ondemand3D and InVivo Dental had more than 5% errors compared with the gold standard. With the fixed threshold protocol, the volume errors were similar (-11.1% to -11.7%) among the programs. In the oropharynx segmentation with the interactive protocol, ITK-Snap, Mimics, OsiriX, and Dolphin3D were statistically significantly different (P 0.05) was found between InVivo Dental and OnDemand3D. All 6 imaging software programs were reliable but had errors in the volume segmentations of the oropharynx. Mimics, Dolphin3D, ITK-Snap, and OsiriX were similar and more accurate than InVivo Dental and Ondemand3D for upper airway assessment. Copyright © 2012 American Association of Orthodontists. Published by

  18. MIA - A free and open source software for gray scale medical image analysis.

    Science.gov (United States)

    Wollny, Gert; Kellman, Peter; Ledesma-Carbayo, María-Jesus; Skinner, Matthew M; Hublin, Jean-Jaques; Hierl, Thomas

    2013-10-11

    Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large.Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers.One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development.Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don't provide an clear approach when one wants to shape a new command line tool from a prototype shell script. The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by

  19. A medical software system for volumetric analysis of cerebral pathologies in magnetic resonance imaging (MRI) data.

    Science.gov (United States)

    Egger, Jan; Kappus, Christoph; Freisleben, Bernd; Nimsky, Christopher

    2012-08-01

    In this contribution, a medical software system for volumetric analysis of different cerebral pathologies in magnetic resonance imaging (MRI) data is presented. The software system is based on a semi-automatic segmentation algorithm and helps to overcome the time-consuming process of volume determination during monitoring of a patient. After imaging, the parameter settings-including a seed point-are set up in the system and an automatic segmentation is performed by a novel graph-based approach. Manually reviewing the result leads to reseeding, adding seed points or an automatic surface mesh generation. The mesh is saved for monitoring the patient and for comparisons with follow-up scans. Based on the mesh, the system performs a voxelization and volume calculation, which leads to diagnosis and therefore further treatment decisions. The overall system has been tested with different cerebral pathologies-glioblastoma multiforme, pituitary adenomas and cerebral aneurysms- and evaluated against manual expert segmentations using the Dice Similarity Coefficient (DSC). Additionally, intra-physician segmentations have been performed to provide a quality measure for the presented system.

  20. Accuracy and initial clinical experience with measurement software (advanced vessel analysis) in three-dimensional imaging

    International Nuclear Information System (INIS)

    Abe, Toshi; Hirohata, Masaru; Tanigawa, Hitoshi

    2002-01-01

    Recently, the clinical benefits of three dimensional (3D) imaging, such as 3D-CTA and 3D-DSA, in cerebro-vascular disease have been widely recognized. Software for quantitative analysis of vascular structure in 3D imaging (advanced vessel analysis: AVA) has been developed. We evaluated AVA with both phantom studies and a few clinical cases. In spiral and curvy aluminum tube phantom studies, the accuracy of diameter measurements was good in 3D images produced from data set generated by multi-detector row CT or rotational angiography. The measurement error was less than 0.03 mm on aluminum tube phantoms that were 3 mm and 5 mm in diameter. In the clinical studies, the differences of carotid artery diameter measurements between 2D-DSA and 3D-DSA was less than 0.3 mm in. The measurement of length, diameter and angle by AVA should provide useful information for planning surgical and endovascular treatments of cerebro-vascular disease. (author)

  1. Free digital image analysis software helps to resolve equivocal scores in HER2 immunohistochemistry.

    Science.gov (United States)

    Helin, Henrik O; Tuominen, Vilppu J; Ylinen, Onni; Helin, Heikki J; Isola, Jorma

    2016-02-01

    Evaluation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) is subject to interobserver variation and lack of reproducibility. Digital image analysis (DIA) has been shown to improve the consistency and accuracy of the evaluation and its use is encouraged in current testing guidelines. We studied whether digital image analysis using a free software application (ImmunoMembrane) can assist in interpreting HER2 IHC in equivocal 2+ cases. We also compared digital photomicrographs with whole-slide images (WSI) as material for ImmunoMembrane DIA. We stained 750 surgical resection specimens of invasive breast cancers immunohistochemically for HER2 and analysed staining with ImmunoMembrane. The ImmunoMembrane DIA scores were compared with the originally responsible pathologists' visual scores, a researcher's visual scores and in situ hybridisation (ISH) results. The originally responsible pathologists reported 9.1 % positive 3+ IHC scores, for the researcher this was 8.4 % and for ImmunoMembrane 9.5 %. Equivocal 2+ scores were 34 % for the pathologists, 43.7 % for the researcher and 10.1 % for ImmunoMembrane. Negative 0/1+ scores were 57.6 % for the pathologists, 46.8 % for the researcher and 80.8 % for ImmunoMembrane. There were six false positive cases, which were classified as 3+ by ImmunoMembrane and negative by ISH. Six cases were false negative defined as 0/1+ by IHC and positive by ISH. ImmunoMembrane DIA using digital photomicrographs and WSI showed almost perfect agreement. In conclusion, digital image analysis by ImmunoMembrane can help to resolve a majority of equivocal 2+ cases in HER2 IHC, which reduces the need for ISH testing.

  2. Integration of XNAT/PACS, DICOM, and research software for automated multi-modal image analysis

    Science.gov (United States)

    Gao, Yurui; Burns, Scott S.; Lauzon, Carolyn B.; Fong, Andrew E.; James, Terry A.; Lubar, Joel F.; Thatcher, Robert W.; Twillie, David A.; Wirt, Michael D.; Zola, Marc A.; Logan, Bret W.; Anderson, Adam W.; Landman, Bennett A.

    2013-03-01

    Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software.

  3. Counting radon tracks in Makrofol detectors with the 'image reduction and analysis facility' (IRAF) software package

    International Nuclear Information System (INIS)

    Hernandez, F.; Gonzalez-Manrique, S.; Karlsson, L.; Hernandez-Armas, J.; Aparicio, A.

    2007-01-01

    Makrofol detectors are commonly used for long-term radon ( 222 Rn) measurements in houses, schools and workplaces. The use of this type of passive detectors for the determination of radon concentrations requires the counting of the nuclear tracks produced by alpha particles on the detecting material. The 'image reduction and analysis facility' (IRAF) software package is a piece of software commonly used in astronomical applications. It allows detailed counting and mapping of sky sections where stars are grouped very closely, even forming clusters. In order to count the nuclear tracks in our Makrofol radon detectors, we have developed an inter-disciplinary application that takes advantage of the similitude that exist between counting stars in a dark sky and tracks in a track-etch detector. Thus, a low cost semi-automatic system has been set up in our laboratory which utilises a commercially available desktop scanner and the IRAF software package. A detailed description of the proposed semi-automatic method and its performance, in comparison to ocular counting, is described in detail here. In addition, the calibration factor for this procedure, 2.97+/-0.07kBqm -3 htrack -1 cm 2 , has been calculated based on the results obtained from exposing 46 detectors to certified radon concentrations. Furthermore, the results of a preliminary radon survey carried out in 62 schools in Tenerife island (Spain), using Makrofol detectors, counted with the mentioned procedure, are briefly presented. The results reported here indicate that the developed procedure permits a fast, accurate and unbiased determination of the radon tracks in a large number of detectors. The measurements carried out in the schools showed that the radon concentrations in at least 12 schools were above 200Bqm -3 and, in two of them, above 400Bqm -3 . Further studies should be performed at those schools following the European Union recommendations about radon concentrations in buildings

  4. Development of a software for monitoring of seismic activity through the analysis of satellite images

    Science.gov (United States)

    Soto-Pinto, C.; Poblete, A.; Arellano-Baeza, A. A.; Sanchez, G.

    2010-12-01

    A software for extraction and analysis of the lineaments has been developed and applied for the tracking of the accumulation/relaxation of stress in the Earth’s crust due to seismic and volcanic activity. A lineament is a straight or a somewhat curved feature in a satellite image, which reflects, at least partially, presence of faults in the crust. The technique of lineament extraction is based on the application of directional filters and Hough transform. The software has been checked for several earthquakes occurred in the Pacific coast of the South America with the magnitude > 4 Mw, analyzing temporal sequences of the ASTER/TERRA multispectral satellite images for the regions around an epicenter. All events were located in the regions with small seasonal variations and limited vegetation to facilitate the tracking of features associated with the seismic activity only. It was found that the number and orientation of lineaments changes significantly about one month before an earthquake approximately, and a few months later the system returns to its initial state. This effect increases with the earthquake magnitude. It also was shown that the behavior of lineaments associated to the volcano seismic activity is opposite to that obtained previously for earthquakes. This discrepancy can be explained assuming that in the last case the main reason of earthquakes is compression and accumulation of strength in the Earth’s crust due to subduction of tectonic plates, whereas in the first case we deal with the inflation of a volcano edifice due to elevation of pressure and magma intrusion.

  5. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.

    Science.gov (United States)

    Appel, R D; Vargas, J R; Palagi, P M; Walther, D; Hochstrasser, D F

    1997-12-01

    After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).

  6. MIA - a free and open source software for gray scale medical image analysis

    OpenAIRE

    Wöllny, Gert; Kellman, Peter; Ledesma Carbayo, María Jesús; Skinner, Matthew M.; Hublin, Jean-Jaques; Hierl, Thomas

    2013-01-01

    Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also a...

  7. DSCImageCalc – Software for Determining Similarity Coefficients for the Analysis of Image Segmentations

    Directory of Open Access Journals (Sweden)

    Tom Lawton

    2017-10-01

    Full Text Available DSCImageCalc is free software for calculating similarity coefficients on segmented images. It is written in Visual BASIC .NET and is available at: https://doi.org/10.6084/m9.figshare.894428. It presently calculates Sørensen-Dice Coefficient, Jaccard Coefficient, Proportional Agreement, Cohen’s Kappa, Goodman & Kruskal’s Gamma, and Rogot-Goldberg Agreement. It also calculates segment centroids and the distance between them. Whilst it was originally designed for calculating Dice coefficients on segmentations of ultrasound images, it has potential for re-use in any field where similarity of image segments is to be analysed; predominantly medical radiology and ecology.

  8. The MicroAnalysis Toolkit: X-ray Fluorescence Image Processing Software

    International Nuclear Information System (INIS)

    Webb, S. M.

    2011-01-01

    The MicroAnalysis Toolkit is an analysis suite designed for the processing of x-ray fluorescence microprobe data. The program contains a wide variety of analysis tools, including image maps, correlation plots, simple image math, image filtering, multiple energy image fitting, semi-quantitative elemental analysis, x-ray fluorescence spectrum analysis, principle component analysis, and tomographic reconstructions. To be as widely useful as possible, data formats from many synchrotron sources can be read by the program with more formats available by request. An overview of the most common features will be presented.

  9. HAZARD ANALYSIS SOFTWARE

    International Nuclear Information System (INIS)

    Sommer, S; Tinh Tran, T.

    2008-01-01

    Washington Safety Management Solutions, LLC developed web-based software to improve the efficiency and consistency of hazard identification and analysis, control selection and classification, and to standardize analysis reporting at Savannah River Site. In the new nuclear age, information technology provides methods to improve the efficiency of the documented safety analysis development process which includes hazard analysis activities. This software provides a web interface that interacts with a relational database to support analysis, record data, and to ensure reporting consistency. A team of subject matter experts participated in a series of meetings to review the associated processes and procedures for requirements and standard practices. Through these meetings, a set of software requirements were developed and compiled into a requirements traceability matrix from which software could be developed. The software was tested to ensure compliance with the requirements. Training was provided to the hazard analysis leads. Hazard analysis teams using the software have verified its operability. The software has been classified as NQA-1, Level D, as it supports the analysis team but does not perform the analysis. The software can be transported to other sites with alternate risk schemes. The software is being used to support the development of 14 hazard analyses. User responses have been positive with a number of suggestions for improvement which are being incorporated as time permits. The software has enforced a uniform implementation of the site procedures. The software has significantly improved the efficiency and standardization of the hazard analysis process

  10. Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software

    Directory of Open Access Journals (Sweden)

    Tânia Perestrelo

    2017-08-01

    Full Text Available Image-based assays, such as alkaline phosphatase staining or immunocytochemistry for pluripotent markers, are common methods used in the stem cell field to assess pluripotency. Although an increased number of image-analysis approaches have been described, there is still a lack of software availability to automatically quantify pluripotency in large images after pluripotency staining. To address this need, we developed a robust and rapid image processing software, Pluri-IQ, which allows the automatic evaluation of pluripotency in large low-magnification images. Using mouse embryonic stem cells (mESC as a model, we combined an automated segmentation algorithm with a supervised machine-learning platform to classify colonies as pluripotent, mixed, or differentiated. In addition, Pluri-IQ allows the automatic comparison between different culture conditions. This efficient user-friendly open-source software can be easily implemented in images derived from pluripotent cells or cells that express pluripotent markers (e.g., OCT4-GFP and can be routinely used, decreasing image assessment bias.

  11. Agreement between clinical estimation and a new quantitative analysis by Photoshop software in fundus and angiographic image variables.

    Science.gov (United States)

    Ramezani, Alireza; Ahmadieh, Hamid; Azarmina, Mohsen; Soheilian, Masoud; Dehghan, Mohammad H; Mohebbi, Mohammad R

    2009-12-01

    To evaluate the validity of a new method for the quantitative analysis of fundus or angiographic images using Photoshop 7.0 (Adobe, USA) software by comparing with clinical evaluation. Four hundred and eighteen fundus and angiographic images of diabetic patients were evaluated by three retina specialists and then by computing using Photoshop 7.0 software. Four variables were selected for comparison: amount of hard exudates (HE) on color pictures, amount of HE on red-free pictures, severity of leakage, and the size of the foveal avascular zone (FAZ). The coefficient of agreement (Kappa) between the two methods in the amount of HE on color and red-free photographs were 85% (0.69) and 79% (0.59), respectively. The agreement for severity of leakage was 72% (0.46). In the two methods for the evaluation of the FAZ size using the magic and lasso software tools, the agreement was 54% (0.09) and 89% (0.77), respectively. Agreement in the estimation of the FAZ size by the lasso magnetic tool was excellent and was almost as good in the quantification of HE on color and on red-free images. Considering the agreement of this new technique for the measurement of variables in fundus images using Photoshop software with the clinical evaluation, this method seems to have sufficient validity to be used for the quantitative analysis of HE, leakage, and FAZ size on the angiograms of diabetic patients.

  12. A virtualized software based on the NVIDIA cuFFT library for image denoising: performance analysis

    DEFF Research Database (Denmark)

    Galletti, Ardelio; Marcellino, Livia; Montella, Raffaele

    2017-01-01

    Abstract Generic Virtualization Service (GVirtuS) is a new solution for enabling GPGPU on Virtual Machines or low powered devices. This paper focuses on the performance analysis that can be obtained using a GPGPU virtualized software. Recently, GVirtuS has been extended in order to support CUDA...... ancillary libraries with good results. Here, our aim is to analyze the applicability of this powerful tool to a real problem, which uses the NVIDIA cuFFT library. As case study we consider a simple denoising algorithm, implementing a virtualized GPU-parallel software based on the convolution theorem...

  13. Time efficiency and diagnostic accuracy of new automated myocardial perfusion analysis software in 320-row CT cardiac imaging

    Energy Technology Data Exchange (ETDEWEB)

    Rief, Matthias; Stenzei, Fabian; Kranz, Anisha; Schlattmann, Peter; Dewey, Marc [Dept. of Radiology, Charite - Universiteitsmedizin Berlin, Berlin (Greece)

    2013-01-15

    We aimed to evaluate the time efficiency and diagnostic accuracy of automated myocardial computed tomography perfusion (CTP) image analysis software. 320-row CTP was performed in 30 patients, and analyses were conducted independently by three different blinded readers by the use of two recent software releases (version 4.6 and novel version 4.71GR001, Toshiba, Tokyo, Japan). Analysis times were compared, and automated epi- and endocardial contour detection was subjectively rated in five categories (excellent, good, fair, poor and very poor). As semi-quantitative perfusion parameters, myocardial attenuation and transmural perfusion ratio (TPR) were calculated for each myocardial segment and agreement was tested by using the intraclass correlation coefficient (ICC). Conventional coronary angiography served as reference standard. The analysis time was significantly reduced with the novel automated software version as compared with the former release (Reader 1: 43:08 ± 11:39 min vs. 09:47 ± 04:51 min, Reader 2: 42:07 ± 06:44 min vs. 09:42 ± 02:50 min and Reader 3: 21:38 ± 3:44 min vs. 07:34 ± 02:12 min; p < 0.001 for all). Epi- and endocardial contour detection for the novel software was rated to be significantly better (p < 0.001) than with the former software. ICCs demonstrated strong agreement (≥ 0.75) for myocardial attenuation in 93% and for TPR in 82%. Diagnostic accuracy for the two software versions was not significantly different (p 0.169) as compared with conventional coronary angiography. The novel automated CTP analysis software offers enhanced time efficiency with an improvement by a factor of about four, while maintaining diagnostic accuracy.

  14. Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

    Science.gov (United States)

    Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

    2009-12-01

    This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the

  15. Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie.

    Science.gov (United States)

    Raman, Babu; Cheung, Agnes; Marten, Mark R

    2002-07-01

    While a variety of software packages are available for analyzing two-dimensional electrophoresis (2-DE) gel images, no comparisons between these packages have been published, making it difficult for end users to determine which package would best meet their needs. The goal here was to develop a set of tests to quantitatively evaluate and then compare two software packages, Melanie 3.0 and Z3, in three of the fundamental steps involved in 2-DE image analysis: (i) spot detection, (ii) gel matching, and (iii) spot quantitation. To test spot detection capability, automatically detected protein spots were compared to manually counted, "real" protein spots. Spot matching efficiency was determined by comparing distorted (both geometrically and nongeometrically) gel images with undistorted original images, and quantitation tests were performed on artificial gels with spots of varying Gaussian volumes. In spot detection tests, Z3 performed better than Melanie 3.0 and required minimal user intervention to detect approximately 89% of the actual protein spots and relatively few extraneous spots. Results from gel matching tests depended on the type of image distortion used. For geometric distortions, Z3 performed better than Melanie 3.0, matching 99% of the spots, even for extreme distortions. For nongeometrical distortions, both Z3 and Melanie 3.0 required user intervention and performed comparably, matching 95% of the spots. In spot quantitation tests, both Z3 and Melanie 3.0 predicted spot volumes relatively well for spot ratios less than 1:6. For higher ratios, Melanie 3.0 did much better. In summary, results suggest Z3 requires less user intervention than Melanie 3.0, thus simplifying differential comparison of 2-DE gel images. Melanie 3.0, however, offers many more optional tools for image editing, spot detection, data reporting and statistical analysis than Z3. All image files used for these tests and updated information on the software are available on the internet

  16. Software safety hazard analysis

    International Nuclear Information System (INIS)

    Lawrence, J.D.

    1996-02-01

    Techniques for analyzing the safety and reliability of analog-based electronic protection systems that serve to mitigate hazards in process control systems have been developed over many years, and are reasonably well understood. An example is the protection system in a nuclear power plant. The extension of these techniques to systems which include digital computers is not well developed, and there is little consensus among software engineering experts and safety experts on how to analyze such systems. One possible technique is to extend hazard analysis to include digital computer-based systems. Software is frequently overlooked during system hazard analyses, but this is unacceptable when the software is in control of a potentially hazardous operation. In such cases, hazard analysis should be extended to fully cover the software. A method for performing software hazard analysis is proposed in this paper

  17. Review of free software tools for image analysis of fluorescence cell micrographs.

    Science.gov (United States)

    Wiesmann, V; Franz, D; Held, C; Münzenmayer, C; Palmisano, R; Wittenberg, T

    2015-01-01

    An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand-alone, Matlab-based, ImageJ-based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure-ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure-ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well-structured menu and intuitive graphical user interface. © 2014 Fraunhofer-Institute for Integrated Circuits IIS Journal of Microscopy © 2014 Royal Microscopical Society.

  18. Initial Work on the Characterization of Additive Manufacturing (3D Printing Using Software Image Analysis

    Directory of Open Access Journals (Sweden)

    Jeremy Straub

    2015-04-01

    Full Text Available A current challenge in additive manufacturing (commonly known as 3D printing is the detection of defects. Detection of defects (or the lack thereof in bespoke industrial manufacturing may be safety critical and reduce or eliminate the need for testing of printed objects. In consumer and prototype printing, early defect detection may facilitate the printer taking corrective measures (or pausing printing and alerting a user, preventing the need to re-print objects after the compounding of a small error occurs. This paper considers one approach to defect detection. It characterizes the efficacy of using a multi-camera system and image processing software to assess printing progress (thus detecting completion failure defects and quality. The potential applications and extrapolations of this type of a system are also discussed.

  19. Software development for dynamic position emission tomography: Dynamic image analysis (DIA) tool

    International Nuclear Information System (INIS)

    Pyeon, Do Yeong; Jung, Young Jin; Kim, Jung Su

    2016-01-01

    Positron Emission Tomography(PET) is nuclear medical tests which is a combination of several compounds with a radioactive isotope that can be injected into body to quantitatively measure the metabolic rate (in the body). Especially, Phenomena that increase (sing) glucose metabolism in cancer tissue using the 18F-FDG (Fluorodeoxyglucose) is utilized widely in cancer diagnosis. And then, Numerous studies have been reported that incidence seems high availability even in the modern diagnosis of dementia and Parkinson's (disease) in brain disease. When using a dynamic PET image including the time information in the static information that is provided for the diagnosis many can increase the accuracy of diagnosis. For this reason, clinical researchers getting great attention but, it is the lack of tools to conduct research. And, it interfered complex mathematical algorithm and programming skills for activation of research. In this study, in order to easy to use and enable research dPET, we developed the software based graphic user interface(GUI). In the future, by many clinical researcher using DIA-Tool is expected to be of great help to dPET research

  20. Software development for dynamic position emission tomography: Dynamic image analysis (DIA) tool

    Energy Technology Data Exchange (ETDEWEB)

    Pyeon, Do Yeong; Jung, Young Jin [Dongseo University, Busan (Korea, Republic of); Kim, Jung Su [Dept. of Radilogical Science, Dongnam Health University, Suwon (Korea, Republic of)

    2016-09-15

    Positron Emission Tomography(PET) is nuclear medical tests which is a combination of several compounds with a radioactive isotope that can be injected into body to quantitatively measure the metabolic rate (in the body). Especially, Phenomena that increase (sing) glucose metabolism in cancer tissue using the 18F-FDG (Fluorodeoxyglucose) is utilized widely in cancer diagnosis. And then, Numerous studies have been reported that incidence seems high availability even in the modern diagnosis of dementia and Parkinson's (disease) in brain disease. When using a dynamic PET image including the time information in the static information that is provided for the diagnosis many can increase the accuracy of diagnosis. For this reason, clinical researchers getting great attention but, it is the lack of tools to conduct research. And, it interfered complex mathematical algorithm and programming skills for activation of research. In this study, in order to easy to use and enable research dPET, we developed the software based graphic user interface(GUI). In the future, by many clinical researcher using DIA-Tool is expected to be of great help to dPET research.

  1. NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

    Science.gov (United States)

    Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

    2018-01-01

    We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

  2. Application of image editing software for forensic detection of image ...

    African Journals Online (AJOL)

    Application of image editing software for forensic detection of image. ... The image editing software's available today is apt for creating visually compelling and sophisticated fake images, ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  3. Method for the calculation of volumetric fraction of retained austenite through the software for analysis of digital images

    International Nuclear Information System (INIS)

    Lombardo, S.; Costa, F.H.; Hashimoto, T.M.; Pereira, M.S.; Abdalla, A.J.

    2010-01-01

    In order to calculate the volume fraction of the retained austenite in aeronautic multiphase steels, it was used a digital analysis software for image processing. The materials studied were steels AISI 43XX with carbon content between 30, 40 and 50%, heat treated by conventional quenching and isothermal cooling in bainitic and intercritical region, characterized by optical microscopy, etching by reagent Sodium Metabisulfite (10%) for 30 seconds, with forced drying. The results were compared with the methods of X-Ray Diffraction and Magnetic Saturation through photomicrographs, showing that with this technic it is possible to quantify the percentage of retained austenite in the martensitic matrix, in the different types of steels. (author)

  4. Reliability and accuracy of three imaging software packages used for 3D analysis of the upper airway on cone beam computed tomography images.

    Science.gov (United States)

    Chen, Hui; van Eijnatten, Maureen; Wolff, Jan; de Lange, Jan; van der Stelt, Paul F; Lobbezoo, Frank; Aarab, Ghizlane

    2017-08-01

    The aim of this study was to assess the reliability and accuracy of three different imaging software packages for three-dimensional analysis of the upper airway using CBCT images. To assess the reliability of the software packages, 15 NewTom 5G ® (QR Systems, Verona, Italy) CBCT data sets were randomly and retrospectively selected. Two observers measured the volume, minimum cross-sectional area and the length of the upper airway using Amira ® (Visage Imaging Inc., Carlsbad, CA), 3Diagnosys ® (3diemme, Cantu, Italy) and OnDemand3D ® (CyberMed, Seoul, Republic of Korea) software packages. The intra- and inter-observer reliability of the upper airway measurements were determined using intraclass correlation coefficients and Bland & Altman agreement tests. To assess the accuracy of the software packages, one NewTom 5G ® CBCT data set was used to print a three-dimensional anthropomorphic phantom with known dimensions to be used as the "gold standard". This phantom was subsequently scanned using a NewTom 5G ® scanner. Based on the CBCT data set of the phantom, one observer measured the volume, minimum cross-sectional area, and length of the upper airway using Amira ® , 3Diagnosys ® , and OnDemand3D ® , and compared these measurements with the gold standard. The intra- and inter-observer reliability of the measurements of the upper airway using the different software packages were excellent (intraclass correlation coefficient ≥0.75). There was excellent agreement between all three software packages in volume, minimum cross-sectional area and length measurements. All software packages underestimated the upper airway volume by -8.8% to -12.3%, the minimum cross-sectional area by -6.2% to -14.6%, and the length by -1.6% to -2.9%. All three software packages offered reliable volume, minimum cross-sectional area and length measurements of the upper airway. The length measurements of the upper airway were the most accurate results in all software packages. All

  5. Software Design for Smile Analysis

    Directory of Open Access Journals (Sweden)

    A. Sarkhosh

    2010-12-01

    Full Text Available Introduction: Esthetics and attractiveness of the smile is one of the major demands in contemporary orthodontic treatment. In order to improve a smile design, it is necessary to record “posed smile” as an intentional, non-pressure, static, natural and reproduciblesmile. The record then should be analyzed to determine its characteristics. In this study,we intended to design and introduce a software to analyze the smile rapidly and precisely in order to produce an attractive smile for the patients.Materials and Methods: For this purpose, a practical study was performed to design multimedia software “Smile Analysis” which can receive patients’ photographs and videographs. After giving records to the software, the operator should mark the points and lines which are displayed on the system’s guide and also define the correct scale for each image. Thirty-three variables are measured by the software and displayed on the report page. Reliability of measurements in both image and video was significantly high(=0.7-1.Results: In order to evaluate intra- operator and inter-operator reliability, five cases were selected randomly. Statistical analysis showed that calculations performed in smile analysis software were both valid and highly reliable (for both video and photo.Conclusion: The results obtained from smile analysis could be used in diagnosis,treatment planning and evaluation of the treatment progress.

  6. Effects of photographic distance on tree crown atributes calculated using urbancrowns image analysis software

    Science.gov (United States)

    Mason F. Patterson; P. Eric Wiseman; Matthew F. Winn; Sang-mook Lee; Philip A. Araman

    2011-01-01

    UrbanCrowns is a software program developed by the USDA Forest Service that computes crown attributes using a side-view digital photograph and a few basic field measurements. From an operational standpoint, it is not known how well the software performs under varying photographic conditions for trees of diverse size, which could impact measurement reproducibility and...

  7. Image analysis

    International Nuclear Information System (INIS)

    Berman, M.; Bischof, L.M.; Breen, E.J.; Peden, G.M.

    1994-01-01

    This paper provides an overview of modern image analysis techniques pertinent to materials science. The usual approach in image analysis contains two basic steps: first, the image is segmented into its constituent components (e.g. individual grains), and second, measurement and quantitative analysis are performed. Usually, the segmentation part of the process is the harder of the two. Consequently, much of the paper concentrates on this aspect, reviewing both fundamental segmentation tools (commonly found in commercial image analysis packages) and more advanced segmentation tools. There is also a review of the most widely used quantitative analysis methods for measuring the size, shape and spatial arrangements of objects. Many of the segmentation and analysis methods are demonstrated using complex real-world examples. Finally, there is a discussion of hardware and software issues. 42 refs., 17 figs

  8. Preliminary Studies for a CBCT Imaging Protocol for Offline Organ Motion Analysis: Registration Software Validation and CTDI Measurements

    International Nuclear Information System (INIS)

    Falco, Maria Daniela; Fontanarosa, Davide; Miceli, Roberto; Carosi, Alessandra; Santoni, Riccardo; D'Andrea, Marco

    2011-01-01

    Cone-beam X-ray volumetric imaging in the treatment room, allows online correction of set-up errors and offline assessment of residual set-up errors and organ motion. In this study the registration algorithm of the X-ray volume imaging software (XVI, Elekta, Crawley, United Kingdom), which manages a commercial cone-beam computed tomography (CBCT)-based positioning system, has been tested using a homemade and an anthropomorphic phantom to: (1) assess its performance in detecting known translational and rotational set-up errors and (2) transfer the transformation matrix of its registrations into a commercial treatment planning system (TPS) for offline organ motion analysis. Furthermore, CBCT dose index has been measured for a particular site (prostate: 120 kV, 1028.8 mAs, approximately 640 frames) using a standard Perspex cylindrical body phantom (diameter 32 cm, length 15 cm) and a 10-cm-long pencil ionization chamber. We have found that known displacements were correctly calculated by the registration software to within 1.3 mm and 0.4 o . For the anthropomorphic phantom, only translational displacements have been considered. Both studies have shown errors within the intrinsic uncertainty of our system for translational displacements (estimated as 0.87 mm) and rotational displacements (estimated as 0.22 o ). The resulting table translations proposed by the system to correct the displacements were also checked with portal images and found to place the isocenter of the plan on the linac isocenter within an error of 1 mm, which is the dimension of the spherical lead marker inserted at the center of the homemade phantom. The registration matrix translated into the TPS image fusion module correctly reproduced the alignment between planning CT scans and CBCT scans. Finally, measurements on the CBCT dose index indicate that CBCT acquisition delivers less dose than conventional CT scans and electronic portal imaging device portals. The registration software was found to be

  9. FITS Liberator: Image processing software

    Science.gov (United States)

    Lindberg Christensen, Lars; Nielsen, Lars Holm; Nielsen, Kaspar K.; Johansen, Teis; Hurt, Robert; de Martin, David

    2012-06-01

    The ESA/ESO/NASA FITS Liberator makes it possible to process and edit astronomical science data in the FITS format to produce stunning images of the universe. Formerly a plugin for Adobe Photoshop, the current version of FITS Liberator is a stand-alone application and no longer requires Photoshop. This image processing software makes it possible to create color images using raw observations from a range of telescopes; the FITS Liberator continues to support the FITS and PDS formats, preferred by astronomers and planetary scientists respectively, which enables data to be processed from a wide range of telescopes and planetary probes, including ESO's Very Large Telescope, the NASA/ESA Hubble Space Telescope, NASA's Spitzer Space Telescope, ESA's XMM-Newton Telescope and Cassini-Huygens or Mars Reconnaissance Orbiter.

  10. Generating statements at whole-body imaging with a workflow-optimized software tool - first experiences with multireader analysis

    International Nuclear Information System (INIS)

    Mueller-Horvat, C.; Plathow, C.; Ludescher, B.; Lichy, M.P.; Claussen, C.D.; Schlemmer, H.P.; Canda, V.; Zindel, C.; Hahn, H.K.; Peitgen, H.O.; Kuhnigk, J.

    2007-01-01

    Introduction: Due to technical innovations in sectional diagram methods, whole-body imaging has increased in importance for clinical radiology, particularly for the diagnosis of systemic tumor disease. Large numbers of images have to be evaluated in increasingly shorter time periods. The aim was to create and evaluate a new software tool to assist and automate the process of diagnosing whole-body datasets. Material and Methods: Thirteen whole-body datasets were evaluated by 3 readers using the conventional system and the new software tool. The times for loading the datasets, examining 5 different regions (head, neck, thorax, abdomen and pelvis/skeletal system) and retrieving a relevant finding for demonstration were acquired. Additionally a Student T-Test was performed. For qualitative analysis the 3 readers used a scale from 0 - 4 (0 = bad, 4 = very good) to assess dataset loading convenience, lesion location assistance, and ease of use. Additionally a kappa value was calculated. Results: The average loading time was 39.7 s (± 5.5) with the conventional system and 6.5 s (± 1.4) (p 0.9). The qualitative analysis showed a significant advantage with respect to convenience (p 0.9). (orig.)

  11. Assessing accumulated hard-tissue debris using micro-computed tomography and free software for image processing and analysis.

    Science.gov (United States)

    De-Deus, Gustavo; Marins, Juliana; Neves, Aline de Almeida; Reis, Claudia; Fidel, Sandra; Versiani, Marco A; Alves, Haimon; Lopes, Ricardo Tadeu; Paciornik, Sidnei

    2014-02-01

    The accumulation of debris occurs after root canal preparation procedures specifically in fins, isthmus, irregularities, and ramifications. The aim of this study was to present a step-by-step description of a new method used to longitudinally identify, measure, and 3-dimensionally map the accumulation of hard-tissue debris inside the root canal after biomechanical preparation using free software for image processing and analysis. Three mandibular molars presenting the mesial root with a large isthmus width and a type II Vertucci's canal configuration were selected and scanned. The specimens were assigned to 1 of 3 experimental approaches: (1) 5.25% sodium hypochlorite + 17% EDTA, (2) bidistilled water, and (3) no irrigation. After root canal preparation, high-resolution scans of the teeth were accomplished, and free software packages were used to register and quantify the amount of accumulated hard-tissue debris in either canal space or isthmus areas. Canal preparation without irrigation resulted in 34.6% of its volume filled with hard-tissue debris, whereas the use of bidistilled water or NaOCl followed by EDTA showed a reduction in the percentage volume of debris to 16% and 11.3%, respectively. The closer the distance to the isthmus area was the larger the amount of accumulated debris regardless of the irrigating protocol used. Through the present method, it was possible to calculate the volume of hard-tissue debris in the isthmuses and in the root canal space. Free-software packages used for image reconstruction, registering, and analysis have shown to be promising for end-user application. Copyright © 2014. Published by Elsevier Inc.

  12. Image quality dependence on image processing software in ...

    African Journals Online (AJOL)

    Image quality dependence on image processing software in computed radiography. ... Agfa CR readers use MUSICA software, and an upgrade with significantly different image ... Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  13. Analysis and optimization techniques for real-time streaming image processing software on general purpose systems

    NARCIS (Netherlands)

    Westmijze, Mark

    2018-01-01

    Commercial Off The Shelf (COTS) Chip Multi-Processor (CMP) systems are for cost reasons often used in industry for soft real-time stream processing. COTS CMP systems typically have a low timing predictability, which makes it difficult to develop software applications for these systems with tight

  14. Automated Software Vulnerability Analysis

    Science.gov (United States)

    Sezer, Emre C.; Kil, Chongkyung; Ning, Peng

    Despite decades of research, software continues to have vulnerabilities. Successful exploitations of these vulnerabilities by attackers cost millions of dollars to businesses and individuals. Unfortunately, most effective defensive measures, such as patching and intrusion prevention systems, require an intimate knowledge of the vulnerabilities. Many systems for detecting attacks have been proposed. However, the analysis of the exploited vulnerabilities is left to security experts and programmers. Both the human effortinvolved and the slow analysis process are unfavorable for timely defensive measure to be deployed. The problem is exacerbated by zero-day attacks.

  15. Comparison of two kinds of skin imaging analysis software: VISIA® from Canfield and IPP® from Media Cybernetics.

    Science.gov (United States)

    Wang, X; Shu, X; Li, Z; Huo, W; Zou, L; Tang, Y; Li, L

    2018-01-27

    Skin imaging analysis, acting as a supplement to noninvasive bioengineering devices, has been widely used in medical cosmetology and cosmetic product evaluation. The main aim of this study is to assess the differences and correlations in measuring skin spots, wrinkles, vascular features, porphyrin, and pore between two commercially available image analysis software. Seventy healthy women were included in the study. Before taking pictures, the dermatologist evaluated subjects' skin conditions. Test sites included the forehead, cheek, and periorbital skin. A 2 × 2 cm cardboard was used to make a mark on the skin surface. Pictures were taken using VISIA ® under three kinds light conditions and analyzed using VISIA ® and IPP ® respectively. (1) Skin pore, red area, ultraviolet spot, brown spot, porphyrin, and wrinkle measured with VISIA ® were correlated with those measured with IPP ® (P < .01). (2) Spot, wrinkle, fine line, brown spot, and red area analyzed with VISIA ® were correlated with age on the forehead and periorbital skin (P < .05). L-value, Crow's feet, ultraviolet spot, brown spot, and red area analyzed with IPP ® were correlated with age on the periorbital skin (P < .05). (3) L-value, spot, wrinkle, fine line, porphyrin, red area, and pore analyzed with VISIA ® and IPP ® showed correlations with the subjective evaluation scores (P < .05). VISIA ® and IPP ® showed acceptable correlation in measuring various skin conditions. VISIA ® showed a high sensibility when measured on the forehead skin. IPP ® is available as an alternative software program to evaluate skin features. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Analysis of open source GIS software

    OpenAIRE

    Božnis, Andrius

    2006-01-01

    GIS is one of the most perspective information technology sciences sphere. GIS conjuncts the digital image analysis and data base systems. This makes GIS wide applicable and very high skills demanding system. There is a lot of commercial GIS software which is well advertised and which functionality is pretty well known, while open source software is forgotten. In this diploma work is made analysis of available open source GIS software on the Internet, in the scope of different projects interr...

  17. Motion correction of PET brain images through deconvolution: I. Theoretical development and analysis in software simulations

    Science.gov (United States)

    Faber, T. L.; Raghunath, N.; Tudorascu, D.; Votaw, J. R.

    2009-02-01

    Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. Existing correction methods that use known patient motion obtained from tracking devices either require multi-frame acquisitions, detailed knowledge of the scanner, or specialized reconstruction algorithms. A deconvolution algorithm has been developed that alleviates these drawbacks by using the reconstructed image to estimate the original non-blurred image using maximum likelihood estimation maximization (MLEM) techniques. A high-resolution digital phantom was created by shape-based interpolation of the digital Hoffman brain phantom. Three different sets of 20 movements were applied to the phantom. For each frame of the motion, sinograms with attenuation and three levels of noise were simulated and then reconstructed using filtered backprojection. The average of the 20 frames was considered the motion blurred image, which was restored with the deconvolution algorithm. After correction, contrast increased from a mean of 2.0, 1.8 and 1.4 in the motion blurred images, for the three increasing amounts of movement, to a mean of 2.5, 2.4 and 2.2. Mean error was reduced by an average of 55% with motion correction. In conclusion, deconvolution can be used for correction of motion blur when subject motion is known.

  18. Motion correction of PET brain images through deconvolution: I. Theoretical development and analysis in software simulations

    Energy Technology Data Exchange (ETDEWEB)

    Faber, T L; Raghunath, N; Tudorascu, D; Votaw, J R [Department of Radiology, Emory University Hospital, 1364 Clifton Road, N.E. Atlanta, GA 30322 (United States)], E-mail: tfaber@emory.edu

    2009-02-07

    Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. Existing correction methods that use known patient motion obtained from tracking devices either require multi-frame acquisitions, detailed knowledge of the scanner, or specialized reconstruction algorithms. A deconvolution algorithm has been developed that alleviates these drawbacks by using the reconstructed image to estimate the original non-blurred image using maximum likelihood estimation maximization (MLEM) techniques. A high-resolution digital phantom was created by shape-based interpolation of the digital Hoffman brain phantom. Three different sets of 20 movements were applied to the phantom. For each frame of the motion, sinograms with attenuation and three levels of noise were simulated and then reconstructed using filtered backprojection. The average of the 20 frames was considered the motion blurred image, which was restored with the deconvolution algorithm. After correction, contrast increased from a mean of 2.0, 1.8 and 1.4 in the motion blurred images, for the three increasing amounts of movement, to a mean of 2.5, 2.4 and 2.2. Mean error was reduced by an average of 55% with motion correction. In conclusion, deconvolution can be used for correction of motion blur when subject motion is known.

  19. Counting radon tracks in Makrofol detectors with the 'image reduction and analysis facility' (IRAF) software package

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, F. [Laboratorio de Fisica Medica y Radioactividad Ambiental, Departamento de Medicina Fisica y Farmacologia, Universidad de La Laguna, 38320 La Laguna, Tenerife (Spain)]. E-mail: fimerall@ull.es; Gonzalez-Manrique, S. [Laboratorio de Fisica Medica y Radioactividad Ambiental, Departamento de Medicina Fisica y Farmacologia, Universidad de La Laguna, 38320 La Laguna, Tenerife (Spain); Karlsson, L. [Laboratorio de Fisica Medica y Radioactividad Ambiental, Departamento de Medicina Fisica y Farmacologia, Universidad de La Laguna, 38320 La Laguna, Tenerife (Spain); Hernandez-Armas, J. [Laboratorio de Fisica Medica y Radioactividad Ambiental, Departamento de Medicina Fisica y Farmacologia, Universidad de La Laguna, 38320 La Laguna, Tenerife (Spain); Aparicio, A. [Instituto de Astrofisica de Canarias, 38200 La Laguna, Tenerife (Spain); Departamento de Astrofisica, Universidad de La Laguna. Avenida. Astrofisico Francisco Sanchez s/n, 38071 La Laguna, Tenerife (Spain)

    2007-03-15

    Makrofol detectors are commonly used for long-term radon ({sup 222}Rn) measurements in houses, schools and workplaces. The use of this type of passive detectors for the determination of radon concentrations requires the counting of the nuclear tracks produced by alpha particles on the detecting material. The 'image reduction and analysis facility' (IRAF) software package is a piece of software commonly used in astronomical applications. It allows detailed counting and mapping of sky sections where stars are grouped very closely, even forming clusters. In order to count the nuclear tracks in our Makrofol radon detectors, we have developed an inter-disciplinary application that takes advantage of the similitude that exist between counting stars in a dark sky and tracks in a track-etch detector. Thus, a low cost semi-automatic system has been set up in our laboratory which utilises a commercially available desktop scanner and the IRAF software package. A detailed description of the proposed semi-automatic method and its performance, in comparison to ocular counting, is described in detail here. In addition, the calibration factor for this procedure, 2.97+/-0.07kBqm{sup -3}htrack{sup -1}cm{sup 2}, has been calculated based on the results obtained from exposing 46 detectors to certified radon concentrations. Furthermore, the results of a preliminary radon survey carried out in 62 schools in Tenerife island (Spain), using Makrofol detectors, counted with the mentioned procedure, are briefly presented. The results reported here indicate that the developed procedure permits a fast, accurate and unbiased determination of the radon tracks in a large number of detectors. The measurements carried out in the schools showed that the radon concentrations in at least 12 schools were above 200Bqm{sup -3} and, in two of them, above 400Bqm{sup -3}. Further studies should be performed at those schools following the European Union recommendations about radon concentrations in

  20. High-throughput image analysis of tumor spheroids: a user-friendly software application to measure the size of spheroids automatically and accurately.

    Science.gov (United States)

    Chen, Wenjin; Wong, Chung; Vosburgh, Evan; Levine, Arnold J; Foran, David J; Xu, Eugenia Y

    2014-07-08

    The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application - SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min on a minimally configured laptop, or around 1 min on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary "Manual Initialize" and "Hand Draw" tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model

  1. Quantification of Abdominal Fat in Obese and Healthy Adolescents Using 3 Tesla Magnetic Resonance Imaging and Free Software for Image Analysis.

    Science.gov (United States)

    Eloi, Juliana Cristina; Epifanio, Matias; de Gonçalves, Marília Maia; Pellicioli, Augusto; Vieira, Patricia Froelich Giora; Dias, Henrique Bregolin; Bruscato, Neide; Soder, Ricardo Bernardi; Santana, João Carlos Batista; Mouzaki, Marialena; Baldisserotto, Matteo

    2017-01-01

    Computed tomography, which uses ionizing radiation and expensive software packages for analysis of scans, can be used to quantify abdominal fat. The objective of this study is to measure abdominal fat with 3T MRI using free software for image analysis and to correlate these findings with anthropometric and laboratory parameters in adolescents. This prospective observational study included 24 overweight/obese and 33 healthy adolescents (mean age 16.55 years). All participants underwent abdominal MRI exams. Visceral and subcutaneous fat area and percentage were correlated with anthropometric parameters, lipid profile, glucose metabolism, and insulin resistance. Student's t test and Mann-Whitney's test was applied. Pearson's chi-square test was used to compare proportions. To determine associations Pearson's linear correlation or Spearman's correlation were used. In both groups, waist circumference (WC) was associated with visceral fat area (P = 0.001 and P = 0.01 respectively), and triglycerides were associated with fat percentage (P = 0.046 and P = 0.071 respectively). In obese individuals, total cholesterol/HDL ratio was associated with visceral fat area (P = 0.03) and percentage (P = 0.09), and insulin and HOMA-IR were associated with visceral fat area (P = 0.001) and percentage (P = 0.005). 3T MRI can provide reliable and good quality images for quantification of visceral and subcutaneous fat by using a free software package. The results demonstrate that WC is a good predictor of visceral fat in obese adolescents and visceral fat area is associated with total cholesterol/HDL ratio, insulin and HOMA-IR.

  2. Clinical software for MR imaging system, 4

    International Nuclear Information System (INIS)

    Shimizu, Koji; Kasai, Akira; Okamura, Shoichi

    1992-01-01

    Magnetic resonance imaging continues to elicit new application software through the recent technological advances of MR equipment. This paper describes several applications of our newly developed clinical software. The fast SE sequence (RISE) has proved to reduce routine examination time and to improve image quality, and ultra-fast FE sequence (SMASH) was found to extend the diagnostic capabilities in the field of cardiac study. Diffusion/perfusion imaging achieved in our MR system showed significant promise for providing novel information regarding tissue characterization. Furthermore, Image quality and practicalities of MR angiography have been improved by advanced imaging sequences and sophisticated post-processing software. (author)

  3. Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

    Science.gov (United States)

    Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

    1997-12-01

    Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

  4. Software quality testing process analysis

    OpenAIRE

    Mera Paz, Julián

    2016-01-01

    Introduction: This article is the result of reading, review, analysis of books, magazines and articles well known for their scientific and research quality, which have addressed the software quality testing process. The author, based on his work experience in software development companies, teaching and other areas, has compiled and selected information to argue and substantiate the importance of the software quality testing process. Methodology: the existing literature on the software qualit...

  5. OSIRIX: open source multimodality image navigation software

    Science.gov (United States)

    Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

    2005-04-01

    The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

  6. Software FMEA analysis for safety-related application software

    International Nuclear Information System (INIS)

    Park, Gee-Yong; Kim, Dong Hoon; Lee, Dong Young

    2014-01-01

    Highlights: • We develop a modified FMEA analysis suited for applying to software architecture. • A template for failure modes on a specific software language is established. • A detailed-level software FMEA analysis on nuclear safety software is presented. - Abstract: A method of a software safety analysis is described in this paper for safety-related application software. The target software system is a software code installed at an Automatic Test and Interface Processor (ATIP) in a digital reactor protection system (DRPS). For the ATIP software safety analysis, at first, an overall safety or hazard analysis is performed over the software architecture and modules, and then a detailed safety analysis based on the software FMEA (Failure Modes and Effect Analysis) method is applied to the ATIP program. For an efficient analysis, the software FMEA analysis is carried out based on the so-called failure-mode template extracted from the function blocks used in the function block diagram (FBD) for the ATIP software. The software safety analysis by the software FMEA analysis, being applied to the ATIP software code, which has been integrated and passed through a very rigorous system test procedure, is proven to be able to provide very valuable results (i.e., software defects) that could not be identified during various system tests

  7. Identifying Image Manipulation Software from Image Features

    Science.gov (United States)

    2015-03-26

    scales”. Educational and Psychological Measurement, 20(1):37, 1960. 7. Committee, Technical Standardization. Exchangeable image file format for digital...Digital Forensics. Springer, 2005. 23. Photography, Technical Committee. Photography and graphic technology - Ex- tended colour encodings for digital image

  8. Software Image J to study soil pore distribution

    Directory of Open Access Journals (Sweden)

    Sabrina Passoni

    2014-04-01

    Full Text Available In the soil science, a direct method that allows the study of soil pore distribution is the bi-dimensional (2D digital image analysis. Such technique provides quantitative results of soil pore shape, number and size. The use of specific softwares for the treatment and processing of images allows a fast and efficient method to quantify the soil porous system. However, due to the high cost of commercial softwares, public ones can be an interesting alternative for soil structure analysis. The objective of this work was to evaluate the quality of data provided by the Image J software (public domain used to characterize the voids of two soils, characterized as Geric Ferralsol and Rhodic Ferralsol, from the southeast region of Brazil. The pore distribution analysis technique from impregnated soil blocks was utilized for this purpose. The 2D image acquisition was carried out by using a CCD camera coupled to a conventional optical microscope. After acquisition and treatment of images, they were processed and analyzed by the software Noesis Visilog 5.4® (chosen as the reference program and ImageJ. The parameters chosen to characterize the soil voids were: shape, number and pore size distribution. For both soils, the results obtained for the image total porosity (%, the total number of pores and the pore size distribution showed that the Image J is a suitable software to be applied in the characterization of the soil sample voids impregnated with resin.

  9. On-Orbit Software Analysis

    Science.gov (United States)

    Moran, Susanne I.

    2004-01-01

    The On-Orbit Software Analysis Research Infusion Project was done by Intrinsyx Technologies Corporation (Intrinsyx) at the National Aeronautics and Space Administration (NASA) Ames Research Center (ARC). The Project was a joint collaborative effort between NASA Codes IC and SL, Kestrel Technology (Kestrel), and Intrinsyx. The primary objectives of the Project were: Discovery and verification of software program properties and dependencies, Detection and isolation of software defects across different versions of software, and Compilation of historical data and technical expertise for future applications

  10. Evaluation of automated image analysis software for the detection of diabetic retinopathy to reduce the ophthalmologists' workload.

    Science.gov (United States)

    Soto-Pedre, Enrique; Navea, Amparo; Millan, Saray; Hernaez-Ortega, Maria C; Morales, Jesús; Desco, Maria C; Pérez, Pablo

    2015-02-01

    To assess the safety and workload reduction of an automated 'disease/no disease' grading system for diabetic retinopathy (DR) within a systematic screening programme. Single 45° macular field image per eye was obtained from consecutive patients attending a regional primary care based DR screening programme in Valencia (Spain). The sensitivity and specificity of automated system operating as 'one or more than one microaneurysm detection for disease presence' grader were determined relative to a manual grading as gold standard. Data on age, gender and diabetes mellitus were also recorded. A total of 5278 patients with diabetes were screened. The median age and duration of diabetes was 69 years and 6.9 years, respectively. Estimated prevalence of DR was 15.6%. The software classified 43.9% of the patients as having no DR and 26.1% as having ungradable images. Detection of DR was achieved with 94.5% sensitivity (95% CI 92.6- 96.5) and 68.8% specificity (95%CI 67.2-70.4). The overall accuracy of the automated system was 72.5% (95%CI 71.1-73.9). The present retinal image processing algorithm that can act as prefilter to flag out images with pathological lesions can be implemented in practice. Our results suggest that it could be considered when implementing DR screening programmes. © 2014 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  11. Analysis of image sharpness reproducibility on a novel engineered micro-CT scanner with variable geometry and embedded recalibration software.

    Science.gov (United States)

    Panetta, D; Belcari, N; Del Guerra, A; Bartolomei, A; Salvadori, P A

    2012-04-01

    This study investigates the reproducibility of the reconstructed image sharpness, after modifications of the geometry setup, for a variable magnification micro-CT (μCT) scanner. All the measurements were performed on a novel engineered μCT scanner for in vivo imaging of small animals (Xalt), which has been recently built at the Institute of Clinical Physiology of the National Research Council (IFC-CNR, Pisa, Italy), in partnership with the University of Pisa. The Xalt scanner is equipped with an integrated software for on-line geometric recalibration, which will be used throughout the experiments. In order to evaluate the losses of image quality due to modifications of the geometry setup, we have made 22 consecutive acquisitions by changing alternatively the system geometry between two different setups (Large FoV - LF, and High Resolution - HR). For each acquisition, the tomographic images have been reconstructed before and after the on-line geometric recalibration. For each reconstruction, the image sharpness was evaluated using two different figures of merit: (i) the percentage contrast on a small bar pattern of fixed frequency (f = 5.5 lp/mm for the LF setup and f = 10 lp/mm for the HR setup) and (ii) the image entropy. We have found that, due to the small-scale mechanical uncertainty (in the order of the voxel size), a recalibration is necessary for each geometric setup after repositioning of the system's components; the resolution losses due to the lack of recalibration are worse for the HR setup (voxel size = 18.4 μm). The integrated on-line recalibration algorithm of the Xalt scanner allowed to perform the recalibration quickly, by restoring the spatial resolution of the system to the reference resolution obtained after the initial (off-line) calibration. Copyright © 2011 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  12. Software architecture analysis tool : software architecture metrics collection

    NARCIS (Netherlands)

    Muskens, J.; Chaudron, M.R.V.; Westgeest, R.

    2002-01-01

    The Software Engineering discipline lacks the ability to evaluate software architectures. Here we describe a tool for software architecture analysis that is based on metrics. Metrics can be used to detect possible problems and bottlenecks in software architectures. Even though metrics do not give a

  13. Software for Simulation of Hyperspectral Images

    Science.gov (United States)

    Richtsmeier, Steven C.; Singer-Berk, Alexander; Bernstein, Lawrence S.

    2002-01-01

    A package of software generates simulated hyperspectral images for use in validating algorithms that generate estimates of Earth-surface spectral reflectance from hyperspectral images acquired by airborne and spaceborne instruments. This software is based on a direct simulation Monte Carlo approach for modeling three-dimensional atmospheric radiative transport as well as surfaces characterized by spatially inhomogeneous bidirectional reflectance distribution functions. In this approach, 'ground truth' is accurately known through input specification of surface and atmospheric properties, and it is practical to consider wide variations of these properties. The software can treat both land and ocean surfaces and the effects of finite clouds with surface shadowing. The spectral/spatial data cubes computed by use of this software can serve both as a substitute for and a supplement to field validation data.

  14. PIV/HPIV Film Analysis Software Package

    Science.gov (United States)

    Blackshire, James L.

    1997-01-01

    A PIV/HPIV film analysis software system was developed that calculates the 2-dimensional spatial autocorrelations of subregions of Particle Image Velocimetry (PIV) or Holographic Particle Image Velocimetry (HPIV) film recordings. The software controls three hardware subsystems including (1) a Kodak Megaplus 1.4 camera and EPIX 4MEG framegrabber subsystem, (2) an IEEE/Unidex 11 precision motion control subsystem, and (3) an Alacron I860 array processor subsystem. The software runs on an IBM PC/AT host computer running either the Microsoft Windows 3.1 or Windows 95 operating system. It is capable of processing five PIV or HPIV displacement vectors per second, and is completely automated with the exception of user input to a configuration file prior to analysis execution for update of various system parameters.

  15. Software development for teleroentgenogram analysis

    Science.gov (United States)

    Goshkoderov, A. A.; Khlebnikov, N. A.; Obabkov, I. N.; Serkov, K. V.; Gajniyarov, I. M.; Aliev, A. A.

    2017-09-01

    A framework for the analysis and calculation of teleroentgenograms was developed. Software development was carried out in the Department of Children's Dentistry and Orthodontics in Ural State Medical University. The software calculates the teleroentgenogram by the original method which was developed in this medical department. Program allows designing its own methods for calculating the teleroentgenograms by new methods. It is planned to use the technology of machine learning (Neural networks) in the software. This will help to make the process of calculating the teleroentgenograms easier because methodological points will be placed automatically.

  16. Software for medical image based phantom modelling

    International Nuclear Information System (INIS)

    Possani, R.G.; Massicano, F.; Coelho, T.S.; Yoriyaz, H.

    2011-01-01

    Latest treatment planning systems depends strongly on CT images, so the tendency is that the dosimetry procedures in nuclear medicine therapy be also based on images, such as magnetic resonance imaging (MRI) or computed tomography (CT), to extract anatomical and histological information, as well as, functional imaging or activities map as PET or SPECT. This information associated with the simulation of radiation transport software is used to estimate internal dose in patients undergoing treatment in nuclear medicine. This work aims to re-engineer the software SCMS, which is an interface software between the Monte Carlo code MCNP, and the medical images, that carry information from the patient in treatment. In other words, the necessary information contained in the images are interpreted and presented in a specific format to the Monte Carlo MCNP code to perform the simulation of radiation transport. Therefore, the user does not need to understand complex process of inputting data on MCNP, as the SCMS is responsible for automatically constructing anatomical data from the patient, as well as the radioactive source data. The SCMS was originally developed in Fortran- 77. In this work it was rewritten in an object-oriented language (JAVA). New features and data options have also been incorporated into the software. Thus, the new software has a number of improvements, such as intuitive GUI and a menu for the selection of the energy spectra correspondent to a specific radioisotope stored in a XML data bank. The new version also supports new materials and the user can specify an image region of interest for the calculation of absorbed dose. (author)

  17. Object-oriented design of medical imaging software.

    Science.gov (United States)

    Ligier, Y; Ratib, O; Logean, M; Girard, C; Perrier, R; Scherrer, J R

    1994-01-01

    A special software package for interactive display and manipulation of medical images was developed at the University Hospital of Geneva, as part of a hospital wide Picture Archiving and Communication System (PACS). This software package, called Osiris, was especially designed to be easily usable and adaptable to the needs of noncomputer-oriented physicians. The Osiris software has been developed to allow the visualization of medical images obtained from any imaging modality. It provides generic manipulation tools, processing tools, and analysis tools more specific to clinical applications. This software, based on an object-oriented paradigm, is portable and extensible. Osiris is available on two different operating systems: the Unix X-11/OSF-Motif based workstations, and the Macintosh family.

  18. Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software.

    Science.gov (United States)

    Moon, Andres; Smith, Geoffrey H; Kong, Jun; Rogers, Thomas E; Ellis, Carla L; Farris, Alton B Brad

    2018-02-01

    Renal allograft rejection diagnosis depends on assessment of parameters such as interstitial inflammation; however, studies have shown interobserver variability regarding interstitial inflammation assessment. Since automated image analysis quantitation can be reproducible, we devised customized analysis methods for CD3+ T-cell staining density as a measure of rejection severity and compared them with established commercial methods along with visual assessment. Renal biopsy CD3 immunohistochemistry slides (n = 45), including renal allografts with various degrees of acute cellular rejection (ACR) were scanned for whole slide images (WSIs). Inflammation was quantitated in the WSIs using pathologist visual assessment, commercial algorithms (Aperio nuclear algorithm for CD3+ cells/mm 2 and Aperio positive pixel count algorithm), and customized open source algorithms developed in ImageJ with thresholding/positive pixel counting (custom CD3+%) and identification of pixels fulfilling "maxima" criteria for CD3 expression (custom CD3+ cells/mm 2 ). Based on visual inspections of "markup" images, CD3 quantitation algorithms produced adequate accuracy. Additionally, CD3 quantitation algorithms correlated between each other and also with visual assessment in a statistically significant manner (r = 0.44 to 0.94, p = 0.003 to algorithms presents salient correlations with established methods of CD3 quantitation. These analysis techniques are promising and highly customizable, providing a form of on-slide "flow cytometry" that can facilitate additional diagnostic accuracy in tissue-based assessments.

  19. Peritoneal vascular density assessment using narrow-band imaging and vascular analysis software, and cytokine analysis in women with and without endometriosis.

    Science.gov (United States)

    Kuroda, Keiji; Kitade, Mari; Kikuchi, Iwaho; Kumakiri, Jun; Matsuoka, Shozo; Kuroda, Masako; Takeda, Satoru

    2010-01-01

    The development and onset of endometriosis is associated with angiogenesis and angiogenic factors including cytokines. We analyzed intrapelvic conditions in women with endometriosis via vascular density assessment of grossly normal peritoneum and determination of cytokine levels in peritoneal fluid. Seventy-three patients underwent laparoscopic surgery because of gynecologic disease including endometriosis in our department using a narrow-band imaging system. Each patient was analyzed for peritoneal vascular density using commercially available vascular analysis software (SolemioENDO ProStudy; Olympus Corp, Tokyo, Japan). Each patient was also subjected to analysis of interleukin 6 (IL-6), IL-8, tumor necrosis factor-alpha, and vascular endothelial growth factor concentrations in peritoneal fluid. We defined 4 groups as follows: group 1, endometriosis: gonadotropin-releasing hormone (GnRH) agonist administration group (n=27); group 2, endometriosis: GnRH agonist nonadministration group (n=15); group 3, no endometriosis: GnRH agonist administration group (n=18); and group 4, no endometriosis: GnRH agonist nonadministration group (n=13). No significant differences in peritoneal vascular density between the 4 groups were found under conventional light; however, under narrow-band light, vascular density in the endometriosis groups (groups 1 and 2) was significantly higher. Cytokine analysis of the 4 groups determined that IL-6 and IL-8 concentrations were significantly higher compared with the no endometriosis groups (groups 3 and 4). Tumor necrosis factor-alpha and vascular endothelial growth factor concentrations were not significantly different between groups. In endometriosis, peritoneal vascular density was significantly higher as assessed using the narrow-band imaging system and SolemioENDO ProStudy, whereas GnRH agonist did not obviously decrease vascular density but IL-6 concentration was lower in the GnRH agonist administration group. Copyright (c) 2010 AAGL

  20. Software

    Energy Technology Data Exchange (ETDEWEB)

    Macedo, R.; Budd, G.; Ross, E.; Wells, P.

    2010-07-15

    The software section of this journal presented new software programs that have been developed to help in the exploration and development of hydrocarbon resources. Software provider IHS Inc. has made additions to its geological and engineering analysis software tool, IHS PETRA, a product used by geoscientists and engineers to visualize, analyze and manage well production, well log, drilling, reservoir, seismic and other related information. IHS PETRA also includes a directional well module and a decline curve analysis module to improve analysis capabilities in unconventional reservoirs. Petris Technology Inc. has developed a software to help manage the large volumes of data. PetrisWinds Enterprise (PWE) helps users find and manage wellbore data, including conventional wireline and MWD core data; analysis core photos and images; waveforms and NMR; and external files documentation. Ottawa-based Ambercore Software Inc. has been collaborating with Nexen on the Petroleum iQ software for steam assisted gravity drainage (SAGD) producers. Petroleum iQ integrates geology and geophysics data with engineering data in 3D and 4D. Calgary-based Envirosoft Corporation has developed a software that reduces the costly and time-consuming effort required to comply with Directive 39 of the Alberta Energy Resources Conservation Board. The product includes an emissions modelling software. Houston-based Seismic Micro-Technology (SMT) has developed the Kingdom software that features the latest in seismic interpretation. Holland-based Joa Oil and Gas and Calgary-based Computer Modelling Group have both supplied the petroleum industry with advanced reservoir simulation software that enables reservoir interpretation. The 2010 software survey included a guide to new software applications designed to facilitate petroleum exploration, drilling and production activities. Oil and gas producers can use the products for a range of functions, including reservoir characterization and accounting. In

  1. Technical note on the validation of a semi-automated image analysis software application for estrogen and progesterone receptor detection in breast cancer

    Science.gov (United States)

    2011-01-01

    Background The immunohistochemical detection of estrogen (ER) and progesterone (PR) receptors in breast cancer is routinely used for prognostic and predictive testing. Whole slide digitalization supported by dedicated software tools allows quantization of the image objects (e.g. cell membrane, nuclei) and an unbiased analysis of immunostaining results. Validation studies of image analysis applications for the detection of ER and PR in breast cancer specimens provided strong concordance between the pathologist's manual assessment of slides and scoring performed using different software applications. Methods The effectiveness of two connected semi-automated image analysis software (NuclearQuant v. 1.13 application for Pannoramic™ Viewer v. 1.14) for determination of ER and PR status in formalin-fixed paraffin embedded breast cancer specimens immunostained with the automated Leica Bond Max system was studied. First the detection algorithm was calibrated to the scores provided an independent assessors (pathologist), using selected areas from 38 small digital slides (created from 16 cases) containing a mean number of 195 cells. Each cell was manually marked and scored according to the Allred-system combining frequency and intensity scores. The performance of the calibrated algorithm was tested on 16 cases (14 invasive ductal carcinoma, 2 invasive lobular carcinoma) against the pathologist's manual scoring of digital slides. Results The detection was calibrated to 87 percent object detection agreement and almost perfect Total Score agreement (Cohen's kappa 0.859, quadratic weighted kappa 0.986) from slight or moderate agreement at the start of the study, using the un-calibrated algorithm. The performance of the application was tested against the pathologist's manual scoring of digital slides on 53 regions of interest of 16 ER and PR slides covering all positivity ranges, and the quadratic weighted kappa provided almost perfect agreement (κ = 0.981) among the two

  2. Salvo: Seismic imaging software for complex geologies

    Energy Technology Data Exchange (ETDEWEB)

    OBER,CURTIS C.; GJERTSEN,ROB; WOMBLE,DAVID E.

    2000-03-01

    This report describes Salvo, a three-dimensional seismic-imaging software for complex geologies. Regions of complex geology, such as overthrusts and salt structures, can cause difficulties for many seismic-imaging algorithms used in production today. The paraxial wave equation and finite-difference methods used within Salvo can produce high-quality seismic images in these difficult regions. However this approach comes with higher computational costs which have been too expensive for standard production. Salvo uses improved numerical algorithms and methods, along with parallel computing, to produce high-quality images and to reduce the computational and the data input/output (I/O) costs. This report documents the numerical algorithms implemented for the paraxial wave equation, including absorbing boundary conditions, phase corrections, imaging conditions, phase encoding, and reduced-source migration. This report also describes I/O algorithms for large seismic data sets and images and parallelization methods used to obtain high efficiencies for both the computations and the I/O of seismic data sets. Finally, this report describes the required steps to compile, port and optimize the Salvo software, and describes the validation data sets used to help verify a working copy of Salvo.

  3. Comparison of performance of object-based image analysis techniques available in open source software (Spring and Orfeo Toolbox/Monteverdi) considering very high spatial resolution data

    Science.gov (United States)

    Teodoro, Ana C.; Araujo, Ricardo

    2016-01-01

    The use of unmanned aerial vehicles (UAVs) for remote sensing applications is becoming more frequent. However, this type of information can result in several software problems related to the huge amount of data available. Object-based image analysis (OBIA) has proven to be superior to pixel-based analysis for very high-resolution images. The main objective of this work was to explore the potentialities of the OBIA methods available in two different open source software applications, Spring and OTB/Monteverdi, in order to generate an urban land cover map. An orthomosaic derived from UAVs was considered, 10 different regions of interest were selected, and two different approaches were followed. The first one (Spring) uses the region growing segmentation algorithm followed by the Bhattacharya classifier. The second approach (OTB/Monteverdi) uses the mean shift segmentation algorithm followed by the support vector machine (SVM) classifier. Two strategies were followed: four classes were considered using Spring and thereafter seven classes were considered for OTB/Monteverdi. The SVM classifier produces slightly better results and presents a shorter processing time. However, the poor spectral resolution of the data (only RGB bands) is an important factor that limits the performance of the classifiers applied.

  4. Histomorphometric analysis of nuclear and cellular volumetric alterations in oral lichen planus, lichenoid lesions and normal oral mucosa using image analysis software.

    Science.gov (United States)

    Venkatesiah, Sowmya S; Kale, Alka D; Hallikeremath, Seema R; Kotrashetti, Vijayalakshmi S

    2013-01-01

    Lichen planus is a chronic inflammatory mucocutaneous disease that clinically and histologically resembles lichenoid lesions, although the latter has a different etiology. Though criteria have been suggested for differentiating oral lichen planus from lichenoid lesions, confusion still prevails. To study the cellular and nuclear volumetric features in the epithelium of normal mucosa, lichen planus, and lichenoid lesions to determine variations if any. A retrospective study was done on 25 histologically diagnosed cases each of oral lichen planus, oral lichenoid lesions, and normal oral mucosa. Cellular and nuclear morphometric measurements were assessed on hematoxylin and eosin sections using image analysis software. Analysis of variance test (ANOVA) and Tukey's post-hoc test. The basal cells of oral lichen planus showed a significant increase in the mean nuclear and cellular areas, and in nuclear volume; there was a significant decrease in the nuclear-cytoplasmic ratio as compared to normal mucosa. The suprabasal cells showed a significant increase in nuclear and cellular areas, nuclear diameter, and nuclear and cellular volumes as compared to normal mucosa. The basal cells of oral lichenoid lesions showed significant difference in the mean cellular area and the mean nuclear-cytoplasmic ratio as compared to normal mucosa, whereas the suprabasal cells differed significantly from normal mucosa in the mean nuclear area and the nuclear and cellular volumes. Morphometry can differentiate lesions of oral lichen planus and oral lichenoid lesions from normal oral mucosa. Thus, morphometry may serve to discriminate between normal and premalignant lichen planus and lichenoid lesions. These lesions might have a high risk for malignant transformation and may behave in a similar manner with respect to malignant transformation.

  5. Imaging Sensor Flight and Test Equipment Software

    Science.gov (United States)

    Freestone, Kathleen; Simeone, Louis; Robertson, Byran; Frankford, Maytha; Trice, David; Wallace, Kevin; Wilkerson, DeLisa

    2007-01-01

    The Lightning Imaging Sensor (LIS) is one of the components onboard the Tropical Rainfall Measuring Mission (TRMM) satellite, and was designed to detect and locate lightning over the tropics. The LIS flight code was developed to run on a single onboard digital signal processor, and has operated the LIS instrument since 1997 when the TRMM satellite was launched. The software provides controller functions to the LIS Real-Time Event Processor (RTEP) and onboard heaters, collects the lightning event data from the RTEP, compresses and formats the data for downlink to the satellite, collects housekeeping data and formats the data for downlink to the satellite, provides command processing and interface to the spacecraft communications and data bus, and provides watchdog functions for error detection. The Special Test Equipment (STE) software was designed to operate specific test equipment used to support the LIS hardware through development, calibration, qualification, and integration with the TRMM spacecraft. The STE software provides the capability to control instrument activation, commanding (including both data formatting and user interfacing), data collection, decompression, and display and image simulation. The LIS STE code was developed for the DOS operating system in the C programming language. Because of the many unique data formats implemented by the flight instrument, the STE software was required to comprehend the same formats, and translate them for the test operator. The hardware interfaces to the LIS instrument using both commercial and custom computer boards, requiring that the STE code integrate this variety into a working system. In addition, the requirement to provide RTEP test capability dictated the need to provide simulations of background image data with short-duration lightning transients superimposed. This led to the development of unique code used to control the location, intensity, and variation above background for simulated lightning strikes

  6. Automatic landslide detection from LiDAR DTM derivatives by geographic-object-based image analysis based on open-source software

    Science.gov (United States)

    Knevels, Raphael; Leopold, Philip; Petschko, Helene

    2017-04-01

    With high-resolution airborne Light Detection and Ranging (LiDAR) data more commonly available, many studies have been performed to facilitate the detailed information on the earth surface and to analyse its limitation. Specifically in the field of natural hazards, digital terrain models (DTM) have been used to map hazardous processes such as landslides mainly by visual interpretation of LiDAR DTM derivatives. However, new approaches are striving towards automatic detection of landslides to speed up the process of generating landslide inventories. These studies usually use a combination of optical imagery and terrain data, and are designed in commercial software packages such as ESRI ArcGIS, Definiens eCognition, or MathWorks MATLAB. The objective of this study was to investigate the potential of open-source software for automatic landslide detection based only on high-resolution LiDAR DTM derivatives in a study area within the federal state of Burgenland, Austria. The study area is very prone to landslides which have been mapped with different methodologies in recent years. The free development environment R was used to integrate open-source geographic information system (GIS) software, such as SAGA (System for Automated Geoscientific Analyses), GRASS (Geographic Resources Analysis Support System), or TauDEM (Terrain Analysis Using Digital Elevation Models). The implemented geographic-object-based image analysis (GEOBIA) consisted of (1) derivation of land surface parameters, such as slope, surface roughness, curvature, or flow direction, (2) finding optimal scale parameter by the use of an objective function, (3) multi-scale segmentation, (4) classification of landslide parts (main scarp, body, flanks) by k-mean thresholding, (5) assessment of the classification performance using a pre-existing landslide inventory, and (6) post-processing analysis for the further use in landslide inventories. The results of the developed open-source approach demonstrated good

  7. Application of Software Safety Analysis Methods

    International Nuclear Information System (INIS)

    Park, G. Y.; Hur, S.; Cheon, S. W.; Kim, D. H.; Lee, D. Y.; Kwon, K. C.; Lee, S. J.; Koo, Y. H.

    2009-01-01

    A fully digitalized reactor protection system, which is called the IDiPS-RPS, was developed through the KNICS project. The IDiPS-RPS has four redundant and separated channels. Each channel is mainly composed of a group of bistable processors which redundantly compare process variables with their corresponding setpoints and a group of coincidence processors that generate a final trip signal when a trip condition is satisfied. Each channel also contains a test processor called the ATIP and a display and command processor called the COM. All the functions were implemented in software. During the development of the safety software, various software safety analysis methods were applied, in parallel to the verification and validation (V and V) activities, along the software development life cycle. The software safety analysis methods employed were the software hazard and operability (Software HAZOP) study, the software fault tree analysis (Software FTA), and the software failure modes and effects analysis (Software FMEA)

  8. MAUS: MICE Analysis User Software

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    The Muon Ionization Cooling Experiment (MICE) has developed the MICE Analysis User Software (MAUS) to simulate and analyse experimental data. It serves as the primary codebase for the experiment, providing for online data quality checks and offline batch simulation and reconstruction. The code is structured in a Map-Reduce framework to allow parallelization whether on a personal machine or in the control room. Various software engineering practices from industry are also used to ensure correct and maintainable physics code, which include unit, functional and integration tests, continuous integration and load testing, code reviews, and distributed version control systems. Lastly, there are various small design decisions like using JSON as the data structure, using SWIG to allow developers to write components in either Python or C++, or using the SCons python-based build system that may be of interest to other experiments.

  9. Software to model AXAF-I image quality

    Science.gov (United States)

    Ahmad, Anees; Feng, Chen

    1995-01-01

    A modular user-friendly computer program for the modeling of grazing-incidence type x-ray optical systems has been developed. This comprehensive computer software GRAZTRACE covers the manipulation of input data, ray tracing with reflectivity and surface deformation effects, convolution with x-ray source shape, and x-ray scattering. The program also includes the capabilities for image analysis, detector scan modeling, and graphical presentation of the results. A number of utilities have been developed to interface the predicted Advanced X-ray Astrophysics Facility-Imaging (AXAF-I) mirror structural and thermal distortions with the ray-trace. This software is written in FORTRAN 77 and runs on a SUN/SPARC station. An interactive command mode version and a batch mode version of the software have been developed.

  10. Digital PIV (DPIV) Software Analysis System

    Science.gov (United States)

    Blackshire, James L.

    1997-01-01

    A software package was developed to provide a Digital PIV (DPIV) capability for NASA LaRC. The system provides an automated image capture, test correlation, and autocorrelation analysis capability for the Kodak Megaplus 1.4 digital camera system for PIV measurements. The package includes three separate programs that, when used together with the PIV data validation algorithm, constitutes a complete DPIV analysis capability. The programs are run on an IBM PC/AT host computer running either Microsoft Windows 3.1 or Windows 95 using a 'quickwin' format that allows simple user interface and output capabilities to the windows environment.

  11. Software Performs Complex Design Analysis

    Science.gov (United States)

    2008-01-01

    Designers use computational fluid dynamics (CFD) to gain greater understanding of the fluid flow phenomena involved in components being designed. They also use finite element analysis (FEA) as a tool to help gain greater understanding of the structural response of components to loads, stresses and strains, and the prediction of failure modes. Automated CFD and FEA engineering design has centered on shape optimization, which has been hindered by two major problems: 1) inadequate shape parameterization algorithms, and 2) inadequate algorithms for CFD and FEA grid modification. Working with software engineers at Stennis Space Center, a NASA commercial partner, Optimal Solutions Software LLC, was able to utilize its revolutionary, one-of-a-kind arbitrary shape deformation (ASD) capability-a major advancement in solving these two aforementioned problems-to optimize the shapes of complex pipe components that transport highly sensitive fluids. The ASD technology solves the problem of inadequate shape parameterization algorithms by allowing the CFD designers to freely create their own shape parameters, therefore eliminating the restriction of only being able to use the computer-aided design (CAD) parameters. The problem of inadequate algorithms for CFD grid modification is solved by the fact that the new software performs a smooth volumetric deformation. This eliminates the extremely costly process of having to remesh the grid for every shape change desired. The program can perform a design change in a markedly reduced amount of time, a process that would traditionally involve the designer returning to the CAD model to reshape and then remesh the shapes, something that has been known to take hours, days-even weeks or months-depending upon the size of the model.

  12. Intercomparison of gamma ray analysis software packages

    International Nuclear Information System (INIS)

    1998-04-01

    The IAEA undertook an intercomparison exercise to review available software for gamma ray spectra analysis. This document describes the methods used in the intercomparison exercise, characterizes the software packages reviewed and presents the results obtained. Only direct results are given without any recommendation for a particular software or method for gamma ray spectra analysis

  13. Infusing Reliability Techniques into Software Safety Analysis

    Science.gov (United States)

    Shi, Ying

    2015-01-01

    Software safety analysis for a large software intensive system is always a challenge. Software safety practitioners need to ensure that software related hazards are completely identified, controlled, and tracked. This paper discusses in detail how to incorporate the traditional reliability techniques into the entire software safety analysis process. In addition, this paper addresses how information can be effectively shared between the various practitioners involved in the software safety analyses. The author has successfully applied the approach to several aerospace applications. Examples are provided to illustrate the key steps of the proposed approach.

  14. Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

    Science.gov (United States)

    Brunner, J; Krummenauer, F; Lehr, H A

    2000-04-01

    Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

  15. Total Mini-Mental State Examination score and regional cerebral blood flow using Z score imaging and automated ROI analysis software in subjects with memory impairment

    International Nuclear Information System (INIS)

    Ikeda, Eiji; Shiozaki, Kazumasa; Takahashi, Nobukazu; Togo, Takashi; Odawara, Toshinari; Oka, Takashi; Inoue, Tomio; Hirayasu, Yoshio

    2008-01-01

    The Mini-Mental State Examination (MMSE) is considered a useful supplementary method to diagnose dementia and evaluate the severity of cognitive disturbance. However, the region of the cerebrum that correlates with the MMSE score is not clear. Recently, a new method was developed to analyze regional cerebral blood flow (rCBF) using a Z score imaging system (eZIS). This system shows changes of rCBF when compared with a normal database. In addition, a three-dimensional stereotaxic region of interest (ROI) template (3DSRT), fully automated ROI analysis software was developed. The objective of this study was to investigate the correlation between rCBF changes and total MMSE score using these new methods. The association between total MMSE score and rCBF changes was investigated in 24 patients (mean age±standard deviation (SD) 71.5±9.2 years; 6 men and 18 women) with memory impairment using eZIS and 3DSRT. Step-wise multiple regression analysis was used for multivariate analysis, with the total MMSE score as the dependent variable and rCBF change in 24 areas as the independent variable. Total MMSE score was significantly correlated only with the reduction of left hippocampal perfusion but not with right (P<0.01). Total MMSE score is an important indicator of left hippocampal function. (author)

  16. Current and future trends in marine image annotation software

    Science.gov (United States)

    Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

    2016-12-01

    Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images

  17. Semiautomated Segmentation and Measurement of Cytoplasmic Vacuoles in a Neutrophil With General-Purpose Image Analysis Software.

    Science.gov (United States)

    Mizukami, Maki; Yamada, Misaki; Fukui, Sayaka; Fujimoto, Nao; Yoshida, Shigeru; Kaga, Sanae; Obata, Keiko; Jin, Shigeki; Miwa, Keiko; Masauzi, Nobuo

    2016-11-01

    Morphological observation of blood or marrow film is still described nonquantitatively. We developed a semiautomatic method for segmenting vacuoles from the cytoplasm using Photoshop (PS) and Image-J (IJ), called PS-IJ, and measured the relative entire cell area (rECA) and relative areas of vacuoles (rAV) in the cytoplasm of neutrophil with PS-IJ. Whole-blood samples were stored at 4°C with ethylenediaminetetraacetate and in two different preserving manners (P1 and P2). Color-tone intensity levels of neutrophil images were semiautomatically compensated using PS, and then vacuole portions were automatically segmented by IJ. The rAV and rECA were measured by counting pixels by IJ. For evaluating the accuracy in segmentations of vacuoles with PS-IJ, the rAV/rECA ratios calculated with results from PS-IJ were compared with those calculated with human eye and IJ (HE-IJ). The rECA and rAV/ in P1 significantly (P < 0.05, P < 0.05) were enlarged and increased, but did not significantly (P = 0.46, P = 0.21) change in P2. The rAV/rECA ratios by PS-IJ were significantly correlated (r = 0.90, P < 0.01) with those by HE-IJ. PS-IJ method can successfully segment vacuoles and measure the rAV and rECA, becoming a useful tool for quantitative description of morphological observation of blood and marrow film. © 2016 Wiley Periodicals, Inc.

  18. Development of Software to Model AXAF-I Image Quality

    Science.gov (United States)

    Ahmad, Anees; Hawkins, Lamar

    1996-01-01

    This draft final report describes the work performed under the delivery order number 145 from May 1995 through August 1996. The scope of work included a number of software development tasks for the performance modeling of AXAF-I. A number of new capabilities and functions have been added to the GT software, which is the command mode version of the GRAZTRACE software, originally developed by MSFC. A structural data interface has been developed for the EAL (old SPAR) finite element analysis FEA program, which is being used by MSFC Structural Analysis group for the analysis of AXAF-I. This interface utility can read the structural deformation file from the EAL and other finite element analysis programs such as NASTRAN and COSMOS/M, and convert the data to a suitable format that can be used for the deformation ray-tracing to predict the image quality for a distorted mirror. There is a provision in this utility to expand the data from finite element models assuming 180 degrees symmetry. This utility has been used to predict image characteristics for the AXAF-I HRMA, when subjected to gravity effects in the horizontal x-ray ground test configuration. The development of the metrology data processing interface software has also been completed. It can read the HDOS FITS format surface map files, manipulate and filter the metrology data, and produce a deformation file, which can be used by GT for ray tracing for the mirror surface figure errors. This utility has been used to determine the optimum alignment (axial spacing and clocking) for the four pairs of AXAF-I mirrors. Based on this optimized alignment, the geometric images and effective focal lengths for the as built mirrors were predicted to cross check the results obtained by Kodak.

  19. Fault tree analysis of KNICS RPS software

    International Nuclear Information System (INIS)

    Park, Gee Yong; Kwon, Kee Choon; Koh, Kwang Yong; Jee, Eun Kyoung; Seong, Poong Hyun; Lee, Dae Hyung

    2008-01-01

    This paper describes the application of a software Fault Tree Analysis (FTA) as one of the analysis techniques for a Software Safety Analysis (SSA) at the design phase and its analysis results for the safety-critical software of a digital reactor protection system, which is called the KNICS RPS, being developed in the KNICS (Korea Nuclear Instrumentation and Control Systems) project. The software modules in the design description were represented by Function Blocks (FBs), and the software FTA was performed based on the well-defined fault tree templates for the FBs. The SSA, which is part of the verification and validation (V and V) activities, was activated at each phase of the software lifecycle for the KNICS RPS. At the design phase, the software HAZOP (Hazard and Operability) and the software FTA were employed in the SSA in such a way that the software HAZOP was performed first and then the software FTA was applied. The software FTA was applied to some critical modules selected from the software HAZOP analysis

  20. Dependability Analysis Methods For Configurable Software

    International Nuclear Information System (INIS)

    Dahll, Gustav; Pulkkinen, Urho

    1996-01-01

    Configurable software systems are systems which are built up by standard software components in the same way as a hardware system is built up by standard hardware components. Such systems are often used in the control of NPPs, also in safety related applications. A reliability analysis of such systems is therefore necessary. This report discusses what configurable software is, and what is particular with respect to reliability assessment of such software. Two very commonly used techniques in traditional reliability analysis, viz. failure mode, effect and criticality analysis (FMECA) and fault tree analysis are investigated. A real example is used to illustrate the discussed methods. Various aspects relevant to the assessment of the software reliability in such systems are discussed. Finally some models for quantitative software reliability assessment applicable on configurable software systems are described. (author)

  1. Reliability analysis of software based safety functions

    International Nuclear Information System (INIS)

    Pulkkinen, U.

    1993-05-01

    The methods applicable in the reliability analysis of software based safety functions are described in the report. Although the safety functions also include other components, the main emphasis in the report is on the reliability analysis of software. The check list type qualitative reliability analysis methods, such as failure mode and effects analysis (FMEA), are described, as well as the software fault tree analysis. The safety analysis based on the Petri nets is discussed. The most essential concepts and models of quantitative software reliability analysis are described. The most common software metrics and their combined use with software reliability models are discussed. The application of software reliability models in PSA is evaluated; it is observed that the recent software reliability models do not produce the estimates needed in PSA directly. As a result from the study some recommendations and conclusions are drawn. The need of formal methods in the analysis and development of software based systems, the applicability of qualitative reliability engineering methods in connection to PSA and the need to make more precise the requirements for software based systems and their analyses in the regulatory guides should be mentioned. (orig.). (46 refs., 13 figs., 1 tab.)

  2. Software architecture analysis of usability

    NARCIS (Netherlands)

    Folmer, Eelke

    2005-01-01

    One of the qualities that has received increased attention in recent decades is usability. A software product with poor usability is likely to fail in a highly competitive market; therefore software developing organizations are paying more and more attention to ensuring the usability of their

  3. Image Analysis

    DEFF Research Database (Denmark)

    The 19th Scandinavian Conference on Image Analysis was held at the IT University of Copenhagen in Denmark during June 15-17, 2015. The SCIA conference series has been an ongoing biannual event for more than 30 years and over the years it has nurtured a world-class regional research and development...... area within the four participating Nordic countries. It is a regional meeting of the International Association for Pattern Recognition (IAPR). We would like to thank all authors who submitted works to this year’s SCIA, the invited speakers, and our Program Committee. In total 67 papers were submitted....... The topics of the accepted papers range from novel applications of vision systems, pattern recognition, machine learning, feature extraction, segmentation, 3D vision, to medical and biomedical image analysis. The papers originate from all the Scandinavian countries and several other European countries...

  4. Digital image processing software system using an array processor

    International Nuclear Information System (INIS)

    Sherwood, R.J.; Portnoff, M.R.; Journeay, C.H.; Twogood, R.E.

    1981-01-01

    A versatile array processor-based system for general-purpose image processing was developed. At the heart of this system is an extensive, flexible software package that incorporates the array processor for effective interactive image processing. The software system is described in detail, and its application to a diverse set of applications at LLNL is briefly discussed. 4 figures, 1 table

  5. IFDOTMETER: A New Software Application for Automated Immunofluorescence Analysis.

    Science.gov (United States)

    Rodríguez-Arribas, Mario; Pizarro-Estrella, Elisa; Gómez-Sánchez, Rubén; Yakhine-Diop, S M S; Gragera-Hidalgo, Antonio; Cristo, Alejandro; Bravo-San Pedro, Jose M; González-Polo, Rosa A; Fuentes, José M

    2016-04-01

    Most laboratories interested in autophagy use different imaging software for managing and analyzing heterogeneous parameters in immunofluorescence experiments (e.g., LC3-puncta quantification and determination of the number and size of lysosomes). One solution would be software that works on a user's laptop or workstation that can access all image settings and provide quick and easy-to-use analysis of data. Thus, we have designed and implemented an application called IFDOTMETER, which can run on all major operating systems because it has been programmed using JAVA (Sun Microsystems). Briefly, IFDOTMETER software has been created to quantify a variety of biological hallmarks, including mitochondrial morphology and nuclear condensation. The program interface is intuitive and user-friendly, making it useful for users not familiar with computer handling. By setting previously defined parameters, the software can automatically analyze a large number of images without the supervision of the researcher. Once analysis is complete, the results are stored in a spreadsheet. Using software for high-throughput cell image analysis offers researchers the possibility of performing comprehensive and precise analysis of a high number of images in an automated manner, making this routine task easier. © 2015 Society for Laboratory Automation and Screening.

  6. Software for fast cameras and image handling on MAST

    International Nuclear Information System (INIS)

    Shibaev, S.

    2008-01-01

    The rapid progress in fast imaging gives new opportunities for fusion research. The data obtained by fast cameras play an important and ever-increasing role in analysis and understanding of plasma phenomena. The fast cameras produce a huge amount of data which creates considerable problems for acquisition, analysis, and storage. We use a number of fast cameras on the Mega-Amp Spherical Tokamak (MAST). They cover several spectral ranges: broadband visible, infra-red and narrow band filtered for spectroscopic studies. These cameras are controlled by programs developed in-house. The programs provide full camera configuration and image acquisition in the MAST shot cycle. Despite the great variety of image sources, all images should be stored in a single format. This simplifies development of data handling tools and hence the data analysis. A universal file format has been developed for MAST images which supports storage in both raw and compressed forms, using either lossless or lossy compression. A number of access and conversion routines have been developed for all languages used on MAST. Two movie-style display tools have been developed-Windows native and Qt based for Linux. The camera control programs run as autonomous data acquisition units with full camera configuration set and stored locally. This allows easy porting of the code to other data acquisition systems. The software developed for MAST fast cameras has been adapted for several other tokamaks where it is in regular use

  7. Image enhancement software for underwater recovery operations: User's manual

    Science.gov (United States)

    Partridge, William J.; Therrien, Charles W.

    1989-06-01

    This report describes software for performing image enhancement on live or recorded video images. The software was developed for operational use during underwater recovery operations at the Naval Undersea Warfare Engineering Station. The image processing is performed on an IBM-PC/AT compatible computer equipped with hardware to digitize and display video images. The software provides the capability to provide contrast enhancement and other similar functions in real time through hardware lookup tables, to automatically perform histogram equalization, to capture one or more frames and average them or apply one of several different processing algorithms to a captured frame. The report is in the form of a user manual for the software and includes guided tutorial and reference sections. A Digital Image Processing Primer in the appendix serves to explain the principle concepts that are used in the image processing.

  8. Gamma-Ray Spectrum Analysis Software GDA

    International Nuclear Information System (INIS)

    Wanabongse, P.

    1998-01-01

    The developmental work on computer software for gamma-ray spectrum analysis has been completed as a software package version 1.02 named GDA, which is an acronym for Gamma-spectrum Deconvolution and Analysis. The software package consists of three 3.5-inch diskettes for setup and a user's manual. GDA software can be installed for using on a personal computer with Windows 95 or Windows NT 4.0 operating system. A computer maybe the type of 80486 CPU with 8 megabytes of memory

  9. Software architecture analysis of usability

    NARCIS (Netherlands)

    Folmer, E; van Gurp, J; Bosch, J; Bastide, R; Palanque, P; Roth, J

    2005-01-01

    Studies of software engineering projects show that a large number of usability related change requests are made after its deployment. Fixing usability problems during the later stages of development often proves to be costly, since many of the necessary changes require changes to the system that

  10. Image formation and image analysis in electron microscopy

    International Nuclear Information System (INIS)

    Heel, M. van.

    1981-01-01

    This thesis covers various aspects of image formation and image analysis in electron microscopy. The imaging of relatively strong objects in partially coherent illumination, the coherence properties of thermionic emission sources and the detection of objects in quantum noise limited images are considered. IMAGIC, a fast, flexible and friendly image analysis software package is described. Intelligent averaging of molecular images is discussed. (C.F.)

  11. Development of Cell Analysis Software for Cultivated Corneal Endothelial Cells.

    Science.gov (United States)

    Okumura, Naoki; Ishida, Naoya; Kakutani, Kazuya; Hongo, Akane; Hiwa, Satoru; Hiroyasu, Tomoyuki; Koizumi, Noriko

    2017-11-01

    To develop analysis software for cultured human corneal endothelial cells (HCECs). Software was designed to recognize cell borders and to provide parameters such as cell density, coefficient of variation, and polygonality of cultured HCECs based on phase contrast images. Cultured HCECs with high or low cell density were incubated with Ca-free and Mg-free phosphate-buffered saline for 10 minutes to reveal the cell borders and were then analyzed with software (n = 50). Phase contrast images showed that cell borders were not distinctly outlined, but these borders became more distinctly outlined after phosphate-buffered saline treatment and were recognized by cell analysis software. The cell density value provided by software was similar to that obtained using manual cell counting by an experienced researcher. Morphometric parameters, such as the coefficient of variation and polygonality, were also produced by software, and these values were significantly correlated with cell density (Pearson correlation coefficients -0.62 and 0.63, respectively). The software described here provides morphometric information from phase contrast images, and it enables subjective and noninvasive quality assessment for tissue engineering therapy of the corneal endothelium.

  12. Multimodality image registration with software: state-of-the-art

    Energy Technology Data Exchange (ETDEWEB)

    Slomka, Piotr J. [Cedars-Sinai Medical Center, AIM Program/Department of Imaging, Los Angeles, CA (United States); University of California, David Geffen School of Medicine, Los Angeles, CA (United States); Baum, Richard P. [Center for PET, Department of Nuclear Medicine, Bad Berka (Germany)

    2009-03-15

    Multimodality image integration of functional and anatomical data can be performed by means of dedicated hybrid imaging systems or by software image co-registration techniques. Hybrid positron emission tomography (PET)/computed tomography (CT) systems have found wide acceptance in oncological imaging, while software registration techniques have a significant role in patient-specific, cost-effective, and radiation dose-effective application of integrated imaging. Software techniques allow accurate (2-3 mm) rigid image registration of brain PET with CT and MRI. Nonlinear techniques are used in whole-body image registration, and recent developments allow for significantly accelerated computing times. Nonlinear software registration of PET with CT or MRI is required for multimodality radiation planning. Difficulties remain in the validation of nonlinear registration of soft tissue organs. The utilization of software-based multimodality image integration in a clinical environment is sometimes hindered by the lack of appropriate picture archiving and communication systems (PACS) infrastructure needed to efficiently and automatically integrate all available images into one common database. In cardiology applications, multimodality PET/single photon emission computed tomography and coronary CT angiography imaging is typically not required unless the results of one of the tests are equivocal. Software image registration is likely to be used in a complementary fashion with hybrid PET/CT or PET/magnetic resonance imaging systems. Software registration of stand-alone scans ''paved the way'' for the clinical application of hybrid scanners, demonstrating practical benefits of image integration before the hybrid dual-modality devices were available. (orig.)

  13. Multimodality image registration with software: state-of-the-art

    International Nuclear Information System (INIS)

    Slomka, Piotr J.; Baum, Richard P.

    2009-01-01

    Multimodality image integration of functional and anatomical data can be performed by means of dedicated hybrid imaging systems or by software image co-registration techniques. Hybrid positron emission tomography (PET)/computed tomography (CT) systems have found wide acceptance in oncological imaging, while software registration techniques have a significant role in patient-specific, cost-effective, and radiation dose-effective application of integrated imaging. Software techniques allow accurate (2-3 mm) rigid image registration of brain PET with CT and MRI. Nonlinear techniques are used in whole-body image registration, and recent developments allow for significantly accelerated computing times. Nonlinear software registration of PET with CT or MRI is required for multimodality radiation planning. Difficulties remain in the validation of nonlinear registration of soft tissue organs. The utilization of software-based multimodality image integration in a clinical environment is sometimes hindered by the lack of appropriate picture archiving and communication systems (PACS) infrastructure needed to efficiently and automatically integrate all available images into one common database. In cardiology applications, multimodality PET/single photon emission computed tomography and coronary CT angiography imaging is typically not required unless the results of one of the tests are equivocal. Software image registration is likely to be used in a complementary fashion with hybrid PET/CT or PET/magnetic resonance imaging systems. Software registration of stand-alone scans ''paved the way'' for the clinical application of hybrid scanners, demonstrating practical benefits of image integration before the hybrid dual-modality devices were available. (orig.)

  14. STAR: Software Toolkit for Analysis Research

    International Nuclear Information System (INIS)

    Doak, J.E.; Prommel, J.M.; Whiteson, R.; Hoffbauer, B.L.; Thomas, T.R.; Helman, P.

    1993-01-01

    Analyzing vast quantities of data from diverse information sources is an increasingly important element for nonproliferation and arms control analysis. Much of the work in this area has used human analysts to assimilate, integrate, and interpret complex information gathered from various sources. With the advent of fast computers, we now have the capability to automate this process thereby shifting this burden away from humans. In addition, there now exist huge data storage capabilities which have made it possible to formulate large integrated databases comprising many thereabouts of information spanning a variety of subjects. We are currently designing a Software Toolkit for Analysis Research (STAR) to address these issues. The goal of STAR is to Produce a research tool that facilitates the development and interchange of algorithms for locating phenomena of interest to nonproliferation and arms control experts. One major component deals with the preparation of information. The ability to manage and effectively transform raw data into a meaningful form is a prerequisite for analysis by any methodology. The relevant information to be analyzed can be either unstructured text structured data, signals, or images. Text can be numerical and/or character, stored in raw data files, databases, streams of bytes, or compressed into bits in formats ranging from fixed, to character-delimited, to a count followed by content The data can be analyzed in real-time or batch mode. Once the data are preprocessed, different analysis techniques can be applied. Some are built using expert knowledge. Others are trained using data collected over a period of time. Currently, we are considering three classes of analyzers for use in our software toolkit: (1) traditional machine learning techniques, (2) the purely statistical system, and (3) expert systems

  15. IMAGE information monitoring and applied graphics software environment. Volume 2. Software description

    International Nuclear Information System (INIS)

    Hallam, J.W.; Ng, K.B.; Upham, G.L.

    1986-09-01

    The EPRI Information Monitoring and Applied Graphics Environment (IMAGE) system is designed for 'fast proto-typing' of advanced concepts for computer-aided plant operations tools. It is a flexible software system which can be used for rapidly creating, dynamically driving and evaluating advanced operator aid displays. The software is written to be both host computer and graphic device independent

  16. Improved Software to Browse the Serial Medical Images for Learning.

    Science.gov (United States)

    Kwon, Koojoo; Chung, Min Suk; Park, Jin Seo; Shin, Byeong Seok; Chung, Beom Sun

    2017-07-01

    The thousands of serial images used for medical pedagogy cannot be included in a printed book; they also cannot be efficiently handled by ordinary image viewer software. The purpose of this study was to provide browsing software to grasp serial medical images efficiently. The primary function of the newly programmed software was to select images using 3 types of interfaces: buttons or a horizontal scroll bar, a vertical scroll bar, and a checkbox. The secondary function was to show the names of the structures that had been outlined on the images. To confirm the functions of the software, 3 different types of image data of cadavers (sectioned and outlined images, volume models of the stomach, and photos of the dissected knees) were inputted. The browsing software was downloadable for free from the homepage (anatomy.co.kr) and available off-line. The data sets provided could be replaced by any developers for their educational achievements. We anticipate that the software will contribute to medical education by allowing users to browse a variety of images. © 2017 The Korean Academy of Medical Sciences.

  17. Objective detection of apoptosis in rat renal tissue sections using light microscopy and free image analysis software with subsequent machine learning: Detection of apoptosis in renal tissue.

    Science.gov (United States)

    Macedo, Nayana Damiani; Buzin, Aline Rodrigues; de Araujo, Isabela Bastos Binotti Abreu; Nogueira, Breno Valentim; de Andrade, Tadeu Uggere; Endringer, Denise Coutinho; Lenz, Dominik

    2017-02-01

    The current study proposes an automated machine learning approach for the quantification of cells in cell death pathways according to DNA fragmentation. A total of 17 images of kidney histological slide samples from male Wistar rats were used. The slides were photographed using an Axio Zeiss Vert.A1 microscope with a 40x objective lens coupled with an Axio Cam MRC Zeiss camera and Zen 2012 software. The images were analyzed using CellProfiler (version 2.1.1) and CellProfiler Analyst open-source software. Out of the 10,378 objects, 4970 (47,9%) were identified as TUNEL positive, and 5408 (52,1%) were identified as TUNEL negative. On average, the sensitivity and specificity values of the machine learning approach were 0.80 and 0.77, respectively. Image cytometry provides a quantitative analytical alternative to the more traditional qualitative methods more commonly used in studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Development of a fatigue analysis software system

    International Nuclear Information System (INIS)

    Choi, B. I.; Lee, H. J.; Han, S. W.; Kim, J. Y.; Hwang, K. H.; Kang, J. Y.

    2001-01-01

    A general purpose fatigue analysis software to predict fatigue lives of mechanical components and structures was developed. This software has some characteristic features including functions of searching weak regions on the free surface in order to reduce computing time significantly, a database of fatigue properties for various materials, and an expert system which can assist any users to get more proper results. This software can be used in the environment consists of commercial finite element packages. Using the software developed fatigue analyses for a SAE keyhole specimen and an automobile knuckle were carried out. It was observed that the results were agree well with those from commercial packages

  19. Numerical methods in software and analysis

    CERN Document Server

    Rice, John R

    1992-01-01

    Numerical Methods, Software, and Analysis, Second Edition introduces science and engineering students to the methods, tools, and ideas of numerical computation. Introductory courses in numerical methods face a fundamental problem-there is too little time to learn too much. This text solves that problem by using high-quality mathematical software. In fact, the objective of the text is to present scientific problem solving using standard mathematical software. This book discusses numerous programs and software packages focusing on the IMSL library (including the PROTRAN system) and ACM Algorithm

  20. Software Process Improvement Using Force Field Analysis ...

    African Journals Online (AJOL)

    An improvement plan is then drawn and implemented. This paper studied the state of Nigerian software development organizations based on selected attributes. Force field analysis is used to partition the factors obtained into driving and restraining forces. An attempt was made to improve the software development process ...

  1. Software for simulation of a computed tomography imaging spectrometer using optical design software

    Science.gov (United States)

    Spuhler, Peter T.; Willer, Mark R.; Volin, Curtis E.; Descour, Michael R.; Dereniak, Eustace L.

    2000-11-01

    Our Imaging Spectrometer Simulation Software known under the name Eikon should improve and speed up the design of a Computed Tomography Imaging Spectrometer (CTIS). Eikon uses existing raytracing software to simulate a virtual instrument. Eikon enables designers to virtually run through the design, calibration and data acquisition, saving significant cost and time when designing an instrument. We anticipate that Eikon simulations will improve future designs of CTIS by allowing engineers to explore more instrument options.

  2. Frequency and analysis of non-clinical errors made in radiology reports using the National Integrated Medical Imaging System voice recognition dictation software.

    Science.gov (United States)

    Motyer, R E; Liddy, S; Torreggiani, W C; Buckley, O

    2016-11-01

    Voice recognition (VR) dictation of radiology reports has become the mainstay of reporting in many institutions worldwide. Despite benefit, such software is not without limitations, and transcription errors have been widely reported. Evaluate the frequency and nature of non-clinical transcription error using VR dictation software. Retrospective audit of 378 finalised radiology reports. Errors were counted and categorised by significance, error type and sub-type. Data regarding imaging modality, report length and dictation time was collected. 67 (17.72 %) reports contained ≥1 errors, with 7 (1.85 %) containing 'significant' and 9 (2.38 %) containing 'very significant' errors. A total of 90 errors were identified from the 378 reports analysed, with 74 (82.22 %) classified as 'insignificant', 7 (7.78 %) as 'significant', 9 (10 %) as 'very significant'. 68 (75.56 %) errors were 'spelling and grammar', 20 (22.22 %) 'missense' and 2 (2.22 %) 'nonsense'. 'Punctuation' error was most common sub-type, accounting for 27 errors (30 %). Complex imaging modalities had higher error rates per report and sentence. Computed tomography contained 0.040 errors per sentence compared to plain film with 0.030. Longer reports had a higher error rate, with reports >25 sentences containing an average of 1.23 errors per report compared to 0-5 sentences containing 0.09. These findings highlight the limitations of VR dictation software. While most error was deemed insignificant, there were occurrences of error with potential to alter report interpretation and patient management. Longer reports and reports on more complex imaging had higher error rates and this should be taken into account by the reporting radiologist.

  3. Predictive images of postoperative levator resection outcome using image processing software.

    Science.gov (United States)

    Mawatari, Yuki; Fukushima, Mikiko

    2016-01-01

    This study aims to evaluate the efficacy of processed images to predict postoperative appearance following levator resection. Analysis involved 109 eyes from 65 patients with blepharoptosis who underwent advancement of levator aponeurosis and Müller's muscle complex (levator resection). Predictive images were prepared from preoperative photographs using the image processing software (Adobe Photoshop ® ). Images of selected eyes were digitally enlarged in an appropriate manner and shown to patients prior to surgery. Approximately 1 month postoperatively, we surveyed our patients using questionnaires. Fifty-six patients (89.2%) were satisfied with their postoperative appearances, and 55 patients (84.8%) positively responded to the usefulness of processed images to predict postoperative appearance. Showing processed images that predict postoperative appearance to patients prior to blepharoptosis surgery can be useful for those patients concerned with their postoperative appearance. This approach may serve as a useful tool to simulate blepharoptosis surgery.

  4. Software to model AXAF image quality

    Science.gov (United States)

    Ahmad, Anees

    1993-01-01

    This draft final report describes the work performed under this delivery order from May 1992 through June 1993. The purpose of this contract was to enhance and develop an integrated optical performance modeling software for complex x-ray optical systems such as AXAF. The GRAZTRACE program developed by the MSFC Optical Systems Branch for modeling VETA-I was used as the starting baseline program. The original program was a large single file program and, therefore, could not be modified very efficiently. The original source code has been reorganized, and a 'Make Utility' has been written to update the original program. The new version of the source code consists of 36 small source files to make it easier for the code developer to manage and modify the program. A user library has also been built and a 'Makelib' utility has been furnished to update the library. With the user library, the users can easily access the GRAZTRACE source files and build a custom library. A user manual for the new version of GRAZTRACE has been compiled. The plotting capability for the 3-D point spread functions and contour plots has been provided in the GRAZTRACE using the graphics package DISPLAY. The Graphics emulator over the network has been set up for programming the graphics routine. The point spread function and the contour plot routines have also been modified to display the plot centroid, and to allow the user to specify the plot range, and the viewing angle options. A Command Mode version of GRAZTRACE has also been developed. More than 60 commands have been implemented in a Code-V like format. The functions covered in this version include data manipulation, performance evaluation, and inquiry and setting of internal parameters. The user manual for these commands has been formatted as in Code-V, showing the command syntax, synopsis, and options. An interactive on-line help system for the command mode has also been accomplished to allow the user to find valid commands, command syntax

  5. Multispectral analysis of multimodal images

    Energy Technology Data Exchange (ETDEWEB)

    Kvinnsland, Yngve; Brekke, Njaal (Dept. of Surgical Sciences, Univ. of Bergen, Bergen (Norway)); Taxt, Torfinn M.; Gruener, Renate (Dept. of Biomedicine, Univ. of Bergen, Bergen (Norway))

    2009-02-15

    An increasing number of multimodal images represent a valuable increase in available image information, but at the same time it complicates the extraction of diagnostic information across the images. Multispectral analysis (MSA) has the potential to simplify this problem substantially as unlimited number of images can be combined, and tissue properties across the images can be extracted automatically. Materials and methods. We have developed a software solution for MSA containing two algorithms for unsupervised classification, an EM-algorithm finding multinormal class descriptions and the k-means clustering algorithm, and two for supervised classification, a Bayesian classifier using multinormal class descriptions and a kNN-algorithm. The software has an efficient user interface for the creation and manipulation of class descriptions, and it has proper tools for displaying the results. Results. The software has been tested on different sets of images. One application is to segment cross-sectional images of brain tissue (T1- and T2-weighted MR images) into its main normal tissues and brain tumors. Another interesting set of images are the perfusion maps and diffusion maps, derived images from raw MR images. The software returns segmentation that seem to be sensible. Discussion. The MSA software appears to be a valuable tool for image analysis with multimodal images at hand. It readily gives a segmentation of image volumes that visually seems to be sensible. However, to really learn how to use MSA, it will be necessary to gain more insight into what tissues the different segments contain, and the upcoming work will therefore be focused on examining the tissues through for example histological sections.

  6. Open-source software platform for medical image segmentation applications

    Science.gov (United States)

    Namías, R.; D'Amato, J. P.; del Fresno, M.

    2017-11-01

    Segmenting 2D and 3D images is a crucial and challenging problem in medical image analysis. Although several image segmentation algorithms have been proposed for different applications, no universal method currently exists. Moreover, their use is usually limited when detection of complex and multiple adjacent objects of interest is needed. In addition, the continually increasing volumes of medical imaging scans require more efficient segmentation software design and highly usable applications. In this context, we present an extension of our previous segmentation framework which allows the combination of existing explicit deformable models in an efficient and transparent way, handling simultaneously different segmentation strategies and interacting with a graphic user interface (GUI). We present the object-oriented design and the general architecture which consist of two layers: the GUI at the top layer, and the processing core filters at the bottom layer. We apply the framework for segmenting different real-case medical image scenarios on public available datasets including bladder and prostate segmentation from 2D MRI, and heart segmentation in 3D CT. Our experiments on these concrete problems show that this framework facilitates complex and multi-object segmentation goals while providing a fast prototyping open-source segmentation tool.

  7. Software for MR imaging system VISTA-E50

    International Nuclear Information System (INIS)

    Nakatao, Shirou; Iino, Mitsutoshi; Fukuda, Kazuhiko

    1989-01-01

    VISTA-E50 has the advantages of high-quality imaging, fast scanning, high patient throughput and easy operation featured by AI (artificial intelligence) technologies, as well as merits of compact, light-weight, space- and energy-saving system. This paper presents system software and clinical application software of VISTA-E50, especially for each function and advantage. (author)

  8. Software safety analysis practice in installation phase

    Energy Technology Data Exchange (ETDEWEB)

    Huang, H. W.; Chen, M. H.; Shyu, S. S., E-mail: hwhwang@iner.gov.t [Institute of Nuclear Energy Research, No. 1000 Wenhua Road, Chiaan Village, Longtan Township, 32546 Taoyuan County, Taiwan (China)

    2010-10-15

    This work performed a software safety analysis in the installation phase of the Lung men nuclear power plant in Taiwan, under the cooperation of Institute of Nuclear Energy Research and Tpc. The US Nuclear Regulatory Commission requests licensee to perform software safety analysis and software verification and validation in each phase of software development life cycle with Branch Technical Position 7-14. In this work, 37 safety grade digital instrumentation and control systems were analyzed by failure mode and effects analysis, which is suggested by IEEE standard 7-4.3.2-2003. During the installation phase, skew tests for safety grade network and point to point tests were performed. The failure mode and effects analysis showed all the single failure modes can be resolved by the redundant means. Most of the common mode failures can be resolved by operator manual actions. (Author)

  9. Software safety analysis practice in installation phase

    International Nuclear Information System (INIS)

    Huang, H. W.; Chen, M. H.; Shyu, S. S.

    2010-10-01

    This work performed a software safety analysis in the installation phase of the Lung men nuclear power plant in Taiwan, under the cooperation of Institute of Nuclear Energy Research and Tpc. The US Nuclear Regulatory Commission requests licensee to perform software safety analysis and software verification and validation in each phase of software development life cycle with Branch Technical Position 7-14. In this work, 37 safety grade digital instrumentation and control systems were analyzed by failure mode and effects analysis, which is suggested by IEEE standard 7-4.3.2-2003. During the installation phase, skew tests for safety grade network and point to point tests were performed. The failure mode and effects analysis showed all the single failure modes can be resolved by the redundant means. Most of the common mode failures can be resolved by operator manual actions. (Author)

  10. Computer-assisted qualitative data analysis software.

    Science.gov (United States)

    Cope, Diane G

    2014-05-01

    Advances in technology have provided new approaches for data collection methods and analysis for researchers. Data collection is no longer limited to paper-and-pencil format, and numerous methods are now available through Internet and electronic resources. With these techniques, researchers are not burdened with entering data manually and data analysis is facilitated by software programs. Quantitative research is supported by the use of computer software and provides ease in the management of large data sets and rapid analysis of numeric statistical methods. New technologies are emerging to support qualitative research with the availability of computer-assisted qualitative data analysis software (CAQDAS).CAQDAS will be presented with a discussion of advantages, limitations, controversial issues, and recommendations for this type of software use.

  11. Earth Observation Services (Image Processing Software)

    Science.gov (United States)

    1992-01-01

    San Diego State University and Environmental Systems Research Institute, with other agencies, have applied satellite imaging and image processing techniques to geographic information systems (GIS) updating. The resulting images display land use and are used by a regional planning agency for applications like mapping vegetation distribution and preserving wildlife habitats. The EOCAP program provides government co-funding to encourage private investment in, and to broaden the use of NASA-developed technology for analyzing information about Earth and ocean resources.

  12. Software for Acquiring Image Data for PIV

    Science.gov (United States)

    Wernet, Mark P.; Cheung, H. M.; Kressler, Brian

    2003-01-01

    PIV Acquisition (PIVACQ) is a computer program for acquisition of data for particle-image velocimetry (PIV). In the PIV system for which PIVACQ was developed, small particles entrained in a flow are illuminated with a sheet of light from a pulsed laser. The illuminated region is monitored by a charge-coupled-device camera that operates in conjunction with a data-acquisition system that includes a frame grabber and a counter-timer board, both installed in a single computer. The camera operates in "frame-straddle" mode where a pair of images can be obtained closely spaced in time (on the order of microseconds). The frame grabber acquires image data from the camera and stores the data in the computer memory. The counter/timer board triggers the camera and synchronizes the pulsing of the laser with acquisition of data from the camera. PIVPROC coordinates all of these functions and provides a graphical user interface, through which the user can control the PIV data-acquisition system. PIVACQ enables the user to acquire a sequence of single-exposure images, display the images, process the images, and then save the images to the computer hard drive. PIVACQ works in conjunction with the PIVPROC program which processes the images of particles into the velocity field in the illuminated plane.

  13. Verification and Validation of a Fingerprint Image Registration Software

    Directory of Open Access Journals (Sweden)

    Liu Yan

    2006-01-01

    Full Text Available The need for reliable identification and authentication is driving the increased use of biometric devices and systems. Verification and validation techniques applicable to these systems are rather immature and ad hoc, yet the consequences of the wide deployment of biometric systems could be significant. In this paper we discuss an approach towards validation and reliability estimation of a fingerprint registration software. Our validation approach includes the following three steps: (a the validation of the source code with respect to the system requirements specification; (b the validation of the optimization algorithm, which is in the core of the registration system; and (c the automation of testing. Since the optimization algorithm is heuristic in nature, mathematical analysis and test results are used to estimate the reliability and perform failure analysis of the image registration module.

  14. Software safety analysis application in installation phase

    International Nuclear Information System (INIS)

    Huang, H. W.; Yih, S.; Wang, L. H.; Liao, B. C.; Lin, J. M.; Kao, T. M.

    2010-01-01

    This work performed a software safety analysis (SSA) in the installation phase of the Lungmen nuclear power plant (LMNPP) in Taiwan, under the cooperation of INER and TPC. The US Nuclear Regulatory Commission (USNRC) requests licensee to perform software safety analysis (SSA) and software verification and validation (SV and V) in each phase of software development life cycle with Branch Technical Position (BTP) 7-14. In this work, 37 safety grade digital instrumentation and control (I and C) systems were analyzed by Failure Mode and Effects Analysis (FMEA), which is suggested by IEEE Standard 7-4.3.2-2003. During the installation phase, skew tests for safety grade network and point to point tests were performed. The FMEA showed all the single failure modes can be resolved by the redundant means. Most of the common mode failures can be resolved by operator manual actions. (authors)

  15. Software criticality analysis of COTS/SOUP

    International Nuclear Information System (INIS)

    Bishop, Peter; Bloomfield, Robin; Clement, Tim; Guerra, Sofia

    2003-01-01

    This paper describes the Software Criticality Analysis (SCA) approach that was developed to support the justification of using commercial off-the-shelf software (COTS) in a safety-related system. The primary objective of SCA is to assess the importance to safety of the software components within the COTS and to show there is segregation between software components with different safety importance. The approach taken was a combination of Hazops based on design documents and on a detailed analysis of the actual code (100 kloc). Considerable effort was spent on validation and ensuring the conservative nature of the results. The results from reverse engineering from the code showed that results based only on architecture and design documents would have been misleading

  16. Software criticality analysis of COTS/SOUP

    Energy Technology Data Exchange (ETDEWEB)

    Bishop, Peter; Bloomfield, Robin; Clement, Tim; Guerra, Sofia

    2003-09-01

    This paper describes the Software Criticality Analysis (SCA) approach that was developed to support the justification of using commercial off-the-shelf software (COTS) in a safety-related system. The primary objective of SCA is to assess the importance to safety of the software components within the COTS and to show there is segregation between software components with different safety importance. The approach taken was a combination of Hazops based on design documents and on a detailed analysis of the actual code (100 kloc). Considerable effort was spent on validation and ensuring the conservative nature of the results. The results from reverse engineering from the code showed that results based only on architecture and design documents would have been misleading.

  17. Development of nuclear imaging instrument and software

    International Nuclear Information System (INIS)

    Kim, Jang Hee; Chung Jae Myung; Nam, Sang Won; Chang, Hyung Uk

    1999-03-01

    In the medical diagnosis, the nuclear medical instrument using the radioactive isotope are commonly utilized. In the foreign countries, the medical application and development of the most advanced nuclear medical instrument such as Single Photon Emission Computer Tomography (SPECT) and position emission tomograph (PET), have been extensively carried out. However, in Korea, such highly expensive instruments have been all, imported, paying foreign currency. Since 1997, much efforts, the development of the radio nuclide medical instrument, the drive of the domestic production, etc. have been made to establish our own technologies and to balance the international payments under the support of the Ministry of Science and Technology. At present time, 180 nuclear imaging instruments are now in operation and 60 of them are analog camera. In analog camera, the vector X-Y monitor is need for are image display. Since the analog camera, signal can not be process in the digital form, we have difficulties to transfer and store the image data. The image displayed at the monitor must be stored in the form of polaroid or X ray film. In order to discard these disadvantages, if we developed the computer interface system, the performance analog camera will be comparable with that of the digital camera. The final objective of the research is that using the interface system developed in this research, we reconstruct the image data transmitted to the personal computer in the form of the generalized data file

  18. gr-MRI: A software package for magnetic resonance imaging using software defined radios

    Science.gov (United States)

    Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

    2016-09-01

    The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

  19. Acoustic Emission Analysis Applet (AEAA) Software

    Science.gov (United States)

    Nichols, Charles T.; Roth, Don J.

    2013-01-01

    NASA Glenn Research and NASA White Sands Test Facility have developed software supporting an automated pressure vessel structural health monitoring (SHM) system based on acoustic emissions (AE). The software, referred to as the Acoustic Emission Analysis Applet (AEAA), provides analysts with a tool that can interrogate data collected on Digital Wave Corp. and Physical Acoustics Corp. software using a wide spectrum of powerful filters and charts. This software can be made to work with any data once the data format is known. The applet will compute basic AE statistics, and statistics as a function of time and pressure (see figure). AEAA provides value added beyond the analysis provided by the respective vendors' analysis software. The software can handle data sets of unlimited size. A wide variety of government and commercial applications could benefit from this technology, notably requalification and usage tests for compressed gas and hydrogen-fueled vehicles. Future enhancements will add features similar to a "check engine" light on a vehicle. Once installed, the system will ultimately be used to alert International Space Station crewmembers to critical structural instabilities, but will have little impact to missions otherwise. Diagnostic information could then be transmitted to experienced technicians on the ground in a timely manner to determine whether pressure vessels have been impacted, are structurally unsound, or can be safely used to complete the mission.

  20. The influence of software filtering in digital mammography image quality

    Science.gov (United States)

    Michail, C.; Spyropoulou, V.; Kalyvas, N.; Valais, I.; Dimitropoulos, N.; Fountos, G.; Kandarakis, I.; Panayiotakis, G.

    2009-05-01

    Breast cancer is one of the most frequently diagnosed cancers among women. Several techniques have been developed to help in the early detection of breast cancer such as conventional and digital x-ray mammography, positron and single-photon emission mammography, etc. A key advantage in digital mammography is that images can be manipulated as simple computer image files. Thus non-dedicated commercially available image manipulation software can be employed to process and store the images. The image processing tools of the Photoshop (CS 2) software usually incorporate digital filters which may be used to reduce image noise, enhance contrast and increase spatial resolution. However, improving an image quality parameter may result in degradation of another. The aim of this work was to investigate the influence of three sharpening filters, named hereafter sharpen, sharpen more and sharpen edges on image resolution and noise. Image resolution was assessed by means of the Modulation Transfer Function (MTF).In conclusion it was found that the correct use of commercial non-dedicated software on digital mammograms may improve some aspects of image quality.

  1. The influence of software filtering in digital mammography image quality

    International Nuclear Information System (INIS)

    Michail, C; Spyropoulou, V; Valais, I; Panayiotakis, G; Kalyvas, N; Fountos, G; Kandarakis, I; Dimitropoulos, N

    2009-01-01

    Breast cancer is one of the most frequently diagnosed cancers among women. Several techniques have been developed to help in the early detection of breast cancer such as conventional and digital x-ray mammography, positron and single-photon emission mammography, etc. A key advantage in digital mammography is that images can be manipulated as simple computer image files. Thus non-dedicated commercially available image manipulation software can be employed to process and store the images. The image processing tools of the Photoshop (CS 2) software usually incorporate digital filters which may be used to reduce image noise, enhance contrast and increase spatial resolution. However, improving an image quality parameter may result in degradation of another. The aim of this work was to investigate the influence of three sharpening filters, named hereafter sharpen, sharpen more and sharpen edges on image resolution and noise. Image resolution was assessed by means of the Modulation Transfer Function (MTF).In conclusion it was found that the correct use of commercial non-dedicated software on digital mammograms may improve some aspects of image quality.

  2. Introducing a New Software for Geodetic Analysis

    Science.gov (United States)

    Hjelle, Geir Arne; Dähnn, Michael; Fausk, Ingrid; Kirkvik, Ann-Silje; Mysen, Eirik

    2017-04-01

    At the Norwegian Mapping Authority, we are currently developing Where, a new software for geodetic analysis. Where is built on our experiences with the Geosat software, and will be able to analyse and combine data from VLBI, SLR, GNSS and DORIS. The software is mainly written in Python which has proved very fruitful. The code is quick to write and the architecture is easily extendable and maintainable, while at the same time taking advantage of well-tested code like the SOFA and IERS libraries. This presentation will show some of the current capabilities of Where, including benchmarks against other software packages, and outline our plans for further progress. In addition we will report on some investigations we have done experimenting with alternative weighting strategies for VLBI.

  3. Software for Graph Analysis and Visualization

    Directory of Open Access Journals (Sweden)

    M. I. Kolomeychenko

    2014-01-01

    Full Text Available This paper describes the software for graph storage, analysis and visualization. The article presents a comparative analysis of existing software for analysis and visualization of graphs, describes the overall architecture of application and basic principles of construction and operation of the main modules. Furthermore, a description of the developed graph storage oriented to storage and processing of large-scale graphs is presented. The developed algorithm for finding communities and implemented algorithms of autolayouts of graphs are the main functionality of the product. The main advantage of the developed software is high speed processing of large size networks (up to millions of nodes and links. Moreover, the proposed graph storage architecture is unique and has no analogues. The developed approaches and algorithms are optimized for operating with big graphs and have high productivity.

  4. Power and performance software analysis and optimization

    CERN Document Server

    Kukunas, Jim

    2015-01-01

    Power and Performance: Software Analysis and Optimization is a guide to solving performance problems in modern Linux systems. Power-efficient chips are no help if the software those chips run on is inefficient. Starting with the necessary architectural background as a foundation, the book demonstrates the proper usage of performance analysis tools in order to pinpoint the cause of performance problems, and includes best practices for handling common performance issues those tools identify. Provides expert perspective from a key member of Intel's optimization team on how processors and memory

  5. Spinal imaging and image analysis

    CERN Document Server

    Yao, Jianhua

    2015-01-01

    This book is instrumental to building a bridge between scientists and clinicians in the field of spine imaging by introducing state-of-the-art computational methods in the context of clinical applications.  Spine imaging via computed tomography, magnetic resonance imaging, and other radiologic imaging modalities, is essential for noninvasively visualizing and assessing spinal pathology. Computational methods support and enhance the physician’s ability to utilize these imaging techniques for diagnosis, non-invasive treatment, and intervention in clinical practice. Chapters cover a broad range of topics encompassing radiological imaging modalities, clinical imaging applications for common spine diseases, image processing, computer-aided diagnosis, quantitative analysis, data reconstruction and visualization, statistical modeling, image-guided spine intervention, and robotic surgery. This volume serves a broad audience as  contributions were written by both clinicians and researchers, which reflects the inte...

  6. Software for imaging phase-shift interference microscope

    Science.gov (United States)

    Malinovski, I.; França, R. S.; Couceiro, I. B.

    2018-03-01

    In recent years absolute interference microscope was created at National Metrology Institute of Brazil (INMETRO). The instrument by principle of operation is imaging phase-shifting interferometer (PSI) equipped with two stabilized lasers of different colour as traceable reference wavelength sources. We report here some progress in development of the software for this instrument. The status of undergoing internal validation and verification of the software is also reported. In contrast with standard PSI method, different methodology of phase evaluation is applied. Therefore, instrument specific procedures for software validation and verification are adapted and discussed.

  7. Retinal Imaging and Image Analysis

    Science.gov (United States)

    Abràmoff, Michael D.; Garvin, Mona K.; Sonka, Milan

    2011-01-01

    Many important eye diseases as well as systemic diseases manifest themselves in the retina. While a number of other anatomical structures contribute to the process of vision, this review focuses on retinal imaging and image analysis. Following a brief overview of the most prevalent causes of blindness in the industrialized world that includes age-related macular degeneration, diabetic retinopathy, and glaucoma, the review is devoted to retinal imaging and image analysis methods and their clinical implications. Methods for 2-D fundus imaging and techniques for 3-D optical coherence tomography (OCT) imaging are reviewed. Special attention is given to quantitative techniques for analysis of fundus photographs with a focus on clinically relevant assessment of retinal vasculature, identification of retinal lesions, assessment of optic nerve head (ONH) shape, building retinal atlases, and to automated methods for population screening for retinal diseases. A separate section is devoted to 3-D analysis of OCT images, describing methods for segmentation and analysis of retinal layers, retinal vasculature, and 2-D/3-D detection of symptomatic exudate-associated derangements, as well as to OCT-based analysis of ONH morphology and shape. Throughout the paper, aspects of image acquisition, image analysis, and clinical relevance are treated together considering their mutually interlinked relationships. PMID:22275207

  8. A tool to include gamma analysis software into a quality assurance program.

    Science.gov (United States)

    Agnew, Christina E; McGarry, Conor K

    2016-03-01

    To provide a tool to enable gamma analysis software algorithms to be included in a quality assurance (QA) program. Four image sets were created comprising two geometric images to independently test the distance to agreement (DTA) and dose difference (DD) elements of the gamma algorithm, a clinical step and shoot IMRT field and a clinical VMAT arc. The images were analysed using global and local gamma analysis with 2 in-house and 8 commercially available software encompassing 15 software versions. The effect of image resolution on gamma pass rates was also investigated. All but one software accurately calculated the gamma passing rate for the geometric images. Variation in global gamma passing rates of 1% at 3%/3mm and over 2% at 1%/1mm was measured between software and software versions with analysis of appropriately sampled images. This study provides a suite of test images and the gamma pass rates achieved for a selection of commercially available software. This image suite will enable validation of gamma analysis software within a QA program and provide a frame of reference by which to compare results reported in the literature from various manufacturers and software versions. Copyright © 2015. Published by Elsevier Ireland Ltd.

  9. Comparison of two three-dimensional cephalometric analysis computer software.

    Science.gov (United States)

    Sawchuk, Dena; Alhadlaq, Adel; Alkhadra, Thamer; Carlyle, Terry D; Kusnoto, Budi; El-Bialy, Tarek

    2014-10-01

    Three-dimensional cephalometric analyses are getting more attraction in orthodontics. The aim of this study was to compare two softwares to evaluate three-dimensional cephalometric analyses of orthodontic treatment outcomes. Twenty cone beam computed tomography images were obtained using i-CAT(®) imaging system from patient's records as part of their regular orthodontic records. The images were analyzed using InVivoDental5.0 (Anatomage Inc.) and 3DCeph™ (University of Illinois at Chicago, Chicago, IL, USA) software. Before and after orthodontic treatments data were analyzed using t-test. Reliability test using interclass correlation coefficient was stronger for InVivoDental5.0 (0.83-0.98) compared with 3DCeph™ (0.51-0.90). Paired t-test comparison of the two softwares shows no statistical significant difference in the measurements made in the two softwares. InVivoDental5.0 measurements are more reproducible and user friendly when compared to 3DCeph™. No statistical difference between the two softwares in linear or angular measurements. 3DCeph™ is more time-consuming in performing three-dimensional analysis compared with InVivoDental5.0.

  10. Computer Software Configuration Item-Specific Flight Software Image Transfer Script Generator

    Science.gov (United States)

    Bolen, Kenny; Greenlaw, Ronald

    2010-01-01

    A K-shell UNIX script enables the International Space Station (ISS) Flight Control Team (FCT) operators in NASA s Mission Control Center (MCC) in Houston to transfer an entire or partial computer software configuration item (CSCI) from a flight software compact disk (CD) to the onboard Portable Computer System (PCS). The tool is designed to read the content stored on a flight software CD and generate individual CSCI transfer scripts that are capable of transferring the flight software content in a given subdirectory on the CD to the scratch directory on the PCS. The flight control team can then transfer the flight software from the PCS scratch directory to the Electronically Erasable Programmable Read Only Memory (EEPROM) of an ISS Multiplexer/ Demultiplexer (MDM) via the Indirect File Transfer capability. The individual CSCI scripts and the CSCI Specific Flight Software Image Transfer Script Generator (CFITSG), when executed a second time, will remove all components from their original execution. The tool will identify errors in the transfer process and create logs of the transferred software for the purposes of configuration management.

  11. Análise da morfometria nuclear: descrição da metodologia e o papel dos softwares de edição de imagem Nuclear morphometric analysis: description of the methodology and the role of image-editing softwares

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo de Andrea

    2008-02-01

    Full Text Available A análise morfométrica de imagens é utilizada em patologia para se obter dados precisos de componentes celulares e teciduais, por meio da mensuração e contagem, que são importantes para o diagnóstico e prognóstico de vários tumores. Essa técnica, mesmo sendo ferramenta útil e de baixo custo, mantém-se restrita a poucos centros de diagnóstico ou pesquisa. O objetivo deste trabalho é apresentar e descrever o método de morfometria nuclear com a utilização complementar de softwares de edição de imagens, fazendo a análise detalhada das etapas críticas do processo. A correção de problemas encontrados durante a captura das imagens, como temperatura e matiz da cor erroneamente ajustados, e de imagens com iluminação desigual provenientes de microscópio mal regulado, é fundamental para a correta análise. Assim, utilizando o recurso máscara de cor disponível em vários softwares de editoração de imagens, é possível selecionar e separar objetos de cores semelhantes, resultando numa imagem final que apresenta somente os objetos de interesse para análise. A morfometria é realizada por meio de softwares específicos como o ImageTool (versão 3.0, que possibilitam a mensuração automática de um ou mais parâmetros, com precisão e em curto intervalo de tempo. A interface do ImageTool permite ainda trabalhar simultaneamente com a imagem original e a imagem processada em que se fez a seleção das cores semelhantes. Dessa forma, pode-se confrontar o objeto que está sendo selecionado com o mesmo objeto na sua imagem original, garantindo assim correta seleção. Esse sistema possibilita conferência interobservador de 100% dos objetos, o que permite desprezar aqueles que posteriormente constatou-se que não deveriam ter sido selecionados e mensurados.The morphometric analysis of images, which comprises measuring and counting, is used in pathology to obtain accurate data of cellular and tissue components that are important for

  12. Software for computerised analysis of cardiotocographic traces.

    Science.gov (United States)

    Romano, M; Bifulco, P; Ruffo, M; Improta, G; Clemente, F; Cesarelli, M

    2016-02-01

    Despite the widespread use of cardiotocography in foetal monitoring, the evaluation of foetal status suffers from a considerable inter and intra-observer variability. In order to overcome the main limitations of visual cardiotocographic assessment, computerised methods to analyse cardiotocographic recordings have been recently developed. In this study, a new software for automated analysis of foetal heart rate is presented. It allows an automatic procedure for measuring the most relevant parameters derivable from cardiotocographic traces. Simulated and real cardiotocographic traces were analysed to test software reliability. In artificial traces, we simulated a set number of events (accelerations, decelerations and contractions) to be recognised. In the case of real signals, instead, results of the computerised analysis were compared with the visual assessment performed by 18 expert clinicians and three performance indexes were computed to gain information about performances of the proposed software. The software showed preliminary performance we judged satisfactory in that the results matched completely the requirements, as proved by tests on artificial signals in which all simulated events were detected from the software. Performance indexes computed in comparison with obstetricians' evaluations are, on the contrary, not so satisfactory; in fact they led to obtain the following values of the statistical parameters: sensitivity equal to 93%, positive predictive value equal to 82% and accuracy equal to 77%. Very probably this arises from the high variability of trace annotation carried out by clinicians. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. GRACAT, Software for grounding and collision analysis

    DEFF Research Database (Denmark)

    Friis-Hansen, Peter; Simonsen, Bo Cerup

    2002-01-01

    and grounding accidents. The software consists of three basic analysis modules and one risk mitigation module: 1) frequency, 2) damage, and 3) consequence. These modules can be used individually or in series and the analyses can be performed in deterministic or probabilistic mode. Finally, in the mitigation...

  14. PySE: Software for extracting sources from radio images

    Science.gov (United States)

    Carbone, D.; Garsden, H.; Spreeuw, H.; Swinbank, J. D.; van der Horst, A. J.; Rowlinson, A.; Broderick, J. W.; Rol, E.; Law, C.; Molenaar, G.; Wijers, R. A. M. J.

    2018-04-01

    PySE is a Python software package for finding and measuring sources in radio telescope images. The software was designed to detect sources in the LOFAR telescope images, but can be used with images from other radio telescopes as well. We introduce the LOFAR Telescope, the context within which PySE was developed, the design of PySE, and describe how it is used. Detailed experiments on the validation and testing of PySE are then presented, along with results of performance testing. We discuss some of the current issues with the algorithms implemented in PySE and their interaction with LOFAR images, concluding with the current status of PySE and its future development.

  15. A specialized plug-in software module for computer-aided quantitative measurement of medical images.

    Science.gov (United States)

    Wang, Q; Zeng, Y J; Huo, P; Hu, J L; Zhang, J H

    2003-12-01

    This paper presents a specialized system for quantitative measurement of medical images. Using Visual C++, we developed a computer-aided software based on Image-Pro Plus (IPP), a software development platform. When transferred to the hard disk of a computer by an MVPCI-V3A frame grabber, medical images can be automatically processed by our own IPP plug-in for immunohistochemical analysis, cytomorphological measurement and blood vessel segmentation. In 34 clinical studies, the system has shown its high stability, reliability and ease of utility.

  16. Digital radiography: optimization of image quality and dose using multi-frequency software.

    Science.gov (United States)

    Precht, H; Gerke, O; Rosendahl, K; Tingberg, A; Waaler, D

    2012-09-01

    New developments in processing of digital radiographs (DR), including multi-frequency processing (MFP), allow optimization of image quality and radiation dose. This is particularly promising in children as they are believed to be more sensitive to ionizing radiation than adults. To examine whether the use of MFP software reduces the radiation dose without compromising quality at DR of the femur in 5-year-old-equivalent anthropomorphic and technical phantoms. A total of 110 images of an anthropomorphic phantom were imaged on a DR system (Canon DR with CXDI-50 C detector and MLT[S] software) and analyzed by three pediatric radiologists using Visual Grading Analysis. In addition, 3,500 images taken of a technical contrast-detail phantom (CDRAD 2.0) provide an objective image-quality assessment. Optimal image-quality was maintained at a dose reduction of 61% with MLT(S) optimized images. Even for images of diagnostic quality, MLT(S) provided a dose reduction of 88% as compared to the reference image. Software impact on image quality was found significant for dose (mAs), dynamic range dark region and frequency band. By optimizing image processing parameters, a significant dose reduction is possible without significant loss of image quality.

  17. Residence time distribution software analysis. User's manual

    International Nuclear Information System (INIS)

    1996-01-01

    Radiotracer applications cover a wide range of industrial activities in chemical and metallurgical processes, water treatment, mineral processing, environmental protection and civil engineering. Experiment design, data acquisition, treatment and interpretation are the basic elements of tracer methodology. The application of radiotracers to determine impulse response as RTD as well as the technical conditions for conducting experiments in industry and in the environment create a need for data processing using special software. Important progress has been made during recent years in the preparation of software programs for data treatment and interpretation. The software package developed for industrial process analysis and diagnosis by the stimulus-response methods contains all the methods for data processing for radiotracer experiments

  18. Improving Software Systems By Flow Control Analysis

    Directory of Open Access Journals (Sweden)

    Piotr Poznanski

    2012-01-01

    Full Text Available Using agile methods during the implementation of the system that meets mission critical requirements can be a real challenge. The change in the system built of dozens or even hundreds of specialized devices with embedded software requires the cooperation of a large group of engineers. This article presents a solution that supports parallel work of groups of system analysts and software developers. Deployment of formal rules to the requirements written in natural language enables using formal analysis of artifacts being a bridge between software and system requirements. Formalism and textual form of requirements allowed the automatic generation of message flow graph for the (sub system, called the “big-picture-model”. Flow diagram analysis helped to avoid a large number of defects whose repair cost in extreme cases could undermine the legitimacy of agile methods in projects of this scale. Retrospectively, a reduction of technical debt was observed. Continuous analysis of the “big picture model” improves the control of the quality parameters of the software architecture. The article also tries to explain why the commercial platform based on UML modeling language may not be sufficient in projects of this complexity.

  19. Intraprocedural dataflow analysis for software product lines

    DEFF Research Database (Denmark)

    Brabrand, Claus; Ribeiro, Márcio; Tolêdo, Társis

    2013-01-01

    Software product lines (SPLs) developed using annotative approaches such as conditional compilation come with an inherent risk of constructing erroneous products. For this reason, it is essential to be able to analyze such SPLs. However, as dataflow analysis techniques are not able to deal with SP...... and memory characteristics on five qualitatively different SPLs. On our benchmarks, the combined analysis strategy is up to almost eight times faster than the brute-force approach....

  20. Automating risk analysis of software design models.

    Science.gov (United States)

    Frydman, Maxime; Ruiz, Guifré; Heymann, Elisa; César, Eduardo; Miller, Barton P

    2014-01-01

    The growth of the internet and networked systems has exposed software to an increased amount of security threats. One of the responses from software developers to these threats is the introduction of security activities in the software development lifecycle. This paper describes an approach to reduce the need for costly human expertise to perform risk analysis in software, which is common in secure development methodologies, by automating threat modeling. Reducing the dependency on security experts aims at reducing the cost of secure development by allowing non-security-aware developers to apply secure development with little to no additional cost, making secure development more accessible. To automate threat modeling two data structures are introduced, identification trees and mitigation trees, to identify threats in software designs and advise mitigation techniques, while taking into account specification requirements and cost concerns. These are the components of our model for automated threat modeling, AutSEC. We validated AutSEC by implementing it in a tool based on data flow diagrams, from the Microsoft security development methodology, and applying it to VOMS, a grid middleware component, to evaluate our model's performance.

  1. Predictive images of postoperative levator resection outcome using image processing software

    Directory of Open Access Journals (Sweden)

    Mawatari Y

    2016-09-01

    Full Text Available Yuki Mawatari,1 Mikiko Fukushima2 1Igo Ophthalmic Clinic, Kagoshima, 2Department of Ophthalmology, Faculty of Life Science, Kumamoto University, Chuo-ku, Kumamoto, Japan Purpose: This study aims to evaluate the efficacy of processed images to predict postoperative appearance following levator resection.Methods: Analysis involved 109 eyes from 65 patients with blepharoptosis who underwent advancement of levator aponeurosis and Müller’s muscle complex (levator resection. Predictive images were prepared from preoperative photographs using the image processing software (Adobe Photoshop®. Images of selected eyes were digitally enlarged in an appropriate manner and shown to patients prior to surgery.Results: Approximately 1 month postoperatively, we surveyed our patients using questionnaires. Fifty-six patients (89.2% were satisfied with their postoperative appearances, and 55 patients (84.8% positively responded to the usefulness of processed images to predict postoperative appearance.Conclusion: Showing processed images that predict postoperative appearance to patients prior to blepharoptosis surgery can be useful for those patients concerned with their postoperative appearance. This approach may serve as a useful tool to simulate blepharoptosis surgery. Keywords: levator resection, blepharoptosis, image processing, Adobe Photoshop® 

  2. Techniques and software architectures for medical visualisation and image processing

    NARCIS (Netherlands)

    Botha, C.P.

    2005-01-01

    This thesis presents a flexible software platform for medical visualisation and image processing, a technique for the segmentation of the shoulder skeleton from CT data and three techniques that make contributions to the field of direct volume rendering. Our primary goal was to investigate the use

  3. The Role and Design of Screen Images in Software Documentation.

    Science.gov (United States)

    van der Meij, Hans

    2000-01-01

    Discussion of learning a new computer software program focuses on how to support the joint handling of a manual, input devices, and screen display. Describes a study that examined three design styles for manuals that included screen images to reduce split-attention problems and discusses theory versus practice and cognitive load theory.…

  4. Hardware and software for image acquisition in nuclear medicine

    International Nuclear Information System (INIS)

    Fideles, E.L.; Vilar, G.; Silva, H.S.

    1992-01-01

    A system for image acquisition and processing in nuclear medicine is presented, including the hardware and software referring to acquisition. The hardware is consisted of an analog-digital conversion card, developed in wire-wape. Its function is digitate the analogic signs provided by gamma camera. The acquisitions are made in list or frame mode. (C.G.C.)

  5. Retinal imaging and image analysis

    NARCIS (Netherlands)

    Abramoff, M.D.; Garvin, Mona K.; Sonka, Milan

    2010-01-01

    Many important eye diseases as well as systemic diseases manifest themselves in the retina. While a number of other anatomical structures contribute to the process of vision, this review focuses on retinal imaging and image analysis. Following a brief overview of the most prevalent causes of

  6. Automated digital image analysis of islet cell mass using Nikon's inverted eclipse Ti microscope and software to improve engraftment may help to advance the therapeutic efficacy and accessibility of islet transplantation across centers.

    Science.gov (United States)

    Gmyr, Valery; Bonner, Caroline; Lukowiak, Bruno; Pawlowski, Valerie; Dellaleau, Nathalie; Belaich, Sandrine; Aluka, Isanga; Moermann, Ericka; Thevenet, Julien; Ezzouaoui, Rimed; Queniat, Gurvan; Pattou, Francois; Kerr-Conte, Julie

    2015-01-01

    Reliable assessment of islet viability, mass, and purity must be met prior to transplanting an islet preparation into patients with type 1 diabetes. The standard method for quantifying human islet preparations is by direct microscopic analysis of dithizone-stained islet samples, but this technique may be susceptible to inter-/intraobserver variability, which may induce false positive/negative islet counts. Here we describe a simple, reliable, automated digital image analysis (ADIA) technique for accurately quantifying islets into total islet number, islet equivalent number (IEQ), and islet purity before islet transplantation. Islets were isolated and purified from n = 42 human pancreata according to the automated method of Ricordi et al. For each preparation, three islet samples were stained with dithizone and expressed as IEQ number. Islets were analyzed manually by microscopy or automatically quantified using Nikon's inverted Eclipse Ti microscope with built-in NIS-Elements Advanced Research (AR) software. The AIDA method significantly enhanced the number of islet preparations eligible for engraftment compared to the standard manual method (p image analysis utilizing the Nikon Instruments software is an unbiased, simple, and reliable teaching tool to comprehensively assess the individual size of each islet cell preparation prior to transplantation. Implementation of this technology to improve engraftment may help to advance the therapeutic efficacy and accessibility of islet transplantation across centers.

  7. Multimodality image analysis work station

    International Nuclear Information System (INIS)

    Ratib, O.; Huang, H.K.

    1989-01-01

    The goal of this project is to design and implement a PACS (picture archiving and communication system) workstation for quantitative analysis of multimodality images. The Macintosh II personal computer was selected for its friendly user interface, its popularity among the academic and medical community, and its low cost. The Macintosh operates as a stand alone workstation where images are imported from a central PACS server through a standard Ethernet network and saved on a local magnetic or optical disk. A video digitizer board allows for direct acquisition of images from sonograms or from digitized cine angiograms. The authors have focused their project on the exploration of new means of communicating quantitative data and information through the use of an interactive and symbolic user interface. The software developed includes a variety of image analysis, algorithms for digitized angiograms, sonograms, scintigraphic images, MR images, and CT scans

  8. Forensic Analysis of Digital Image Tampering

    Science.gov (United States)

    2004-12-01

    analysis of when each method fails, which Chapter 4 discusses. Finally, a test image containing an invisible watermark using LSB steganography is...2.2 – Example of invisible watermark using Steganography Software F5 ............. 8 Figure 2.3 – Example of copy-move image forgery [12...used to embed the hidden watermark is Steganography Software F5 version 11+ discussed in Section 2.2. Original JPEG Image – 580 x 435 – 17.4

  9. Data to Pictures to Data: Outreach Imaging Software and Metadata

    Science.gov (United States)

    Levay, Z.

    2011-07-01

    A convergence between astronomy science and digital photography has enabled a steady stream of visually rich imagery from state-of-the-art data. The accessibility of hardware and software has facilitated an explosion of astronomical images for outreach, from space-based observatories, ground-based professional facilities and among the vibrant amateur astrophotography community. Producing imagery from science data involves a combination of custom software to understand FITS data (FITS Liberator), off-the-shelf, industry-standard software to composite multi-wavelength data and edit digital photographs (Adobe Photoshop), and application of photo/image-processing techniques. Some additional effort is needed to close the loop and enable this imagery to be conveniently available for various purposes beyond web and print publication. The metadata paradigms in digital photography are now complying with FITS and science software to carry information such as keyword tags and world coordinates, enabling these images to be usable in more sophisticated, imaginative ways exemplified by Sky in Google Earth and World Wide Telescope.

  10. Software for the acquisition and proses of Gammagraphy images

    International Nuclear Information System (INIS)

    De la Hoz Olivera, J.; Hernandez Garcia, J.

    1999-01-01

    In Cuba, the piece of equipment most widespread in Gammagraphy studies is the rectilinear scanner. In the years 1997-98, all such equipment was coupled to the microcomputer by specialists from Nuclear Research and Service Center and Marie Curie Oncological Hospital, both in Camaguey city. The results went beyond expectations, which allowed for the continuation of work in these departments with quality higher than that of the original version. This paper describes the software for acquiring and processing the images. The acquisition software is a wizard application that guides technicians through the different steps of the study and allows for the use of the computer in other tasks during the study. MDI (Multiple Document Interface) is the image processing software, which makes it possible for technicians to simultaneously visualize several studies for comparison, to apply several image processing techniques, to insert comments on the study and to show anatomical marks, to mention only a few advantages. The software were developed in Delphi 3.0 for Windows 95 or higher

  11. Utility of noise addition image made by using water phantom and image addition and subtraction software

    International Nuclear Information System (INIS)

    Watanabe, Ryo; Aoki, Takahiro; Hayano, Mizuho; Ogawa, Masato; Mituzono, Hiroki; Watanabe, Yuka

    2010-01-01

    In optimizing exposures, it is very important to evaluate the impact of image noise on image quality. To realize this, there is a need to evaluate how much image noise will make the subject disease invisible. But generally it is very difficult to shoot images of different quality in a clinical examination. Thus, a method to create a noise addition image by adding the image noise to raw data has been reported. However, this approach requires a special system, so it is difficult to implement in many facilities. We have invented a method to easily create a noise addition image by using the water phantom and image add-subtract software that accompanies the device. To create a noise addition image, first we made a noise image by subtracting the water phantom with different standard deviation (SD). A noise addition image was then created by adding the noise image to the original image. By using this method, a simulation image with intergraded SD can be created from the original. Moreover, the noise frequency component of the created noise addition image is as same as the real image. Thus, the relationship of image quality to SD in the clinical image can be evaluated. Although this method is an easy method of LDSI creation on image data, a noise addition image can be easily created by using image addition and subtraction software and water phantom, and this can be implemented in many facilities. (author)

  12. Development of neutron activation analysis software

    International Nuclear Information System (INIS)

    Wang Liyu

    1987-10-01

    The software for quantitative neutron activation analysis was developed to run under the MS/DOS operating system. The programmes of the IBM/SPAN include: spectra file transfer from and to a Canberra Series 35 multichannel analyzer, spectrum evaluation routines, calibration subprogrammes, and quantitative analysis. The programmes for spectrum analysis include fitting routine for separation of multiple lines by reproducing the peak shape with a combination of Gaussian and exponential terms. The programmes were tested on an IBM/AT-compatible computer. The programmes and the sources are available costfree for the IAEA projects of Technical Cooperation. 7 refs, 3 figs

  13. Adobe Photoshop images software in the verification of radiation portal

    International Nuclear Information System (INIS)

    Ouyang Shuigen; Wang Xiaohu; Liu Zhiqiang; Wei Xiyi; Qi Yong

    2010-01-01

    Objective: To investigate the value of Adobe Photoshop images software in the verification of radiation portal. Methods: The portal and simulation films or CT reconstruction images were imported into computer using a scanner. The image size, gray scale and contrast scale were adjusted with Adobe Photoshop images software, then image registration and measurement were completed. Results: By the comparison between portal image and simulation image, the set-up errors in right-left, superior-inferior and anterior-posterior directions were (1.11 ± 1.37) mm, (1.33 ± 1.25) mm and (0.83±0.79) mm in the head and neck;(1.44±1.03) mm,(1.6±1.52) mm and (1.34±1.17) mm in the thorax;(1.53±0.86) mm, (1.83 ± 1.19) mm and (1.67 ± 0.68)mm in the abdomen; (1.93 ± I. 83) mm, (1.59 ± 1.07)mm and (0.85 ± 0.72)mm in the pelvic cavity. Conclusions: Accurate radiation portal verification and position measurement can be completed by using Adobe Photoshop, which is a simple, safe and reliable method. (authors)

  14. IUE Data Analysis Software for Personal Computers

    Science.gov (United States)

    Thompson, R.; Caplinger, J.; Taylor, L.; Lawton , P.

    1996-01-01

    This report summarizes the work performed for the program titled, "IUE Data Analysis Software for Personal Computers" awarded under Astrophysics Data Program NRA 92-OSSA-15. The work performed was completed over a 2-year period starting in April 1994. As a result of the project, 450 IDL routines and eight database tables are now available for distribution for Power Macintosh computers and Personal Computers running Windows 3.1.

  15. The application of image processing software: Photoshop in environmental design

    Science.gov (United States)

    Dong, Baohua; Zhang, Chunmi; Zhuo, Chen

    2011-02-01

    In the process of environmental design and creation, the design sketch holds a very important position in that it not only illuminates the design's idea and concept but also shows the design's visual effects to the client. In the field of environmental design, computer aided design has made significant improvement. Many types of specialized design software for environmental performance of the drawings and post artistic processing have been implemented. Additionally, with the use of this software, working efficiency has greatly increased and drawings have become more specific and more specialized. By analyzing the application of photoshop image processing software in environmental design and comparing and contrasting traditional hand drawing and drawing with modern technology, this essay will further explore the way for computer technology to play a bigger role in environmental design.

  16. Application of Metric-based Software Reliability Analysis to Example Software

    International Nuclear Information System (INIS)

    Kim, Man Cheol; Smidts, Carol

    2008-07-01

    The software reliability of TELLERFAST ATM software is analyzed by using two metric-based software reliability analysis methods, a state transition diagram-based method and a test coverage-based method. The procedures for the software reliability analysis by using the two methods and the analysis results are provided in this report. It is found that the two methods have a relation of complementary cooperation, and therefore further researches on combining the two methods to reflect the benefit of the complementary cooperative effect to the software reliability analysis are recommended

  17. JEM-X science analysis software

    DEFF Research Database (Denmark)

    Westergaard, Niels Jørgen Stenfeldt; Kretschmar, P.; Oxborrow, Carol Anne

    2003-01-01

    The science analysis of the data from JEM-X on INTEGRAL is performed through a number of levels including corrections, good time selection, imaging and source finding, spectrum and light-curve extraction. These levels consist of individual executables and the running of the complete analysis...

  18. Imaging of jaw with dental CT software program: Normal Anatomy

    International Nuclear Information System (INIS)

    Kim, Myong Gon; Seo, Kwang Hee; Jung, Hak Young; Sung, Nak Kwan; Chung, Duk Soo; Kim, Ok Dong; Lee, Young Hwan

    1994-01-01

    Dental CT software program can provide reformatted cross-sectional and panoramic images that cannot be obtained with conventional axial and direct coronal CT scan. The purpose of this study is to describe the method of the technique and to identify the precise anatomy of jaw. We evaluated 13 mandibles and 7 maxillae of 15 subjects without bony disease who were being considered for endosseous dental implants. Reformatted images obtained by the use of bone algorithm performed on GE HiSpeed Advantage CT scanner were retrospectively reviewed for detailed anatomy of jaw. Anatomy related to neurovascular bundle(mandibular foramen, inferior alveolar canal, mental foramen, canal for incisive artery, nutrient canal, lingual foramen and mylohyoid groove), muscular insertion(mylohyoid line, superior and inferior genial tubercle and digastric fossa) and other anatomy(submandibular fossa, sublingual fossa, contour of alveolar process, oblique line, retromolar fossa, temporal crest and retromolar triangle) were well delineated in mandible. In maxilla, anatomy related to neurovascular bundle(greater palatine foramen and groove, nasopalatine canal and incisive foramen) and other anatomy(alveolar process, maxillary sinus and nasal fossa) were also well delineated. Reformatted images using dental CT software program provided excellent delineation of the jaw anatomy. Therefore, dental CT software program can play an important role in the preoperative assessment of mandible and maxilla for dental implants and other surgical conditions

  19. Specdata: Automated Analysis Software for Broadband Spectra

    Science.gov (United States)

    Oliveira, Jasmine N.; Martin-Drumel, Marie-Aline; McCarthy, Michael C.

    2017-06-01

    With the advancement of chirped-pulse techniques, broadband rotational spectra with a few tens to several hundred GHz of spectral coverage are now routinely recorded. When studying multi-component mixtures that might result, for example, with the use of an electrical discharge, lines of new chemical species are often obscured by those of known compounds, and analysis can be laborious. To address this issue, we have developed SPECdata, an open source, interactive tool which is designed to simplify and greatly accelerate the spectral analysis and discovery. Our software tool combines both automated and manual components that free the user from computation, while giving him/her considerable flexibility to assign, manipulate, interpret and export their analysis. The automated - and key - component of the new software is a database query system that rapidly assigns transitions of known species in an experimental spectrum. For each experiment, the software identifies spectral features, and subsequently assigns them to known molecules within an in-house database (Pickett .cat files, list of frequencies...), or those catalogued in Splatalogue (using automatic on-line queries). With suggested assignments, the control is then handed over to the user who can choose to accept, decline or add additional species. Data visualization, statistical information, and interactive widgets assist the user in making decisions about their data. SPECdata has several other useful features intended to improve the user experience. Exporting a full report of the analysis, or a peak file in which assigned lines are removed are among several options. A user may also save their progress to continue at another time. Additional features of SPECdata help the user to maintain and expand their database for future use. A user-friendly interface allows one to search, upload, edit or update catalog or experiment entries.

  20. Software development processes and analysis software: a mismatch and a novel framework

    International Nuclear Information System (INIS)

    Kelly, D.; Harauz, J.

    2011-01-01

    This paper discusses the salient characteristics of analysis software and the impact of those characteristics on its development. From this discussion, it can be seen that mainstream software development processes, usually characterized as Plan Driven or Agile, are built upon assumptions that are mismatched to the development and maintenance of analysis software. We propose a novel software development framework that would match the process normally observed in the development of analysis software. In the discussion of this framework, we suggest areas of research and directions for future work. (author)

  1. CMS Computing Software and Analysis Challenge 2006

    Energy Technology Data Exchange (ETDEWEB)

    De Filippis, N. [Dipartimento interateneo di Fisica M. Merlin and INFN Bari, Via Amendola 173, 70126 Bari (Italy)

    2007-10-15

    The CMS (Compact Muon Solenoid) collaboration is making a big effort to test the workflow and the dataflow associated with the data handling model. With this purpose the computing, software and analysis Challenge 2006, namely CSA06, started the 15th of September. It was a 50 million event exercise that included all the steps of the analysis chain, like the prompt reconstruction, the data streaming, calibration and alignment iterative executions, the data distribution to regional sites, up to the end-user analysis. Grid tools provided by the LCG project are also experimented to gain access to the data and the resources by providing a user friendly interface to the physicists submitting the production and the analysis jobs. An overview of the status and results of the CSA06 is presented in this work.

  2. CMS Computing Software and Analysis Challenge 2006

    International Nuclear Information System (INIS)

    De Filippis, N.

    2007-01-01

    The CMS (Compact Muon Solenoid) collaboration is making a big effort to test the workflow and the dataflow associated with the data handling model. With this purpose the computing, software and analysis Challenge 2006, namely CSA06, started the 15th of September. It was a 50 million event exercise that included all the steps of the analysis chain, like the prompt reconstruction, the data streaming, calibration and alignment iterative executions, the data distribution to regional sites, up to the end-user analysis. Grid tools provided by the LCG project are also experimented to gain access to the data and the resources by providing a user friendly interface to the physicists submitting the production and the analysis jobs. An overview of the status and results of the CSA06 is presented in this work

  3. Uncertainty in the use of MAMA software to measure particle morphological parameters from SEM images

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Daniel S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Tandon, Lav [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-06-05

    The MAMA software package developed at LANL is designed to make morphological measurements on a wide variety of digital images of objects. At LANL, we have focused on using MAMA to measure scanning electron microscope (SEM) images of particles, as this is a critical part of our forensic analysis of interdicted radiologic materials. In order to successfully use MAMA to make such measurements, we must understand the level of uncertainty involved in the process, so that we can rigorously support our quantitative conclusions.

  4. Software components for medical image visualization and surgical planning

    Science.gov (United States)

    Starreveld, Yves P.; Gobbi, David G.; Finnis, Kirk; Peters, Terence M.

    2001-05-01

    Purpose: The development of new applications in medical image visualization and surgical planning requires the completion of many common tasks such as image reading and re-sampling, segmentation, volume rendering, and surface display. Intra-operative use requires an interface to a tracking system and image registration, and the application requires basic, easy to understand user interface components. Rapid changes in computer and end-application hardware, as well as in operating systems and network environments make it desirable to have a hardware and operating system as an independent collection of reusable software components that can be assembled rapidly to prototype new applications. Methods: Using the OpenGL based Visualization Toolkit as a base, we have developed a set of components that implement the above mentioned tasks. The components are written in both C++ and Python, but all are accessible from Python, a byte compiled scripting language. The components have been used on the Red Hat Linux, Silicon Graphics Iris, Microsoft Windows, and Apple OS X platforms. Rigorous object-oriented software design methods have been applied to ensure hardware independence and a standard application programming interface (API). There are components to acquire, display, and register images from MRI, MRA, CT, Computed Rotational Angiography (CRA), Digital Subtraction Angiography (DSA), 2D and 3D ultrasound, video and physiological recordings. Interfaces to various tracking systems for intra-operative use have also been implemented. Results: The described components have been implemented and tested. To date they have been used to create image manipulation and viewing tools, a deep brain functional atlas, a 3D ultrasound acquisition and display platform, a prototype minimally invasive robotic coronary artery bypass graft planning system, a tracked neuro-endoscope guidance system and a frame-based stereotaxy neurosurgery planning tool. The frame-based stereotaxy module has been

  5. PARAGON-IPS: A Portable Imaging Software System For Multiple Generations Of Image Processing Hardware

    Science.gov (United States)

    Montelione, John

    1989-07-01

    Paragon-IPS is a comprehensive software system which is available on virtually all generations of image processing hardware. It is designed for an image processing department or a scientist and engineer who is doing image processing full-time. It is being used by leading R&D labs in government agencies and Fortune 500 companies. Applications include reconnaissance, non-destructive testing, remote sensing, medical imaging, etc.

  6. Static analysis of software the abstract interpretation

    CERN Document Server

    Boulanger, Jean-Louis

    2013-01-01

    The existing literature currently available to students and researchers is very general, covering only the formal techniques of static analysis. This book presents real examples of the formal techniques called ""abstract interpretation"" currently being used in various industrial fields: railway, aeronautics, space, automotive, etc. The purpose of this book is to present students and researchers, in a single book, with the wealth of experience of people who are intrinsically involved in the realization and evaluation of software-based safety critical systems. As the authors are people curr

  7. A new paradigm for the development of analysis software

    International Nuclear Information System (INIS)

    Kelly, D.; Harauz, J.

    2012-01-01

    For the CANDU industry, analysis software is an important tool for scientists and engineers to examine issues related to safety, operation, and design. However, the software quality assurance approach currently used for these tools assumes the software is the delivered product. In this paper, we present a model that shifts the emphasis from software being the end-product to software being support for the end-product, the science. We describe a novel software development paradigm that supports this shift and provides the groundwork for re-examining the quality assurance practices used for analysis software. (author)

  8. Clinical validation of semi-automated software for volumetric and dynamic contrast enhancement analysis of soft tissue venous malformations on magnetic resonance imaging examination

    Energy Technology Data Exchange (ETDEWEB)

    Caty, Veronique [Hopital Maisonneuve-Rosemont, Universite de Montreal, Department of Radiology, Montreal, QC (Canada); Kauffmann, Claude; Giroux, Marie-France; Oliva, Vincent; Therasse, Eric [Centre Hospitalier de l' Universite de Montreal (CHUM), Universite de Montreal and Research Centre, CHUM (CRCHUM), Department of Radiology, Montreal, QC (Canada); Dubois, Josee [Centre Hospitalier Universitaire Sainte-Justine et Universite de Montreal, Department of Radiology, Montreal, QC (Canada); Mansour, Asmaa [Institut de Cardiologie de Montreal, Heart Institute Coordinating Centre, Montreal, QC (Canada); Piche, Nicolas [Object Research System, Montreal, QC (Canada); Soulez, Gilles [Centre Hospitalier de l' Universite de Montreal (CHUM), Universite de Montreal and Research Centre, CHUM (CRCHUM), Department of Radiology, Montreal, QC (Canada); CHUM - Hopital Notre-Dame, Department of Radiology, Montreal, Quebec (Canada)

    2014-02-15

    To evaluate venous malformation (VM) volume and contrast-enhancement analysis on magnetic resonance imaging (MRI) compared with diameter evaluation. Baseline MRI was undertaken in 44 patients, 20 of whom were followed by MRI after sclerotherapy. All patients underwent short-tau inversion recovery (STIR) acquisitions and dynamic contrast assessment. VM diameters in three orthogonal directions were measured to obtain the largest and mean diameters. Volumetric reconstruction of VM was generated from two orthogonal STIR sequences and fused with acquisitions after contrast medium injection. Reproducibility (interclass correlation coefficients [ICCs]) of diameter and volume measurements was estimated. VM size variations in diameter and volume after sclerotherapy and contrast enhancement before sclerotherapy were compared in patients with clinical success or failure. Inter-observer ICCs were similar for diameter and volume measurements at baseline and follow-up (range 0.87-0.99). Higher percentages of size reduction after sclerotherapy were observed with volume (32.6 ± 30.7 %) than with diameter measurements (14.4 ± 21.4 %; P = 0.037). Contrast enhancement values were estimated at 65.3 ± 27.5 % and 84 ± 13 % in patients with clinical failure and success respectively (P = 0.056). Venous malformation volume was as reproducible as diameter measurement and more sensitive in detecting therapeutic responses. Patients with better clinical outcome tend to have stronger malformation enhancement. (orig.)

  9. Modularity analysis of automotive control software

    OpenAIRE

    Dajsuren, Y.; Brand, van den, M.G.J.; Serebrenik, A.

    2013-01-01

    A design language and tool like MATLAB/Simulink is used for the graphical modelling and simulation of automotive control software. As the functionality based on electronics and software systems increases in motor vehicles, it is becoming increasingly important for system/software architects and control engineers in the automotive industry to ensure the quality of the highly complex MATLAB/Simulink control software. For automotive software, modularity is recognized as being a crucial quality a...

  10. JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

    Science.gov (United States)

    Lelièvre, Peter G.; Grey, Melissa

    2017-08-01

    Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

  11. Mirion--a software package for automatic processing of mass spectrometric images.

    Science.gov (United States)

    Paschke, C; Leisner, A; Hester, A; Maass, K; Guenther, S; Bouschen, W; Spengler, B

    2013-08-01

    Mass spectrometric imaging (MSI) techniques are of growing interest for the Life Sciences. In recent years, the development of new instruments employing ion sources that are tailored for spatial scanning allowed the acquisition of large data sets. A subsequent data processing, however, is still a bottleneck in the analytical process, as a manual data interpretation is impossible within a reasonable time frame. The transformation of mass spectrometric data into spatial distribution images of detected compounds turned out to be the most appropriate method to visualize the results of such scans, as humans are able to interpret images faster and easier than plain numbers. Image generation, thus, is a time-consuming and complex yet very efficient task. The free software package "Mirion," presented in this paper, allows the handling and analysis of data sets acquired by mass spectrometry imaging. Mirion can be used for image processing of MSI data obtained from many different sources, as it uses the HUPO-PSI-based standard data format imzML, which is implemented in the proprietary software of most of the mass spectrometer companies. Different graphical representations of the recorded data are available. Furthermore, automatic calculation and overlay of mass spectrometric images promotes direct comparison of different analytes for data evaluation. The program also includes tools for image processing and image analysis.

  12. The ESA's Space Trajectory Analysis software suite

    Science.gov (United States)

    Ortega, Guillermo

    The European Space Agency (ESA) initiated in 2005 an internal activity to develop an open source software suite involving university science departments and research institutions all over the world. This project is called the "Space Trajectory Analysis" or STA. This article describes the birth of STA and its present configuration. One of the STA aims is to promote the exchange of technical ideas, and raise knowledge and competence in the areas of applied mathematics, space engineering, and informatics at University level. Conceived as a research and education tool to support the analysis phase of a space mission, STA is able to visualize a wide range of space trajectories. These include among others ascent, re-entry, descent and landing trajectories, orbits around planets and moons, interplanetary trajectories, rendezvous trajectories, etc. The article explains that STA project is an original idea of the Technical Directorate of ESA. It was born in August 2005 to provide a framework in astrodynamics research at University level. As research and education software applicable to Academia, a number of Universities support this development by joining ESA in leading the development. ESA and Universities partnership are expressed in the STA Steering Board. Together with ESA, each University has a chair in the board whose tasks are develop, control, promote, maintain, and expand the software suite. The article describes that STA provides calculations in the fields of spacecraft tracking, attitude analysis, coverage and visibility analysis, orbit determination, position and velocity of solar system bodies, etc. STA implements the concept of "space scenario" composed of Solar system bodies, spacecraft, ground stations, pads, etc. It is able to propagate the orbit of a spacecraft where orbital propagators are included. STA is able to compute communication links between objects of a scenario (coverage, line of sight), and to represent the trajectory computations and

  13. Open source software in a practical approach for post processing of radiologic images.

    Science.gov (United States)

    Valeri, Gianluca; Mazza, Francesco Antonino; Maggi, Stefania; Aramini, Daniele; La Riccia, Luigi; Mazzoni, Giovanni; Giovagnoni, Andrea

    2015-03-01

    The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images. We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points. Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10. OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

  14. Effective Results Analysis for the Similar Software Products’ Orthogonality

    Directory of Open Access Journals (Sweden)

    Ion Ivan

    2009-10-01

    Full Text Available It is defined the concept of similar software. There are established conditions of archiving the software components. It is carried out the orthogonality evaluation and the correlation between the orthogonality and the complexity of the homogenous software components is analyzed. Shall proceed to build groups of similar software products, belonging to the orthogonality intervals. There are presented in graphical form the results of the analysis. There are detailed aspects of the functioning of the software product allocated for the orthogonality.

  15. Vertical bone measurements from cone beam computed tomography images using different software packages

    Energy Technology Data Exchange (ETDEWEB)

    Vasconcelos, Taruska Ventorini; Neves, Frederico Sampaio; Moraes, Livia Almeida Bueno; Freitas, Deborah Queiroz, E-mail: tataventorini@hotmail.com [Universidade Estadual de Campinas (UNICAMP), Piracicaba, SP (Brazil). Faculdade de Odontologia

    2015-03-01

    This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (‑0.11 and ‑0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p > 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data. (author)

  16. Vertical bone measurements from cone beam computed tomography images using different software packages

    International Nuclear Information System (INIS)

    Vasconcelos, Taruska Ventorini; Neves, Frederico Sampaio; Moraes, Livia Almeida Bueno; Freitas, Deborah Queiroz

    2015-01-01

    This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (‑0.11 and ‑0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p > 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data. (author)

  17. Modularity analysis of automotive control software

    NARCIS (Netherlands)

    Dajsuren, Y.; Brand, van den M.G.J.; Serebrenik, A.

    2013-01-01

    A design language and tool like MATLAB/Simulink is used for the graphical modelling and simulation of automotive control software. As the functionality based on electronics and software systems increases in motor vehicles, it is becoming increasingly important for system/software architects and

  18. Elementary study on γ analysis software for low level measurement

    International Nuclear Information System (INIS)

    Ruan Guanglin; Huang Xianguo; Xing Shixiong

    2001-01-01

    The difficulty in using fashion γ analysis software in low level measurement is discussed. The ROI report file of ORTEC operation system has been chosen as interface file to write γ analysis software for low-level measurement. The author gives software flowchart and applied example and discusses the existent problems

  19. Comparison of quality control software tools for diffusion tensor imaging.

    Science.gov (United States)

    Liu, Bilan; Zhu, Tong; Zhong, Jianhui

    2015-04-01

    Image quality of diffusion tensor imaging (DTI) is critical for image interpretation, diagnostic accuracy and efficiency. However, DTI is susceptible to numerous detrimental artifacts that may impair the reliability and validity of the obtained data. Although many quality control (QC) software tools are being developed and are widely used and each has its different tradeoffs, there is still no general agreement on an image quality control routine for DTIs, and the practical impact of these tradeoffs is not well studied. An objective comparison that identifies the pros and cons of each of the QC tools will be helpful for the users to make the best choice among tools for specific DTI applications. This study aims to quantitatively compare the effectiveness of three popular QC tools including DTI studio (Johns Hopkins University), DTIprep (University of North Carolina at Chapel Hill, University of Iowa and University of Utah) and TORTOISE (National Institute of Health). Both synthetic and in vivo human brain data were used to quantify adverse effects of major DTI artifacts to tensor calculation as well as the effectiveness of different QC tools in identifying and correcting these artifacts. The technical basis of each tool was discussed, and the ways in which particular techniques affect the output of each of the tools were analyzed. The different functions and I/O formats that three QC tools provide for building a general DTI processing pipeline and integration with other popular image processing tools were also discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Software architecture for intelligent image processing using Prolog

    Science.gov (United States)

    Jones, Andrew C.; Batchelor, Bruce G.

    1994-10-01

    We describe a prototype system for interactive image processing using Prolog, implemented by the first author on an Apple Macintosh computer. This system is inspired by Prolog+, but differs from it in two particularly important respects. The first is that whereas Prolog+ assumes the availability of dedicated image processing hardware, with which the Prolog system communicates, our present system implements image processing functions in software using the C programming language. The second difference is that although our present system supports Prolog+ commands, these are implemented in terms of lower-level Prolog predicates which provide a more flexible approach to image manipulation. We discuss the impact of the Apple Macintosh operating system upon the implementation of the image-processing functions, and the interface between these functions and the Prolog system. We also explain how the Prolog+ commands have been implemented. The system described in this paper is a fairly early prototype, and we outline how we intend to develop the system, a task which is expedited by the extensible architecture we have implemented.

  1. Visual querying and analysis of large software repositories

    NARCIS (Netherlands)

    Voinea, Lucian; Telea, Alexandru

    We present a software framework for mining software repositories. Our extensible framework enables the integration of data extraction from repositories with data analysis and interactive visualization. We demonstrate the applicability of the framework by presenting several case studies performed on

  2. Specific developed phantoms and software to assess radiological equipment image quality

    Energy Technology Data Exchange (ETDEWEB)

    Verdu, G., E-mail: gverdu@iqn.upv.es [Universidad Politecnica de Valencia (Spain). Dept. de Ingenieria Quimica y Nuclear; Mayo, P., E-mail: p.mayo@titaniast.com [TITANIA Servicios Teconologicos, Valencia (Spain); Rodenas, F., E-mail: frodenas@mat.upv.es [Universidad Politecnica de Valencia (Spain). Dept. de Matematica Aplicada; Campayo, J.M., E-mail: j.campayo@lainsa.com [Logistica y Acondicionamientos Industriales S.A.U (LAINSA), Valencia (Spain)

    2011-07-01

    The use of radiographic phantoms specifically designed to evaluate the operation of the radiographic equipment lets the study of the image quality obtained by this equipment in an objective way. In digital radiographic equipment, the analysis of the image quality can be automatized because the acquisition of the image is possible in different technologies that are, computerized radiography or phosphor plate and direct radiography or detector. In this work we have shown an application to assess automatically the constancy quality image in the image chain of the radiographic equipment. This application is integrated by designed radiographic phantoms which are adapted to conventional, dental equipment and specific developed software for the automatic evaluation of the phantom image quality. The software is based on digital image processing techniques that let the automatic detection of the different phantom tests by edge detector, morphological operators, threshold histogram techniques, etc. The utility developed is enough sensitive to the radiographic equipment of operating conditions of voltage (kV) and charge (mAs). It is a friendly user programme connected with a data base of the hospital or clinic where it has been used. After the phantom image processing the user can obtain an inform with a resume of the imaging system state with accepting and constancy results. (author)

  3. Specific developed phantoms and software to assess radiological equipment image quality

    International Nuclear Information System (INIS)

    Verdu, G.; Rodenas, F.

    2011-01-01

    The use of radiographic phantoms specifically designed to evaluate the operation of the radiographic equipment lets the study of the image quality obtained by this equipment in an objective way. In digital radiographic equipment, the analysis of the image quality can be automatized because the acquisition of the image is possible in different technologies that are, computerized radiography or phosphor plate and direct radiography or detector. In this work we have shown an application to assess automatically the constancy quality image in the image chain of the radiographic equipment. This application is integrated by designed radiographic phantoms which are adapted to conventional, dental equipment and specific developed software for the automatic evaluation of the phantom image quality. The software is based on digital image processing techniques that let the automatic detection of the different phantom tests by edge detector, morphological operators, threshold histogram techniques, etc. The utility developed is enough sensitive to the radiographic equipment of operating conditions of voltage (kV) and charge (mAs). It is a friendly user programme connected with a data base of the hospital or clinic where it has been used. After the phantom image processing the user can obtain an inform with a resume of the imaging system state with accepting and constancy results. (author)

  4. Microscopy image segmentation tool: Robust image data analysis

    Energy Technology Data Exchange (ETDEWEB)

    Valmianski, Ilya, E-mail: ivalmian@ucsd.edu; Monton, Carlos; Schuller, Ivan K. [Department of Physics and Center for Advanced Nanoscience, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093 (United States)

    2014-03-15

    We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

  5. Microscopy image segmentation tool: Robust image data analysis

    Science.gov (United States)

    Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

    2014-03-01

    We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

  6. Microscopy image segmentation tool: Robust image data analysis

    International Nuclear Information System (INIS)

    Valmianski, Ilya; Monton, Carlos; Schuller, Ivan K.

    2014-01-01

    We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy

  7. Software applications for flux balance analysis.

    Science.gov (United States)

    Lakshmanan, Meiyappan; Koh, Geoffrey; Chung, Bevan K S; Lee, Dong-Yup

    2014-01-01

    Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overall, most of the applications are able to perform basic features of model creation and FBA simulation. COBRA toolbox, OptFlux and FASIMU are versatile to support advanced in silico algorithms to identify environmental and genetic targets for strain design. SurreyFBA, WEbcoli, Acorn, FAME, GEMSiRV and MetaFluxNet are the distinct tools which provide the user friendly interfaces in model handling. In terms of software architecture, FBA-SimVis and OptFlux have the flexible environments as they enable the plug-in/add-on feature to aid prospective functional extensions. Notably, an increasing trend towards the implementation of more tailored e-services such as central model repository and assistance to collaborative efforts was observed among the web-based applications with the help of advanced web-technologies. Furthermore, most recent applications such as the Model SEED, FAME, MetaFlux and MicrobesFlux have even included several routines to facilitate the reconstruction of genome-scale metabolic models. Finally, a brief discussion on the future directions of FBA applications was made for the benefit of potential tool developers.

  8. SOFTWARE FOR IMAGE PROCESSING OF IRON-CARBONACEOUS ALLOY MICROSTRUCTURES

    Directory of Open Access Journals (Sweden)

    A. N. Chichko

    2011-01-01

    Full Text Available The paper proposes a mathematical apparatus for image processing of a cast-iron microstructure of a pearlite class that has casually distributed graphite inclusions in the structure the software has been developed and it allows to determine statistical functions concerning distribution of graphite inclusion characteristics according to areas, perimeters and distances between inclusions. The paper shows that computer processing of gray pig-iron microstructure image makes it possible to classify microstructures on the basis of statistical distribution of a graphite phase which are considered as indiscernible while applying conventional metallographic methods and it has practical significance for investigation of the interrelations – «workability – cast iron microstructure».

  9. Standardizing Activation Analysis: New Software for Photon Activation Analysis

    Science.gov (United States)

    Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

    2011-06-01

    Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

  10. Standardizing Activation Analysis: New Software for Photon Activation Analysis

    International Nuclear Information System (INIS)

    Sun, Z. J.; Wells, D.; Green, J.; Segebade, C.

    2011-01-01

    Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

  11. 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.

  12. LANDSAFE: LANDING SITE RISK ANALYSIS SOFTWARE FRAMEWORK

    Directory of Open Access Journals (Sweden)

    R. Schmidt

    2012-08-01

    Full Text Available The European Space Agency (ESA is planning a Lunar Lander mission in the 2018 timeframe that will demonstrate precise soft landing at the polar regions of the Moon. To ensure a safe and successful landing a careful risk analysis has to be carried out. This is comprised of identifying favorable target areas and evaluating the surface conditions in these areas. Features like craters, boulders, steep slopes, rough surfaces and shadow areas have to be identified in order to assess the risk associated to a landing site in terms of a successful touchdown and subsequent surface operation of the lander. In addition, global illumination conditions at the landing site have to be simulated and analyzed. The Landing Site Risk Analysis software framework (LandSAfe is a system for the analysis, selection and certification of safe landing sites on the lunar surface. LandSAfe generates several data products including high resolution digital terrain models (DTMs, hazard maps, illumination maps, temperature maps and surface reflectance maps which assist the user in evaluating potential landing site candidates. This paper presents the LandSAfe system and describes the methods and products of the different modules. For one candidate landing site on the rim of Shackleton crater at the south pole of the Moon a high resolution DTM is showcased.

  13. PuMA: the Porous Microstructure Analysis software

    Science.gov (United States)

    Ferguson, Joseph C.; Panerai, Francesco; Borner, Arnaud; Mansour, Nagi N.

    2018-01-01

    The Porous Microstructure Analysis (PuMA) software has been developed in order to compute effective material properties and perform material response simulations on digitized microstructures of porous media. PuMA is able to import digital three-dimensional images obtained from X-ray microtomography or to generate artificial microstructures. PuMA also provides a module for interactive 3D visualizations. Version 2.1 includes modules to compute porosity, volume fractions, and surface area. Two finite difference Laplace solvers have been implemented to compute the continuum tortuosity factor, effective thermal conductivity, and effective electrical conductivity. A random method has been developed to compute tortuosity factors from the continuum to rarefied regimes. Representative elementary volume analysis can be performed on each property. The software also includes a time-dependent, particle-based model for the oxidation of fibrous materials. PuMA was developed for Linux operating systems and is available as a NASA software under a US & Foreign release.

  14. Multi-institutional Validation Study of Commercially Available Deformable Image Registration Software for Thoracic Images

    International Nuclear Information System (INIS)

    Kadoya, Noriyuki; Nakajima, Yujiro; Saito, Masahide; Miyabe, Yuki; Kurooka, Masahiko; Kito, Satoshi; Fujita, Yukio; Sasaki, Motoharu; Arai, Kazuhiro; Tani, Kensuke; Yagi, Masashi; Wakita, Akihisa; Tohyama, Naoki; Jingu, Keiichi

    2016-01-01

    Purpose: To assess the accuracy of the commercially available deformable image registration (DIR) software for thoracic images at multiple institutions. Methods and Materials: Thoracic 4-dimensional (4D) CT images of 10 patients with esophageal or lung cancer were used. Datasets for these patients were provided by DIR-lab ( (dir-lab.com)) and included a coordinate list of anatomic landmarks (300 bronchial bifurcations) that had been manually identified. Deformable image registration was performed between the peak-inhale and -exhale images. Deformable image registration error was determined by calculating the difference at each landmark point between the displacement calculated by DIR software and that calculated by the landmark. Results: Eleven institutions participated in this study: 4 used RayStation (RaySearch Laboratories, Stockholm, Sweden), 5 used MIM Software (Cleveland, OH), and 3 used Velocity (Varian Medical Systems, Palo Alto, CA). The ranges of the average absolute registration errors over all cases were as follows: 0.48 to 1.51 mm (right-left), 0.53 to 2.86 mm (anterior-posterior), 0.85 to 4.46 mm (superior-inferior), and 1.26 to 6.20 mm (3-dimensional). For each DIR software package, the average 3-dimensional registration error (range) was as follows: RayStation, 3.28 mm (1.26-3.91 mm); MIM Software, 3.29 mm (2.17-3.61 mm); and Velocity, 5.01 mm (4.02-6.20 mm). These results demonstrate that there was moderate variation among institutions, although the DIR software was the same. Conclusions: We evaluated the commercially available DIR software using thoracic 4D-CT images from multiple centers. Our results demonstrated that DIR accuracy differed among institutions because it was dependent on both the DIR software and procedure. Our results could be helpful for establishing prospective clinical trials and for the widespread use of DIR software. In addition, for clinical care, we should try to find the optimal DIR procedure using thoracic 4D

  15. A New Effort for Atmospherical Forecast: Meteorological Image Processing Software (MIPS) for Astronomical Observations

    Science.gov (United States)

    Shameoni Niaei, M.; Kilic, Y.; Yildiran, B. E.; Yüzlükoglu, F.; Yesilyaprak, C.

    2016-12-01

    We have described a new software (MIPS) about the analysis and image processing of the meteorological satellite (Meteosat) data for an astronomical observatory. This software will be able to help to make some atmospherical forecast (cloud, humidity, rain) using meteosat data for robotic telescopes. MIPS uses a python library for Eumetsat data that aims to be completely open-source and licenced under GNU/General Public Licence (GPL). MIPS is a platform independent and uses h5py, numpy, and PIL with the general-purpose and high-level programming language Python and the QT framework.

  16. Software patterns, knowledge maps, and domain analysis

    CERN Document Server

    Fayad, Mohamed E; Hegde, Srikanth GK; Basia, Anshu; Vakil, Ashka

    2014-01-01

    Preface AcknowledgmentsAuthors INTRODUCTIONAn Overview of Knowledge MapsIntroduction: Key Concepts-Software Stable Models, Knowledge Maps, Pattern Language, Goals, Capabilities (Enduring Business Themes + Business Objects) The Motivation The Problem The Objectives Overview of Software Stability Concepts Overview of Knowledge Maps Pattern Languages versus Knowledge Maps: A Brief ComparisonThe Solution Knowledge Maps Methodology or Concurrent Software Development ModelWhy Knowledge Maps? Research Methodology Undertaken Research Verification and Validation The Stratification of This Book Summary

  17. Free and open source software for the manipulation of digital images.

    Science.gov (United States)

    Solomon, Robert W

    2009-06-01

    Free and open source software is a type of software that is nearly as powerful as commercial software but is freely downloadable. This software can do almost everything that the expensive programs can. GIMP (gnu image manipulation program) is the free program that is comparable to Photoshop, and versions are available for Windows, Macintosh, and Linux platforms. This article briefly describes how GIMP can be installed and used to manipulate radiology images. It is no longer necessary to budget large amounts of money for high-quality software to achieve the goals of image processing and document creation because free and open source software is available for the user to download at will.

  18. The SAVI Vulnerability Analysis Software Package

    International Nuclear Information System (INIS)

    Mc Aniff, R.J.; Paulus, W.K.; Key, B.; Simpkins, B.

    1987-01-01

    SAVI (Systematic Analysis of Vulnerability to Intrusion) is a new PC-based software package for modeling Physical Protection Systems (PPS). SAVI utilizes a path analysis approach based on the Adversary Sequence Diagram (ASD) methodology. A highly interactive interface allows the user to accurately model complex facilities, maintain a library of these models on disk, and calculate the most vulnerable paths through any facility. Recommendations are provided to help the user choose facility upgrades which should reduce identified path vulnerabilities. Pop-up windows throughout SAVI are used for the input and display of information. A menu at the top of the screen presents all options to the user. These options are further explained on a message line directly below the menu. A diagram on the screen graphically represents the current protection system model. All input is checked for errors, and data are presented in a logical and clear manner. Print utilities provide the user with hard copies of all information and calculated results

  19. Social network analysis in software process improvement

    DEFF Research Database (Denmark)

    Nielsen, Peter Axel; Tjørnehøj, Gitte

    2010-01-01

    Software process improvement in small organisation is often problematic and communication and knowledge sharing is more informal. To improve software processes we need to understand how they communicate and share knowledge. In this article have studied the company SmallSoft through action research...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-15

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

  1. Effective Results Analysis for the Similar Software Products’ Orthogonality

    OpenAIRE

    Ion Ivan; Daniel Milodin

    2009-01-01

    It is defined the concept of similar software. There are established conditions of archiving the software components. It is carried out the orthogonality evaluation and the correlation between the orthogonality and the complexity of the homogenous software components is analyzed. Shall proceed to build groups of similar software products, belonging to the orthogonality intervals. There are presented in graphical form the results of the analysis. There are detailed aspects of the functioning o...

  2. Astronomical Image and Data Analysis

    CERN Document Server

    Starck, J.-L

    2006-01-01

    With information and scale as central themes, this comprehensive survey explains how to handle real problems in astronomical data analysis using a modern arsenal of powerful techniques. It treats those innovative methods of image, signal, and data processing that are proving to be both effective and widely relevant. The authors are leaders in this rapidly developing field and draw upon decades of experience. They have been playing leading roles in international projects such as the Virtual Observatory and the Grid. The book addresses not only students and professional astronomers and astrophysicists, but also serious amateur astronomers and specialists in earth observation, medical imaging, and data mining. The coverage includes chapters or appendices on: detection and filtering; image compression; multichannel, multiscale, and catalog data analytical methods; wavelets transforms, Picard iteration, and software tools. This second edition of Starck and Murtagh's highly appreciated reference again deals with to...

  3. A software tool for automatic classification and segmentation of 2D/3D medical images

    International Nuclear Information System (INIS)

    Strzelecki, Michal; Szczypinski, Piotr; Materka, Andrzej; Klepaczko, Artur

    2013-01-01

    Modern medical diagnosis utilizes techniques of visualization of human internal organs (CT, MRI) or of its metabolism (PET). However, evaluation of acquired images made by human experts is usually subjective and qualitative only. Quantitative analysis of MR data, including tissue classification and segmentation, is necessary to perform e.g. attenuation compensation, motion detection, and correction of partial volume effect in PET images, acquired with PET/MR scanners. This article presents briefly a MaZda software package, which supports 2D and 3D medical image analysis aiming at quantification of image texture. MaZda implements procedures for evaluation, selection and extraction of highly discriminative texture attributes combined with various classification, visualization and segmentation tools. Examples of MaZda application in medical studies are also provided

  4. A software tool for automatic classification and segmentation of 2D/3D medical images

    Energy Technology Data Exchange (ETDEWEB)

    Strzelecki, Michal, E-mail: michal.strzelecki@p.lodz.pl [Institute of Electronics, Technical University of Lodz, Wolczanska 211/215, 90-924 Lodz (Poland); Szczypinski, Piotr; Materka, Andrzej; Klepaczko, Artur [Institute of Electronics, Technical University of Lodz, Wolczanska 211/215, 90-924 Lodz (Poland)

    2013-02-21

    Modern medical diagnosis utilizes techniques of visualization of human internal organs (CT, MRI) or of its metabolism (PET). However, evaluation of acquired images made by human experts is usually subjective and qualitative only. Quantitative analysis of MR data, including tissue classification and segmentation, is necessary to perform e.g. attenuation compensation, motion detection, and correction of partial volume effect in PET images, acquired with PET/MR scanners. This article presents briefly a MaZda software package, which supports 2D and 3D medical image analysis aiming at quantification of image texture. MaZda implements procedures for evaluation, selection and extraction of highly discriminative texture attributes combined with various classification, visualization and segmentation tools. Examples of MaZda application in medical studies are also provided.

  5. Hardware and software design considerations in engineering an image processing workstation

    International Nuclear Information System (INIS)

    Feingold, E.; Seshadri, S.B.; Tretiak, O.J.

    1986-01-01

    The use of densitometry in autoradiography is not novel, but computer-assisted video densitometry is gaining increasing popularity. This is because functional mapping with radionuclides, such as the 2-deoxyglucose (2-DG) technique, produces enormous numbers of images which require quite detailed analysis and quantification. Effective use of the data contained in 2-DG autoradiograms is almost unfeasible if computer assisted image analysis is not utilized, and a video densitometric system (one that uses a television camera to scan the autoradiogram) is both suitable and economical. This paper will describe the software and hardware design and implementation of one such image analysis system: the DUMAs system and the BRAIN software package. This chapter describes the results of the authors' development effort. Since the user interface is paramount, the next section describes the BRAIN software. In the following section, they describe the issues relevant to selecting the DUMAS hardware and some of the alternatives considered. In the concluding section, they summarize the status of the DUMAS/BRAIN project and look at future developments

  6. The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images

    International Nuclear Information System (INIS)

    Shahidi, Shoaleh; Bahrampour, Ehsan; Soltanimehr, Elham; Zamani, Ali; Oshagh, Morteza; Moattari, Marzieh; Mehdizadeh, Alireza

    2014-01-01

    Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods

  7. COMPARATIVE ANALYSIS OF SOFTWARE DEVELOPMENT MODELS

    OpenAIRE

    Sandeep Kaur*

    2017-01-01

    No geek is unfamiliar with the concept of software development life cycle (SDLC). This research deals with the various SDLC models covering waterfall, spiral, and iterative, agile, V-shaped, prototype model. In the modern era, all the software systems are fallible as they can’t stand with certainty. So, it is tried to compare all aspects of the various models, their pros and cons so that it could be easy to choose a particular model at the time of need

  8. CAX a software for automated spectrum analysis

    International Nuclear Information System (INIS)

    Zahn, Guilherme S.; Genezini, Frederico A.

    2017-01-01

    In this work, the scripting capabilities of Genie-2000 were used to develop a software that automatically analyses all spectrum files in either Ortec's CHN or Canberra's MCA or CNF formats in a folder, generating two output files: a print-ready text le (.DAT) and a Comma-Separated Values (.CSV) le which can be easily imported in any major spreadsheet software. This software, named CAX ('Convert and Analyse for eXcel'), uses Genie-2000's functions to import spectrum files into Genie's native CNF format and analyze the converted spectra. The software can also, if requested, import energy and FWHM calibrations from a stored calibrated spectrum. The print-ready output le (.DAT) is generated by Genie-2000 using a customized script, and the CSV le is generated by a custom-built DAT2CSV software which generates a CSV le that complies to the Brazilian standards, with commas as a decimal indicator and semicolons as eld separators. This software is already used in the daily routines in IPEN's Neutron Activation Laboratory, greatly reducing the time required for sample analyses, as well as reducing the possibility of transcription errors. (author)

  9. CAX a software for automated spectrum analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zahn, Guilherme S.; Genezini, Frederico A., E-mail: gzahn@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (CRPq/IPEN/CNEN-SP), Sao Paulo, SP (Brazil). Centro do Reator de Pesquisas

    2017-11-01

    In this work, the scripting capabilities of Genie-2000 were used to develop a software that automatically analyses all spectrum files in either Ortec's CHN or Canberra's MCA or CNF formats in a folder, generating two output files: a print-ready text le (.DAT) and a Comma-Separated Values (.CSV) le which can be easily imported in any major spreadsheet software. This software, named CAX ('Convert and Analyse for eXcel'), uses Genie-2000's functions to import spectrum files into Genie's native CNF format and analyze the converted spectra. The software can also, if requested, import energy and FWHM calibrations from a stored calibrated spectrum. The print-ready output le (.DAT) is generated by Genie-2000 using a customized script, and the CSV le is generated by a custom-built DAT2CSV software which generates a CSV le that complies to the Brazilian standards, with commas as a decimal indicator and semicolons as eld separators. This software is already used in the daily routines in IPEN's Neutron Activation Laboratory, greatly reducing the time required for sample analyses, as well as reducing the possibility of transcription errors. (author)

  10. Development of a New VLBI Data Analysis Software

    Science.gov (United States)

    Bolotin, Sergei; Gipson, John M.; MacMillan, Daniel S.

    2010-01-01

    We present an overview of a new VLBI analysis software under development at NASA GSFC. The new software will replace CALC/SOLVE and many related utility programs. It will have the capabilities of the current system as well as incorporate new models and data analysis techniques. In this paper we give a conceptual overview of the new software. We formulate the main goals of the software. The software should be flexible and modular to implement models and estimation techniques that currently exist or will appear in future. On the other hand it should be reliable and possess production quality for processing standard VLBI sessions. Also, it needs to be capable of processing observations from a fully deployed network of VLBI2010 stations in a reasonable time. We describe the software development process and outline the software architecture.

  11. Evaluation of a software package for automated quality assessment of contrast detail images-comparison with subjective visual assessment

    International Nuclear Information System (INIS)

    Pascoal, A; Lawinski, C P; Honey, I; Blake, P

    2005-01-01

    Contrast detail analysis is commonly used to assess image quality (IQ) associated with diagnostic imaging systems. Applications include routine assessment of equipment performance and optimization studies. Most frequently, the evaluation of contrast detail images involves human observers visually detecting the threshold contrast detail combinations in the image. However, the subjective nature of human perception and the variations in the decision threshold pose limits to the minimum image quality variations detectable with reliability. Objective methods of assessment of image quality such as automated scoring have the potential to overcome the above limitations. A software package (CDRAD analyser) developed for automated scoring of images produced with the CDRAD test object was evaluated. Its performance to assess absolute and relative IQ was compared with that of an average observer. Results show that the software does not mimic the absolute performance of the average observer. The software proved more sensitive and was able to detect smaller low-contrast variations. The observer's performance was superior to the software's in the detection of smaller details. Both scoring methods showed frequent agreement in the detection of image quality variations resulting from changes in kVp and KERMA detector , which indicates the potential to use the software CDRAD analyser for assessment of relative IQ

  12. Continuous software quality analysis for the ATLAS experiment

    CERN Document Server

    Washbrook, Andrew; The ATLAS collaboration

    2017-01-01

    The software for the ATLAS experiment on the Large Hadron Collider at CERN has evolved over many years to meet the demands of Monte Carlo simulation, particle detector reconstruction and data analysis. At present over 3.8 million lines of C++ code (and close to 6 million total lines of code) are maintained by an active worldwide developer community. In order to run the experiment software efficiently at hundreds of computing centres it is essential to maintain a high level of software quality standards. The methods proposed to improve software quality practices by incorporating checks into the new ATLAS software build infrastructure.

  13. Application of Scion image software to the simultaneous determination of curcuminoids in turmeric (Curcuma longa).

    Science.gov (United States)

    Sotanaphun, Uthai; Phattanawasin, Panadda; Sriphong, Lawan

    2009-01-01

    Curcumin, desmethoxycurcumin and bisdesmethoxycurcumin are bioactive constituents of turmeric (Curcuma longa). Owing to their different potency, quality control of turmeric based on the content of each curcuminoid is more reliable than that based on total curcuminoids. However, to perform such an assay, high-cost instrument is needed. To develop a simple and low-cost method for the simultaneous quantification of three curcuminoids in turmeric using TLC and the public-domain software Scion Image. The image of a TLC chromatogram of turmeric extract was recorded using a digital scanner. The density of the TLC spot of each curcuminoid was analysed by the Scion Image software. The density value was transformed to concentration by comparison with the calibration curve of standard curcuminoids developed on the same TLC plate. The polynomial regression data for all curcuminoids showed good linear relationship with R(2) > 0.99 in the concentration range of 0.375-6 microg/spot. The limits of detection and quantitation were 43-73 and 143-242 ng/spot, respectively. The method gave adequate precision, accuracy and recovery. The contents of each curcuminoid determined using this method were not significantly different from those determined using the TLC densitometric method. TLC image analysis using Scion Image is shown to be a reliable method for the simultaneous analysis of the content of each curcuminoid in turmeric.

  14. Technical Note: DIRART- A software suite for deformable image registration and adaptive radiotherapy research

    International Nuclear Information System (INIS)

    Yang Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu Yu; Murty Goddu, S.; Mutic, Sasa; Deasy, Joseph O.; Low, Daniel A.

    2011-01-01

    Purpose: Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). Methods: DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. Results: DIRART provides a set of image processing/registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. Conclusions: By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research.

  15. Software Piracy in Research: A Moral Analysis.

    Science.gov (United States)

    Santillanes, Gary; Felder, Ryan Marshall

    2015-08-01

    Researchers in virtually every discipline rely on sophisticated proprietary software for their work. However, some researchers are unable to afford the licenses and instead procure the software illegally. We discuss the prohibition of software piracy by intellectual property laws, and argue that the moral basis for the copyright law offers the possibility of cases where software piracy may be morally justified. The ethics codes that scientific institutions abide by are informed by a rule-consequentialist logic: by preserving personal rights to authored works, people able to do so will be incentivized to create. By showing that the law has this rule-consequentialist grounding, we suggest that scientists who blindly adopt their institutional ethics codes will commit themselves to accepting that software piracy could be morally justified, in some cases. We hope that this conclusion will spark debate over important tensions between ethics codes, copyright law, and the underlying moral basis for these regulations. We conclude by offering practical solutions (other than piracy) for researchers.

  16. A proposal for performing software safety hazard analysis

    International Nuclear Information System (INIS)

    Lawrence, J.D.; Gallagher, J.M.

    1997-01-01

    Techniques for analyzing the safety and reliability of analog-based electronic protection systems that serve to mitigate hazards in process control systems have been developed over many years, and are reasonably understood. An example is the protection system in a nuclear power plant. The extension of these techniques to systems which include digital computers is not well developed, and there is little consensus among software engineering experts and safety experts on how to analyze such systems. One possible technique is to extend hazard analysis to include digital computer-based systems. Software is frequently overlooked during system hazard analyses, but this is unacceptable when the software is in control of a potentially hazardous operation. In such cases, hazard analysis should be extended to fully cover the software. A method for performing software hazard analysis is proposed in this paper. The method concentrates on finding hazards during the early stages of the software life cycle, using an extension of HAZOP

  17. INFOS: spectrum fitting software for NMR analysis

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Albert A., E-mail: alsi@nmr.phys.chem.ethz.ch [ETH Zürich, Physical Chemistry (Switzerland)

    2017-02-15

    Software for fitting of NMR spectra in MATLAB is presented. Spectra are fitted in the frequency domain, using Fourier transformed lineshapes, which are derived using the experimental acquisition and processing parameters. This yields more accurate fits compared to common fitting methods that use Lorentzian or Gaussian functions. Furthermore, a very time-efficient algorithm for calculating and fitting spectra has been developed. The software also performs initial peak picking, followed by subsequent fitting and refinement of the peak list, by iteratively adding and removing peaks to improve the overall fit. Estimation of error on fitting parameters is performed using a Monte-Carlo approach. Many fitting options allow the software to be flexible enough for a wide array of applications, while still being straightforward to set up with minimal user input.

  18. Digitized hand-wrist radiographs: comparison of subjective and software-derived image quality at various compression ratios.

    Science.gov (United States)

    McCord, Layne K; Scarfe, William C; Naylor, Rachel H; Scheetz, James P; Silveira, Anibal; Gillespie, Kevin R

    2007-05-01

    The objectives of this study were to compare the effect of JPEG 2000 compression of hand-wrist radiographs on observer image quality qualitative assessment and to compare with a software-derived quantitative image quality index. Fifteen hand-wrist radiographs were digitized and saved as TIFF and JPEG 2000 images at 4 levels of compression (20:1, 40:1, 60:1, and 80:1). The images, including rereads, were viewed by 13 orthodontic residents who determined the image quality rating on a scale of 1 to 5. A quantitative analysis was also performed by using a readily available software based on the human visual system (Image Quality Measure Computer Program, version 6.2, Mitre, Bedford, Mass). ANOVA was used to determine the optimal compression level (P quality. When we used quantitative indexes, the JPEG 2000 images had lower quality at all compression ratios compared with the original TIFF images. There was excellent correlation (R2 >0.92) between qualitative and quantitative indexes. Image Quality Measure indexes are more sensitive than subjective image quality assessments in quantifying image degradation with compression. There is potential for this software-based quantitative method in determining the optimal compression ratio for any image without the use of subjective raters.

  19. Oncological image analysis.

    Science.gov (United States)

    Brady, Sir Michael; Highnam, Ralph; Irving, Benjamin; Schnabel, Julia A

    2016-10-01

    Cancer is one of the world's major healthcare challenges and, as such, an important application of medical image analysis. After a brief introduction to cancer, we summarise some of the major developments in oncological image analysis over the past 20 years, but concentrating those in the authors' laboratories, and then outline opportunities and challenges for the next decade. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Comparison of two three-dimensional cephalometric analysis computer software

    OpenAIRE

    Sawchuk, Dena; Alhadlaq, Adel; Alkhadra, Thamer; Carlyle, Terry D; Kusnoto, Budi; El-Bialy, Tarek

    2014-01-01

    Background: Three-dimensional cephalometric analyses are getting more attraction in orthodontics. The aim of this study was to compare two softwares to evaluate three-dimensional cephalometric analyses of orthodontic treatment outcomes. Materials and Methods: Twenty cone beam computed tomography images were obtained using i-CAT® imaging system from patient's records as part of their regular orthodontic records. The images were analyzed using InVivoDental5.0 (Anatomage Inc.) and 3DCeph™ (Unive...

  1. Development of Software to Model AXAF-I Image Quality

    Science.gov (United States)

    Geary, Joseph; Hawkins, Lamar; Ahmad, Anees; Gong, Qian

    1997-01-01

    This report describes work conducted on Delivery Order 181 between October 1996 through June 1997. During this period software was written to: compute axial PSD's from RDOS AXAF-I mirror surface maps; plot axial surface errors and compute PSD's from HDOS "Big 8" axial scans; plot PSD's from FITS format PSD files; plot band-limited RMS vs axial and azimuthal position for multiple PSD files; combine and organize PSD's from multiple mirror surface measurements formatted as input to GRAZTRACE; modify GRAZTRACE to read FITS formatted PSD files; evaluate AXAF-I test results; improve and expand the capabilities of the GT x-ray mirror analysis package. During this period work began on a more user-friendly manual for the GT program, and improvements were made to the on-line help manual.

  2. Gabor Analysis for Imaging

    DEFF Research Database (Denmark)

    Christensen, Ole; Feichtinger, Hans G.; Paukner, Stephan

    2015-01-01

    , it characterizes a function by its transform over phase space, which is the time–frequency plane (TF-plane) in a musical context or the location–wave-number domain in the context of image processing. Since the transition from the signal domain to the phase space domain introduces an enormous amount of data...... of the generalities relevant for an understanding of Gabor analysis of functions on Rd. We pay special attention to the case d = 2, which is the most important case for image processing and image analysis applications. The chapter is organized as follows. Section 2 presents central tools from functional analysis......, the application of Gabor expansions to image representation is considered in Sect. 6....

  3. Ultrasonic image analysis and image-guided interventions.

    Science.gov (United States)

    Noble, J Alison; Navab, Nassir; Becher, H

    2011-08-06

    The fields of medical image analysis and computer-aided interventions deal with reducing the large volume of digital images (X-ray, computed tomography, magnetic resonance imaging (MRI), positron emission tomography and ultrasound (US)) to more meaningful clinical information using software algorithms. US is a core imaging modality employed in these areas, both in its own right and used in conjunction with the other imaging modalities. It is receiving increased interest owing to the recent introduction of three-dimensional US, significant improvements in US image quality, and better understanding of how to design algorithms which exploit the unique strengths and properties of this real-time imaging modality. This article reviews the current state of art in US image analysis and its application in image-guided interventions. The article concludes by giving a perspective from clinical cardiology which is one of the most advanced areas of clinical application of US image analysis and describing some probable future trends in this important area of ultrasonic imaging research.

  4. Using Deep Learning Algorithm to Enhance Image-review Software for Surveillance Cameras

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Yonggang

    2018-05-07

    We propose the development of proven deep learning algorithms to flag objects and events of interest in Next Generation Surveillance System (NGSS) surveillance to make IAEA image review more efficient. Video surveillance is one of the core monitoring technologies used by the IAEA Department of Safeguards when implementing safeguards at nuclear facilities worldwide. The current image review software GARS has limited automated functions, such as scene-change detection, black image detection and missing scene analysis, but struggles with highly cluttered backgrounds. A cutting-edge algorithm to be developed in this project will enable efficient and effective searches in images and video streams by identifying and tracking safeguards relevant objects and detect anomalies in their vicinity. In this project, we will develop the algorithm, test it with the IAEA surveillance cameras and data sets collected at simulated nuclear facilities at BNL and SNL, and implement it in a software program for potential integration into the IAEA’s IRAP (Integrated Review and Analysis Program).

  5. Research and Development on Food Nutrition Statistical Analysis Software System

    OpenAIRE

    Du Li; Ke Yun

    2013-01-01

    Designing and developing a set of food nutrition component statistical analysis software can realize the automation of nutrition calculation, improve the nutrition processional professional’s working efficiency and achieve the informatization of the nutrition propaganda and education. In the software development process, the software engineering method and database technology are used to calculate the human daily nutritional intake and the intelligent system is used to evaluate the user’s hea...

  6. ESTERR-PRO: A Setup Verification Software System Using Electronic Portal Imaging

    Directory of Open Access Journals (Sweden)

    Pantelis A. Asvestas

    2007-01-01

    Full Text Available The purpose of the paper is to present and evaluate the performance of a new software-based registration system for patient setup verification, during radiotherapy, using electronic portal images. The estimation of setup errors, using the proposed system, can be accomplished by means of two alternate registration methods. (a The portal image of the current fraction of the treatment is registered directly with the reference image (digitally reconstructed radiograph (DRR or simulator image using a modified manual technique. (b The portal image of the current fraction of the treatment is registered with the portal image of the first fraction of the treatment (reference portal image by applying a nearly automated technique based on self-organizing maps, whereas the reference portal has already been registered with a DRR or a simulator image. The proposed system was tested on phantom data and on data from six patients. The root mean square error (RMSE of the setup estimates was 0.8±0.3 (mean value ± standard deviation for the phantom data and 0.3±0.3 for the patient data, respectively, by applying the two methodologies. Furthermore, statistical analysis by means of the Wilcoxon nonparametric signed test showed that the results that were obtained by the two methods did not differ significantly (P value >0.05.

  7. Cross-instrument Analysis Correlation Software

    Energy Technology Data Exchange (ETDEWEB)

    2017-06-28

    This program has been designed to assist with the tracking of a sample from one analytical instrument to another such as SEM, microscopes, micro x-ray diffraction and other instruments where particular positions/locations on the sample are examined, photographed, etc. The software is designed to easily enter the position of fiducials and locations of interest such that in a future session in the same of different instrument the positions of interest can be re-found through using the known location fiducials in the current and reference session to transform the point into the current sessions coordinate system. The software is dialog box driven guiding the user through the necessary data entry and program choices. Information is stored in a series of text based extensible markup language (XML) files.

  8. Nuclear Fuel Depletion Analysis Using Matlab Software

    Science.gov (United States)

    Faghihi, F.; Nematollahi, M. R.

    Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the 239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.

  9. Image fusion between whole body FDG PET images and whole body MRI images using a full-automatic mutual information-based multimodality image registration software

    International Nuclear Information System (INIS)

    Uchida, Yoshitaka; Nakano, Yoshitada; Fujibuchi, Toshiou; Isobe, Tomoko; Kazama, Toshiki; Ito, Hisao

    2006-01-01

    We attempted image fusion between whole body PET and whole body MRI of thirty patients using a full-automatic mutual information (MI) -based multimodality image registration software and evaluated accuracy of this method and impact of the coregistrated imaging on diagnostic accuracy. For 25 of 30 fused images in body area, translating gaps were within 6 mm in all axes and rotating gaps were within 2 degrees around all axes. In head and neck area, considerably much gaps caused by difference of head inclination at imaging occurred in 16 patients, however these gaps were able to decrease by fused separately. In 6 patients, diagnostic accuracy using PET/MRI fused images was superior compared by PET image alone. This work shows that whole body FDG PET images and whole body MRI images can be automatically fused using MI-based multimodality image registration software accurately and this technique can add useful information when evaluating FDG PET images. (author)

  10. A study of software safety analysis system for safety-critical software

    International Nuclear Information System (INIS)

    Chang, H. S.; Shin, H. K.; Chang, Y. W.; Jung, J. C.; Kim, J. H.; Han, H. H.; Son, H. S.

    2004-01-01

    The core factors and requirements for the safety-critical software traced and the methodology adopted in each stage of software life cycle are presented. In concept phase, Failure Modes and Effects Analysis (FMEA) for the system has been performed. The feasibility evaluation of selected safety parameter was performed and Preliminary Hazards Analysis list was prepared using HAZOP(Hazard and Operability) technique. And the check list for management control has been produced via walk-through technique. Based on the evaluation of the check list, activities to be performed in requirement phase have been determined. In the design phase, hazard analysis has been performed to check the safety capability of the system with regard to safety software algorithm using Fault Tree Analysis (FTA). In the test phase, the test items based on FMEA have been checked for fitness guided by an accident scenario. The pressurizer low pressure trip algorithm has been selected to apply FTA method to software safety analysis as a sample. By applying CASE tool, the requirements traceability of safety critical system has been enhanced during all of software life cycle phases

  11. Change Impact Analysis of Crosscutting in Software Architectural Design

    NARCIS (Netherlands)

    van den Berg, Klaas

    2006-01-01

    Software architectures should be amenable to changes in user requirements and implementation technology. The analysis of the impact of these changes can be based on traceability of architectural design elements. Design elements have dependencies with other software artifacts but also evolve in time.

  12. Integrated analysis software for bulk power system stability

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, T; Nagao, T; Takahashi, K [Central Research Inst. of Electric Power Industry, Tokyo (Japan)

    1994-12-31

    This paper presents Central Research Inst.of Electric Power Industry - CRIEPI`s - own developed three softwares for bulk power network analysis and the user support system which arranges tremendous data necessary for these softwares with easy and high reliability. (author) 3 refs., 7 figs., 2 tabs.

  13. Evaluation of a breast software model for 2D and 3D X-ray imaging studies of the breast.

    Science.gov (United States)

    Baneva, Yanka; Bliznakova, Kristina; Cockmartin, Lesley; Marinov, Stoyko; Buliev, Ivan; Mettivier, Giovanni; Bosmans, Hilde; Russo, Paolo; Marshall, Nicholas; Bliznakov, Zhivko

    2017-09-01

    In X-ray imaging, test objects reproducing breast anatomy characteristics are realized to optimize issues such as image processing or reconstruction, lesion detection performance, image quality and radiation induced detriment. Recently, a physical phantom with a structured background has been introduced for both 2D mammography and breast tomosynthesis. A software version of this phantom and a few related versions are now available and a comparison between these 3D software phantoms and the physical phantom will be presented. The software breast phantom simulates a semi-cylindrical container filled with spherical beads of different diameters. Four computational breast phantoms were generated with a dedicated software application and for two of these, physical phantoms are also available and they are used for the side by side comparison. Planar projections in mammography and tomosynthesis were simulated under identical incident air kerma conditions. Tomosynthesis slices were reconstructed with an in-house developed reconstruction software. In addition to a visual comparison, parameters like fractal dimension, power law exponent β and second order statistics (skewness, kurtosis) of planar projections and tomosynthesis reconstructed images were compared. Visually, an excellent agreement between simulated and real planar and tomosynthesis images is observed. The comparison shows also an overall very good agreement between parameters evaluated from simulated and experimental images. The computational breast phantoms showed a close match with their physical versions. The detailed mathematical analysis of the images confirms the agreement between real and simulated 2D mammography and tomosynthesis images. The software phantom is ready for optimization purpose and extrapolation of the phantom to other breast imaging techniques. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  14. Continuous Software Quality analysis for the ATLAS experiment

    CERN Document Server

    Washbrook, Andrew; The ATLAS collaboration

    2017-01-01

    The regular application of software quality tools in large collaborative projects is required to reduce code defects to an acceptable level. If left unchecked the accumulation of defects invariably results in performance degradation at scale and problems with the long-term maintainability of the code. Although software quality tools are effective for identification there remains a non-trivial sociological challenge to resolve defects in a timely manner. This is a ongoing concern for the ATLAS software which has evolved over many years to meet the demands of Monte Carlo simulation, detector reconstruction and data analysis. At present over 3.8 million lines of C++ code (and close to 6 million total lines of code) are maintained by a community of hundreds of developers worldwide. It is therefore preferable to address code defects before they are introduced into a widely used software release. Recent wholesale changes to the ATLAS software infrastructure have provided an ideal opportunity to apply software quali...

  15. Digital image analysis

    DEFF Research Database (Denmark)

    Riber-Hansen, Rikke; Vainer, Ben; Steiniche, Torben

    2012-01-01

    Digital image analysis (DIA) is increasingly implemented in histopathological research to facilitate truly quantitative measurements, decrease inter-observer variation and reduce hands-on time. Originally, efforts were made to enable DIA to reproduce manually obtained results on histological slides...... reproducibility, application of stereology-based quantitative measurements, time consumption, optimization of histological slides, regions of interest selection and recent developments in staining and imaging techniques....

  16. Software Users Manual (SUM): Extended Testability Analysis (ETA) Tool

    Science.gov (United States)

    Maul, William A.; Fulton, Christopher E.

    2011-01-01

    This software user manual describes the implementation and use the Extended Testability Analysis (ETA) Tool. The ETA Tool is a software program that augments the analysis and reporting capabilities of a commercial-off-the-shelf (COTS) testability analysis software package called the Testability Engineering And Maintenance System (TEAMS) Designer. An initial diagnostic assessment is performed by the TEAMS Designer software using a qualitative, directed-graph model of the system being analyzed. The ETA Tool utilizes system design information captured within the diagnostic model and testability analysis output from the TEAMS Designer software to create a series of six reports for various system engineering needs. The ETA Tool allows the user to perform additional studies on the testability analysis results by determining the detection sensitivity to the loss of certain sensors or tests. The ETA Tool was developed to support design and development of the NASA Ares I Crew Launch Vehicle. The diagnostic analysis provided by the ETA Tool was proven to be valuable system engineering output that provided consistency in the verification of system engineering requirements. This software user manual provides a description of each output report generated by the ETA Tool. The manual also describes the example diagnostic model and supporting documentation - also provided with the ETA Tool software release package - that were used to generate the reports presented in the manual

  17. An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging

    International Nuclear Information System (INIS)

    Messroghli, Daniel R; Rudolph, Andre; Abdel-Aty, Hassan; Wassmuth, Ralf; Kühne, Titus; Dietz, Rainer; Schulz-Menger, Jeanette

    2010-01-01

    In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI) T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet

  18. An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Kühne Titus

    2010-07-01

    Full Text Available Abstract Background In magnetic resonance (MR imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. Results After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. Conclusions MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

  19. New software developments for quality mesh generation and optimization from biomedical imaging data.

    Science.gov (United States)

    Yu, Zeyun; Wang, Jun; Gao, Zhanheng; Xu, Ming; Hoshijima, Masahiko

    2014-01-01

    In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  20. GWAMA: software for genome-wide association meta-analysis

    Directory of Open Access Journals (Sweden)

    Mägi Reedik

    2010-05-01

    Full Text Available Abstract Background Despite the recent success of genome-wide association studies in identifying novel loci contributing effects to complex human traits, such as type 2 diabetes and obesity, much of the genetic component of variation in these phenotypes remains unexplained. One way to improving power to detect further novel loci is through meta-analysis of studies from the same population, increasing the sample size over any individual study. Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies. Results We have developed flexible, open-source software for the meta-analysis of genome-wide association studies. The software incorporates a variety of error trapping facilities, and provides a range of meta-analysis summary statistics. The software is distributed with scripts that allow simple formatting of files containing the results of each association study and generate graphical summaries of genome-wide meta-analysis results. Conclusions The GWAMA (Genome-Wide Association Meta-Analysis software has been developed to perform meta-analysis of summary statistics generated from genome-wide association studies of dichotomous phenotypes or quantitative traits. Software with source files, documentation and example data files are freely available online at http://www.well.ox.ac.uk/GWAMA.

  1. Free and open-source software application for the evaluation of coronary computed tomography angiography images.

    Science.gov (United States)

    Hadlich, Marcelo Souza; Oliveira, Gláucia Maria Moraes; Feijóo, Raúl A; Azevedo, Clerio F; Tura, Bernardo Rangel; Ziemer, Paulo Gustavo Portela; Blanco, Pablo Javier; Pina, Gustavo; Meira, Márcio; Souza e Silva, Nelson Albuquerque de

    2012-10-01

    The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions 70% in the ADA was lower, but this is also observed when the anatomical reference standard is used.

  2. Long-term preservation of analysis software environment

    International Nuclear Information System (INIS)

    Toppe Larsen, Dag; Blomer, Jakob; Buncic, Predrag; Charalampidis, Ioannis; Haratyunyan, Artem

    2012-01-01

    Long-term preservation of scientific data represents a challenge to experiments, especially regarding the analysis software. Preserving data is not enough; the full software and hardware environment is needed. Virtual machines (VMs) make it possible to preserve hardware “in software”. A complete infrastructure package has been developed for easy deployment and management of VMs, based on CERN virtual machine (CernVM). Further, a HTTP-based file system, CernVM file system (CVMFS), is used for the distribution of the software. It is possible to process data with any given software version, and a matching, regenerated VM version. A point-and-click web user interface is being developed for setting up the complete processing chain, including VM and software versions, number and type of processing nodes, and the particular type of analysis and data. This paradigm also allows for distributed cloud-computing on private and public clouds, for both legacy and contemporary experiments.

  3. Software para análise quantitativa da deglutição Swallowing quantitative analysis software

    Directory of Open Access Journals (Sweden)

    André Augusto Spadotto

    2008-02-01

    Full Text Available OBJETIVO: Apresentar um software que permita uma análise detalhada da dinâmica da deglutição. MATERIAIS E MÉTODOS: Participaram deste estudo dez indivíduos após acidente vascular encefálico, sendo seis do gênero masculino, com idade média de 57,6 anos. Foi realizada videofluoroscopia da deglutição e as imagens foram digitalizadas em microcomputador, com posterior análise do tempo do trânsito faríngeo da deglutição, por meio de um cronômetro e do software. RESULTADOS: O tempo médio do trânsito faríngeo da deglutição apresentou-se diferente quando comparados os métodos utilizados (cronômetro e software. CONCLUSÃO: Este software é um instrumento de análise dos parâmetros tempo e velocidade da deglutição, propiciando melhor compreensão da dinâmica da deglutição, com reflexos tanto na abordagem clínica dos pacientes com disfagia como para fins de pesquisa científica.OBJECTIVE: The present paper is aimed at introducing a software to allow a detailed analysis of the swallowing dynamics. MATERIALS AND METHODS: The sample included ten (six male and four female stroke patients, with mean age of 57.6 years. Swallowing videofluoroscopy was performed and images were digitized for posterior analysis of the pharyngeal transit time with the aid of a chronometer and the software. RESULTS: Differences were observed in the average pharyngeal swallowing transit time as a result of measurements with chronometer and software. CONCLUSION: This software is a useful tool for the analysis of parameters such as swallowing time and speed, allowing a better understanding of the swallowing dynamics, both in the clinical approach of patients with oropharyngeal dysphagia and for scientific research purposes.

  4. VAP3D: a software for dosimetric analysis and visualization of phantons

    International Nuclear Information System (INIS)

    Lima, Lindeval Fernandes de; Lima, Fernando Roberto de Andrade

    2011-01-01

    The anthropomorphic models used in computational dosimetry of the ionizing radiation, usually called voxel phantom, are produced from image stacks CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) obtained from patient or volunteer scanning. These phantoms are the geometry to be radiated in the computing arrangements of exposure, using a Monte Carlo code, allowing the estimation of the energy deposited in each voxel of the virtual body. From these data collected in the simulation, it is possible to evaluate the average absorbed dose in various organs and tissues radiosensitive cataloged by the International Commission on Radiological Protection (ICRP). Therefore, a computational model of the exhibition is constituted primarily by the Monte Carlo code to simulate the transport, deposition and interaction of radiation and the phantom being irradiated. The construction of voxel phantoms requires computer skills like a transformation format of images, compression of 2D images for 3D image construction, quantization, resampling and image segmentation, among others. Hardly the computational dosimetry researcher finds all these skills into a single software and often this results in a decrease in the pace of their research or the use, sometimes inadequate, the alternative tools. This paper presents the VAP3D (Visualization and Analysis of Phantoms), a software developed with Qt/VTK with C++, in order to operationalize some of the tasks mentioned above. The current version has been based on DIP software (Digital Imaging Processing), containing the File menu, Conversions and tools, where the user interacts with the software. (author)

  5. The development of gamma imaging system's aided software using matlab GUI

    International Nuclear Information System (INIS)

    Yang Yapeng; Xu Yuan; Jin Gen

    2011-01-01

    The RadCam 2000 gamma imaging system's software supplied by the manufacture cannot be run when the PC disconnected to the system's hardware, also cannot be used to analysis the results acquired, therefore, we have developed easyRadCam using Matlab GUI with the ability of generating the 'hot point' three-dimensional distribution by importing the results acquired, giving the counts distribution versus channel number. After the system be calibrated, we can get the energy spectrum, even the type of nuclides exist. (authors)

  6. Development of design and analysis software for advanced nuclear system

    International Nuclear Information System (INIS)

    Wu Yican; Hu Liqin; Long Pengcheng; Luo Yuetong; Li Yazhou; Zeng Qin; Lu Lei; Zhang Junjun; Zou Jun; Xu Dezheng; Bai Yunqing; Zhou Tao; Chen Hongli; Peng Lei; Song Yong; Huang Qunying

    2010-01-01

    A series of professional codes, which are necessary software tools and data libraries for advanced nuclear system design and analysis, were developed by the FDS Team, including the codes of automatic modeling, physics and engineering calculation, virtual simulation and visualization, system engineering and safety analysis and the related database management etc. The development of these software series was proposed as an exercise of development of nuclear informatics. This paper introduced the main functions and key techniques of the software series, as well as some tests and practical applications. (authors)

  7. 'TISUCROMA': A Software for Color Processing of Biological Tissue's Images

    International Nuclear Information System (INIS)

    Arista Romeu, Eduardo J.; La Rosa Vazquez, Jose Manuel de; Valor, Alma; Stolik, Suren

    2016-01-01

    In this work a software intended to plot and analyze digital image RGB histograms from normal and abnormal regions of biological tissue. The obtained RGB histograms from each zone can be used to show the image in only one color or the mixture of some of them. The Software was developed in Lab View to process the images in a laptop. Some medical application examples are shown. (Author)

  8. Use of a russian software and hardware complex for quantitative analysis of coronary angiograms

    International Nuclear Information System (INIS)

    Savchenko, A.P.; Pavlov, N.A.; Myasnikova, A.L.

    1996-01-01

    The software and hardware complex developed by the Cardiology Research Center, Russian Academy of Medical Sciences, jointly with the Technomash Research Production Association on the basis of a IBM 386DX personal computer equipped with a VS-100 video controller and a DS P31 VS signal processor board. Testing has indicated that it provides a qualitative image and a quantitative analysis both of phantoms and real images of coronarograms, but more accurately in the analysis of the image obtained from a film projector. Clinical tests have shown that the software and hardware complex may yield a rather qualitative image and calculate the required diameter of a vessel, virtually without prolonging the time of intervention. 4 refs.; 3 figs. 1 tab

  9. Software for X-Ray Images Calculation of Hydrogen Compression Device in Megabar Pressure Range

    Science.gov (United States)

    Egorov, Nikolay; Bykov, Alexander; Pavlov, Valery

    2007-06-01

    Software for x-ray images simulation is described. The software is a part of x-ray method used for investigation of an equation of state of hydrogen in a megabar pressure range. A graphical interface that clearly and simply allows users to input data for x-ray image calculation: properties of the studied device, parameters of the x-ray radiation source, parameters of the x-ray radiation recorder, the experiment geometry; to represent the calculation results and efficiently transmit them to other software for processing. The calculation time is minimized. This makes it possible to perform calculations in a dialogue regime. The software is written in ``MATLAB'' system.

  10. Change impact analysis for software product lines

    Directory of Open Access Journals (Sweden)

    Jihen Maâzoun

    2016-10-01

    Full Text Available A software product line (SPL represents a family of products in a given application domain. Each SPL is constructed to provide for the derivation of new products by covering a wide range of features in its domain. Nevertheless, over time, some domain features may become obsolete with the apparition of new features while others may become refined. Accordingly, the SPL must be maintained to account for the domain evolution. Such evolution requires a means for managing the impact of changes on the SPL models, including the feature model and design. This paper presents an automated method that analyzes feature model evolution, traces their impact on the SPL design, and offers a set of recommendations to ensure the consistency of both models. The proposed method defines a set of new metrics adapted to SPL evolution to identify the effort needed to maintain the SPL models consistently and with a quality as good as the original models. The method and its tool are illustrated through an example of an SPL in the Text Editing domain. In addition, they are experimentally evaluated in terms of both the quality of the maintained SPL models and the precision of the impact change management.

  11. Dispersion analysis of biotoxins using HPAC software

    International Nuclear Information System (INIS)

    Wu, A.; Nurthen, N.; Horstman, A.; Watson, R.; Phillips, M.

    2009-01-01

    Biotoxins are emerging threat agents produced by living organisms: bacteria, plants, or animals. Biotoxins are generally classified as cyanotoxins, hemotoxins, necrotoxins, neurotoxins, and cytotoxins. The application of classical biotoxins as weapons of terror has been realized because of extreme potency and lethality; ease of production, transport, and misuse; and the need for prolonged intensive care among affected persons. Recently, emerging biotoxins, such as ricin and T2 micotoxin have been clandestinely used by either terrorist groups or military combat operations. It is thus highly desirable to have a modeling system to simulate dispersions of biotoxins in a terrorist attack scenario in order to provide prompt technical support and casualty estimation to the first responders and military rescuers. The Hazard Prediction and Assessment Capability (HPAC) automated software system provides the means to accurately predict the effects of hazardous material released into the atmosphere and its impact on civilian and military populations. The system uses integrated source terms, high-resolution weather forecasts and atmospheric transport and dispersion analyses to model hazard areas produced by military or terrorist incidents and industrial accidents. We have successfully incorporated physical, chemical, epidemiological and biological characteristics of a variety of biotoxins into the HPAC system and have conducted numerous analyses for our emergency responders. The health effects caused by these hazards are closely reflected in HPAC output results.(author)

  12. OST: analysis tool for real time software by simulation of material and software environments

    International Nuclear Information System (INIS)

    Boulc'h; Le Meur; Lapassat; Salichon; Segalard

    1988-07-01

    The utilization of microprocessors systems in a nuclear installation control oblige a great operation safety in the installation operation and in the environment protection. For the safety analysis of these installations the Institute of Protection and Nuclear Safety (IPSN) will dispose tools which permit to make controls during all the life of the software. The simulation and test tool (OST) which have been created is completely made by softwares. It is used on VAX calculators and can be easily transportable on other calculators [fr

  13. An evaluation on the accuracy of the indirect digital images densitometry by modified Photoshop software

    Directory of Open Access Journals (Sweden)

    Bashizadeh Fakhar H.

    2004-06-01

    Full Text Available Statement of Problem: One of the major goals, in most dental researches, is to measure bone destruction or deposition due to the progression or regression of disease. Failure of human eyes to detect minor radiographic density changes resulted in more accurate methods such as optical densitometry and direct or indirect digital densitometry."nPurpose: The aim of this study was to determine the accuracy of a newly proposed method of indirect digital densitometry using modified Photoshop software."nMaterials and Methods: Radiographs from 37 samples of urografin solution with three concentrations (12.5%, 25% and 37.5% were taken on dental radiographic films no.2 and digitized by a scanner. A region with 800*800 pixels was cropped from each image and compressed with the Joint Photographic Experts Group (JPEG compression algorithm and saved. These new images were then put into registration with new algorithm using MATLAB software version 6.1. This algorithm assigned each image and average pixel value (between 0 and 255. The association between concentration and calculated values for each image was tested with regression analysis and the meaning fullness of differences between calculated values was also analysis by ANOVA test. Tukey HSD and Alpha Krunbach were used whenever needs."nResults: Regression analysis revealed significant correlation between concentration and calculated average pixel value (r=0.883. The differences between average of pixels value for different concentration was significant (P=0.0001. Pixel values showed a good intra- sample and intra-group repeatability (Alpha Krunbach: a=99.96%, a=99.68%."nConclusion: This method due to its high accuracy, easy usage and densitometer independency can be considered as a suitable alternative for conventional densitometry methods.

  14. Power Analysis Software for Educational Researchers

    Science.gov (United States)

    Peng, Chao-Ying Joanne; Long, Haiying; Abaci, Serdar

    2012-01-01

    Given the importance of statistical power analysis in quantitative research and the repeated emphasis on it by American Educational Research Association/American Psychological Association journals, the authors examined the reporting practice of power analysis by the quantitative studies published in 12 education/psychology journals between 2005…

  15. Development and applications of Kramers-Kronig PEELS analysis software

    International Nuclear Information System (INIS)

    Fan, X. D.; Peng, J.L.; Bursill, L.A.

    1997-01-01

    A Kramers-Kronig analysis program is developed as a custom function for the GATAN parallel electron energy loss spectroscopy (PEELS) software package EL/P. When used with a JEOL 4000EX high-resolution transmission electron microscope this program allows to measure the dielectric functions of materials with an energy resolution of approx 1.4eV. The imaginary part of the dielectric function is particularly useful, since it allows the magnitude of the band gap to be determined for relatively wide-gap materials. More importantly, changes in the gap may be monitored at high spatial resolution, when used in conjunction with the HRTEM images. The principles of the method are described and applications are presented for Type-1a gem quality diamond, before and after neutron irradiation. The former shows a band gap of about 5.8 eV, as expected, whereas for the latter the gap appears to be effectively collapsed. The core-loss spectra confirm that Type-1a diamond has pure sp 3 tetrahedral bonding, whereas the neutron irradiated diamond has mixed sp 2 /sp 3 bonding. Analysis of the low-loss spectra for the neutron-irradiated specimen yielded density 1.6 g/cm 3 , approximately half that of diamond. 10 refs., 2 figs

  16. Analysis of Variance: What Is Your Statistical Software Actually Doing?

    Science.gov (United States)

    Li, Jian; Lomax, Richard G.

    2011-01-01

    Users assume statistical software packages produce accurate results. In this article, the authors systematically examined Statistical Package for the Social Sciences (SPSS) and Statistical Analysis System (SAS) for 3 analysis of variance (ANOVA) designs, mixed-effects ANOVA, fixed-effects analysis of covariance (ANCOVA), and nested ANOVA. For each…

  17. Adapted wavelet analysis from theory to software

    CERN Document Server

    Wickerhauser, Mladen Victor

    1994-01-01

    This detail-oriented text is intended for engineers and applied mathematicians who must write computer programs to perform wavelet and related analysis on real data. It contains an overview of mathematical prerequisites and proceeds to describe hands-on programming techniques to implement special programs for signal analysis and other applications. From the table of contents: - Mathematical Preliminaries - Programming Techniques - The Discrete Fourier Transform - Local Trigonometric Transforms - Quadrature Filters - The Discrete Wavelet Transform - Wavelet Packets - The Best Basis Algorithm - Multidimensional Library Trees - Time-Frequency Analysis - Some Applications - Solutions to Some of the Exercises - List of Symbols - Quadrature Filter Coefficients

  18. Development of Emittance Analysis Software for Ion Beam Characterization

    International Nuclear Information System (INIS)

    Padilla, M.J.; Liu, Yuan

    2007-01-01

    Transverse beam emittance is a crucial property of charged particle beams that describes their angular and spatial spread. It is a figure of merit frequently used to determine the quality of ion beams, the compatibility of an ion beam with a given beam transport system, and the ability to suppress neighboring isotopes at on-line mass separator facilities. Generally, a high-quality beam is characterized by a small emittance. In order to determine and improve the quality of ion beams used at the Holifield Radioactive Ion Beam Facility (HRIBF) for nuclear physics and nuclear astrophysics research, the emittances of the ion beams are measured at the off-line Ion Source Test Facilities. In this project, emittance analysis software was developed to perform various data processing tasks for noise reduction, to evaluate root-mean-square emittance, Twiss parameters, and area emittance of different beam fractions. The software also provides 2D and 3D graphical views of the emittance data, beam profiles, emittance contours, and RMS. Noise exclusion is essential for accurate determination of beam emittance values. A Self-Consistent, Unbiased Elliptical Exclusion (SCUBEEx) method is employed. Numerical data analysis techniques such as interpolation and nonlinear fitting are also incorporated into the software. The software will provide a simplified, fast tool for comprehensive emittance analysis. The main functions of the software package have been completed. In preliminary tests with experimental emittance data, the analysis results using the software were shown to be accurate

  19. DEVELOPMENT OF EMITTANCE ANALYSIS SOFTWARE FOR ION BEAM CHARACTERIZATION

    Energy Technology Data Exchange (ETDEWEB)

    Padilla, M. J.; Liu, Y.

    2007-01-01

    Transverse beam emittance is a crucial property of charged particle beams that describes their angular and spatial spread. It is a fi gure of merit frequently used to determine the quality of ion beams, the compatibility of an ion beam with a given beam transport system, and the ability to suppress neighboring isotopes at on-line mass separator facilities. Generally a high quality beam is characterized by a small emittance. In order to determine and improve the quality of ion beams used at the Holifi eld Radioactive Ion beam Facility (HRIBF) for nuclear physics and nuclear astrophysics research, the emittances of the ion beams are measured at the off-line Ion Source Test Facilities. In this project, emittance analysis software was developed to perform various data processing tasks for noise reduction, to evaluate root-mean-square emittance, Twiss parameters, and area emittance of different beam fractions. The software also provides 2D and 3D graphical views of the emittance data, beam profi les, emittance contours, and RMS. Noise exclusion is essential for accurate determination of beam emittance values. A Self-Consistent, Unbiased Elliptical Exclusion (SCUBEEx) method is employed. Numerical data analysis techniques such as interpolation and nonlinear fi tting are also incorporated into the software. The software will provide a simplifi ed, fast tool for comprehensive emittance analysis. The main functions of the software package have been completed. In preliminary tests with experimental emittance data, the analysis results using the software were shown to be accurate.

  20. NeuronMetrics: software for semi-automated processing of cultured neuron images.

    Science.gov (United States)

    Narro, Martha L; Yang, Fan; Kraft, Robert; Wenk, Carola; Efrat, Alon; Restifo, Linda L

    2007-03-23

    Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of approximately 60 2D images is 1.0-2.5 h, from a folder of images to a table of numeric data. NeuronMetrics' output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery.

  1. Automated Freedom from Interference Analysis for Automotive Software

    OpenAIRE

    Leitner-Fischer , Florian; Leue , Stefan; Liu , Sirui

    2016-01-01

    International audience; Freedom from Interference for automotive software systems developed according to the ISO 26262 standard means that a fault in a less safety critical software component will not lead to a fault in a more safety critical component. It is an important concern in the realm of functional safety for automotive systems. We present an automated method for the analysis of concurrency-related interferences based on the QuantUM approach and tool that we have previously developed....

  2. Software safety analysis techniques for developing safety critical software in the digital protection system of the LMR

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jang Soo; Cheon, Se Woo; Kim, Chang Hoi; Sim, Yun Sub

    2001-02-01

    This report has described the software safety analysis techniques and the engineering guidelines for developing safety critical software to identify the state of the art in this field and to give the software safety engineer a trail map between the code and standards layer and the design methodology and documents layer. We have surveyed the management aspects of software safety activities during the software lifecycle in order to improve the safety. After identifying the conventional safety analysis techniques for systems, we have surveyed in details the software safety analysis techniques, software FMEA(Failure Mode and Effects Analysis), software HAZOP(Hazard and Operability Analysis), and software FTA(Fault Tree Analysis). We have also surveyed the state of the art in the software reliability assessment techniques. The most important results from the reliability techniques are not the specific probability numbers generated, but the insights into the risk importance of software features. To defend against potential common-mode failures, high quality, defense-in-depth, and diversity are considered to be key elements in digital I and C system design. To minimize the possibility of CMFs and thus increase the plant reliability, we have provided D-in-D and D analysis guidelines.

  3. Software safety analysis techniques for developing safety critical software in the digital protection system of the LMR

    International Nuclear Information System (INIS)

    Lee, Jang Soo; Cheon, Se Woo; Kim, Chang Hoi; Sim, Yun Sub

    2001-02-01

    This report has described the software safety analysis techniques and the engineering guidelines for developing safety critical software to identify the state of the art in this field and to give the software safety engineer a trail map between the code and standards layer and the design methodology and documents layer. We have surveyed the management aspects of software safety activities during the software lifecycle in order to improve the safety. After identifying the conventional safety analysis techniques for systems, we have surveyed in details the software safety analysis techniques, software FMEA(Failure Mode and Effects Analysis), software HAZOP(Hazard and Operability Analysis), and software FTA(Fault Tree Analysis). We have also surveyed the state of the art in the software reliability assessment techniques. The most important results from the reliability techniques are not the specific probability numbers generated, but the insights into the risk importance of software features. To defend against potential common-mode failures, high quality, defense-in-depth, and diversity are considered to be key elements in digital I and C system design. To minimize the possibility of CMFs and thus increase the plant reliability, we have provided D-in-D and D analysis guidelines

  4. Imaging C. elegans embryos using an epifluorescent microscope and open source software.

    Science.gov (United States)

    Verbrugghe, Koen J C; Chan, Raymond C

    2011-03-24

    Cellular processes, such as chromosome assembly, segregation and cytokinesis,are inherently dynamic. Time-lapse imaging of living cells, using fluorescent-labeled reporter proteins or differential interference contrast (DIC) microscopy, allows for the examination of the temporal progression of these dynamic events which is otherwise inferred from analysis of fixed samples(1,2). Moreover, the study of the developmental regulations of cellular processes necessitates conducting time-lapse experiments on an intact organism during development. The Caenorhabiditis elegans embryo is light-transparent and has a rapid, invariant developmental program with a known cell lineage(3), thus providing an ideal experiment model for studying questions in cell biology(4,5)and development(6-9). C. elegans is amendable to genetic manipulation by forward genetics (based on random mutagenesis(10,11)) and reverse genetics to target specific genes (based on RNAi-mediated interference and targeted mutagenesis(12-15)). In addition, transgenic animals can be readily created to express fluorescently tagged proteins or reporters(16,17). These traits combine to make it easy to identify the genetic pathways regulating fundamental cellular and developmental processes in vivo(18-21). In this protocol we present methods for live imaging of C. elegans embryos using DIC optics or GFP fluorescence on a compound epifluorescent microscope. We demonstrate the ease with which readily available microscopes, typically used for fixed sample imaging, can also be applied for time-lapse analysis using open-source software to automate the imaging process.

  5. Development of output user interface software to support analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wahanani, Nursinta Adi, E-mail: sintaadi@batan.go.id; Natsir, Khairina, E-mail: sintaadi@batan.go.id; Hartini, Entin, E-mail: sintaadi@batan.go.id [Center for Development of Nuclear Informatics - National Nuclear Energy Agency, PUSPIPTEK, Serpong, Tangerang, Banten (Indonesia)

    2014-09-30

    Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this software 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu{sup 239} and Pu{sup 241}. Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis.

  6. Development of output user interface software to support analysis

    International Nuclear Information System (INIS)

    Wahanani, Nursinta Adi; Natsir, Khairina; Hartini, Entin

    2014-01-01

    Data processing software packages such as VSOP and MCNPX are softwares that has been scientifically proven and complete. The result of VSOP and MCNPX are huge and complex text files. In the analyze process, user need additional processing like Microsoft Excel to show informative result. This research develop an user interface software for output of VSOP and MCNPX. VSOP program output is used to support neutronic analysis and MCNPX program output is used to support burn-up analysis. Software development using iterative development methods which allow for revision and addition of features according to user needs. Processing time with this software 500 times faster than with conventional methods using Microsoft Excel. PYTHON is used as a programming language, because Python is available for all major operating systems: Windows, Linux/Unix, OS/2, Mac, Amiga, among others. Values that support neutronic analysis are k-eff, burn-up and mass Pu 239 and Pu 241 . Burn-up analysis used the mass inventory values of actinide (Thorium, Plutonium, Neptunium and Uranium). Values are visualized in graphical shape to support analysis

  7. LANDSAFE: LANDING SITE RISK ANALYSIS SOFTWARE FRAMEWORK

    OpenAIRE

    Schmidt, Ralph; Bostelmann, Jonas; Cornet, Yves; Heipke, Christian; Philippe, Christian; Poncelet, Nadia; de Rosa, Diego; Vandeloise, Yannick

    2012-01-01

    The European Space Agency (ESA) is planning a Lunar Lander mission in the 2018 timeframe that will demonstrate precise soft landing at the polar regions of the Moon. To ensure a safe and successful landing a careful risk analysis has to be carried out. This is comprised of identifying favorable target areas and evaluating the surface conditions in these areas. Features like craters, boulders, steep slopes, rough surfaces and shadow areas have to be identified in order to assess the risk assoc...

  8. Multiattribute selection of acute stroke imaging software platform for Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) clinical trial.

    Science.gov (United States)

    Churilov, Leonid; Liu, Daniel; Ma, Henry; Christensen, Soren; Nagakane, Yoshinari; Campbell, Bruce; Parsons, Mark W; Levi, Christopher R; Davis, Stephen M; Donnan, Geoffrey A

    2013-04-01

    The appropriateness of a software platform for rapid MRI assessment of the amount of salvageable brain tissue after stroke is critical for both the validity of the Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) Clinical Trial of stroke thrombolysis beyond 4.5 hours and for stroke patient care outcomes. The objective of this research is to develop and implement a methodology for selecting the acute stroke imaging software platform most appropriate for the setting of a multi-centre clinical trial. A multi-disciplinary decision making panel formulated the set of preferentially independent evaluation attributes. Alternative Multi-Attribute Value Measurement methods were used to identify the best imaging software platform followed by sensitivity analysis to ensure the validity and robustness of the proposed solution. Four alternative imaging software platforms were identified. RApid processing of PerfusIon and Diffusion (RAPID) software was selected as the most appropriate for the needs of the EXTEND trial. A theoretically grounded generic multi-attribute selection methodology for imaging software was developed and implemented. The developed methodology assured both a high quality decision outcome and a rational and transparent decision process. This development contributes to stroke literature in the area of comprehensive evaluation of MRI clinical software. At the time of evaluation, RAPID software presented the most appropriate imaging software platform for use in the EXTEND clinical trial. The proposed multi-attribute imaging software evaluation methodology is based on sound theoretical foundations of multiple criteria decision analysis and can be successfully used for choosing the most appropriate imaging software while ensuring both robust decision process and outcomes. © 2012 The Authors. International Journal of Stroke © 2012 World Stroke Organization.

  9. Development of evaluation method for software safety analysis techniques

    International Nuclear Information System (INIS)

    Huang, H.; Tu, W.; Shih, C.; Chen, C.; Yang, W.; Yih, S.; Kuo, C.; Chen, M.

    2006-01-01

    Full text: Full text: Following the massive adoption of digital Instrumentation and Control (I and C) system for nuclear power plant (NPP), various Software Safety Analysis (SSA) techniques are used to evaluate the NPP safety for adopting appropriate digital I and C system, and then to reduce risk to acceptable level. However, each technique has its specific advantage and disadvantage. If the two or more techniques can be complementarily incorporated, the SSA combination would be more acceptable. As a result, if proper evaluation criteria are available, the analyst can then choose appropriate technique combination to perform analysis on the basis of resources. This research evaluated the applicable software safety analysis techniques nowadays, such as, Preliminary Hazard Analysis (PHA), Failure Modes and Effects Analysis (FMEA), Fault Tree Analysis (FTA), Markov chain modeling, Dynamic Flowgraph Methodology (DFM), and simulation-based model analysis; and then determined indexes in view of their characteristics, which include dynamic capability, completeness, achievability, detail, signal/ noise ratio, complexity, and implementation cost. These indexes may help the decision makers and the software safety analysts to choose the best SSA combination arrange their own software safety plan. By this proposed method, the analysts can evaluate various SSA combinations for specific purpose. According to the case study results, the traditional PHA + FMEA + FTA (with failure rate) + Markov chain modeling (without transfer rate) combination is not competitive due to the dilemma for obtaining acceptable software failure rates. However, the systematic architecture of FTA and Markov chain modeling is still valuable for realizing the software fault structure. The system centric techniques, such as DFM and Simulation-based model analysis, show the advantage on dynamic capability, achievability, detail, signal/noise ratio. However, their disadvantage are the completeness complexity

  10. The role and design of screen images in software documentation.

    NARCIS (Netherlands)

    van der Meij, Hans

    2000-01-01

    Software documentation for the novice user typically must try to achieve at least three goals: to support basic knowledge and skills development; to prevent or support the handling of mistakes, and to support the joint handling of manual, input device and screen. This paper concentrates on the

  11. How to do Meta-Analysis using HLM software

    OpenAIRE

    Petscher, Yaacov

    2013-01-01

    This is a step-by-step presentation of how to run a meta-analysis using HLM software. Because it's a variance known model, it is not run through the GUI, but batch mode. These slides show how to prepare the data and run the analysis.

  12. A relational approach to support software architecture analysis

    NARCIS (Netherlands)

    Feijs, L.M.G.; Krikhaar, R.L.; van Ommering, R.C.

    1998-01-01

    This paper reports on our experience with a relational approach to support the analysis of existing software architectures. The analysis options provide for visualization and view calculation. The approach has been applied for reverse engineering. It is also possible to check concrete designs

  13. Development of data acquisition and analysis software for multichannel detectors

    International Nuclear Information System (INIS)

    Chung, Y.

    1988-06-01

    This report describes the development of data acquisition and analysis software for Apple Macintosh computers, capable of controlling two multichannel detectors. With the help of outstanding graphics capabilities, easy-to-use user interface, and several other built-in convenience features, this application has enhanced the productivity and the efficiency of data analysis. 2 refs., 6 figs

  14. Radio-science performance analysis software

    Science.gov (United States)

    Morabito, D. D.; Asmar, S. W.

    1995-02-01

    The Radio Science Systems Group (RSSG) provides various support functions for several flight project radio-science teams. Among these support functions are uplink and sequence planning, real-time operations monitoring and support, data validation, archiving and distribution functions, and data processing and analysis. This article describes the support functions that encompass radio-science data performance analysis. The primary tool used by the RSSG to fulfill this support function is the STBLTY program set. STBLTY is used to reconstruct observable frequencies and calculate model frequencies, frequency residuals, frequency stability in terms of Allan deviation, reconstructed phase, frequency and phase power spectral density, and frequency drift rates. In the case of one-way data, using an ultrastable oscillator (USO) as a frequency reference, the program set computes the spacecraft transmitted frequency and maintains a database containing the in-flight history of the USO measurements. The program set also produces graphical displays. Some examples and discussions on operating the program set on Galileo and Ulysses data will be presented.

  15. An Imaging And Graphics Workstation For Image Sequence Analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-01-01

    This paper describes an application-specific engineering workstation designed and developed to analyze imagery sequences from a variety of sources. The system combines the software and hardware environment of the modern graphic-oriented workstations with the digital image acquisition, processing and display techniques. The objective is to achieve automation and high throughput for many data reduction tasks involving metric studies of image sequences. The applications of such an automated data reduction tool include analysis of the trajectory and attitude of aircraft, missile, stores and other flying objects in various flight regimes including launch and separation as well as regular flight maneuvers. The workstation can also be used in an on-line or off-line mode to study three-dimensional motion of aircraft models in simulated flight conditions such as wind tunnels. The system's key features are: 1) Acquisition and storage of image sequences by digitizing real-time video or frames from a film strip; 2) computer-controlled movie loop playback, slow motion and freeze frame display combined with digital image sharpening, noise reduction, contrast enhancement and interactive image magnification; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored image sequence; 4) automatic and manual field-of-view and spatial calibration; 5) image sequence data base generation and management, including the measurement data products; 6) off-line analysis software for trajectory plotting and statistical analysis; 7) model-based estimation and tracking of object attitude angles; and 8) interface to a variety of video players and film transport sub-systems.

  16. Confirmatory Factor Analysis Alternative: Free, Accessible CBID Software.

    Science.gov (United States)

    Bott, Marjorie; Karanevich, Alex G; Garrard, Lili; Price, Larry R; Mudaranthakam, Dinesh Pal; Gajewski, Byron

    2018-02-01

    New software that performs Classical and Bayesian Instrument Development (CBID) is reported that seamlessly integrates expert (content validity) and participant data (construct validity) to produce entire reliability estimates with smaller sample requirements. The free CBID software can be accessed through a website and used by clinical investigators in new instrument development. Demonstrations are presented of the three approaches using the CBID software: (a) traditional confirmatory factor analysis (CFA), (b) Bayesian CFA using flat uninformative prior, and (c) Bayesian CFA using content expert data (informative prior). Outcomes of usability testing demonstrate the need to make the user-friendly, free CBID software available to interdisciplinary researchers. CBID has the potential to be a new and expeditious method for instrument development, adding to our current measurement toolbox. This allows for the development of new instruments for measuring determinants of health in smaller diverse populations or populations of rare diseases.

  17. A 'Toolbox' Equivalent Process for Safety Analysis Software

    International Nuclear Information System (INIS)

    O'Kula, K.R.; Eng, Tony

    2004-01-01

    Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 2002-1 (Quality Assurance for Safety-Related Software) identified a number of quality assurance issues on the use of software in Department of Energy (DOE) facilities for analyzing hazards, and designing and operating controls that prevent or mitigate potential accidents. The development and maintenance of a collection, or 'toolbox', of multiple-site use, standard solution, Software Quality Assurance (SQA)-compliant safety software is one of the major improvements identified in the associated DOE Implementation Plan (IP). The DOE safety analysis toolbox will contain a set of appropriately quality-assured, configuration-controlled, safety analysis codes, recognized for DOE-broad, safety basis applications. Currently, six widely applied safety analysis computer codes have been designated for toolbox consideration. While the toolbox concept considerably reduces SQA burdens among DOE users of these codes, many users of unique, single-purpose, or single-site software may still have sufficient technical justification to continue use of their computer code of choice, but are thwarted by the multiple-site condition on toolbox candidate software. The process discussed here provides a roadmap for an equivalency argument, i.e., establishing satisfactory SQA credentials for single-site software that can be deemed ''toolbox-equivalent''. The process is based on the model established to meet IP Commitment 4.2.1.2: Establish SQA criteria for the safety analysis ''toolbox'' codes. Implementing criteria that establish the set of prescriptive SQA requirements are based on implementation plan/procedures from the Savannah River Site, also incorporating aspects of those from the Waste Isolation Pilot Plant (SNL component) and the Yucca Mountain Project. The major requirements are met with evidence of a software quality assurance plan, software requirements and design documentation, user's instructions, test report, a

  18. The ImageJ ecosystem: An open platform for biomedical image analysis.

    Science.gov (United States)

    Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

    2015-01-01

    Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

  19. FORECAST: Regulatory effects cost analysis software annual

    International Nuclear Information System (INIS)

    Lopez, B.; Sciacca, F.W.

    1991-11-01

    Over the past several years the NRC has developed a generic cost methodology for the quantification of cost/economic impacts associated with a wide range of new or revised regulatory requirements. This methodology has been developed to aid the NRC in preparing Regulatory Impact Analyses (RIAs). These generic costing methods can be useful in quantifying impacts both to industry and to the NRC. The FORECAST program was developed to facilitate the use of the generic costing methodology. This PC program integrates the major cost considerations that may be required because of a regulatory change. FORECAST automates much of the calculations typically needed in an RIA and thus reduces the time and labor required to perform these analysis. More importantly, its integrated and consistent treatment of the different cost elements should help assure comprehensiveness, uniformity, and accuracy in the preparation of needed cost estimates

  20. Equipment Obsolescence Analysis and Management Software

    Energy Technology Data Exchange (ETDEWEB)

    Redmond, J.; Carret, L.; Shaon, S.; Schultz, C.

    2015-07-01

    The procurement engineering resources at Nuclear Power Plants (NPPs) are experiencing increasing backlog for procurement items primarily due to the inability to order the original replacement parts. The level of effort and time required to prepare procurement packages is increasing since the number of obsolete parts are increasing exponentially. Procurement packages for obsolete components and parts are much more complex and take more time to prepare because of the need to perform equivalency evaluations, testing requirements and test acceptance criteria development, commercial grade dedication or equipment qualification, and increasing efforts to verify that no fraudulent or counterfeit parts are procured. This problem will be further compounded when NPPs pursue license renewal and approval for plant-life extension. Advanced planning and advanced knowledge of equipment obsolescence is required to allow for sufficient time to properly procure replacement parts for obsolete items. The uncertain supply chain capability due to obsolescence is a real problem and can cause a risk to reliable plant operations due to the potential for a lack of available spare parts and replacement components to support outages and unplanned component failures. Advanced notification of obsolescence is increasingly more important to ensure that adequate time and planning is scheduled to procure the proper replacement parts. A thorough analysis of Original Equipment Manufacturer (OEM) availability and inventory as well as an analysis of failure rates and usage rates is required to predict critical part needs to allow for early identification of obsolescence issues so that a planned and controlled strategy to qualify replacement equipment can be implemented. (Author)

  1. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  2. The software analysis project for the Office of Human Resources

    Science.gov (United States)

    Tureman, Robert L., Jr.

    1994-01-01

    There were two major sections of the project for the Office of Human Resources (OHR). The first section was to conduct a planning study to analyze software use with the goal of recommending software purchases and determining whether the need exists for a file server. The second section was analysis and distribution planning for retirement planning computer program entitled VISION provided by NASA Headquarters. The software planning study was developed to help OHR analyze the current administrative desktop computing environment and make decisions regarding software acquisition and implementation. There were three major areas addressed by the study: current environment new software requirements, and strategies regarding the implementation of a server in the Office. To gather data on current environment, employees were surveyed and an inventory of computers were produced. The surveys were compiled and analyzed by the ASEE fellow with interpretation help by OHR staff. New software requirements represented a compilation and analysis of the surveyed requests of OHR personnel. Finally, the information on the use of a server represents research done by the ASEE fellow and analysis of survey data to determine software requirements for a server. This included selection of a methodology to estimate the number of copies of each software program required given current use and estimated growth. The report presents the results of the computing survey, a description of the current computing environment, recommenations for changes in the computing environment, current software needs, management advantages of using a server, and management considerations in the implementation of a server. In addition, detailed specifications were presented for the hardware and software recommendations to offer a complete picture to OHR management. The retirement planning computer program available to NASA employees will aid in long-range retirement planning. The intended audience is the NASA civil

  3. Evaluation of Co-rich manganese deposits by image analysis and photogrammetric techniques

    Digital Repository Service at National Institute of Oceanography (India)

    Yamazaki, T.; Sharma, R.; Tsurusaki, K.

    Stereo-seabed photographs of Co-rich manganese deposits on a mid-Pacific seamount, were analysed using an image analysis software for coverage estimation and size classification of nodules, and a photogrammetric software for calculation of height...

  4. Software package for the design and analysis of DNA origami structures

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Nielsen, Morten Muhlig; Dong, Mingdong

    was observed on the mica surface with a fraction of the dolphin nanostructures showing extensive tail flexibility of approximately 90 degrees. The Java editor and tools are free software distributed under the GNU license. The open architecture of the editor makes it easy for the scientific community......A software package was developed for the semi-automated design of DNA origamis and further data analysis of Atomic Force Microscopy (AFM) images. As an example, we design the shape of a bottlenose dolphin and analyze it by means of high resolution AFM imaging. A high yield of DNA dolphins...... to contribute new tools and functionalities. Documentation, tutorials and software will be made available online....

  5. Software for muscle fibre type classification and analysis

    Czech Academy of Sciences Publication Activity Database

    Karen, Petr; Števanec, M.; Smerdu, V.; Cvetko, E.; Kubínová, Lucie; Eržen, I.

    2009-01-01

    Roč. 53, č. 2 (2009), s. 87-95 ISSN 1121-760X R&D Projects: GA MŠk(CZ) LC06063; GA MŠk(CZ) MEB090910 Institutional research plan: CEZ:AV0Z50110509 Keywords : muscle fiber types * myosin heavy chain isoforms * image processing Subject RIV: JC - Computer Hardware ; Software Impact factor: 0.886, year: 2009

  6. GiA Roots: software for the high throughput analysis of plant root system architecture

    Science.gov (United States)

    2012-01-01

    Background Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks. Results We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user. Conclusions We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis. PMID:22834569

  7. ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

    Science.gov (United States)

    Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

    2016-04-01

    The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. Optimising MR perfusion imaging: comparison of different software-based approaches in acute ischaemic stroke

    Energy Technology Data Exchange (ETDEWEB)

    Schaafs, Lars-Arne [Charite-Universitaetsmedizin, Department of Radiology, Berlin (Germany); Charite-Universitaetsmedizin, Academic Neuroradiology, Department of Neurology and Center for Stroke Research, Berlin (Germany); Porter, David [Fraunhofer Institute for Medical Image Computing MEVIS, Bremen (Germany); Audebert, Heinrich J. [Charite-Universitaetsmedizin, Department of Neurology with Experimental Neurology, Berlin (Germany); Fiebach, Jochen B.; Villringer, Kersten [Charite-Universitaetsmedizin, Academic Neuroradiology, Department of Neurology and Center for Stroke Research, Berlin (Germany)

    2016-11-15

    Perfusion imaging (PI) is susceptible to confounding factors such as motion artefacts as well as delay and dispersion (D/D). We evaluate the influence of different post-processing algorithms on hypoperfusion assessment in PI analysis software packages to improve the clinical accuracy of stroke PI. Fifty patients with acute ischaemic stroke underwent MRI imaging in the first 24 h after onset. Diverging approaches to motion and D/D correction were applied. The calculated MTT and CBF perfusion maps were assessed by volumetry of lesions and tested for agreement with a standard approach and with the final lesion volume (FLV) on day 6 in patients with persisting vessel occlusion. MTT map lesion volumes were significantly smaller throughout the software packages with correction of motion and D/D when compared to the commonly used approach with no correction (p = 0.001-0.022). Volumes on CBF maps did not differ significantly (p = 0.207-0.925). All packages with advanced post-processing algorithms showed a high level of agreement with FLV (ICC = 0.704-0.879). Correction of D/D had a significant influence on estimated lesion volumes and leads to significantly smaller lesion volumes on MTT maps. This may improve patient selection. (orig.)

  9. Optimising MR perfusion imaging: comparison of different software-based approaches in acute ischaemic stroke

    International Nuclear Information System (INIS)

    Schaafs, Lars-Arne; Porter, David; Audebert, Heinrich J.; Fiebach, Jochen B.; Villringer, Kersten

    2016-01-01

    Perfusion imaging (PI) is susceptible to confounding factors such as motion artefacts as well as delay and dispersion (D/D). We evaluate the influence of different post-processing algorithms on hypoperfusion assessment in PI analysis software packages to improve the clinical accuracy of stroke PI. Fifty patients with acute ischaemic stroke underwent MRI imaging in the first 24 h after onset. Diverging approaches to motion and D/D correction were applied. The calculated MTT and CBF perfusion maps were assessed by volumetry of lesions and tested for agreement with a standard approach and with the final lesion volume (FLV) on day 6 in patients with persisting vessel occlusion. MTT map lesion volumes were significantly smaller throughout the software packages with correction of motion and D/D when compared to the commonly used approach with no correction (p = 0.001-0.022). Volumes on CBF maps did not differ significantly (p = 0.207-0.925). All packages with advanced post-processing algorithms showed a high level of agreement with FLV (ICC = 0.704-0.879). Correction of D/D had a significant influence on estimated lesion volumes and leads to significantly smaller lesion volumes on MTT maps. This may improve patient selection. (orig.)

  10. RATIO_TOOL - SOFTWARE FOR COMPUTING IMAGE RATIOS

    Science.gov (United States)

    Yates, G. L.

    1994-01-01

    Geological studies analyze spectral data in order to gain information on surface materials. RATIO_TOOL is an interactive program for viewing and analyzing large multispectral image data sets that have been created by an imaging spectrometer. While the standard approach to classification of multispectral data is to match the spectrum for each input pixel against a library of known mineral spectra, RATIO_TOOL uses ratios of spectral bands in order to spot significant areas of interest within a multispectral image. Each image band can be viewed iteratively, or a selected image band of the data set can be requested and displayed. When the image ratios are computed, the result is displayed as a gray scale image. At this point a histogram option helps in viewing the distribution of values. A thresholding option can then be used to segment the ratio image result into two to four classes. The segmented image is then color coded to indicate threshold classes and displayed alongside the gray scale image. RATIO_TOOL is written in C language for Sun series computers running SunOS 4.0 and later. It requires the XView toolkit and the OpenWindows window manager (version 2.0 or 3.0). The XView toolkit is distributed with Open Windows. A color monitor is also required. The standard distribution medium for RATIO_TOOL is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation is included on the program media. RATIO_TOOL was developed in 1992 and is a copyrighted work with all copyright vested in NASA. Sun, SunOS, and OpenWindows are trademarks of Sun Microsystems, Inc. UNIX is a registered trademark of AT&T Bell Laboratories.

  11. Diffusion tensor imaging of the median nerve: intra-, inter-reader agreement, and agreement between two software packages

    International Nuclear Information System (INIS)

    Guggenberger, Roman; Nanz, Daniel; Puippe, Gilbert; Andreisek, Gustav; Rufibach, Kaspar; White, Lawrence M.; Sussman, Marshall S.

    2012-01-01

    To assess intra-, inter-reader agreement, and the agreement between two software packages for magnetic resonance diffusion tensor imaging (DTI) measurements of the median nerve. Fifteen healthy volunteers (seven men, eight women; mean age, 31.2 years) underwent DTI of both wrists at 1.5 T. Fractional anisotropy (FA) and apparent diffusion coefficient (ADC) of the median nerve were measured by three readers using two commonly used software packages. Measurements were repeated by two readers after 6 weeks. Intraclass correlation coefficients (ICC) and Bland-Altman analysis were used for statistical analysis. ICCs for intra-reader agreement ranged from 0.87 to 0.99, for inter-reader agreement from 0.62 to 0.83, and between the two software packages from 0.63 to 0.82. Bland-Altman analysis showed no differences for intra- and inter-reader agreement and agreement between software packages. The intra-, inter-reader, and agreement between software packages for DTI measurements of the median nerve were moderate to substantial suggesting that user- and software-dependent factors contribute little to variance in DTI measurements. (orig.)

  12. Development of interactive software for fuel management analysis

    International Nuclear Information System (INIS)

    Graves, H.W. Jr.

    1986-01-01

    Electronic computation plays a central part in engineering analysis of all types. Utilization of microcomputers for calculations that were formerly carried out on large mainframe computers presents a unique opportunity to develop software that not only takes advantage of the lower cost of using these machines, but also increases the efficiency of the engineers performing these calculations. This paper reviews the use of electronic computers in engineering analysis, discusses the potential for microcomputer utilization in this area, and describes a series of steps to be followed in software development that can yield significant gains in engineering design efficiency

  13. IMAGE information monitoring and applied graphics software environment. Volume 4. Applications description

    International Nuclear Information System (INIS)

    Hallam, J.W.; Ng, K.B.; Upham, G.L.

    1986-09-01

    The EPRI Information Monitoring and Applied Graphics Environment (IMAGE) system is designed for 'fast proto-typing' of advanced concepts for computer-aided plant operations tools. It is a flexible software system which can be used for rapidly creating, dynamically driving and evaluating advanced operator aid displays. The software is written to be both host computer and graphic device independent. This four volume report includes an Executive Overview of the IMAGE package (Volume 1), followed by Software Description (Volume II), User's Guide (Volume III), and Description of Example Applications (Volume IV)

  14. Applications of the BEam Cross section Analysis Software (BECAS)

    DEFF Research Database (Denmark)

    Blasques, José Pedro Albergaria Amaral; Bitsche, Robert; Fedorov, Vladimir

    2013-01-01

    A newly developed framework is presented for structural design and analysis of long slender beam-like structures, e.g., wind turbine blades. The framework is based on the BEam Cross section Analysis Software – BECAS – a finite element based cross section analysis tool. BECAS is used for the gener......A newly developed framework is presented for structural design and analysis of long slender beam-like structures, e.g., wind turbine blades. The framework is based on the BEam Cross section Analysis Software – BECAS – a finite element based cross section analysis tool. BECAS is used...... for the generation of beam finite element models which correctly account for effects stemming from material anisotropy and inhomogeneity in cross sections of arbitrary geometry. These type of modelling approach allows for an accurate yet computationally inexpensive representation of a general class of three...

  15. Detection of patient setup errors with a portal image - DRR registration software application.

    Science.gov (United States)

    Sutherland, Kenneth; Ishikawa, Masayori; Bengua, Gerard; Ito, Yoichi M; Miyamoto, Yoshiko; Shirato, Hiroki

    2011-02-18

    The purpose of this study was to evaluate a custom portal image - digitally reconstructed radiograph (DRR) registration software application. The software works by transforming the portal image into the coordinate space of the DRR image using three control points placed on each image by the user, and displaying the fused image. In order to test statistically that the software actually improves setup error estimation, an intra- and interobserver phantom study was performed. Portal images of anthropomorphic thoracic and pelvis phantoms with virtually placed irradiation fields at known setup errors were prepared. A group of five doctors was first asked to estimate the setup errors by examining the portal and DRR image side-by-side, not using the software. A second group of four technicians then estimated the same set of images using the registration software. These two groups of human subjects were then compared with an auto-registration feature of the software, which is based on the mutual information between the portal and DRR images. For the thoracic case, the average distance between the actual setup error and the estimated error was 4.3 ± 3.0 mm for doctors using the side-by-side method, 2.1 ± 2.4 mm for technicians using the registration method, and 0.8 ± 0.4mm for the automatic algorithm. For the pelvis case, the average distance between the actual setup error and estimated error was 2.0 ± 0.5 mm for the doctors using the side-by-side method, 2.5 ± 0.4 mm for technicians using the registration method, and 2.0 ± 1.0 mm for the automatic algorithm. The ability of humans to estimate offset values improved statistically using our software for the chest phantom that we tested. Setup error estimation was further improved using our automatic error estimation algorithm. Estimations were not statistically different for the pelvis case. Consistency improved using the software for both the chest and pelvis phantoms. We also tested the automatic algorithm with a

  16. Digital image processing and analysis human and computer vision applications with CVIPtools

    CERN Document Server

    Umbaugh, Scott E

    2010-01-01

    Section I Introduction to Digital Image Processing and AnalysisDigital Image Processing and AnalysisOverviewImage Analysis and Computer VisionImage Processing and Human VisionKey PointsExercisesReferencesFurther ReadingComputer Imaging SystemsImaging Systems OverviewImage Formation and SensingCVIPtools SoftwareImage RepresentationKey PointsExercisesSupplementary ExercisesReferencesFurther ReadingSection II Digital Image Analysis and Computer VisionIntroduction to Digital Image AnalysisIntroductionPreprocessingBinary Image AnalysisKey PointsExercisesSupplementary ExercisesReferencesFurther Read

  17. Initial Investigation of Software-Based Bone-Suppressed Imaging

    International Nuclear Information System (INIS)

    Park, Eunpyeong; Youn, Hanbean; Kim, Ho Kyung

    2015-01-01

    Chest radiography is the most widely used imaging modality in medicine. However, the diagnostic performance of chest radiography is deteriorated by the anatomical background of the patient. So, dual energy imaging (DEI) has recently been emerged and demonstrated an improved. However, the typical DEI requires more than two projections, hence causing additional patient dose. The motion artifact is another concern in the DEI. In this study, we investigate DEI-like bone-suppressed imaging based on the post processing of a single radiograph. To obtain bone-only images, we use the artificial neural network (ANN) method with the error backpropagation-based machine learning approach. The computational load of learning process of the ANN is too heavy for a practical implementation because we use the gradient descent method for the error backpropagation. We will use a more advanced error propagation method for the learning process

  18. Development of Software for Measurement and Analysis of Solar Radiation

    International Nuclear Information System (INIS)

    Mohamad Idris Taib; Abul Adli Anuar; Noor Ezati Shuib

    2015-01-01

    This software was under development using LabVIEW to be using with StellarNet spectrometers system with USB communication to computer. LabVIEW have capabilities in hardware interfacing, graphical user interfacing and mathematical calculation including array manipulation and processing. This software read data from StellarNet spectrometer in real-time and then processed for analysis. Several measurement of solar radiation and analysis have been done. Solar radiation involved mainly infra-red, visible light and ultra-violet. With solar radiation spectrum data, information of weather and suitability of plant can be gathered and analyzed. Furthermore, optimization of utilization and safety precaution of solar radiation can be planned. Using this software, more research and development in utilization and safety of solar radiation can be explored. (author)

  19. Free software for performing physical analysis of systems for digital radiography and mammography

    Energy Technology Data Exchange (ETDEWEB)

    Donini, Bruno; Lanconelli, Nico, E-mail: nico.lanconelli@unibo.it [Alma Mater Studiorum, Department of Physics and Astronomy, University of Bologna, Bologna 40127 (Italy); Rivetti, Stefano [Fisica Medica, Ospedale di Sassuolo S.p.A., Sassuolo 41049 (Italy); Bertolini, Marco [Medical Physics Unit, Azienda Ospedaliera ASMN, Istituto di Ricovero e Cura a Carattere Scientifico, Reggio Emilia 42123 (Italy)

    2014-05-15

    Purpose: In this paper, the authors present a free software for assisting users in achieving the physical characterization of x-ray digital systems and image quality checks. Methods: The program was developed as a plugin of a well-known public-domain suite ImageJ. The software can assist users in calculating various physical parameters such as the response curve (also termed signal transfer property), modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE). It also includes the computation of some image quality checks: defective pixel analysis, uniformity, dark analysis, and lag. Results: The software was made available in 2009 and has been used during the last couple of years by many users who gave us valuable feedback for improving its usability. It was tested for achieving the physical characterization of several clinical systems for digital radiography and mammography. Various published papers made use of the outcomes of the plugin. Conclusions: This software is potentially beneficial to a variety of users: physicists working in hospitals, staff working in radiological departments, such as medical physicists, physicians, engineers. The plugin, together with a brief user manual, are freely available and can be found online ( http://www.medphys.it/downloads.htm ). With our plugin users can estimate all three most important parameters used for physical characterization (MTF, NPS, and also DQE). The plugin can run on any operating system equipped with ImageJ suite. The authors validated the software by comparing MTF and NPS curves on a common set of images with those obtained with other dedicated programs, achieving a very good agreement.

  20. Free software for performing physical analysis of systems for digital radiography and mammography.

    Science.gov (United States)

    Donini, Bruno; Rivetti, Stefano; Lanconelli, Nico; Bertolini, Marco

    2014-05-01

    In this paper, the authors present a free software for assisting users in achieving the physical characterization of x-ray digital systems and image quality checks. The program was developed as a plugin of a well-known public-domain suite ImageJ. The software can assist users in calculating various physical parameters such as the response curve (also termed signal transfer property), modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE). It also includes the computation of some image quality checks: defective pixel analysis, uniformity, dark analysis, and lag. The software was made available in 2009 and has been used during the last couple of years by many users who gave us valuable feedback for improving its usability. It was tested for achieving the physical characterization of several clinical systems for digital radiography and mammography. Various published papers made use of the outcomes of the plugin. This software is potentially beneficial to a variety of users: physicists working in hospitals, staff working in radiological departments, such as medical physicists, physicians, engineers. The plugin, together with a brief user manual, are freely available and can be found online (www.medphys.it/downloads.htm). With our plugin users can estimate all three most important parameters used for physical characterization (MTF, NPS, and also DQE). The plugin can run on any operating system equipped with ImageJ suite. The authors validated the software by comparing MTF and NPS curves on a common set of images with those obtained with other dedicated programs, achieving a very good agreement.

  1. Free software for performing physical analysis of systems for digital radiography and mammography

    International Nuclear Information System (INIS)

    Donini, Bruno; Lanconelli, Nico; Rivetti, Stefano; Bertolini, Marco

    2014-01-01

    Purpose: In this paper, the authors present a free software for assisting users in achieving the physical characterization of x-ray digital systems and image quality checks. Methods: The program was developed as a plugin of a well-known public-domain suite ImageJ. The software can assist users in calculating various physical parameters such as the response curve (also termed signal transfer property), modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE). It also includes the computation of some image quality checks: defective pixel analysis, uniformity, dark analysis, and lag. Results: The software was made available in 2009 and has been used during the last couple of years by many users who gave us valuable feedback for improving its usability. It was tested for achieving the physical characterization of several clinical systems for digital radiography and mammography. Various published papers made use of the outcomes of the plugin. Conclusions: This software is potentially beneficial to a variety of users: physicists working in hospitals, staff working in radiological departments, such as medical physicists, physicians, engineers. The plugin, together with a brief user manual, are freely available and can be found online ( http://www.medphys.it/downloads.htm ). With our plugin users can estimate all three most important parameters used for physical characterization (MTF, NPS, and also DQE). The plugin can run on any operating system equipped with ImageJ suite. The authors validated the software by comparing MTF and NPS curves on a common set of images with those obtained with other dedicated programs, achieving a very good agreement

  2. Polarization information processing and software system design for simultaneously imaging polarimetry

    Science.gov (United States)

    Wang, Yahui; Liu, Jing; Jin, Weiqi; Wen, Renjie

    2015-08-01

    Simultaneous imaging polarimetry can realize real-time polarization imaging of the dynamic scene, which has wide application prospect. This paper first briefly illustrates the design of the double separate Wollaston Prism simultaneous imaging polarimetry, and then emphases are put on the polarization information processing methods and software system design for the designed polarimetry. Polarization information processing methods consist of adaptive image segmentation, high-accuracy image registration, instrument matrix calibration. Morphological image processing was used for image segmentation by taking dilation of an image; The accuracy of image registration can reach 0.1 pixel based on the spatial and frequency domain cross-correlation; Instrument matrix calibration adopted four-point calibration method. The software system was implemented under Windows environment based on C++ programming language, which realized synchronous polarization images acquisition and preservation, image processing and polarization information extraction and display. Polarization data obtained with the designed polarimetry shows that: the polarization information processing methods and its software system effectively performs live realize polarization measurement of the four Stokes parameters of a scene. The polarization information processing methods effectively improved the polarization detection accuracy.

  3. New tools for digital medical image processing implemented in DIP software

    International Nuclear Information System (INIS)

    Araujo, Erica A.C.; Santana, Ivan E.; Lima, Fernando R.A.; Viera, Jose W.

    2011-01-01

    The anthropomorphic models used in computational dosimetry, also called phantoms, are mostly built from stacks of images CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) obtained from scans of patients or volunteers. The construction of voxel phantoms requires computational processing for transforming image formats, dimensional image compression (2D) to form three-dimensional arrays (3D), quantization, resampling, enhancement, restoration and image segmentation, among others. Hardly the computational dosimetry researcher finds all these skills into a single software and often it results in a decreased development of their research or inadequate use of alternative tools. The need to integrate the various tasks of the original digital image processing to obtain an image that can be used in a computational model of exposure led to the development of software DIP (Digital Image Processing). This software reads, writes and edits binary files containing the 3D matrix corresponding to a stack of cross-sectional images of a given geometry that can be a human body or other volume of interest. It can also read any type of computer image and do conversions. When the task involves only one output image, it is saved in the JPEG standard Windows. When it involves a stack of images, the binary output file is called SGI (Interactive Graphic Simulations, a symbol already used in other publications of the Research Group in Numerical Dosimetry). The following paper presents the third version of the DIP software and emphasizes the new tools it implemented. Currently it has the menus Basics, Views, Spatial Domain, Frequency Domain, Segmentations and Study. Each menu contains items and subitems with features that generally require an image as input and produce an image or an attribute in the output. (author)

  4. Evaluation of peak-fitting software for gamma spectrum analysis

    International Nuclear Information System (INIS)

    Zahn, Guilherme S.; Genezini, Frederico A.; Moralles, Mauricio

    2009-01-01

    In all applications of gamma-ray spectroscopy, one of the most important and delicate parts of the data analysis is the fitting of the gamma-ray spectra, where information as the number of counts, the position of the centroid and the width, for instance, are associated with each peak of each spectrum. There's a huge choice of computer programs that perform this type of analysis, and the most commonly used in routine work are the ones that automatically locate and fit the peaks; this fit can be made in several different ways - the most common ways are to fit a Gaussian function to each peak or simply to integrate the area under the peak, but some software go far beyond and include several small corrections to the simple Gaussian peak function, in order to compensate for secondary effects. In this work several gamma-ray spectroscopy software are compared in the task of finding and fitting the gamma-ray peaks in spectra taken with standard sources of 137 Cs, 60 Co, 133 Ba and 152 Eu. The results show that all of the automatic software can be properly used in the task of finding and fitting peaks, with the exception of GammaVision; also, it was possible to verify that the automatic peak-fitting software did perform as well as - and sometimes even better than - a manual peak-fitting software. (author)

  5. A software for digital image processing used in constructions of voxels phantoms

    International Nuclear Information System (INIS)

    Vieira, Jose Wilson; Fernando Roberto de Andrade

    2008-01-01

    This paper presents, based on menus and menu items, the second version of software DIP-Digital Image Processing, that reads, edits and writes binary files containing the matrix 3D corresponding to a transversal voxels images of a certain geometry that may be a human body or other volume of interest

  6. Report of AAPM Task Group 162: Software for planar image quality metrology.

    Science.gov (United States)

    Samei, Ehsan; Ikejimba, Lynda C; Harrawood, Brian P; Rong, John; Cunningham, Ian A; Flynn, Michael J

    2018-02-01

    The AAPM Task Group 162 aimed to provide a standardized approach for the assessment of image quality in planar imaging systems. This report offers a description of the approach as well as the details of the resultant software bundle to measure detective quantum efficiency (DQE) as well as its basis components and derivatives. The methodology and the associated software include the characterization of the noise power spectrum (NPS) from planar images acquired under specific acquisition conditions, modulation transfer function (MTF) using an edge test object, the DQE, and effective DQE (eDQE). First, a methodological framework is provided to highlight the theoretical basis of the work. Then, a step-by-step guide is included to assist in proper execution of each component of the code. Lastly, an evaluation of the method is included to validate its accuracy against model-based and experimental data. The code was built using a Macintosh OSX operating system. The software package contains all the source codes to permit an experienced user to build the suite on a Linux or other *nix type system. The package further includes manuals and sample images and scripts to demonstrate use of the software for new users. The results of the code are in close alignment with theoretical expectations and published results of experimental data. The methodology and the software package offered in AAPM TG162 can be used as baseline for characterization of inherent image quality attributes of planar imaging systems. © 2017 American Association of Physicists in Medicine.

  7. UTOOLS: microcomputer software for spatial analysis and landscape visualization.

    Science.gov (United States)

    Alan A. Ager; Robert J. McGaughey

    1997-01-01

    UTOOLS is a collection of programs designed to integrate various spatial data in a way that allows versatile spatial analysis and visualization. The programs were designed for watershed-scale assessments in which a wide array of resource data must be integrated, analyzed, and interpreted. UTOOLS software combines raster, attribute, and vector data into "spatial...

  8. Using Business Analysis Software in a Business Intelligence Course

    Science.gov (United States)

    Elizondo, Juan; Parzinger, Monica J.; Welch, Orion J.

    2011-01-01

    This paper presents an example of a project used in an undergraduate business intelligence class which integrates concepts from statistics, marketing, and information systems disciplines. SAS Enterprise Miner software is used as the foundation for predictive analysis and data mining. The course culminates with a competition and the project is used…

  9. Application of software technology to automatic test data analysis

    Science.gov (United States)

    Stagner, J. R.

    1991-01-01

    The verification process for a major software subsystem was partially automated as part of a feasibility demonstration. The methods employed are generally useful and applicable to other types of subsystems. The effort resulted in substantial savings in test engineer analysis time and offers a method for inclusion of automatic verification as a part of regression testing.

  10. WinDAM C earthen embankment internal erosion analysis software

    Science.gov (United States)

    Two primary causes of dam failure are overtopping and internal erosion. For the purpose of evaluating dam safety for existing earthen embankment dams and proposed earthen embankment dams, Windows Dam Analysis Modules C (WinDAM C) software will simulate either internal erosion or erosion resulting f...

  11. ANALYSIS OF CONTEMPORARY SOFTWARE BEING USED FOR FORWARDING SERVICES

    Directory of Open Access Journals (Sweden)

    Naumov, V.

    2013-01-01

    Full Text Available The role of information technologies in the forwarding services has been specified. The typical structure of the logistic sites providing the search of requests of freight owners and carriers has been described. The analysis of the software for transportation companies was conducted. The perspective directions of improvement of forwarding services process have been revealed.

  12. A report on digital image processing and analysis

    International Nuclear Information System (INIS)

    Singh, B.; Alex, J.; Haridasan, G.

    1989-01-01

    This report presents developments in software, connected with digital image processing and analysis in the Centre. In image processing, one resorts to either alteration of grey level values so as to enhance features in the image or resorts to transform domain operations for restoration or filtering. Typical transform domain operations like Karhunen-Loeve transforms are statistical in nature and are used for a good registration of images or template - matching. Image analysis procedures segment grey level images into images contained within selectable windows, for the purpose of estimating geometrical features in the image, like area, perimeter, projections etc. In short, in image processing both the input and output are images, whereas in image analyses, the input is an image whereas the output is a set of numbers and graphs. (author). 19 refs

  13. IDP: Image and data processing (software) in C++

    Energy Technology Data Exchange (ETDEWEB)

    Lehman, S. [Lawrence Livermore National Lab., CA (United States)

    1994-11-15

    IDP++(Image and Data Processing in C++) is a complied, multidimensional, multi-data type, signal processing environment written in C++. It is being developed within the Radar Ocean Imaging group and is intended as a partial replacement for View. IDP++ takes advantage of the latest object-oriented compiler technology to provide `information hiding.` Users need only know C, not C++. Signals are treated like any other variable with a defined set of operators and functions in an intuitive manner. IDP++ is being designed for real-time environment where interpreted signal processing packages are less efficient.

  14. Software optimization for electrical conductivity imaging in polycrystalline diamond cutters

    Energy Technology Data Exchange (ETDEWEB)

    Bogdanov, G.; Ludwig, R. [Department of Electrical and Computer Engineering, Worcester Polytechnic Institute, 100 Institute Rd, Worcester, MA 01609 (United States); Wiggins, J.; Bertagnolli, K. [US Synthetic, 1260 South 1600 West, Orem, UT 84058 (United States)

    2014-02-18

    We previously reported on an electrical conductivity imaging instrument developed for measurements on polycrystalline diamond cutters. These cylindrical cutters for oil and gas drilling feature a thick polycrystalline diamond layer on a tungsten carbide substrate. The instrument uses electrical impedance tomography to profile the conductivity in the diamond table. Conductivity images must be acquired quickly, on the order of 5 sec per cutter, to be useful in the manufacturing process. This paper reports on successful efforts to optimize the conductivity reconstruction routine, porting major portions of it to NVIDIA GPUs, including a custom CUDA kernel for Jacobian computation.

  15. Image compression software for the SOHO LASCO and EIT experiments

    Science.gov (United States)

    Grunes, Mitchell R.; Howard, Russell A.; Hoppel, Karl; Mango, Stephen A.; Wang, Dennis

    1994-01-01

    This paper describes the lossless and lossy image compression algorithms to be used on board the Solar Heliospheric Observatory (SOHO) in conjunction with the Large Angle Spectrometric Coronograph and Extreme Ultraviolet Imaging Telescope experiments. It also shows preliminary results obtained using similar prior imagery and discusses the lossy compression artifacts which will result. This paper is in part intended for the use of SOHO investigators who need to understand the results of SOHO compression in order to better allocate the transmission bits which they have been allocated.

  16. A Knowledge-based Environment for Software Process Performance Analysis

    Directory of Open Access Journals (Sweden)

    Natália Chaves Lessa Schots

    2015-08-01

    Full Text Available Background: Process performance analysis is a key step for implementing continuous improvement in software organizations. However, the knowledge to execute such analysis is not trivial and the person responsible to executing it must be provided with appropriate support. Aim: This paper presents a knowledge-based environment, named SPEAKER, proposed for supporting software organizations during the execution of process performance analysis. SPEAKER comprises a body of knowledge and a set of activities and tasks for software process performance analysis along with supporting tools to executing these activities and tasks. Method: We conducted an informal literature reviews and a systematic mapping study, which provided basic requirements for the proposed environment. We implemented the SPEAKER environment integrating supporting tools for the execution of activities and tasks of performance analysis and the knowledge necessary to execute them, in order to meet the variability presented by the characteristics of these activities. Results: In this paper, we describe each SPEAKER module and the individual evaluations of these modules, and also present an example of use comprising how the environment can guide the user through a specific performance analysis activity. Conclusion: Although we only conducted individual evaluations of SPEAKER’s modules, the example of use indicates the feasibility of the proposed environment. Therefore, the environment as a whole will be further evaluated to verify if it attains its goal of assisting in the execution of process performance analysis by non-specialist people.

  17. Image sequence analysis workstation for multipoint motion analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-08-01

    This paper describes an application-specific engineering workstation designed and developed to analyze motion of objects from video sequences. The system combines the software and hardware environment of a modem graphic-oriented workstation with the digital image acquisition, processing and display techniques. In addition to automation and Increase In throughput of data reduction tasks, the objective of the system Is to provide less invasive methods of measurement by offering the ability to track objects that are more complex than reflective markers. Grey level Image processing and spatial/temporal adaptation of the processing parameters is used for location and tracking of more complex features of objects under uncontrolled lighting and background conditions. The applications of such an automated and noninvasive measurement tool include analysis of the trajectory and attitude of rigid bodies such as human limbs, robots, aircraft in flight, etc. The system's key features are: 1) Acquisition and storage of Image sequences by digitizing and storing real-time video; 2) computer-controlled movie loop playback, freeze frame display, and digital Image enhancement; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored Image sequence; 4) model-based estimation and tracking of the six degrees of freedom of a rigid body: 5) field-of-view and spatial calibration: 6) Image sequence and measurement data base management; and 7) offline analysis software for trajectory plotting and statistical analysis.

  18. Application of an image processing software for quantitative autoradiography

    International Nuclear Information System (INIS)

    Sobeslavsky, E.; Bergmann, R.; Kretzschmar, M.; Wenzel, U.

    1993-01-01

    The present communication deals with the utilization of an image processing device for quantitative whole-body autoradiography, cell counting and also for interpretation of chromatograms. It is shown that the system parameters allow an adequate and precise determination of optical density values. Also shown are the main error sources limiting the applicability of the system. (orig.)

  19. Synchronized analysis of testbeam data with the Judith software

    CERN Document Server

    McGoldrick, Garrin; Gorišek, Andrej

    2014-01-01

    The Judith software performs pixel detector analysis tasks utilizing two different data streams such as those produced by the reference and tested devices typically found in a testbeam. This software addresses and fixes problems arising from the desynchronization of the two simultaneously triggered data streams by detecting missed triggers in either of the streams. The software can perform all tasks required to generate particle tracks using multiple detector planes: it can align the planes, cluster hits and generate tracks from these clusters. This information can then be used to measure the properties of a particle detector with very fine spatial resolution. It was tested at DESY in the Kartel telescope, a silicon tracking detector, with ATLAS Diamond Beam Monitor modules as a device under test.

  20. One-Click Data Analysis Software for Science Operations

    Science.gov (United States)

    Navarro, Vicente

    2015-12-01

    One of the important activities of ESA Science Operations Centre is to provide Data Analysis Software (DAS) to enable users and scientists to process data further to higher levels. During operations and post-operations, Data Analysis Software (DAS) is fully maintained and updated for new OS and library releases. Nonetheless, once a Mission goes into the "legacy" phase, there are very limited funds and long-term preservation becomes more and more difficult. Building on Virtual Machine (VM), Cloud computing and Software as a Service (SaaS) technologies, this project has aimed at providing long-term preservation of Data Analysis Software for the following missions: - PIA for ISO (1995) - SAS for XMM-Newton (1999) - Hipe for Herschel (2009) - EXIA for EXOSAT (1983) Following goals have guided the architecture: - Support for all operations, post-operations and archive/legacy phases. - Support for local (user's computer) and cloud environments (ESAC-Cloud, Amazon - AWS). - Support for expert users, requiring full capabilities. - Provision of a simple web-based interface. This talk describes the architecture, challenges, results and lessons learnt gathered in this project.

  1. Application of econometric and ecology analysis methods in physics software

    Science.gov (United States)

    Han, Min Cheol; Hoff, Gabriela; Kim, Chan Hyeong; Kim, Sung Hun; Grazia Pia, Maria; Ronchieri, Elisabetta; Saracco, Paolo

    2017-10-01

    Some data analysis methods typically used in econometric studies and in ecology have been evaluated and applied in physics software environments. They concern the evolution of observables through objective identification of change points and trends, and measurements of inequality, diversity and evenness across a data set. Within each analysis area, various statistical tests and measures have been examined. This conference paper summarizes a brief overview of some of these methods.

  2. Carotid artery stenosis: Performance of advanced vessel analysis software in evaluating CTA

    International Nuclear Information System (INIS)

    Tsiflikas, Ilias; Biermann, Christina; Thomas, Christoph; Ketelsen, Dominik; Claussen, Claus D.; Heuschmid, Martin

    2012-01-01

    Objectives: The aim of this study was to evaluate time efficiency and diagnostic reproducibility of an advanced vessel analysis software for diagnosis of carotid artery stenosis. Material and methods: 40 patients with suspected carotid artery stenosis received head and neck DE-CTA as part of their pre-interventional workup. Acquired data were evaluated by 2 independent radiologists. Stenosis grading was performed by MPR eyeballing with freely adjustable MPRs and with a preliminary prototype of the meanwhile available client-server and advanced visualization software syngo.via CT Vascular (Siemens Healthcare, Erlangen, Germany). Stenoses were graded according to the following 5 categories: I: 0%, II: 1–50%, III: 51–69%, IV: 70–99% and V: total occlusion. Furthermore, time to diagnosis for each carotid artery was recorded. Results: Both readers achieved very good specificity values and good respectively very good sensitivity values without significant differences between both reading methods. Furthermore, there was a very good correlation between both readers for both reading methods without significant differences (kappa value: standard image interpretation k = 0.809; advanced vessel analysis software k = 0.863). Using advanced vessel analysis software resulted in a significant time saving (p < 0.0001) for both readers. Time to diagnosis could be decreased by approximately 55%. Conclusions: Advanced vessel analysis application CT Vascular of the new imaging software syngo.via (Siemens Healthcare, Forchheim, Germany) provides a high rate of reproducibility in assessment of carotid artery stenosis. Furthermore a significant time saving in comparison to standard image interpretation is achievable

  3. Carotid artery stenosis: Performance of advanced vessel analysis software in evaluating CTA

    Energy Technology Data Exchange (ETDEWEB)

    Tsiflikas, Ilias, E-mail: ilias.tsiflikas@med.uni-tuebingen.de [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Biermann, Christina, E-mail: christina.biermann@siemens.com [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Siemens AG, Siemens Healthcare Consulting, Allee am Röthelheimpark 3A, 91052 Erlangen (Germany); Thomas, Christoph, E-mail: christoph.thomas@med.uni-tuebingen.de [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Ketelsen, Dominik, E-mail: dominik.ketelsen@med.uni-tuebingen.de [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Claussen, Claus D., E-mail: claus.claussen@med.uni-tuebingen.de [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany); Heuschmid, Martin, E-mail: martin.heuschmid@med.uni-tuebingen.de [University Hospital of Tuebingen, Diagnostic and Interventional Radiology, Hoppe-Seyler-Str. 3, 72076 Tuebingen (Germany)

    2012-09-15

    Objectives: The aim of this study was to evaluate time efficiency and diagnostic reproducibility of an advanced vessel analysis software for diagnosis of carotid artery stenosis. Material and methods: 40 patients with suspected carotid artery stenosis received head and neck DE-CTA as part of their pre-interventional workup. Acquired data were evaluated by 2 independent radiologists. Stenosis grading was performed by MPR eyeballing with freely adjustable MPRs and with a preliminary prototype of the meanwhile available client-server and advanced visualization software syngo.via CT Vascular (Siemens Healthcare, Erlangen, Germany). Stenoses were graded according to the following 5 categories: I: 0%, II: 1–50%, III: 51–69%, IV: 70–99% and V: total occlusion. Furthermore, time to diagnosis for each carotid artery was recorded. Results: Both readers achieved very good specificity values and good respectively very good sensitivity values without significant differences between both reading methods. Furthermore, there was a very good correlation between both readers for both reading methods without significant differences (kappa value: standard image interpretation k = 0.809; advanced vessel analysis software k = 0.863). Using advanced vessel analysis software resulted in a significant time saving (p < 0.0001) for both readers. Time to diagnosis could be decreased by approximately 55%. Conclusions: Advanced vessel analysis application CT Vascular of the new imaging software syngo.via (Siemens Healthcare, Forchheim, Germany) provides a high rate of reproducibility in assessment of carotid artery stenosis. Furthermore a significant time saving in comparison to standard image interpretation is achievable.

  4. Reliability evaluation of I-123 ADAM SPECT imaging using SPM software and AAL ROI methods

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Bang-Hung [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Tsai, Sung-Yi [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Imaging Medical, St.Martin De Porres Hospital, Chia-Yi, Taiwan (China); Wang, Shyh-Jen [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China); Department of Nuclear Medicine, Taipei Veterans General Hospital, Taiwan (China); Su, Tung-Ping; Chou, Yuan-Hwa [Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan (China); Chen, Chia-Chieh [Institute of Nuclear Energy Research, Longtan, Taiwan (China); Chen, Jyh-Cheng, E-mail: jcchen@ym.edu.tw [Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taipei, Taiwan (China)

    2011-08-21

    The level of serotonin was regulated by serotonin transporter (SERT), which is a decisive protein in regulation of serotonin neurotransmission system. Many psychiatric disorders and therapies were also related to concentration of cerebral serotonin. I-123 ADAM was the novel radiopharmaceutical to image SERT in brain. The aim of this study was to measure reliability of SERT densities of healthy volunteers by automated anatomical labeling (AAL) method. Furthermore, we also used statistic parametric mapping (SPM) on a voxel by voxel analysis to find difference of cortex between test and retest of I-123 ADAM single photon emission computed tomography (SPECT) images. Twenty-one healthy volunteers were scanned twice with SPECT at 4 h after intravenous administration of 185 MBq of {sup 123}I-ADAM. The image matrix size was 128x128 and pixel size was 3.9 mm. All images were obtained through filtered back-projection (FBP) reconstruction algorithm. Region of interest (ROI) definition was performed based on the AAL brain template in PMOD version 2.95 software package. ROI demarcations were placed on midbrain, pons, striatum, and cerebellum. All images were spatially normalized to the SPECT MNI (Montreal Neurological Institute) templates supplied with SPM2. And each image was transformed into standard stereotactic space, which was matched to the Talairach and Tournoux atlas. Then differences across scans were statistically estimated on a voxel by voxel analysis using paired t-test (population main effect: 2 cond's, 1 scan/cond.), which was applied to compare concentration of SERT between the test and retest cerebral scans. The average of specific uptake ratio (SUR: target/cerebellum-1) of {sup 123}I-ADAM binding to SERT in midbrain was 1.78{+-}0.27, pons was 1.21{+-}0.53, and striatum was 0.79{+-}0.13. The cronbach's {alpha} of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2

  5. Decision Engines for Software Analysis Using Satisfiability Modulo Theories Solvers

    Science.gov (United States)

    Bjorner, Nikolaj

    2010-01-01

    The area of software analysis, testing and verification is now undergoing a revolution thanks to the use of automated and scalable support for logical methods. A well-recognized premise is that at the core of software analysis engines is invariably a component using logical formulas for describing states and transformations between system states. The process of using this information for discovering and checking program properties (including such important properties as safety and security) amounts to automatic theorem proving. In particular, theorem provers that directly support common software constructs offer a compelling basis. Such provers are commonly called satisfiability modulo theories (SMT) solvers. Z3 is a state-of-the-art SMT solver. It is developed at Microsoft Research. It can be used to check the satisfiability of logical formulas over one or more theories such as arithmetic, bit-vectors, lists, records and arrays. The talk describes some of the technology behind modern SMT solvers, including the solver Z3. Z3 is currently mainly targeted at solving problems that arise in software analysis and verification. It has been applied to various contexts, such as systems for dynamic symbolic simulation (Pex, SAGE, Vigilante), for program verification and extended static checking (Spec#/Boggie, VCC, HAVOC), for software model checking (Yogi, SLAM), model-based design (FORMULA), security protocol code (F7), program run-time analysis and invariant generation (VS3). We will describe how it integrates support for a variety of theories that arise naturally in the context of the applications. There are several new promising avenues and the talk will touch on some of these and the challenges related to SMT solvers. Proceedings

  6. Software Toolbox for Low-Frequency Conductivity and Current Density Imaging Using MRI.

    Science.gov (United States)

    Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-11-01

    Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes. Low-frequency conductivity and current density imaging using MRI includes

  7. Image fusion using MIM software via picture archiving and communication system

    International Nuclear Information System (INIS)

    Gu Zhaoxiang; Jiang Maosong

    2001-01-01

    The preliminary studies of the multimodality image registration and fusion were performed using an image fusion software and a picture archiving and communication system (PACS) to explore the methodology. Original image voluminal data were acquired with a CT scanner, MR and dual-head coincidence SPECT, respectively. The data sets from all imaging devices were queried, retrieved, transferred and accessed via DICOM PACS. The image fusion was performed at the SPECT ICON work-station, where the MIM (Medical Image Merge) fusion software was installed. The images were created by re-slicing original volume on the fly. The image volumes were aligned by translation and rotation of these view ports with respect to the original volume orientation. The transparency factor and contrast were adjusted in order that both volumes can be visualized in the merged images. The image volume data of CT, MR and nuclear medicine were transferred, accessed and loaded via PACS successfully. The perfect fused images of chest CT/ 18 F-FDG and brain MR/SPECT were obtained. These results showed that image fusion technique using PACS was feasible and practical. Further experimentation and larger validation studies were needed to explore the full potential of the clinical use

  8. Advantages and Disadvantages in Image Processing with Free Software in Radiology.

    Science.gov (United States)

    Mujika, Katrin Muradas; Méndez, Juan Antonio Juanes; de Miguel, Andrés Framiñan

    2018-01-15

    Currently, there are sophisticated applications that make it possible to visualize medical images and even to manipulate them. These software applications are of great interest, both from a teaching and a radiological perspective. In addition, some of these applications are known as Free Open Source Software because they are free and the source code is freely available, and therefore it can be easily obtained even on personal computers. Two examples of free open source software are Osirix Lite® and 3D Slicer®. However, this last group of free applications have limitations in its use. For the radiological field, manipulating and post-processing images is increasingly important. Consequently, sophisticated computing tools that combine software and hardware to process medical images are needed. In radiology, graphic workstations allow their users to process, review, analyse, communicate and exchange multidimensional digital images acquired with different image-capturing radiological devices. These radiological devices are basically CT (Computerised Tomography), MRI (Magnetic Resonance Imaging), PET (Positron Emission Tomography), etc. Nevertheless, the programs included in these workstations have a high cost which always depends on the software provider and is always subject to its norms and requirements. With this study, we aim to present the advantages and disadvantages of these radiological image visualization systems in the advanced management of radiological studies. We will compare the features of the VITREA2® and AW VolumeShare 5® radiology workstation with free open source software applications like OsiriX® and 3D Slicer®, with examples from specific studies.

  9. Knickpoint finder: A software tool that improves neotectonic analysis

    Science.gov (United States)

    Queiroz, G. L.; Salamuni, E.; Nascimento, E. R.

    2015-03-01

    This work presents a new software tool for morphometric analysis of drainage networks based on the methods of Hack (1973) and Etchebehere et al. (2004). This tool is applicable to studies of morphotectonics and neotectonics. The software used a digital elevation model (DEM) to identify the relief breakpoints along drainage profiles (knickpoints). The program was coded in Python for use on the ArcGIS platform and is called Knickpoint Finder. A study area was selected to test and evaluate the software's ability to analyze and identify neotectonic morphostructures based on the morphology of the terrain. For an assessment of its validity, we chose an area of the James River basin, which covers most of the Piedmont area of Virginia (USA), which is an area of constant intraplate seismicity and non-orogenic active tectonics and exhibits a relatively homogeneous geodesic surface currently being altered by the seismogenic features of the region. After using the tool in the chosen area, we found that the knickpoint locations are associated with the geologic structures, epicenters of recent earthquakes, and drainages with rectilinear anomalies. The regional analysis demanded the use of a spatial representation of the data after processing using Knickpoint Finder. The results were satisfactory in terms of the correlation of dense areas of knickpoints with active lineaments and the rapidity of the identification of deformed areas. Therefore, this software tool may be considered useful in neotectonic analyses of large areas and may be applied to any area where there is DEM coverage.

  10. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    Directory of Open Access Journals (Sweden)

    Yu-Hua Dean Fang

    2014-01-01

    Full Text Available Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC. Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.. Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita.

  11. Objective analysis of image quality of video image capture systems

    Science.gov (United States)

    Rowberg, Alan H.

    1990-07-01

    As Picture Archiving and Communication System (PACS) technology has matured, video image capture has become a common way of capturing digital images from many modalities. While digital interfaces, such as those which use the ACR/NEMA standard, will become more common in the future, and are preferred because of the accuracy of image transfer, video image capture will be the dominant method in the short term, and may continue to be used for some time because of the low cost and high speed often associated with such devices. Currently, virtually all installed systems use methods of digitizing the video signal that is produced for display on the scanner viewing console itself. A series of digital test images have been developed for display on either a GE CT9800 or a GE Signa MRI scanner. These images have been captured with each of five commercially available image capture systems, and the resultant images digitally transferred on floppy disk to a PC1286 computer containing Optimast' image analysis software. Here the images can be displayed in a comparative manner for visual evaluation, in addition to being analyzed statistically. Each of the images have been designed to support certain tests, including noise, accuracy, linearity, gray scale range, stability, slew rate, and pixel alignment. These image capture systems vary widely in these characteristics, in addition to the presence or absence of other artifacts, such as shading and moire pattern. Other accessories such as video distribution amplifiers and noise filters can also add or modify artifacts seen in the captured images, often giving unusual results. Each image is described, together with the tests which were performed using them. One image contains alternating black and white lines, each one pixel wide, after equilibration strips ten pixels wide. While some systems have a slew rate fast enough to track this correctly, others blur it to an average shade of gray, and do not resolve the lines, or give

  12. Software-assisted small bowel motility analysis using free-breathing MRI: feasibility study.

    Science.gov (United States)

    Bickelhaupt, Sebastian; Froehlich, Johannes M; Cattin, Roger; Raible, Stephan; Bouquet, Hanspeter; Bill, Urs; Patak, Michael A

    2014-01-01

    To validate a software prototype allowing for small bowel motility analysis in free breathing by comparing it to manual measurements. In all, 25 patients (15 male, 10 female; mean age 39 years) were included in this Institutional Review Board-approved, retrospective study. Magnetic resonance imaging (MRI) was performed on a 1.5T system after standardized preparation acquiring motility sequences in free breathing over 69-84 seconds. Small bowel motility was analyzed manually and with the software. Functional parameters, measurement time, and reproducibility were compared using the coefficient of variance and paired Student's t-test. Correlation was analyzed using Pearson's correlation coefficient and linear regression. The 25 segments were analyzed twice both by hand and using the software with automatic breathing correction. All assessed parameters significantly correlated between the methods (P software (3.90%, standard deviation [SD] ± 5.69) than manual examinations (9.77%, SD ± 11.08). The time needed was significantly less (P software (4.52 minutes, SD ± 1.58) compared to manual measurement, lasting 17.48 minutes for manual (SD ± 1.75 minutes). The use of the software proves reliable and faster small bowel motility measurements in free-breathing MRI compared to manual analyses. The new technique allows for analyses of prolonged sequences acquired in free breathing, improving the informative value of the examinations by amplifying the evaluable data. Copyright © 2013 Wiley Periodicals, Inc.

  13. Predictive images of postoperative levator resection outcome using image processing software

    OpenAIRE

    Mawatari, Yuki; Fukushima, Mikiko

    2016-01-01

    Yuki Mawatari,1 Mikiko Fukushima2 1Igo Ophthalmic Clinic, Kagoshima, 2Department of Ophthalmology, Faculty of Life Science, Kumamoto University, Chuo-ku, Kumamoto, Japan Purpose: This study aims to evaluate the efficacy of processed images to predict postoperative appearance following levator resection.Methods: Analysis involved 109 eyes from 65 patients with blepharoptosis who underwent advancement of levator aponeurosis and Müller’s muscle complex (levator resection). P...

  14. STARS software tool for analysis of reliability and safety

    International Nuclear Information System (INIS)

    Poucet, A.; Guagnini, E.

    1989-01-01

    This paper reports on the STARS (Software Tool for the Analysis of Reliability and Safety) project aims at developing an integrated set of Computer Aided Reliability Analysis tools for the various tasks involved in systems safety and reliability analysis including hazard identification, qualitative analysis, logic model construction and evaluation. The expert system technology offers the most promising perspective for developing a Computer Aided Reliability Analysis tool. Combined with graphics and analysis capabilities, it can provide a natural engineering oriented environment for computer assisted reliability and safety modelling and analysis. For hazard identification and fault tree construction, a frame/rule based expert system is used, in which the deductive (goal driven) reasoning and the heuristic, applied during manual fault tree construction, is modelled. Expert system can explain their reasoning so that the analyst can become aware of the why and the how results are being obtained. Hence, the learning aspect involved in manual reliability and safety analysis can be maintained and improved

  15. Medical image registration for analysis

    International Nuclear Information System (INIS)

    Petrovic, V.

    2006-01-01

    Full text: Image registration techniques represent a rich family of image processing and analysis tools that aim to provide spatial correspondences across sets of medical images of similar and disparate anatomies and modalities. Image registration is a fundamental and usually the first step in medical image analysis and this paper presents a number of advanced techniques as well as demonstrates some of the advanced medical image analysis techniques they make possible. A number of both rigid and non-rigid medical image alignment algorithms of equivalent and merely consistent anatomical structures respectively are presented. The algorithms are compared in terms of their practical aims, inputs, computational complexity and level of operator (e.g. diagnostician) interaction. In particular, the focus of the methods discussion is placed on the applications and practical benefits of medical image registration. Results of medical image registration on a number of different imaging modalities and anatomies are presented demonstrating the accuracy and robustness of their application. Medical image registration is quickly becoming ubiquitous in medical imaging departments with the results of such algorithms increasingly used in complex medical image analysis and diagnostics. This paper aims to demonstrate at least part of the reason why

  16. Design and Applications of Rapid Image Tile Producing Software Based on Mosaic Dataset

    Science.gov (United States)

    Zha, Z.; Huang, W.; Wang, C.; Tang, D.; Zhu, L.

    2018-04-01

    Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

  17. DESIGN AND APPLICATIONS OF RAPID IMAGE TILE PRODUCING SOFTWARE BASED ON MOSAIC DATASET

    Directory of Open Access Journals (Sweden)

    Z. Zha

    2018-04-01

    Full Text Available Map tile technology is widely used in web geographic information services. How to efficiently produce map tiles is key technology for rapid service of images on web. In this paper, a rapid producing software for image tile data based on mosaic dataset is designed, meanwhile, the flow of tile producing is given. Key technologies such as cluster processing, map representation, tile checking, tile conversion and compression in memory are discussed. Accomplished by software development and tested by actual image data, the results show that this software has a high degree of automation, would be able to effectively reducing the number of IO and improve the tile producing efficiency. Moreover, the manual operations would be reduced significantly.

  18. STAMPS: development and verification of swallowing kinematic analysis software.

    Science.gov (United States)

    Lee, Woo Hyung; Chun, Changmook; Seo, Han Gil; Lee, Seung Hak; Oh, Byung-Mo

    2017-10-17

    Swallowing impairment is a common complication in various geriatric and neurodegenerative diseases. Swallowing kinematic analysis is essential to quantitatively evaluate the swallowing motion of the oropharyngeal structures. This study aims to develop a novel swallowing kinematic analysis software, called spatio-temporal analyzer for motion and physiologic study (STAMPS), and verify its validity and reliability. STAMPS was developed in MATLAB, which is one of the most popular platforms for biomedical analysis. This software was constructed to acquire, process, and analyze the data of swallowing motion. The target of swallowing structures includes bony structures (hyoid bone, mandible, maxilla, and cervical vertebral bodies), cartilages (epiglottis and arytenoid), soft tissues (larynx and upper esophageal sphincter), and food bolus. Numerous functions are available for the spatiotemporal parameters of the swallowing structures. Testing for validity and reliability was performed in 10 dysphagia patients with diverse etiologies and using the instrumental swallowing model which was designed to mimic the motion of the hyoid bone and the epiglottis. The intra- and inter-rater reliability tests showed excellent agreement for displacement and moderate to excellent agreement for velocity. The Pearson correlation coefficients between the measured and instrumental reference values were nearly 1.00 (P software is expected to be useful for researchers who are interested in the swallowing motion analysis.

  19. MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

    Science.gov (United States)

    Bokhart, Mark T.; Nazari, Milad; Garrard, Kenneth P.; Muddiman, David C.

    2018-01-01

    A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. [Figure not available: see fulltext.

  20. Software Method for Computed Tomography Cylinder Data Unwrapping, Re-slicing, and Analysis

    Science.gov (United States)

    Roth, Don J.

    2013-01-01

    A software method has been developed that is applicable for analyzing cylindrical and partially cylindrical objects inspected using computed tomography (CT). This method involves unwrapping and re-slicing data so that the CT data from the cylindrical object can be viewed as a series of 2D sheets (or flattened onion skins ) in addition to a series of top view slices and 3D volume rendering. The advantages of viewing the data in this fashion are as follows: (1) the use of standard and specialized image processing and analysis methods is facilitated having 2D array data versus a volume rendering; (2) accurate lateral dimensional analysis of flaws is possible in the unwrapped sheets versus volume rendering; (3) flaws in the part jump out at the inspector with the proper contrast expansion settings in the unwrapped sheets; and (4) it is much easier for the inspector to locate flaws in the unwrapped sheets versus top view slices for very thin cylinders. The method is fully automated and requires no input from the user except proper voxel dimension from the CT experiment and wall thickness of the part. The software is available in 32-bit and 64-bit versions, and can be used with binary data (8- and 16-bit) and BMP type CT image sets. The software has memory (RAM) and hard-drive based modes. The advantage of the (64-bit) RAM-based mode is speed (and is very practical for users of 64-bit Windows operating systems and computers having 16 GB or more RAM). The advantage of the hard-drive based analysis is one can work with essentially unlimited-sized data sets. Separate windows are spawned for the unwrapped/re-sliced data view and any image processing interactive capability. Individual unwrapped images and un -wrapped image series can be saved in common image formats. More information is available at http://www.grc.nasa.gov/WWW/OptInstr/ NDE_CT_CylinderUnwrapper.html.

  1. Research and development of the software for visualizing nuclear reactor and neutronics analysis

    International Nuclear Information System (INIS)

    Okui, Shota; Sekimoto, Hiroshi

    2009-01-01

    It is not easy to image three-dimensional construct of a nuclear reactor with only its two-dimensional figure because it contains a number of structures and its construction is very complicated. Several visualization softwares for the nuclear reactor or some other plant exist, but require high skills and their operation is not simple. In this study, we developed nuclear reactor visualization software, called 'Visual Reactor (VR)', which does not require specific skills. We added the neutronics analysis code to that software. This code executes cell calculation, neutron diffusion calculation and nuclide burnup calculation by itself without any other codes. We tried to treat simple physics model in order to perform these calculation in a short time. Neutronics characteristics, such as neutron flux and power density distribution, are visualized on structure of nuclear reactor. Target operating system is Microsoft Windows XP or Vista. VR is utilized to figure out the structure of nuclear reactor and whole picture of neutronics characteristics. (author)

  2. Effectiveness of an Automatic Tracking Software in Underwater Motion Analysis

    Directory of Open Access Journals (Sweden)

    Fabrício A. Magalhaes

    2013-12-01

    Full Text Available Tracking of markers placed on anatomical landmarks is a common practice in sports science to perform the kinematic analysis that interests both athletes and coaches. Although different software programs have been developed to automatically track markers and/or features, none of them was specifically designed to analyze underwater motion. Hence, this study aimed to evaluate the effectiveness of a software developed for automatic tracking of underwater movements (DVP, based on the Kanade-Lucas-Tomasi feature tracker. Twenty-one video recordings of different aquatic exercises (n = 2940 markers’ positions were manually tracked to determine the markers’ center coordinates. Then, the videos were automatically tracked using DVP and a commercially available software (COM. Since tracking techniques may produce false targets, an operator was instructed to stop the automatic procedure and to correct the position of the cursor when the distance between the calculated marker’s coordinate and the reference one was higher than 4 pixels. The proportion of manual interventions required by the software was used as a measure of the degree of automation. Overall, manual interventions were 10.4% lower for DVP (7.4% than for COM (17.8%. Moreover, when examining the different exercise modes separately, the percentage of manual interventions was 5.6% to 29.3% lower for DVP than for COM. Similar results were observed when analyzing the type of marker rather than the type of exercise, with 9.9% less manual interventions for DVP than for COM. In conclusion, based on these results, the developed automatic tracking software presented can be used as a valid and useful tool for underwater motion analysis.

  3. Model Based Analysis and Test Generation for Flight Software

    Science.gov (United States)

    Pasareanu, Corina S.; Schumann, Johann M.; Mehlitz, Peter C.; Lowry, Mike R.; Karsai, Gabor; Nine, Harmon; Neema, Sandeep

    2009-01-01

    We describe a framework for model-based analysis and test case generation in the context of a heterogeneous model-based development paradigm that uses and combines Math- Works and UML 2.0 models and the associated code generation tools. This paradigm poses novel challenges to analysis and test case generation that, to the best of our knowledge, have not been addressed before. The framework is based on a common intermediate representation for different modeling formalisms and leverages and extends model checking and symbolic execution tools for model analysis and test case generation, respectively. We discuss the application of our framework to software models for a NASA flight mission.

  4. Hardware and software constructs for a vibration analysis network

    International Nuclear Information System (INIS)

    Cook, S.A.; Crowe, R.D.; Toffer, H.

    1985-01-01

    Vibration level monitoring and analysis has been initiated at N Reactor, the dual purpose reactor operated at Hanford, Washington by UNC Nuclear Industries (UNC) for the Department of Energy (DOE). The machinery to be monitored was located in several buildings scattered over the plant site, necessitating an approach using satellite stations to collect, monitor and temporarily store data. The satellite stations are, in turn, linked to a centralized processing computer for further analysis. The advantages of a networked data analysis system are discussed in this paper along with the hardware and software required to implement such a system

  5. Calibration Analysis Software for the ATLAS Pixel Detector

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00372086; The ATLAS collaboration

    2016-01-01

    The calibration of the ATLAS Pixel detector at LHC fulfils two main purposes: to tune the front-end configuration parameters for establishing the best operational settings and to measure the tuning performance through a subset of scans. An analysis framework has been set up in order to take actions on the detector given the outcome of a calibration scan (e.g. to create a mask for disabling noisy pixels). The software framework to control all aspects of the Pixel detector scans and analyses is called Calibration Console. The introduction of a new layer, equipped with new Front End-I4 Chips, required an update the Console architecture. It now handles scans and scans analyses applied together to chips with different characteristics. An overview of the newly developed Calibration Analysis Software will be presented, together with some preliminary result.

  6. Using Statistical Analysis Software to Advance Nitro Plasticizer Wettability

    Energy Technology Data Exchange (ETDEWEB)

    Shear, Trevor Allan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-08-29

    Statistical analysis in science is an extremely powerful tool that is often underutilized. Additionally, it is frequently the case that data is misinterpreted or not used to its fullest extent. Utilizing the advanced software JMP®, many aspects of experimental design and data analysis can be evaluated and improved. This overview will detail the features of JMP® and how they were used to advance a project, resulting in time and cost savings, as well as the collection of scientifically sound data. The project analyzed in this report addresses the inability of a nitro plasticizer to coat a gold coated quartz crystal sensor used in a quartz crystal microbalance. Through the use of the JMP® software, the wettability of the nitro plasticizer was increased by over 200% using an atmospheric plasma pen, ensuring good sample preparation and reliable results.

  7. Spectrum analysis on quality requirements consideration in software design documents.

    Science.gov (United States)

    Kaiya, Haruhiko; Umemura, Masahiro; Ogata, Shinpei; Kaijiri, Kenji

    2013-12-01

    Software quality requirements defined in the requirements analysis stage should be implemented in the final products, such as source codes and system deployment. To guarantee this meta-requirement, quality requirements should be considered in the intermediate stages, such as the design stage or the architectural definition stage. We propose a novel method for checking whether quality requirements are considered in the design stage. In this method, a technique called "spectrum analysis for quality requirements" is applied not only to requirements specifications but also to design documents. The technique enables us to derive the spectrum of a document, and quality requirements considerations in the document are numerically represented in the spectrum. We can thus objectively identify whether the considerations of quality requirements in a requirements document are adapted to its design document. To validate the method, we applied it to commercial software systems with the help of a supporting tool, and we confirmed that the method worked well.

  8. Software for a measuring facility for activation analysis

    International Nuclear Information System (INIS)

    De Keyser, A.; De Roost, E.

    1985-01-01

    A software package has been developed for an APPLE P.C. The programs are intended to control an automated measuring station for photon activation analysis at GELINA, the linear accelerator of C.B.N.M. at Geel (Belgium). They allow to set-up a measuring scheme, to execute it under computer control, to accumulate and store 2 K-spectra using a built-in ADC and to output the results as listings, plots or evaluated reports

  9. Phenomenology and Qualitative Data Analysis Software (QDAS): A Careful Reconciliation

    OpenAIRE

    Brian Kelleher Sohn

    2017-01-01

    An oft-cited phenomenological methodologist, Max VAN MANEN (2014), claims that qualitative data analysis software (QDAS) is not an appropriate tool for phenomenological research. Yet phenomenologists rarely describe how phenomenology is to be done: pencil, paper, computer? DAVIDSON and DI GREGORIO (2011) urge QDAS contrarians such as VAN MANEN to get over their methodological loyalties and join the digital world, claiming that all qualitative researchers, whatever their methodology, perform p...

  10. Nuclear analysis software. Pt. 1: Spectrum transfer and reformatting (SPEDAC)

    International Nuclear Information System (INIS)

    1991-01-01

    GANAAS (Gamma, Activity, and Neutron Activation Analysis System) is one in the family of software packages developed under the auspices of the International Atomic Energy Agency. Primarily, the package was intended to support the IAEA Technical Assistance and Cooperation projects in developing countries. However, it is open domain software that can be copied and used by anybody, except for commercial purposes. All the nuclear analysis software provided by the IAEA has the same design philosophy and similar structure. The intention was to provide the user with maximum flexibility, at the same time with a simple and logical organization that requires minimum digging through the manuals. GANAAS is a modular system. It consists of several programmes that can be installed on the hard disk as the are needed. Obviously, some parts of they system are required in all cases. Those are installed at the beginning, without consulting the operator. GANAAS offers the opportunity to expand and improve the system. The gamma spectrum evaluation programmes using different fitting algorithms can be added to GANAAS, under the condition that the format of their input and output files corresponds to the rules of GANAAS. The same applies to the quantitative analysis parts of the programme

  11. Effect of software manipulation (Photoshop) of digitised retinal images on the grading of diabetic retinopathy.

    Science.gov (United States)

    George, L D; Lusty, J; Owens, D R; Ollerton, R L

    1999-08-01

    To determine whether software processing of digitised retinal images using a "sharpen" filter improves the ability to grade diabetic retinopathy. 150 macula centred retinal images were taken as 35 mm colour transparencies representing a spectrum of diabetic retinopathy, digitised, and graded in random order before and after the application of a sharpen filter (Adobe Photoshop). Digital enhancement of contrast and brightness was performed and a X2 digital zoom was utilised. The grades from the unenhanced and enhanced digitised images were compared with the same retinal fields viewed as slides. Overall agreement in retinopathy grade from the digitised images improved from 83.3% (125/150) to 94.0% (141/150) with sight threatening diabetic retinopathy (STDR) correctly identified in 95.5% (84/88) and 98.9% (87/88) of cases when using unenhanced and enhanced images respectively. In total, five images were overgraded and four undergraded from the enhanced images compared with 17 and eight images respectively when using unenhanced images. This study demonstrates that the already good agreement in grading performance can be further improved by software manipulation or processing of digitised retinal images.

  12. Freud: a software suite for high-throughput simulation analysis

    Science.gov (United States)

    Harper, Eric; Spellings, Matthew; Anderson, Joshua; Glotzer, Sharon

    Computer simulation is an indispensable tool for the study of a wide variety of systems. As simulations scale to fill petascale and exascale supercomputing clusters, so too does the size of the data produced, as well as the difficulty in analyzing these data. We present Freud, an analysis software suite for efficient analysis of simulation data. Freud makes no assumptions about the system being analyzed, allowing for general analysis methods to be applied to nearly any type of simulation. Freud includes standard analysis methods such as the radial distribution function, as well as new methods including the potential of mean force and torque and local crystal environment analysis. Freud combines a Python interface with fast, parallel C + + analysis routines to run efficiently on laptops, workstations, and supercomputing clusters. Data analysis on clusters reduces data transfer requirements, a prohibitive cost for petascale computing. Used in conjunction with simulation software, Freud allows for smart simulations that adapt to the current state of the system, enabling the study of phenomena such as nucleation and growth, intelligent investigation of phases and phase transitions, and determination of effective pair potentials.

  13. MCID: A Software Tool to Provide Monte Carlo Driven Dosimetric Calculations Using Multimodality NM Images

    International Nuclear Information System (INIS)

    Vergara Gil, Alex; Torres Aroche, Leonel A; Coca Péreza, Marco A; Pacilio, Massimiliano; Botta, Francesca; Cremonesi, Marta

    2016-01-01

    Aim: In this work, a new software tool (named MCID) to calculate patient specific absorbed dose in molecular radiotherapy, based on Monte Carlo simulation, is presented. Materials & Methods: The inputs for MCID are two co-registered medical images containing anatomical (CT) and functional (PET or SPECT) information of the patient. The anatomical image is converted to a density map, and tissues segmentation is provided considering compositions and densities from ICRU 44 and ICRP; the functional image provides the cumulative activity map at voxel level (figure 1). MCID creates an input file for Monte Carlo (MC) codes such as MCNP5 and GATE, and converts the MC outputs into an absorbed dose image. Results: The developed tool allows estimating dose distributions for non-uniform activities distributions and non-homogeneous tissues. It includes tools for delineation of volumes of interest, and dosimetric data analysis. Procedures to decrease the calculation time are implemented in order to allow its use in clinical settings. Dose–volume histograms are computed and presented from the obtained dosimetric maps as well as dose statistics such as mean, minimum and maximum dose values; the results can be saved in common medical image formats (Interfile, DICOM, Analyze, MetaImage). The MCID was validated by comparing estimated dose values versus reference data, such as gold standards phantoms (OLINDA´s spheres) and other MC simulations of non-homogeneous phantoms. A good agreement was obtained in spheres ranged 1g to 1kg of mass and in non-homogeneous phantoms. Clinical studies were also examined. Dosimetric evaluations in patients undergoing 153Sm-EDTMP therapy for osseous metastases showed non-significant differences with calculations performed by traditional methods. The possibility of creating input files to perform the simulations using the Gate Code has increased the MCID applications and improved its functionality, Different clinical situations including PET and SPECT

  14. MR image analysis: Longitudinal cardiac motion influences left ventricular measurements

    International Nuclear Information System (INIS)

    Berkovic, Patrick; Hemmink, Maarten; Parizel, Paul M.; Vrints, Christiaan J.; Paelinck, Bernard P.

    2010-01-01

    Background: Software for the analysis of left ventricular (LV) volumes and mass using border detection in short-axis images only, is hampered by through-plane cardiac motion. Therefore we aimed to evaluate software that involves longitudinal cardiac motion. Methods: Twenty-three consecutive patients underwent 1.5-Tesla cine magnetic resonance (MR) imaging of the entire heart in the long-axis and short-axis orientation with breath-hold steady-state free precession imaging. Offline analysis was performed using software that uses short-axis images (Medis MASS) and software that includes two-chamber and four-chamber images to involve longitudinal LV expansion and shortening (CAAS-MRV). Intraobserver and interobserver reproducibility was assessed by using Bland-Altman analysis. Results: Compared with MASS software, CAAS-MRV resulted in significantly smaller end-diastolic (156 ± 48 ml versus 167 ± 52 ml, p = 0.001) and end-systolic LV volumes (79 ± 48 ml versus 94 ± 52 ml, p < 0.001). In addition, CAAS-MRV resulted in higher LV ejection fraction (52 ± 14% versus 46 ± 13%, p < 0.001) and calculated LV mass (154 ± 52 g versus 142 ± 52 g, p = 0.004). Intraobserver and interobserver limits of agreement were similar for both methods. Conclusion: MR analysis of LV volumes and mass involving long-axis LV motion is a highly reproducible method, resulting in smaller LV volumes, higher ejection fraction and calculated LV mass.

  15. SU-F-I-43: A Software-Based Statistical Method to Compute Low Contrast Detectability in Computed Tomography Images

    Energy Technology Data Exchange (ETDEWEB)

    Chacko, M; Aldoohan, S [University of Oklahoma Health Sciences Center, Oklahoma City, OK (United States)

    2016-06-15

    Purpose: The low contrast detectability (LCD) of a CT scanner is its ability to detect and display faint lesions. The current approach to quantify LCD is achieved using vendor-specific methods and phantoms, typically by subjectively observing the smallest size object at a contrast level above phantom background. However, this approach does not yield clinically applicable values for LCD. The current study proposes a statistical LCD metric using software tools to not only to assess scanner performance, but also to quantify the key factors affecting LCD. This approach was developed using uniform QC phantoms, and its applicability was then extended under simulated clinical conditions. Methods: MATLAB software was developed to compute LCD using a uniform image of a QC phantom. For a given virtual object size, the software randomly samples the image within a selected area, and uses statistical analysis based on Student’s t-distribution to compute the LCD as the minimal Hounsfield Unit’s that can be distinguished from the background at the 95% confidence level. Its validity was assessed by comparison with the behavior of a known QC phantom under various scan protocols and a tissue-mimicking phantom. The contributions of beam quality and scattered radiation upon the computed LCD were quantified by using various external beam-hardening filters and phantom lengths. Results: As expected, the LCD was inversely related to object size under all scan conditions. The type of image reconstruction kernel filter and tissue/organ type strongly influenced the background noise characteristics and therefore, the computed LCD for the associated image. Conclusion: The proposed metric and its associated software tools are vendor-independent and can be used to analyze any LCD scanner performance. Furthermore, the method employed can be used in conjunction with the relationships established in this study between LCD and tissue type to extend these concepts to patients’ clinical CT

  16. EVALUATION OF PATCHY ATROPHY SECONDARY TO HIGH MYOPIA BY SEMIAUTOMATED SOFTWARE FOR FUNDUS AUTOFLUORESCENCE ANALYSIS.

    Science.gov (United States)

    Miere, Alexandra; Capuano, Vittorio; Serra, Rita; Jung, Camille; Souied, Eric; Querques, Giuseppe

    2017-05-31

    To evaluate the progression of patchy atrophy in high myopia using semiautomated software for fundus autofluorescence (FAF) analysis. The medical records and multimodal imaging of 21 consecutive highly myopic patients with macular chorioretinal patchy atrophy (PA) were retrospectively analyzed. All patients underwent repeated fundus autofluorescence and spectral domain optical coherence tomography over at least 12 months. Color fundus photography was also performed in a subset of patients. Total atrophy area was measured on FAF images using Region Finder semiautomated software embedded in Spectralis (Heidelberg Engineering, Heidelberg, Germany) at baseline and during follow-up visits. Region Finder was compared with manually measured PA on FAF images. Twenty-two eyes of 21 patients (14 women, 7 men; mean age 62.8 + 13.0 years, range 32-84 years) were included. Mean PA area using Region Finder was 2.77 ± 2.91 SD mm at baseline, 3.12 ± 2.68 mm at Month 6, 3.43 ± 2.68 mm at Month 12, and 3.73 ± 2.74 mm at Month 18 (overall P autofluorescence analysis by Region Finder semiautomated software provides accurate measurements of lesion area and allows us to quantify the progression of PA in high myopia. In our series, PA enlarged significantly over at least 12 months, and its progression seemed to be related to the lesion size at baseline.

  17. IMMAN: free software for information theory-based chemometric analysis.

    Science.gov (United States)

    Urias, Ricardo W Pino; Barigye, Stephen J; Marrero-Ponce, Yovani; García-Jacas, César R; Valdes-Martiní, José R; Perez-Gimenez, Facundo

    2015-05-01

    The features and theoretical background of a new and free computational program for chemometric analysis denominated IMMAN (acronym for Information theory-based CheMoMetrics ANalysis) are presented. This is multi-platform software developed in the Java programming language, designed with a remarkably user-friendly graphical interface for the computation of a collection of information-theoretic functions adapted for rank-based unsupervised and supervised feature selection tasks. A total of 20 feature selection parameters are presented, with the unsupervised and supervised frameworks represented by 10 approaches in each case. Several information-theoretic parameters traditionally used as molecular descriptors (MDs) are adapted for use as unsupervised rank-based feature selection methods. On the other hand, a generalization scheme for the previously defined differential Shannon's entropy is discussed, as well as the introduction of Jeffreys information measure for supervised feature selection. Moreover, well-known information-theoretic feature selection parameters, such as information gain, gain ratio, and symmetrical uncertainty are incorporated to the IMMAN software ( http://mobiosd-hub.com/imman-soft/ ), following an equal-interval discretization approach. IMMAN offers data pre-processing functionalities, such as missing values processing, dataset partitioning, and browsing. Moreover, single parameter or ensemble (multi-criteria) ranking options are provided. Consequently, this software is suitable for tasks like dimensionality reduction, feature ranking, as well as comparative diversity analysis of data matrices. Simple examples of applications performed with this program are presented. A comparative study between IMMAN and WEKA feature selection tools using the Arcene dataset was performed, demonstrating similar behavior. In addition, it is revealed that the use of IMMAN unsupervised feature selection methods improves the performance of both IMMAN and WEKA

  18. Analysis of signal acquisition in GPS receiver software

    Directory of Open Access Journals (Sweden)

    Vlada S. Sokolović

    2011-01-01

    Full Text Available This paper presents a critical analysis of the flow signal processing carried out in GPS receiver software, which served as a basis for a critical comparison of different signal processing architectures within the GPS receiver. It is possible to achieve Increased flexibility and reduction of GPS device commercial costs, including those of mobile devices, by using radio technology software (SDR, Software Defined Radio. The SDR application can be realized when certain hardware components in a GPS receiver are replaced. Signal processing in the SDR is implemented using a programmable DSP (Digital Signal Processing or FPGA (Field Programmable Gate Array circuit, which allows a simple change of digital signal processing algorithms and a simple change of the receiver parameters. The starting point of the research is the signal generated on the satellite the structure of which is shown in the paper. Based on the GPS signal structure, a receiver is realized with a task to extract an appropriate signal from the spectrum and detect it. Based on collected navigation data, the receiver calculates the position of the end user. The signal coming from the satellite may be at the carrier frequencies of L1 and L2. Since the SPS is used in the civil service, all the tests shown in the work were performed on the L1 signal. The signal coming to the receiver is generated in the spread spectrum technology and is situated below the level of noise. Such signals often interfere with signals from the environment which presents a difficulty for a receiver to perform proper detection and signal processing. Therefore, signal processing technology is continually being improved, aiming at more accurate and faster signal processing. All tests were carried out on a signal acquired from the satellite using the SE4110 input circuit used for filtering, amplification and signal selection. The samples of the received signal were forwarded to a computer for data post processing, i. e

  19. Development of HydroImage, A User Friendly Hydrogeophysical Characterization Software

    Energy Technology Data Exchange (ETDEWEB)

    Mok, Chin Man [GSI Environmental; Hubbard, Susan [Lawrence Berkeley National Laboratory; Chen, Jinsong [Lawrence Berkeley National Laboratory; Suribhatla, Raghu [AMEC E& I; Kaback, Dawn Samara [AMEC E& I

    2014-01-29

    HydroImage, user friendly software that utilizes high-resolution geophysical data for estimating hydrogeological parameters in subsurface strate, was developed under this grant. HydroImage runs on a personal computer platform to promote broad use by hydrogeologists to further understanding of subsurface processes that govern contaminant fate, transport, and remediation. The unique software provides estimates of hydrogeological properties over continuous volumes of the subsurface, whereas previous approaches only allow estimation of point locations. thus, this unique tool can be used to significantly enhance site conceptual models and improve design and operation of remediation systems. The HydroImage technical approach uses statistical models to integrate geophysical data with borehole geological data and hydrological measurements to produce hydrogeological parameter estimates as 2-D or 3-D images.

  20. MMX-I: data-processing software for multimodal X-ray imaging and tomography.

    Science.gov (United States)

    Bergamaschi, Antoine; Medjoubi, Kadda; Messaoudi, Cédric; Marco, Sergio; Somogyi, Andrea

    2016-05-01

    A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors' knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.

  1. Quantitative analysis of receptor imaging

    International Nuclear Information System (INIS)

    Fu Zhanli; Wang Rongfu

    2004-01-01

    Model-based methods for quantitative analysis of receptor imaging, including kinetic, graphical and equilibrium methods, are introduced in detail. Some technical problem facing quantitative analysis of receptor imaging, such as the correction for in vivo metabolism of the tracer and the radioactivity contribution from blood volume within ROI, and the estimation of the nondisplaceable ligand concentration, is also reviewed briefly

  2. Introduction to Medical Image Analysis

    DEFF Research Database (Denmark)

    Paulsen, Rasmus Reinhold; Moeslund, Thomas B.

    of the book is to present the fascinating world of medical image analysis in an easy and interesting way. Compared to many standard books on image analysis, the approach we have chosen is less mathematical and more casual. Some of the key algorithms are exemplified in C-code. Please note that the code...

  3. An Ibm PC/AT-Based Image Acquisition And Processing System For Quantitative Image Analysis

    Science.gov (United States)

    Kim, Yongmin; Alexander, Thomas

    1986-06-01

    In recent years, a large number of applications have been developed for image processing systems in the area of biological imaging. We have already finished the development of a dedicated microcomputer-based image processing and analysis system for quantitative microscopy. The system's primary function has been to facilitate and ultimately automate quantitative image analysis tasks such as the measurement of cellular DNA contents. We have recognized from this development experience, and interaction with system users, biologists and technicians, that the increasingly widespread use of image processing systems, and the development and application of new techniques for utilizing the capabilities of such systems, would generate a need for some kind of inexpensive general purpose image acquisition and processing system specially tailored for the needs of the medical community. We are currently engaged in the development and testing of hardware and software for a fairly high-performance image processing computer system based on a popular personal computer. In this paper, we describe the design and development of this system. Biological image processing computer systems have now reached a level of hardware and software refinement where they could become convenient image analysis tools for biologists. The development of a general purpose image processing system for quantitative image analysis that is inexpensive, flexible, and easy-to-use represents a significant step towards making the microscopic digital image processing techniques more widely applicable not only in a research environment as a biologist's workstation, but also in clinical environments as a diagnostic tool.

  4. Open source software and crowdsourcing for energy analysis

    International Nuclear Information System (INIS)

    Bazilian, Morgan; Rice, Andrew; Rotich, Juliana; Howells, Mark; DeCarolis, Joseph; Macmillan, Stuart; Brooks, Cameron; Bauer, Florian; Liebreich, Michael

    2012-01-01

    Informed energy decision making requires effective software, high-quality input data, and a suitably trained user community. Developing these resources can be expensive and time consuming. Even when data and tools are intended for public re-use they often come with technical, legal, economic and social barriers that make them difficult to adopt, adapt and combine for use in new contexts. We focus on the promise of open, publically accessible software and data as well as crowdsourcing techniques to develop robust energy analysis tools that can deliver crucial, policy-relevant insight, particularly in developing countries, where planning resources are highly constrained—and the need to adapt these resources and methods to the local context is high. We survey existing research, which argues that these techniques can produce high-quality results, and also explore the potential role that linked, open data can play in both supporting the modelling process and in enhancing public engagement with energy issues. - Highlights: ► We focus on the promise of open, publicly accessible software and data. ► These emerging techniques can produce high-quality results for energy analysis. ► Developing economies require new techniques for energy planning.

  5. Software engineering methods for the visualization in the modeling of radiation imaging system

    International Nuclear Information System (INIS)

    Tang Jie; Zhang Li; Chen Zhiqiang; Zhao Ziran; XiaoYongshun

    2003-01-01

    This thesis has accomplished the research in visualization in the modeling of radiation imaging system, and a visualize software was developed using OpenGL and Visual C++ tools. It can load any model files, which are made by the user for every component of the radiation image system, and easily manages the module dynamic link library (DLL) designed by the user for possible movements of those components

  6. X-ray image processing software for computing object size and object location coordinates from acquired optical and x-ray images

    International Nuclear Information System (INIS)

    Tiwari, Akash; Tiwari, Shyam Sunder; Tiwari, Railesha; Panday, Lokesh; Panday, Jeet; Suri, Nitin

    2004-01-01

    X-ray and Visible image data processing software has been developed in Visual Basic for real time online and offline image information processing for NDT and Medical Applications. Software computes two dimension image size parameters from its sharp boundary lines by raster scanning the image contrast data. Code accepts bit map image data and hunts for multiple tumors of different sizes that may be present in the image definition and then computes size of each tumor and locates its approximate center for registering its location coordinates. Presence of foreign metal and glass balls industrial product such as chocolate and other food items imaged out using x-ray imaging technique are detected by the software and their size and position co-ordinates are computed by the software. Paper discusses ways and means to compute size and coordinated of air bubble like objects present in the x-ray and optical images and their multiple existences in image of interest. (author)

  7. New analysis software for Viking Lander meteorological data

    Directory of Open Access Journals (Sweden)

    O. Kemppinen

    2013-02-01

    Full Text Available We have developed a set of tools that enable us to process Viking Lander meteorological data beyond what has been previously publicly available. Besides providing data for new periods of time, the existing data periods have been augmented by enhancing the data resolution significantly. This was accomplished by first transferring the original Prime computer version of the data analysis software to a standard Linux platform, and then by modifying the software to be able to process the data despite irregularities in the original raw data and reverse engineering various parameter files. In addition to this, the processing pipeline has been streamlined, making processing the data faster and easier. As a case example of new data, freshly processed Viking Lander 1 and 2 temperature records are described and briefly analyzed in ways that have not been previously possible due to the lack of data.

  8. OVERVIEW OF THE SAPHIRE PROBABILISTIC RISK ANALYSIS SOFTWARE

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Curtis L.; Wood, Ted; Knudsen, James; Ma, Zhegang

    2016-10-01

    The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) is a software application developed for performing a complete probabilistic risk assessment (PRA) using a personal computer (PC) running the Microsoft Windows operating system. SAPHIRE Version 8 is funded by the U.S. Nuclear Regulatory Commission (NRC) and developed by the Idaho National Laboratory (INL). INL's primary role in this project is that of software developer and tester. However, INL also plays an important role in technology transfer by interfacing and supporting SAPHIRE users, who constitute a wide range of PRA practitioners from the NRC, national laboratories, the private sector, and foreign countries. In this paper, we provide an overview of the current technical capabilities found in SAPHIRE Version 8, including the user interface and enhanced solving algorithms.

  9. Spatial resolution measurements by Radia diagnostic software with SEDENTEXCT image quality phantom in cone beam CT for dental use.

    Science.gov (United States)

    Watanabe, Hiroshi; Nomura, Yoshikazu; Kuribayashi, Ami; Kurabayashi, Tohru

    2018-02-01

    We aimed to employ the Radia diagnostic software with the safety and efficacy of a new emerging dental X-ray modality (SEDENTEXCT) image quality (IQ) phantom in CT, and to evaluate its validity. The SEDENTEXCT IQ phantom and Radia diagnostic software were employed. The phantom was scanned using one medical full-body CT and two dentomaxillofacial cone beam CTs. The obtained images were imported to the Radia software, and the spatial resolution outputs were evaluated. The oversampling method was employed using our original wire phantom as a reference. The resultant modulation transfer function (MTF) curves were compared. The null hypothesis was that MTF curves generated using both methods would be in agreement. One-way analysis of variance tests were applied to the f50 and f10 values from the MTF curves. The f10 values were subjectively confirmed by observing the line pair modules. The Radia software reported the MTF curves on the xy-plane of the CT scans, but could not return f50 and f10 values on the z-axis. The null hypothesis concerning the reported MTF curves on the xy-plane was rejected. There were significant differences between the results of the Radia software and our reference method, except for f10 values in CS9300. These findings were consistent with our line pair observations. We evaluated the validity of the Radia software with the SEDENTEXCT IQ phantom. The data provided were semi-automatic, albeit with problems and statistically different from our reference. We hope the manufacturer will overcome these limitations.

  10. Efficacy of an Intra-Operative Imaging Software System for Anatomic Anterior Cruciate Ligament Reconstruction Surgery

    Directory of Open Access Journals (Sweden)

    Xudong Zhang

    2012-01-01

    Full Text Available An imaging software system was studied for improving the performance of anatomic anterior cruciate ligament (ACL reconstruction which requires identifying ACL insertion sites for bone tunnel placement. This software predicts and displays the insertion sites based on the literature data and patient-specific bony landmarks. Twenty orthopaedic surgeons performed simulated arthroscopic ACL surgeries on 20 knee specimens, first without and then with the visual guidance by fluoroscopic imaging, and their tunnel entry positions were recorded. The native ACL insertion morphologies of individual specimens were quantified in relation to CT-based bone models and then used to evaluate the software-generated insertion locations. Results suggested that the system was effective in leading surgeons to predetermined locations while the application of averaged insertion morphological information in individual surgeries can be susceptible to inaccuracy and uncertainty. Implications on challenges associated with developing engineering solutions to aid in re-creating or recognizing anatomy in surgical care delivery are discussed.

  11. MMX-I: data-processing software for multimodal X-ray imaging and tomography

    Energy Technology Data Exchange (ETDEWEB)

    Bergamaschi, Antoine, E-mail: antoine.bergamaschi@synchrotron-soleil.fr; Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint-Aubin, 91192 Gif sur Yvette (France); Messaoudi, Cédric; Marco, Sergio [Université Paris-Saclay, CNRS, Université Paris-Saclay, F-91405 Orsay (France); Institut Curie, INSERM, PSL Reseach University, F-91405 Orsay (France); Somogyi, Andrea [Synchrotron SOLEIL, BP 48, Saint-Aubin, 91192 Gif sur Yvette (France)

    2016-04-12

    The MMX-I open-source software has been developed for processing and reconstruction of large multimodal X-ray imaging and tomography datasets. The recent version of MMX-I is optimized for scanning X-ray fluorescence, phase-, absorption- and dark-field contrast techniques. This, together with its implementation in Java, makes MMX-I a versatile and friendly user tool for X-ray imaging. A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors’ knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.

  12. 76 FR 60939 - Metal Fatigue Analysis Performed by Computer Software

    Science.gov (United States)

    2011-09-30

    ... Software AGENCY: Nuclear Regulatory Commission. ACTION: Regulatory issue summary; request for comment... computer software package, WESTEMS TM , to demonstrate compliance with Section III, ``Rules for... Software Addressees All holders of, and applicants for, a power reactor operating license or construction...

  13. A software architectural framework specification for neutron activation analysis

    International Nuclear Information System (INIS)

    Preston, J.A.; Grant, C.N.

    2013-01-01

    Neutron Activation Analysis (NAA) is a sensitive multi-element nuclear analytical technique that has been routinely applied by research reactor (RR) facilities to environmental, nutritional, health related, geological and geochemical studies. As RR facilities face calls to increase their research output and impact, with existing or reducing budgets, automation of NAA offers a possible solution. However, automation has many challenges, not the least of which is a lack of system architecture standards to establish acceptable mechanisms for the various hardware/software and software/software interactions among data acquisition systems, specialised hardware such as sample changers, sample loaders, and data processing modules. This lack of standardization often results in automation hardware and software being incompatible with existing system components, in a facility looking to automate its NAA operations. This limits the availability of automation to a few RR facilities with adequate budgets or in-house engineering resources. What is needed is a modern open system architecture for NAA, that provides the required set of functionalities. This paper describes such an 'architectural framework' (OpenNAA), and portions of a reference implementation. As an example of the benefits, calculations indicate that applying this architecture to the compilation and QA steps associated with the analysis of 35 elements in 140 samples, with 14 SRM's, can reduce the time required by over 80 %. The adoption of open standards in the nuclear industry has been very successful over the years in promoting interchangeability and maximising the lifetime and output of nuclear measurement systems. OpenNAA will provide similar benefits within the NAA application space, safeguarding user investments in their current system, while providing a solid path for development into the future. (author)

  14. Development of automatic navigation measuring system using template-matching software in image guided neurosurgery

    International Nuclear Information System (INIS)

    Watanabe, Yohei; Hayashi, Yuichiro; Fujii, Masazumi; Wakabayashi, Toshihiko; Kimura, Miyuki; Tsuzaka, Masatoshi; Sugiura, Akihiro

    2010-01-01

    An image-guided neurosurgery and neuronavigation system based on magnetic resonance imaging has been used as an indispensable tool for resection of brain tumors. Therefore, accuracy of the neuronavigation system, provided by periodic quality assurance (QA), is essential for image-guided neurosurgery. Two types of accuracy index, fiducial registration error (FRE) and target registration error (TRE), have been used to evaluate navigation accuracy. FRE shows navigation accuracy on points that have been registered. On the other hand, TRE shows navigation accuracy on points such as tumor, skin, and fiducial markers. This study shows that TRE is more reliable than FRE. However, calculation of TRE is a time-consuming, subjective task. Software for QA was developed to compute TRE. This software calculates TRE automatically by an image processing technique, such as automatic template matching. TRE was calculated by the software and compared with the results obtained by manual calculation. Using the software made it possible to achieve a reliable QA system. (author)

  15. Hyperspectral image analysis. A tutorial

    DEFF Research Database (Denmark)

    Amigo Rubio, Jose Manuel; Babamoradi, Hamid; Elcoroaristizabal Martin, Saioa

    2015-01-01

    This tutorial aims at providing guidelines and practical tools to assist with the analysis of hyperspectral images. Topics like hyperspectral image acquisition, image pre-processing, multivariate exploratory analysis, hyperspectral image resolution, classification and final digital image processi...... to differentiate between several types of plastics by using Near infrared hyperspectral imaging and Partial Least Squares - Discriminant Analysis. Thus, the reader is guided through every single step and oriented in order to adapt those strategies to the user's case....... will be exposed, and some guidelines given and discussed. Due to the broad character of current applications and the vast number of multivariate methods available, this paper has focused on an industrial chemical framework to explain, in a step-wise manner, how to develop a classification methodology...

  16. Hyperspectral image analysis. A tutorial

    International Nuclear Information System (INIS)

    Amigo, José Manuel; Babamoradi, Hamid; Elcoroaristizabal, Saioa

    2015-01-01

    This tutorial aims at providing guidelines and practical tools to assist with the analysis of hyperspectral images. Topics like hyperspectral image acquisition, image pre-processing, multivariate exploratory analysis, hyperspectral image resolution, classification and final digital image processing will be exposed, and some guidelines given and discussed. Due to the broad character of current applications and the vast number of multivariate methods available, this paper has focused on an industrial chemical framework to explain, in a step-wise manner, how to develop a classification methodology to differentiate between several types of plastics by using Near infrared hyperspectral imaging and Partial Least Squares – Discriminant Analysis. Thus, the reader is guided through every single step and oriented in order to adapt those strategies to the user's case. - Highlights: • Comprehensive tutorial of Hyperspectral Image analysis. • Hierarchical discrimination of six classes of plastics containing flame retardant. • Step by step guidelines to perform class-modeling on hyperspectral images. • Fusion of multivariate data analysis and digital image processing methods. • Promising methodology for real-time detection of plastics containing flame retardant.

  17. Software for tomographic analysis: application in ceramic filters

    International Nuclear Information System (INIS)

    Figuerola, W.B.; Assis, J.T.; Oliveira, L.F.; Lopes, R.T.

    2001-01-01

    New methods for acquiring data have been developed with the technological advances. With this, it has been possible to obtain more precise data and, consequently produce results with greater reliability. Among the variety of acquisition methods available, those that have volume description, as CT (Computerized Tomography) and NMR (Nuclear Magnetic Resonance) stand out. The models of volumetric data (group of data that describe a solid object from a three dimensional space) are being greatly used in diversity of areas as a way of inspection, modeling and simulation of objects in a three - dimensional space. Applications of this model are already found in Mechanic Engineering, Geosciences, Medicine and other areas. In the area of engineering it is sometimes necessary to use industrial CT as the only non-invasive form of inspection the interior of pieces without destroying them. The 3D micro focus X-ray tomography is one technique of non destructive testing used in the most different areas of science and technology, given its capacity to generate clean images (practically free of the unhappiness effect) and high resolution reconstructions. The unsharpness effect minimization and space resolution improvement are consequences of the focal spot size reduction in the X-ray micro focus tube to dimensions smaller than 50 mm. The ceramic filters are used in a wide area in the metallurgic industry, particularly in the cast aluminum where they are used to clean the waste coming through the liquid aluminum. The ceramic filters used in this work are manufactured by FUSICO (German company) and they are constructed from foams. They are manufactured at three models: 10, 20 and 30 ppi (porous per inch). In this paper we present the development of software to analyze and characterize ceramic filters, which can be divided in four stages. This software was developed in C++ language, using objects oriented programming. It is also capable of being executed in multiple platforms (Windows

  18. Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

    Science.gov (United States)

    Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

    2017-06-28

    High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. [Landmark-based automatic registration of serial cross-sectional images of Chinese digital human using Photoshop and Matlab software].

    Science.gov (United States)

    Su, Xiu-yun; Pei, Guo-xian; Yu, Bin; Hu, Yan-ling; Li, Jin; Huang, Qian; Li, Xu; Zhang, Yuan-zhi

    2007-12-01

    This paper describes automatic registration of the serial cross-sectional images of Chinese digital human by projective registration method based on the landmarks using the commercially available software Photoshop and Matlab. During cadaver embedment for acquisition of the Chinese digital human images, 4 rods were placed parallel to the vertical axis of the frozen cadaver to allow orientation. Projective distortion of the rod positions on the cross-sectional images was inevitable due to even slight changes of the relative position of the camera. The original cross-sectional images were first processed using Photoshop software firstly to obtain the images of the orientation rods, and the centroid coordinate of every rod image was acquired with Matlab software. With the average coordinate value of the rods as the fiducial point, two-dimensional projective transformation coefficient of each image was determined. Projective transformation was then carried out and projective distortion from each original serial image was eliminated. The rectified cross-sectional images were again processed using Photoshop to obtain the image of the first orientation rod, the coordinate value of first rod image was calculated using Matlab software, and the cross-sectional images were cut into images of the same size according to the first rod spatial coordinate, to achieve automatic registration of the serial cross-sectional images. sing Photoshop and Matlab softwares, projective transformation can accurately accomplish the image registration for the serial images with simpler calculation processes and easier computer processing.

  20. BIM Software Capability and Interoperability Analysis : An analytical approach toward structural usage of BIM software (S-BIM)

    OpenAIRE

    A. Taher, Ali

    2016-01-01

    This study focused on the structuralanalysis of BIM models. Different commercial software (Autodesk products and Rhinoceros)are presented through modelling and analysis of different structures with varying complexity,section properties, geometry, and material. Beside the commercial software, differentarchitectural and different tools for structural analysis are evaluated (dynamo, grasshopper,add-on tool, direct link, indirect link via IFC). BIM and Structural BIM (S-BIM)

  1. UPVapor: Cofrentes nuclear power plant production results analysis software

    International Nuclear Information System (INIS)

    Curiel, M.; Palomo, M. J.; Baraza, A.; Vaquer, J.

    2010-10-01

    UPVapor software version 02 has been developed for the Cofrentes nuclear power plant Data Analysis Department (Spain). It is an analysis graphical environment in which users have available all the plant variables registered in the process computer system (SIEC). In order to perform this, UPVapor software has many advanced graphic tools for work simplicity, as well as a friendly environment easy to use and with many configuration possibilities. Plant variables are classified in the same way that they are in SIEC computer and these values are taken from it through the network of Iberdrola. UPVapor can generate two different types of graphics: evolution graphs and X Y graphs. The first ones analyse the evolution up to twenty plant variables in a user's defined time period and according to historic plant files. Many tools are available: cursors, graphic configuration, mobile means, non valid data visualization ... Moreover, a particular analysis configuration can be saved, as a pre selection, giving the possibility of charging pre selection directly and developing quick monitoring of a group of preselected plant variables. In X Y graphs, it is possible to analyse a variable value against another variable in a defined time. As an option, users can filter previous data depending on a variable certain range, with the possibility of programming up to five filters. As well as the other graph, X Y graph has many configurations, saving and printing options. With UPVapor software, data analysts can save a valuable time during daily work and, as it is of easy utilization, it permits to other users to perform their own analysis without ask the analysts to develop. Besides, it can be used from any work centre with access to network framework. (Author)

  2. UPVapor: Cofrentes nuclear power plant production results analysis software

    Energy Technology Data Exchange (ETDEWEB)

    Curiel, M. [Logistica y Acondicionamientos Industriales SAU, Sorolla Center, local 10, Av. de las Cortes Valencianas No. 58, 46015 Valencia (Spain); Palomo, M. J. [ISIRYM, Universidad Politecnica de Valencia, Camino de Vera s/n, Valencia (Spain); Baraza, A. [Iberdrola Generacion S. A., Central Nuclear Cofrentes, Carretera Almansa Requena s/n, 04662 Cofrentes, Valencia (Spain); Vaquer, J., E-mail: m.curiel@lainsa.co [TITANIA Servicios Tecnologicos SL, Sorolla Center, local 10, Av. de las Cortes Valencianas No. 58, 46015 Valencia (Spain)

    2010-10-15

    UPVapor software version 02 has been developed for the Cofrentes nuclear power plant Data Analysis Department (Spain). It is an analysis graphical environment in which users have available all the plant variables registered in the process computer system (SIEC). In order to perform this, UPVapor software has many advanced graphic tools for work simplicity, as well as a friendly environment easy to use and with many configuration possibilities. Plant variables are classified in the same way that they are in SIEC computer and these values are taken from it through the network of Iberdrola. UPVapor can generate two different types of graphics: evolution graphs and X Y graphs. The first ones analyse the evolution up to twenty plant variables in a user's defined time period and according to historic plant files. Many tools are available: cursors, graphic configuration, mobile means, non valid data visualization ... Moreover, a particular analysis configuration can be saved, as a pre selection, giving the possibility of charging pre selection directly and developing quick monitoring of a group of preselected plant variables. In X Y graphs, it is possible to analyse a variable value against another variable in a defined time. As an option, users can filter previous data depending on a variable certain range, with the possibility of programming up to five filters. As well as the other graph, X Y graph has many configurations, saving and printing options. With UPVapor software, data analysts can save a valuable time during daily work and, as it is of easy utilization, it permits to other users to perform their own analysis without ask the analysts to develop. Besides, it can be used from any work centre with access to network framework. (Author)

  3. Automated daily quality control analysis for mammography in a multi-unit imaging center.

    Science.gov (United States)

    Sundell, Veli-Matti; Mäkelä, Teemu; Meaney, Alexander; Kaasalainen, Touko; Savolainen, Sauli

    2018-01-01

    Background The high requirements for mammography image quality necessitate a systematic quality assurance process. Digital imaging allows automation of the image quality analysis, which can potentially improve repeatability and objectivity compared to a visual evaluation made by the users. Purpose To develop an automatic image quality analysis software for daily mammography quality control in a multi-unit imaging center. Material and Methods An automated image quality analysis software using the discrete wavelet transform and multiresolution analysis was developed for the American College of Radiology accreditation phantom. The software was validated by analyzing 60 randomly selected phantom images from six mammography systems and 20 phantom images with different dose levels from one mammography system. The results were compared to a visual analysis made by four reviewers. Additionally, long-term image quality trends of a full-field digital mammography system and a computed radiography mammography system were investigated. Results The automated software produced feature detection levels comparable to visual analysis. The agreement was good in the case of fibers, while the software detected somewhat more microcalcifications and characteristic masses. Long-term follow-up via a quality assurance web portal demonstrated the feasibility of using the software for monitoring the performance of mammography systems in a multi-unit imaging center. Conclusion Automated image quality analysis enables monitoring the performance of digital mammography systems in an efficient, centralized manner.

  4. Stochastic geometry for image analysis

    CERN Document Server

    Descombes, Xavier

    2013-01-01

    This book develops the stochastic geometry framework for image analysis purpose. Two main frameworks are  described: marked point process and random closed sets models. We derive the main issues for defining an appropriate model. The algorithms for sampling and optimizing the models as well as for estimating parameters are reviewed.  Numerous applications, covering remote sensing images, biological and medical imaging, are detailed.  This book provides all the necessary tools for developing an image analysis application based on modern stochastic modeling.

  5. CT, MRI and PET image fusion using the ProSoma 3D simulation software

    International Nuclear Information System (INIS)

    Dalah, E.; Bradley, D.A.; Nisbet, A.; Reise, S.

    2008-01-01

    Full text: Multi-modality imaging is involved in almost all oncology applications focusing on the extent of disease and target volume delineation. Commercial image fusion software packages are becoming available but require comprehensive evaluation to ensure reliability of fusion and the underpinning registration algorithm particularly for radiotherapy. The present work seeks to assess such accuracy for a number of available registration methods provided by the commercial package ProSoma. A NEMA body phantom was used in evaluating CT, MR and PET images. In addition, discussion is provided concerning the choice and geometry of fiducial markers in phantom studies and the effect of window-level on target size, in particular in regard to the application of multi modality imaging in treatment planning. In general, the accuracy of fusion of multi-modality images was within 0.5-1.5 mm of actual feature diameters and < 2 ml volume of actual values, particularly in CT images. (author)

  6. Semiautomatic digital imaging system for cytogenetic analysis

    International Nuclear Information System (INIS)

    Chaubey, R.C.; Chauhan, P.C.; Bannur, S.V.; Kulgod, S.V.; Chadda, V.K.; Nigam, R.K.

    1999-08-01

    The paper describes a digital image processing system, developed indigenously at BARC for size measurement of microscopic biological objects such as cell, nucleus and micronucleus in mouse bone marrow; cytochalasin-B blocked human lymphocytes in-vitro; numerical counting and karyotyping of metaphase chromosomes of human lymphocytes. Errors in karyotyping of chromosomes by the imaging system may creep in due to lack of well-defined position of centromere or extensive bending of chromosomes, which may result due to poor quality of preparation. Good metaphase preparations are mandatory for precise and accurate analysis by the system. Additional new morphological parameters about each chromosome have to be incorporated to improve the accuracy of karyotyping. Though the experienced cytogenetisist is the final judge; however, the system assists him/her to carryout analysis much faster as compared to manual scoring. Further, experimental studies are in progress to validate different software packages developed for various cytogenetic applications. (author)

  7. Analysis of mice tumor models using dynamic MRI data and a dedicated software platform

    Energy Technology Data Exchange (ETDEWEB)

    Alfke, H.; Maurer, E.; Klose, K.J. [Philipps Univ. Marburg (Germany). Dept. of Radiology; Kohle, S.; Rascher-Friesenhausen, R.; Behrens, S.; Peitgen, H.O. [MeVis - Center for Medical Diagnostic Systems and Visualization, Bremen (Germany); Celik, I. [Philipps Univ. Marburg (Germany). Inst. for Theoretical Surgery; Heverhagen, J.T. [Philipps Univ. Marburg (Germany). Dept. of Radiology; Ohio State Univ., Columbus (United States). Dept. of Radiology

    2004-09-01

    Purpose: To implement a software platform (DynaVision) dedicated to analyze data from functional imaging of tumors with different mathematical approaches, and to test the software platform in pancreatic carcinoma xenografts in mice with severe combined immunodeficiency disease (SCID). Materials and Methods: A software program was developed for extraction and visualization of tissue perfusion parameters from dynamic contrast-enhanced images. This includes regional parameter calculation from enhancement curves, parametric images (e.g., blood flow), animation, 3D visualization, two-compartment modeling a mode for comparing different datasets (e.g., therapy monitoring), and motion correction. We analyzed xenograft tumors from two pancreatic carcinoma cell lines (B x PC3 and ASPC1) implanted in 14 SCID mice after injection of Gd-DTPA into the tail vein. These data were correlated with histopathological findings. Results: Image analysis was completed in approximately 15 minutes per data set. The possibility of drawing and editing ROIs within the whole data set makes it easy to obtain quantitative data from the intensity-time curves. In one animal, motion artifacts reduced the image quality to a greater extent but data analysis was still possible after motion correction. Dynamic MRI of mice tumor models revealed a highly heterogeneous distribution of the contrast-enhancement curves and derived parameters, which correlated with differences in histopathology. ASPc1 tumors showed a more hypervascular type of curves with faster and higher signal enhancement rate (wash-in) and a faster signal decrease (wash-out). BXPC3 tumors showed a more hypovascular type with slower wash-in and wash-out. This correlated with the biological properties of the tumors. (orig.)

  8. Analysis of mice tumor models using dynamic MRI data and a dedicated software platform

    International Nuclear Information System (INIS)

    Alfke, H.; Maurer, E.; Klose, K.J.; Celik, I.; Heverhagen, J.T.; Ohio State Univ., Columbus

    2004-01-01

    Purpose: To implement a software platform (DynaVision) dedicated to analyze data from functional imaging of tumors with different mathematical approaches, and to test the software platform in pancreatic carcinoma xenografts in mice with severe combined immunodeficiency disease (SCID). Materials and Methods: A software program was developed for extraction and visualization of tissue perfusion parameters from dynamic contrast-enhanced images. This includes regional parameter calculation from enhancement curves, parametric images (e.g., blood flow), animation, 3D visualization, two-compartment modeling a mode for comparing different datasets (e.g., therapy monitoring), and motion correction. We analyzed xenograft tumors from two pancreatic carcinoma cell lines (B x PC3 and ASPC1) implanted in 14 SCID mice after injection of Gd-DTPA into the tail vein. These data were correlated with histopathological findings. Results: Image analysis was completed in approximately 15 minutes per data set. The possibility of drawing and editing ROIs within the whole data set makes it easy to obtain quantitative data from the intensity-time curves. In one animal, motion artifacts reduced the image quality to a greater extent but data analysis was still possible after motion correction. Dynamic MRI of mice tumor models revealed a highly heterogeneous distribution of the contrast-enhancement curves and derived parameters, which correlated with differences in histopathology. ASPc1 tumors showed a more hypervascular type of curves with faster and higher signal enhancement rate (wash-in) and a faster signal decrease (wash-out). BXPC3 tumors showed a more hypovascular type with slower wash-in and wash-out. This correlated with the biological properties of the tumors. (orig.)

  9. International Atomic Energy Agency intercomparison of ion beam analysis software

    Energy Technology Data Exchange (ETDEWEB)

    Barradas, N.P. [Instituto Tecnologico e Nuclear, Estrada Nacional No. 10, Apartado 21, 2686-953 Sacavem (Portugal); Centro de Fisica Nuclear da Universidade de Lisboa, Avenida do Professor Gama Pinto 2, 1649-003 Lisboa (Portugal)], E-mail: nunoni@itn.pt; Arstila, K. [K.U. Leuven, Instituut voor Kern-en Stralingsfysica, Celestijnenlaan 200D, B-3001 Leuven (Belgium); Battistig, G. [MFA Research Institute for Technical Physics and Materials Science, P.O. Box 49, H-1525 Budapest (Hungary); Bianconi, M. [CNR-IMM-Sezione di Bologna, Via P. Gobetti, 101, I-40129 Bologna (Italy); Dytlewski, N. [International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, A-1400 Vienna (Austria); Jeynes, C. [Surrey Ion Beam Centre, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom); Kotai, E. [KFKI Research Institute for Particle and Nuclear Physics, P.O. Box 49, H-1525 Budapest (Hungary); Lulli, G. [CNR-IMM-Sezione di Bologna, Via P. Gobetti, 101, I-40129 Bologna (Italy); Mayer, M. [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, Boltzmannstrasse 2, D-85748 Garching (Germany); Rauhala, E. [Accelerator Laboratory, Department of Physics, University of Helsinki, P.O. Box 43, FIN-00014 Helsinki (Finland); Szilagyi, E. [KFKI Research Institute for Particle and Nuclear Physics, P.O. Box 49, H-1525 Budapest (Hungary); Thompson, M. [Department of MS and E/Bard Hall 328, Cornell University, Ithaca, NY 14853 (United States)

    2007-09-15

    Ion beam analysis (IBA) includes a group of techniques for the determination of elemental concentration depth profiles of thin film materials. Often the final results rely on simulations, fits and calculations, made by dedicated codes written for specific techniques. Here we evaluate numerical codes dedicated to the analysis of Rutherford backscattering spectrometry, non-Rutherford elastic backscattering spectrometry, elastic recoil detection analysis and non-resonant nuclear reaction analysis data. Several software packages have been presented and made available to the community. New codes regularly appear, and old codes continue to be used and occasionally updated and expanded. However, those codes have to date not been validated, or even compared to each other. Consequently, IBA practitioners use codes whose validity, correctness and accuracy have never been validated beyond the authors' efforts. In this work, we present the results of an IBA software intercomparison exercise, where seven different packages participated. These were DEPTH, GISA, DataFurnace (NDF), RBX, RUMP, SIMNRA (all analytical codes) and MCERD (a Monte Carlo code). In a first step, a series of simulations were defined, testing different capabilities of the codes, for fixed conditions. In a second step, a set of real experimental data were analysed. The main conclusion is that the codes perform well within the limits of their design, and that the largest differences in the results obtained are due to differences in the fundamental databases used (stopping power and scattering cross section). In particular, spectra can be calculated including Rutherford cross sections with screening, energy resolution convolutions including energy straggling, and pileup effects, with agreement between the codes available at the 0.1% level. This same agreement is also available for the non-RBS techniques. This agreement is not limited to calculation of spectra from particular structures with predetermined

  10. FIMTrack: An open source tracking and locomotion analysis software for small animals.

    Directory of Open Access Journals (Sweden)

    Benjamin Risse

    2017-05-01

    Full Text Available Imaging and analyzing the locomotion behavior of small animals such as Drosophila larvae or C. elegans worms has become an integral subject of biological research. In the past we have introduced FIM, a novel imaging system feasible to extract high contrast images. This system in combination with the associated tracking software FIMTrack is already used by many groups all over the world. However, so far there has not been an in-depth discussion of the technical aspects. Here we elaborate on the implementation details of FIMTrack and give an in-depth explanation of the used algorithms. Among others, the software offers several tracking strategies to cover a wide range of different model organisms, locomotion types, and camera properties. Furthermore, the software facilitates stimuli-based analysis in combination with built-in manual tracking and correction functionalities. All features are integrated in an easy-to-use graphical user interface. To demonstrate the potential of FIMTrack we provide an evaluation of its accuracy using manually labeled data. The source code is available under the GNU GPLv3 at https://github.com/i-git/FIMTrack and pre-compiled binaries for Windows and Mac are available at http://fim.uni-muenster.de.

  11. Research and Development of Statistical Analysis Software System of Maize Seedling Experiment

    OpenAIRE

    Hui Cao

    2014-01-01

    In this study, software engineer measures were used to develop a set of software system for maize seedling experiments statistics and analysis works. During development works, B/S structure software design method was used and a set of statistics indicators for maize seedling evaluation were established. The experiments results indicated that this set of software system could finish quality statistics and analysis for maize seedling very well. The development of this software system explored a...

  12. Automated image analysis in the study of collagenous colitis

    DEFF Research Database (Denmark)

    Fiehn, Anne-Marie Kanstrup; Kristensson, Martin; Engel, Ulla

    2016-01-01

    PURPOSE: The aim of this study was to develop an automated image analysis software to measure the thickness of the subepithelial collagenous band in colon biopsies with collagenous colitis (CC) and incomplete CC (CCi). The software measures the thickness of the collagenous band on microscopic...... slides stained with Van Gieson (VG). PATIENTS AND METHODS: A training set consisting of ten biopsies diagnosed as CC, CCi, and normal colon mucosa was used to develop the automated image analysis (VG app) to match the assessment by a pathologist. The study set consisted of biopsies from 75 patients...

  13. A Parallel Software Pipeline for DMET Microarray Genotyping Data Analysis

    Directory of Open Access Journals (Sweden)

    Giuseppe Agapito

    2018-06-01

    Full Text Available Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS, Genome-Wide Association Studies (GWAS, Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective. A side effect of high-throughput methodologies is the massive amount of data produced for each single experiment, that poses several challenges (e.g., high execution time and required memory to bioinformatic software. Thus a main requirement of modern bioinformatic softwares, is the use of good software engineering methods and efficient programming techniques, able to face those challenges, that include the use of parallel programming and efficient and compact data structures. This paper presents the design and the experimentation of a comprehensive software pipeline, named microPipe, for the preprocessing, annotation and analysis of microarray-based Single Nucleotide Polymorphism (SNP genotyping data. A use case in pharmacogenomics is presented. The main advantages of using microPipe are: the reduction of errors that may happen when trying to make data compatible among different tools; the possibility to analyze in parallel huge datasets; the easy annotation and integration of data. microPipe is available under Creative Commons license, and is freely downloadable for academic and not-for-profit institutions.

  14. Comparison of two software versions for assessment of body-composition analysis by DXA

    DEFF Research Database (Denmark)

    Vozarova, B; Wang, J; Weyer, C

    2001-01-01

    To compare two software versions provided by Lunar CO: for assessment of body composition analysis by DXA.......To compare two software versions provided by Lunar CO: for assessment of body composition analysis by DXA....

  15. A software to digital image processing to be used in the voxel phantom development.

    Science.gov (United States)

    Vieira, J W; Lima, F R A

    2009-11-15

    Anthropomorphic models used in computational dosimetry, also denominated phantoms, are based on digital images recorded from scanning of real people by Computed Tomography (CT) or Magnetic Resonance Imaging (MRI). The voxel phantom construction requests computational processing for transformations of image formats, to compact two-dimensional (2-D) images forming of three-dimensional (3-D) matrices, image sampling and quantization, image enhancement, restoration and segmentation, among others. Hardly the researcher of computational dosimetry will find all these available abilities in single software, and almost always this difficulty presents as a result the decrease of the rhythm of his researches or the use, sometimes inadequate, of alternative tools. The need to integrate the several tasks mentioned above to obtain an image that can be used in an exposure computational model motivated the development of the Digital Image Processing (DIP) software, mainly to solve particular problems in Dissertations and Thesis developed by members of the Grupo de Pesquisa em Dosimetria Numérica (GDN/CNPq). Because of this particular objective, the software uses the Portuguese idiom in their implementations and interfaces. This paper presents the second version of the DIP, whose main changes are the more formal organization on menus and menu items, and menu for digital image segmentation. Currently, the DIP contains the menus Fundamentos, Visualizações, Domínio Espacial, Domínio de Frequências, Segmentações and Estudos. Each menu contains items and sub-items with functionalities that, usually, request an image as input and produce an image or an attribute in the output. The DIP reads edits and writes binary files containing the 3-D matrix corresponding to a stack of axial images from a given geometry that can be a human body or other volume of interest. It also can read any type of computational image and to make conversions. When the task involves only an output image

  16. IHE cross-enterprise document sharing for imaging: interoperability testing software

    Directory of Open Access Journals (Sweden)

    Renaud Bérubé

    2010-09-01

    Full Text Available Abstract Background With the deployments of Electronic Health Records (EHR, interoperability testing in healthcare is becoming crucial. EHR enables access to prior diagnostic information in order to assist in health decisions. It is a virtual system that results from the cooperation of several heterogeneous distributed systems. Interoperability between peers is therefore essential. Achieving interoperability requires various types of testing. Implementations need to be tested using software that simulates communication partners, and that provides test data and test plans. Results In this paper we describe a software that is used to test systems that are involved in sharing medical images within the EHR. Our software is used as part of the Integrating the Healthcare Enterprise (IHE testing process to test the Cross Enterprise Document Sharing for imaging (XDS-I integration profile. We describe its architecture and functionalities; we also expose the challenges encountered and discuss the elected design solutions. Conclusions EHR is being deployed in several countries. The EHR infrastructure will be continuously evolving to embrace advances in the information technology domain. Our software is built on a web framework to allow for an easy evolution with web technology. The testing software is publicly available; it can be used by system implementers to test their implementations. It can also be used by site integrators to verify and test the interoperability of systems, or by developers to understand specifications ambiguities, or to resolve implementations difficulties.

  17. Meta-Analyst: software for meta-analysis of binary, continuous and diagnostic data

    Directory of Open Access Journals (Sweden)

    Schmid Christopher H

    2009-12-01

    Full Text Available Abstract Background Meta-analysis is increasingly used as a key source of evidence synthesis to inform clinical practice. The theory and statistical foundations of meta-analysis continually evolve, providing solutions to many new and challenging problems. In practice, most meta-analyses are performed in general statistical packages or dedicated meta-analysis programs. Results Herein, we introduce Meta-Analyst, a novel, powerful, intuitive, and free meta-analysis program for the meta-analysis of a variety of problems. Meta-Analyst is implemented in C# atop of the Microsoft .NET framework, and features a graphical user interface. The software performs several meta-analysis and meta-regression models for binary and continuous outcomes, as well as analyses for diagnostic and prognostic test studies in the frequentist and Bayesian frameworks. Moreover, Meta-Analyst includes a flexible tool to edit and customize generated meta-analysis graphs (e.g., forest plots and provides output in many formats (images, Adobe PDF, Microsoft Word-ready RTF. The software architecture employed allows for rapid changes to be made to either the Graphical User Interface (GUI or to the analytic modules. We verified the numerical precision of Meta-Analyst by comparing its output with that from standard meta-analysis routines in Stata over a large database of 11,803 meta-analyses of binary outcome data, and 6,881 meta-analyses of continuous outcome data from the Cochrane Library of Systematic Reviews. Results from analyses of diagnostic and prognostic test studies have been verified in a limited number of meta-analyses versus MetaDisc and MetaTest. Bayesian statistical analyses use the OpenBUGS calculation engine (and are thus as accurate as the standalone OpenBUGS software. Conclusion We have developed and validated a new program for conducting meta-analyses that combines the advantages of existing software for this task.

  18. Utilizing a Photo-Analysis Software for Content Identifying Method (CIM

    Directory of Open Access Journals (Sweden)

    Nejad Nasim Sahraei

    2015-01-01

    Full Text Available Content Identifying Methodology or (CIM was developed to measure public preferences in order to reveal the common characteristics of landscapes and aspects of underlying perceptions including the individual's reactions to content and spatial configuration, therefore, it can assist with the identification of factors that influenced preference. Regarding the analysis of landscape photographs through CIM, there are several studies utilizing image analysis software, such as Adobe Photoshop, in order to identify the physical contents in the scenes. This study attempts to evaluate public’s ‘preferences for aesthetic qualities of pedestrian bridges in urban areas through a photo-questionnaire survey, in which respondents evaluated images of pedestrian bridges in urban areas. Two groups of images were evaluated as the most and least preferred scenes that concern the highest and lowest mean scores respectively. These two groups were analyzed by CIM and also evaluated based on the respondent’s description of each group to reveal the pattern of preferences and the factors that may affect them. Digimizer Software was employed to triangulate the two approaches and to determine the role of these factors on people’s preferences. This study attempts to introduce the useful software for image analysis which can measure the physical contents and also their spatial organization in the scenes. According to the findings, it is revealed that Digimizer could be a useful tool in CIM approaches through preference studies that utilizes photographs in place of the actual landscape in order to determine the most important factors in public preferences for pedestrian bridges in urban areas.

  19. Graph based communication analysis for hardware/software codesign

    DEFF Research Database (Denmark)

    Knudsen, Peter Voigt; Madsen, Jan

    1999-01-01

    In this paper we present a coarse grain CDFG (Control/Data Flow Graph) model suitable for hardware/software partitioning of single processes and demonstrate how it is necessary to perform various transformations on the graph structure before partitioning in order to achieve a structure that allows...... for accurate estimation of communication overhead between nodes mapped to different processors. In particular, we demonstrate how various transformations of control structures can lead to a more accurate communication analysis and more efficient implementations. The purpose of the transformations is to obtain...

  20. Development of RCM analysis software for Korean nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Ho; Choi, Kwang Hee; Jeong, Hyeong Jong [Korea Electric Power Research Institute, Taejon (Korea, Republic of)

    1999-12-31

    A software called KEPCO RCM workstation (KRCM) has been developed to optimize the maintenance strategies of Korean nuclear power plants. The program modules of the KRCM were designed in a manner that combines EPRI methodologies and KEPRI analysis technique. The KRCM is being applied to the three pilot system, chemical and volume control system, main steam system, and compressed air system of Yonggwang Units 1 and 2. In addition, the KRCM can be utilized as a tool to meet a part of the requirements of maintenance rule (MR) imposed by U.S. NRC. 3 refs., 4 figs. (Author)

  1. Development of RCM analysis software for Korean nuclear power plants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Young Ho; Choi, Kwang Hee; Jeong, Hyeong Jong [Korea Electric Power Research Institute, Taejon (Korea, Republic of)

    1998-12-31

    A software called KEPCO RCM workstation (KRCM) has been developed to optimize the maintenance strategies of Korean nuclear power plants. The program modules of the KRCM were designed in a manner that combines EPRI methodologies and KEPRI analysis technique. The KRCM is being applied to the three pilot system, chemical and volume control system, main steam system, and compressed air system of Yonggwang Units 1 and 2. In addition, the KRCM can be utilized as a tool to meet a part of the requirements of maintenance rule (MR) imposed by U.S. NRC. 3 refs., 4 figs. (Author)

  2. Discriminant Analysis of the Effects of Software Cost Drivers on ...

    African Journals Online (AJOL)

    The paper work investigates the effect of software cost drivers on project schedule estimation of software development projects in Nigeria. Specifically, the paper determines the extent to which software cost variables affect our software project time schedule in our environment. Such studies are lacking in the recent ...

  3. Tool Support for Parametric Analysis of Large Software Simulation Systems

    Science.gov (United States)

    Schumann, Johann; Gundy-Burlet, Karen; Pasareanu, Corina; Menzies, Tim; Barrett, Tony

    2008-01-01

    The analysis of large and complex parameterized software systems, e.g., systems simulation in aerospace, is very complicated and time-consuming due to the large parameter space, and the complex, highly coupled nonlinear nature of the different system components. Thus, such systems are generally validated only in regions local to anticipated operating points rather than through characterization of the entire feasible operational envelope of the system. We have addressed the factors deterring such an analysis with a tool to support envelope assessment: we utilize a combination of advanced Monte Carlo generation with n-factor combinatorial parameter variations to limit the number of cases, but still explore important interactions in the parameter space in a systematic fashion. Additional test-cases, automatically generated from models (e.g., UML, Simulink, Stateflow) improve the coverage. The distributed test runs of the software system produce vast amounts of data, making manual analysis impossible. Our tool automatically analyzes the generated data through a combination of unsupervised Bayesian clustering techniques (AutoBayes) and supervised learning of critical parameter ranges using the treatment learner TAR3. The tool has been developed around the Trick simulation environment, which is widely used within NASA. We will present this tool with a GN&C (Guidance, Navigation and Control) simulation of a small satellite system.

  4. Development of a software for INAA analysis automation

    International Nuclear Information System (INIS)

    Zahn, Guilherme S.; Genezini, Frederico A.; Figueiredo, Ana Maria G.; Ticianelli, Regina B.

    2013-01-01

    In this work, a software to automate the post-counting tasks in comparative INAA has been developed that aims to become more flexible than the available options, integrating itself with some of the routines currently in use in the IPEN Activation Analysis Laboratory and allowing the user to choose between a fully-automatic analysis or an Excel-oriented one. The software makes use of the Genie 2000 data importing and analysis routines and stores each 'energy-counts-uncertainty' table as a separate ASCII file that can be used later on if required by the analyst. Moreover, it generates an Excel-compatible CSV (comma separated values) file with only the relevant results from the analyses for each sample or comparator, as well as the results of the concentration calculations and the results obtained with four different statistical tools (unweighted average, weighted average, normalized residuals and Rajeval technique), allowing the analyst to double-check the results. Finally, a 'summary' CSV file is also produced, with the final concentration results obtained for each element in each sample. (author)

  5. OsiriX: an open-source software for navigating in multidimensional DICOM images.

    Science.gov (United States)

    Rosset, Antoine; Spadola, Luca; Ratib, Osman

    2004-09-01

    A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

  6. Clinical evaluation of reducing acquisition time on single-photon emission computed tomography image quality using proprietary resolution recovery software.

    Science.gov (United States)

    Aldridge, Matthew D; Waddington, Wendy W; Dickson, John C; Prakash, Vineet; Ell, Peter J; Bomanji, Jamshed B

    2013-11-01

    A three-dimensional model-based resolution recovery (RR) reconstruction algorithm that compensates for collimator-detector response, resulting in an improvement in reconstructed spatial resolution and signal-to-noise ratio of single-photon emission computed tomography (SPECT) images, was tested. The software is said to retain image quality even with reduced acquisition time. Clinically, any improvement in patient throughput without loss of quality is to be welcomed. Furthermore, future restrictions in radiotracer supplies may add value to this type of data analysis. The aims of this study were to assess improvement in image quality using the software and to evaluate the potential of performing reduced time acquisitions for bone and parathyroid SPECT applications. Data acquisition was performed using the local standard SPECT/CT protocols for 99mTc-hydroxymethylene diphosphonate bone and 99mTc-methoxyisobutylisonitrile parathyroid SPECT imaging. The principal modification applied was the acquisition of an eight-frame gated data set acquired using an ECG simulator with a fixed signal as the trigger. This had the effect of partitioning the data such that the effect of reduced time acquisitions could be assessed without conferring additional scanning time on the patient. The set of summed data sets was then independently reconstructed using the RR software to permit a blinded assessment of the effect of acquired counts upon reconstructed image quality as adjudged by three experienced observers. Data sets reconstructed with the RR software were compared with the local standard processing protocols; filtered back-projection and ordered-subset expectation-maximization. Thirty SPECT studies were assessed (20 bone and 10 parathyroid). The images reconstructed with the RR algorithm showed improved image quality for both full-time and half-time acquisitions over local current processing protocols (Pimproved image quality compared with local processing protocols and has been

  7. CONTEXT BASED FOOD IMAGE ANALYSIS

    OpenAIRE

    He, Ye; Xu, Chang; Khanna, Nitin; Boushey, Carol J.; Delp, Edward J.

    2013-01-01

    We are developing a dietary assessment system that records daily food intake through the use of food images. Recognizing food in an image is difficult due to large visual variance with respect to eating or preparation conditions. This task becomes even more challenging when different foods have similar visual appearance. In this paper we propose to incorporate two types of contextual dietary information, food co-occurrence patterns and personalized learning models, in food image analysis to r...

  8. TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies.

    Science.gov (United States)

    Klein, Johannes; Leupold, Stefan; Biegler, Ilona; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter

    2012-09-01

    Time-lapse imaging in combination with fluorescence microscopy techniques enable the investigation of gene regulatory circuits and uncovered phenomena like culture heterogeneity. In this context, computational image processing for the analysis of single cell behaviour plays an increasing role in systems biology and mathematical modelling approaches. Consequently, we developed a software package with graphical user interface for the analysis of single bacterial cell behaviour. A new software called TLM-Tracker allows for the flexible and user-friendly interpretation for the segmentation, tracking and lineage analysis of microbial cells in time-lapse movies. The software package, including manual, tutorial video and examples, is available as Matlab code or executable binaries at http://www.tlmtracker.tu-bs.de.

  9. SOFTWARE FOR REGIONS OF INTEREST RETRIEVAL ON MEDICAL 3D IMAGES

    Directory of Open Access Journals (Sweden)

    G. G. Stromov

    2014-01-01

    Full Text Available Background. Implementation of software for areas of interest retrieval in 3D medical images is described in this article. It has been tested against large volume of model MRIs.Material and methods. We tested software against normal and pathological (severe multiple sclerosis model MRIs from tge BrainWeb resource. Technological stack is based on open-source cross-platform solutions. We implemented storage system on Maria DB (an open-sourced fork of MySQL with P/SQL extensions. Python 2.7 scripting was used for automatization of extract-transform-load operations. The computational core is written on Java 7 with Spring framework 3. MongoDB was used as a cache in the cluster of workstations. Maven 3 was chosen as a dependency manager and build system, the project is hosted at Github.Results. As testing on SSMU's LAN has showed, software has been developed is quite efficiently retrieves ROIs are matching for the morphological substratum on pathological MRIs.Conclusion. Automation of a diagnostic process using medical imaging allows to level down the subjective component in decision making and increase the availability of hi-tech medicine. Software has shown in the article is a complex solution for ROI retrieving and segmentation process on model medical images in full-automated mode.We would like to thank Robert Vincent for great help with consulting of usage the BrainWeb resource.

  10. Portable image-manipulation software: what is the extra development cost?

    Science.gov (United States)

    Ligier, Y; Ratib, O; Funk, M; Perrier, R; Girard, C; Logean, M

    1992-08-01

    A hospital-wide picture archiving and communication system (PACS) project is currently under development at the University Hospital of Geneva. The visualization and manipulation of images provided by different imaging modalities constitutes one of the most challenging component of a PACS. It was necessary to provide this visualization software on a number of types of workstations because of the varying requirements imposed by the range of clinical uses it must serve. The user interface must be the same, independent of the underlying workstation. In addition to a standard set of image-manipulation and processing tools, there is a need for more specific clinical tools that can be easily adapted to specific medical requirements. To achieve this goal, it was elected to develop a modular and portable software called OSIRIS. This software is available on two different operating systems (the UNIX standard X-11/OSF-Motif based workstations and the Macintosh family) and can be easily ported to other systems. The extra effort required to design such software in a modular and portable way was worthwhile because it resulted in a platform that can be easily expanded and adapted to a variety of specific clinical applications. Its portability allows users to benefit from the rapidly evolving workstation technology and to adapt the performance to suit their needs.

  11. Models for composing software : an analysis of software composition and objects

    NARCIS (Netherlands)

    Bergmans, Lodewijk

    1999-01-01

    In this report, we investigate component-based software construction with a focus on composition. In particular we try to analyze the requirements and issues for components and software composition. As a means to understand this research area, we introduce a canonical model for representing

  12. PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development

    DEFF Research Database (Denmark)

    Martin, Sarah F.; Falkenberg, Heiner; Dyrlund, Thomas Franck

    2013-01-01

    , including arguments for community-wide open source software development and “big data” compatible solutions for the future. For the meantime, we have laid out ten top tips for data processing. With these at hand, a first large-scale proteomics analysis hopefully becomes less daunting to navigate.......However there is clearly a real need for robust tools, standard operating procedures and general acceptance of best practises. Thus we submit to the proteomics community a call for a community-wide open set of proteomics analysis challenges—PROTEINCHALLENGE—that directly target and compare data analysis workflows......In large-scale proteomics studies there is a temptation, after months of experimental work, to plug resulting data into a convenient—if poorly implemented—set of tools, which may neither do the data justice nor help answer the scientific question. In this paper we have captured key concerns...

  13. Open Source software and social networks: Disruptive alternatives for medical imaging

    International Nuclear Information System (INIS)

    Ratib, Osman; Rosset, Antoine; Heuberger, Joris

    2011-01-01

    In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. Methods: This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Observations: Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate

  14. Open Source software and social networks: Disruptive alternatives for medical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ratib, Osman, E-mail: osman.ratib@hcuge.ch [Department of Medical Imaging and Information Sciences, University Hospital of Geneva, 24, rue Micheli-du-Crest, 1205 Geneva (Switzerland); Rosset, Antoine; Heuberger, Joris [Department of Medical Imaging and Information Sciences, University Hospital of Geneva, 24, rue Micheli-du-Crest, 1205 Geneva (Switzerland)

    2011-05-15

    In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. Methods: This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Observations: Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily

  15. Open Source software and social networks: disruptive alternatives for medical imaging.

    Science.gov (United States)

    Ratib, Osman; Rosset, Antoine; Heuberger, Joris

    2011-05-01

    In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate and exchange information

  16. Imaging mass spectrometry statistical analysis.

    Science.gov (United States)

    Jones, Emrys A; Deininger, Sören-Oliver; Hogendoorn, Pancras C W; Deelder, André M; McDonnell, Liam A

    2012-08-30

    Imaging mass spectrometry is increasingly used to identify new candidate biomarkers. This clinical application of imaging mass spectrometry is highly multidisciplinary: expertise in mass spectrometry is necessary to acquire high quality data, histology is required to accurately label the origin of each pixel's mass spectrum, disease biology is necessary to understand the potential meaning of the imaging mass spectrometry results, and statistics to assess the confidence of any findings. Imaging mass spectrometry data analysis is further complicated because of the unique nature of the data (within the mass spectrometry field); several of the assumptions implicit in the analysis of LC-MS/profiling datasets are not applicable to imaging. The very large size of imaging datasets and the reporting of many data analysis routines, combined with inadequate training and accessible reviews, have exacerbated this problem. In this paper we provide an accessible review of the nature of imaging data and the different strategies by which the data may be analyzed. Particular attention is paid to the assumptions of the data analysis routines to ensure that the reader is apprised of their correct usage in imaging mass spectrometry research. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. UV imaging in pharmaceutical analysis

    DEFF Research Database (Denmark)

    Østergaard, Jesper

    2018-01-01

    UV imaging provides spatially and temporally resolved absorbance measurements, which are highly useful in pharmaceutical analysis. Commercial UV imaging instrumentation was originally developed as a detector for separation sciences, but the main use is in the area of in vitro dissolution...

  18. Hazard Analysis of Software Requirements Specification for Process Module of FPGA-based Controllers in NPP

    Energy Technology Data Exchange (ETDEWEB)

    Jung; Sejin; Kim, Eui-Sub; Yoo, Junbeom [Konkuk University, Seoul (Korea, Republic of); Keum, Jong Yong; Lee, Jang-Soo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    Software in PLC, FPGA which are used to develop I and C system also should be analyzed to hazards and risks before used. NUREG/CR-6430 proposes the method for performing software hazard analysis. It suggests analysis technique for software affected hazards and it reveals that software hazard analysis should be performed with the aspects of software life cycle such as requirements analysis, design, detailed design, implements. It also provides the guide phrases for applying software hazard analysis. HAZOP (Hazard and operability analysis) is one of the analysis technique which is introduced in NUREG/CR-6430 and it is useful technique to use guide phrases. HAZOP is sometimes used to analyze the safety of software. Analysis method of NUREG/CR-6430 had been used in Korea nuclear power plant software for PLC development. Appropriate guide phrases and analysis process are selected to apply efficiently and NUREG/CR-6430 provides applicable methods for software hazard analysis is identified in these researches. We perform software hazard analysis of FPGA software requirements specification with two approaches which are NUREG/CR-6430 and HAZOP with using general GW. We also perform the comparative analysis with them. NUREG/CR-6430 approach has several pros and cons comparing with the HAZOP with general guide words and approach. It is enough applicable to analyze the software requirements specification of FPGA.

  19. Methods in quantitative image analysis.

    Science.gov (United States)

    Oberholzer, M; Ostreicher, M; Christen, H; Brühlmann, M

    1996-05-01

    The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic-noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the grey values describing the brightness of every point within the image, named a pixel. The information is stored in bits. Eight bits are summarised in one byte. Therefore, grey values can have a value between 0 and 256 (2(8)). The human eye seems to be quite content with a display of 5-bit images (corresponding to 64 different grey values). In a digitised image, the pixel grey values can vary within regions that are uniform in the original scene: the image is noisy. The noise is mainly manifested in the background of the image. For an optimal discrimination between different objects or features in an image, uniformity of illumination in the whole image is required. These defects can be minimised by shading correction [subtraction of a background (white) image from the original image, pixel per pixel, or division of the original image by the background image]. The brightness of an image represented by its grey values can be analysed for every single pixel or for a group of pixels. The most frequently used pixel-based image descriptors are optical density, integrated optical density, the histogram of the grey values, mean grey value and entropy. The distribution of the grey values existing within an image is one of the most important characteristics of the image. However, the histogram gives no information about the texture of the image. The simplest way to improve the contrast of an image is to expand the brightness scale by spreading the histogram out to the full available range. Rules for transforming the grey value

  20. Don't Blame the Software: Using Qualitative Data Analysis Software Successfully in Doctoral Research

    Directory of Open Access Journals (Sweden)

    Michelle Salmona

    2016-07-01

    Full Text Available In this article, we explore the learning experiences of doctoral candidates as they use qualitative data analysis software (QDAS. Of particular interest is the process of adopting technology during the development of research methodology. Using an action research approach, data was gathered over five years from advanced doctoral research candidates and supervisors. The technology acceptance model (TAM was then applied as a theoretical analytic lens for better understanding how students interact with new technology. Findings relate to two significant barriers which doctoral students confront: 1. aligning perceptions of ease of use and usefulness is essential in overcoming resistance to technological change; 2. transparency into the research process through technology promotes insights into methodological challenges. Transitioning through both barriers requires a competent foundation in qualitative research. The study acknowledges the importance of higher degree research, curriculum reform and doctoral supervision in post-graduate research training together with their interconnected relationships in support of high-quality inquiry. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs1603117

  1. eXtended CASA Line Analysis Software Suite (XCLASS)

    Science.gov (United States)

    Möller, T.; Endres, C.; Schilke, P.

    2017-02-01

    The eXtended CASA Line Analysis Software Suite (XCLASS) is a toolbox for the Common Astronomy Software Applications package (CASA) containing new functions for modeling interferometric and single dish data. Among the tools is the myXCLASS program which calculates synthetic spectra by solving the radiative transfer equation for an isothermal object in one dimension, whereas the finite source size and dust attenuation are considered as well. Molecular data required by the myXCLASS program are taken from an embedded SQLite3 database containing entries from the Cologne Database for Molecular Spectroscopy (CDMS) and JPL using the Virtual Atomic and Molecular Data Center (VAMDC) portal. Additionally, the toolbox provides an interface for the model optimizer package Modeling and Analysis Generic Interface for eXternal numerical codes (MAGIX), which helps to find the best description of observational data using myXCLASS (or another external model program), that is, finding the parameter set that most closely reproduces the data. http://www.astro.uni-koeln.de/projects/schilke/myXCLASSInterface A copy of the code is available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/598/A7

  2. Oxygen octahedra picker: A software tool to extract quantitative information from STEM images

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yi, E-mail: y.wang@fkf.mpg.de; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y.; Aken, Peter A. van

    2016-09-15

    In perovskite oxide based materials and hetero-structures there are often strong correlations between oxygen octahedral distortions and functionality. Thus, atomistic understanding of the octahedral distortion, which requires accurate measurements of atomic column positions, will greatly help to engineer their properties. Here, we report the development of a software tool to extract quantitative information of the lattice and of BO{sub 6} octahedral distortions from STEM images. Center-of-mass and 2D Gaussian fitting methods are implemented to locate positions of individual atom columns. The precision of atomic column distance measurements is evaluated on both simulated and experimental images. The application of the software tool is demonstrated using practical examples. - Highlights: • We report a software tool for mapping atomic positions from HAADF and ABF images. • It enables quantification of both crystal lattice and oxygen octahedral distortions. • We test the measurement accuracy and precision on simulated and experimental images. • It works well for different orientations of perovskite structures and interfaces.

  3. MedXViewer: an extensible web-enabled software package for medical imaging

    Science.gov (United States)

    Looney, P. T.; Young, K. C.; Mackenzie, Alistair; Halling-Brown, Mark D.

    2014-03-01

    MedXViewer (Medical eXtensible Viewer) is an application designed to allow workstation-independent, PACS-less viewing and interaction with anonymised medical images (e.g. observer studies). The application was initially implemented for use in digital mammography and tomosynthesis but the flexible software design allows it to be easily extended to other imaging modalities. Regions of interest can be identified by a user and any associated information about a mark, an image or a study can be added. The questions and settings can be easily configured depending on the need of the research allowing both ROC and FROC studies to be performed. The extensible nature of the design allows for other functionality and hanging protocols to be available for each study. Panning, windowing, zooming and moving through slices are all available while modality-specific features can be easily enabled e.g. quadrant zooming in mammographic studies. MedXViewer can integrate with a web-based image database allowing results and images to be stored centrally. The software and images can be downloaded remotely from this centralised data-store. Alternatively, the software can run without a network connection where the images and results can be encrypted and stored locally on a machine or external drive. Due to the advanced workstation-style functionality, the simple deployment on heterogeneous systems over the internet without a requirement for administrative access and the ability to utilise a centralised database, MedXViewer has been used for running remote paper-less observer studies and is capable of providing a training infrastructure and co-ordinating remote collaborative viewing sessions (e.g. cancer reviews, interesting cases).

  4. Evaluation of three methods for retrospective correction of vignetting on medical microscopy images utilizing two open source software tools.

    Science.gov (United States)

    Babaloukas, Georgios; Tentolouris, Nicholas; Liatis, Stavros; Sklavounou, Alexandra; Perrea, Despoina

    2011-12-01

    Correction of vignetting on images obtained by a digital camera mounted on a microscope is essential before applying image analysis. The aim of this study is to evaluate three methods for retrospective correction of vignetting on medical microscopy images and compare them with a prospective correction method. One digital image from four different tissues was used and a vignetting effect was applied on each of these images. The resulted vignetted image was replicated four times and in each replica a different method for vignetting correction was applied with fiji and gimp software tools. The highest peak signal-to-noise ratio from the comparison of each method to the original image was obtained from the prospective method in all tissues. The morphological filtering method provided the highest peak signal-to-noise ratio value amongst the retrospective methods. The prospective method is suggested as the method of choice for correction of vignetting and if it is not applicable, then the morphological filtering may be suggested as the retrospective alternative method. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

  5. Impact on dose and image quality of a software-based scatter correction in mammography.

    Science.gov (United States)

    Monserrat, Teresa; Prieto, Elena; Barbés, Benigno; Pina, Luis; Elizalde, Arlette; Fernández, Belén

    2017-01-01

    Background In 2014, Siemens developed a new software-based scatter correction (Progressive Reconstruction Intelligently Minimizing Exposure [PRIME]), enabling grid-less digital mammography. Purpose To compare doses and image quality between PRIME (grid-less) and standard (with anti-scatter grid) modes. Material and Methods Contrast-to-noise ratio (CNR) was measured for various polymethylmethacrylate (PMMA) thicknesses and dose values provided by the mammograph were recorded. CDMAM phantom images were acquired for various PMMA thicknesses and inverse Image Quality Figure (IQF inv ) was calculated. Values of incident entrance surface air kerma (ESAK) and average glandular dose (AGD) were obtained from the DICOM header for a total of 1088 pairs of clinical cases. Two experienced radiologists compared subjectively the image quality of a total of 149 pairs of clinical cases. Results CNR values were higher and doses were lower in PRIME mode for all thicknesses. IQF inv values in PRIME mode were lower for all thicknesses except for 40 mm of PMMA equivalent, in which IQF inv was slightly greater in PRIME mode. A mean reduction of 10% in ESAK and 12% in AGD in PRIME mode with respect to standard mode was obtained. The clinical image quality in PRIME and standard acquisitions resulted to be similar in most of the cases (84% for the first radiologist and 67% for the second one). Conclusion The use of PRIME software reduces, in average, the dose of radiation to the breast without affecting image quality. This reduction is greater for thinner and denser breasts.

  6. AROSICS: An Automated and Robust Open-Source Image Co-Registration Software for Multi-Sensor Satellite Data

    Directory of Open Access Journals (Sweden)

    Daniel Scheffler

    2017-07-01

    Full Text Available Geospatial co-registration is a mandatory prerequisite when dealing with remote sensing data. Inter- or intra-sensoral misregistration will negatively affect any subsequent image analysis, specifically when processing multi-sensoral or multi-temporal data. In recent decades, many algorithms have been developed to enable manual, semi- or fully automatic displacement correction. Especially in the context of big data processing and the development of automated processing chains that aim to be applicable to different remote sensing systems, there is a strong need for efficient, accurate and generally usable co-registration. Here, we present AROSICS (Automated and Robust Open-Source Image Co-Registration Software, a Python-based open-source software including an easy-to-use user interface for automatic detection and correction of sub-pixel misalignments between various remote sensing datasets. It is independent of spatial or spectral characteristics and robust against high degrees of cloud coverage and spectral and temporal land cover dynamics. The co-registration is based on phase correlation for sub-pixel shift estimation in the frequency domain utilizing the Fourier shift theorem in a moving-window manner. A dense grid of spatial shift vectors can be created and automatically filtered by combining various validation and quality estimation metrics. Additionally, the software supports the masking of, e.g., clouds and cloud shadows to exclude such areas from spatial shift detection. The software has been tested on more than 9000 satellite images acquired by different sensors. The results are evaluated exemplarily for two inter-sensoral and two intra-sensoral use cases and show registration results in the sub-pixel range with root mean square error fits around 0.3 pixels and better.

  7. System and software safety analysis for the ERA control computer

    International Nuclear Information System (INIS)

    Beerthuizen, P.G.; Kruidhof, W.

    2001-01-01

    The European Robotic Arm (ERA) is a seven degrees of freedom relocatable anthropomorphic robotic manipulator system, to be used in manned space operation on the International Space Station, supporting the assembly and external servicing of the Russian segment. The safety design concept and implementation of the ERA is described, in particular with respect to the central computer's software design. A top-down analysis and specification process is used to down flow the safety aspects of the ERA system towards the subsystems, which are produced by a consortium of companies in many countries. The user requirements documents and the critical function list are the key documents in this process. Bottom-up analysis (FMECA) and test, on both subsystem and system level, are the basis for safety verification. A number of examples show the use of the approach and methods used

  8. Compositional Solution Space Quantification for Probabilistic Software Analysis

    Science.gov (United States)

    Borges, Mateus; Pasareanu, Corina S.; Filieri, Antonio; d'Amorim, Marcelo; Visser, Willem

    2014-01-01

    Probabilistic software analysis aims at quantifying how likely a target event is to occur during program execution. Current approaches rely on symbolic execution to identify the conditions to reach the target event and try to quantify the fraction of the input domain satisfying these conditions. Precise quantification is usually limited to linear constraints, while only approximate solutions can be provided in general through statistical approaches. However, statistical approaches may fail to converge to an acceptable accuracy within a reasonable time. We present a compositional statistical approach for the efficient quantification of solution spaces for arbitrarily complex constraints over bounded floating-point domains. The approach leverages interval constraint propagation to improve the accuracy of the estimation by focusing the sampling on the regions of the input domain containing the sought solutions. Preliminary experiments show significant improvement on previous approaches both in results accuracy and analysis time.

  9. HistFitter software framework for statistical data analysis

    CERN Document Server

    Baak, M.; Côte, D.; Koutsman, A.; Lorenz, J.; Short, D.

    2015-01-01

    We present a software framework for statistical data analysis, called HistFitter, that has been used extensively by the ATLAS Collaboration to analyze big datasets originating from proton-proton collisions at the Large Hadron Collider at CERN. Since 2012 HistFitter has been the standard statistical tool in searches for supersymmetric particles performed by ATLAS. HistFitter is a programmable and flexible framework to build, book-keep, fit, interpret and present results of data models of nearly arbitrary complexity. Starting from an object-oriented configuration, defined by users, the framework builds probability density functions that are automatically fitted to data and interpreted with statistical tests. A key innovation of HistFitter is its design, which is rooted in core analysis strategies of particle physics. The concepts of control, signal and validation regions are woven into its very fabric. These are progressively treated with statistically rigorous built-in methods. Being capable of working with mu...

  10. APERO, AN OPEN SOURCE BUNDLE ADJUSMENT SOFTWARE FOR AUTOMATIC CALIBRATION AND ORIENTATION OF SET OF IMAGES

    Directory of Open Access Journals (Sweden)

    M. Pierrot Deseilligny

    2012-09-01

    Full Text Available IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

  11. 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.

  12. Image analysis enhancement and interpretation

    International Nuclear Information System (INIS)

    Glauert, A.M.

    1978-01-01

    The necessary practical and mathematical background are provided for the analysis of an electron microscope image in order to extract the maximum amount of structural information. Instrumental methods of image enhancement are described, including the use of the energy-selecting electron microscope and the scanning transmission electron microscope. The problems of image interpretation are considered with particular reference to the limitations imposed by radiation damage and specimen thickness. A brief survey is given of the methods for producing a three-dimensional structure from a series of two-dimensional projections, although emphasis is really given on the analysis, processing and interpretation of the two-dimensional projection of a structure. (Auth.)

  13. Image Analysis of Eccentric Photorefraction

    Directory of Open Access Journals (Sweden)

    J. Dušek

    2004-01-01

    Full Text Available This article deals with image and data analysis of the recorded video-sequences of strabistic infants. It describes a unique noninvasive measuring system based on two measuring methods (position of I. Purkynje image with relation to the centre of the lens and eccentric photorefraction for infants. The whole process is divided into three steps. The aim of the first step is to obtain video sequences on our special system (Eye Movement Analyser. Image analysis of the recorded sequences is performed in order to obtain curves of basic eye reactions (accommodation and convergence. The last step is to calibrate of these curves to corresponding units (diopter and degrees of movement.

  14. Introduction to Medical Image Analysis

    DEFF Research Database (Denmark)

    Paulsen, Rasmus Reinhold; Moeslund, Thomas B.

    This book is a result of a collaboration between DTU Informatics at the Technical University of Denmark and the Laboratory of Computer Vision and Media Technology at Aalborg University. It is partly based on the book ”Image and Video Processing”, second edition by Thomas Moeslund. The aim...... of the book is to present the fascinating world of medical image analysis in an easy and interesting way. Compared to many standard books on image analysis, the approach we have chosen is less mathematical and more casual. Some of the key algorithms are exemplified in C-code. Please note that the code...

  15. Shape analysis in medical image analysis

    CERN Document Server

    Tavares, João

    2014-01-01

    This book contains thirteen contributions from invited experts of international recognition addressing important issues in shape analysis in medical image analysis, including techniques for image segmentation, registration, modelling and classification, and applications in biology, as well as in cardiac, brain, spine, chest, lung and clinical practice. This volume treats topics such as, anatomic and functional shape representation and matching; shape-based medical image segmentation; shape registration; statistical shape analysis; shape deformation; shape-based abnormity detection; shape tracking and longitudinal shape analysis; machine learning for shape modeling and analysis; shape-based computer-aided-diagnosis; shape-based medical navigation; benchmark and validation of shape representation, analysis and modeling algorithms. This work will be of interest to researchers, students, and manufacturers in the fields of artificial intelligence, bioengineering, biomechanics, computational mechanics, computationa...

  16. ROCView: prototype software for data collection in jackknife alternative free-response receiver operating characteristic analysis

    Science.gov (United States)

    Thompson, J; Hogg, P; Thompson, S; Manning, D; Szczepura, K

    2012-01-01

    ROCView has been developed as an image display and response capture (IDRC) solution to image display and consistent recording of reader responses in relation to the free-response receiver operating characteristic paradigm. A web-based solution to IDRC for observer response studies allows observations to be completed from any location, assuming that display performance and viewing conditions are consistent with the study being completed. The simplistic functionality of the software allows observations to be completed without supervision. ROCView can display images from multiple modalities, in a randomised order if required. Following registration, observers are prompted to begin their image evaluation. All data are recorded via mouse clicks, one to localise (mark) and one to score confidence (rate) using either an ordinal or continuous rating scale. Up to nine “mark-rating” pairs can be made per image. Unmarked images are given a default score of zero. Upon completion of the study, both true-positive and false-positive reports can be downloaded and adapted for analysis. ROCView has the potential to be a useful tool in the assessment of modality performance difference for a range of imaging methods. PMID:22573294

  17. Optical granulometric analysis of sedimentary deposits by color segmentation-based software: OPTGRAN-CS

    Science.gov (United States)

    Chávez, G. Moreno; Sarocchi, D.; Santana, E. Arce; Borselli, L.

    2015-12-01

    The study of grain size distribution is fundamental for understanding sedimentological environments. Through these analyses, clast erosion, transport and deposition processes can be interpreted and modeled. However, grain size distribution analysis can be difficult in some outcrops due to the number and complexity of the arrangement of clasts and matrix and their physical size. Despite various technological advances, it is almost impossible to get the full grain size distribution (blocks to sand grain size) with a single method or instrument of analysis. For this reason development in this area continues to be fundamental. In recent years, various methods of particle size analysis by automatic image processing have been developed, due to their potential advantages with respect to classical ones; speed and final detailed content of information (virtually for each analyzed particle). In this framework, we have developed a novel algorithm and software for grain size distribution analysis, based on color image segmentation using an entropy-controlled quadratic Markov measure field algorithm and the Rosiwal method for counting intersections between clast and linear transects in the images. We test the novel algorithm in different sedimentary deposit types from 14 varieties of sedimentological environments. The results of the new algorithm were compared with grain counts performed manually by the same Rosiwal methods applied by experts. The new algorithm has the same accuracy as a classical manual count process, but the application of this innovative methodology is much easier and dramatically less time-consuming. The final productivity of the new software for analysis of clasts deposits after recording field outcrop images can be increased significantly.

  18. An Analysis of Related Software Cycles Among Organizations, People and the Software Industry

    National Research Council Canada - National Science Library

    Moore, Robert; Adams, Brady

    2008-01-01

    .... This thesis intends to explore the moderating factors of these three distinct and disjointed cycles and propose courses of action towards mitigating various issues and problems inherent in the software upgrade process...

  19. 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

  20. Artificial intelligence and medical imaging. Expert systems and image analysis

    International Nuclear Information System (INIS)

    Wackenheim, A.; Zoellner, G.; Horviller, S.; Jacqmain, T.

    1987-01-01

    This paper gives an overview on the existing systems for automated image analysis and interpretation in medical imaging, especially in radiology. The example of ORFEVRE, the system for the analysis of CAT-scan images of the cervical triplet (c3-c5) by image analysis and subsequent expert-system is given and discussed in detail. Possible extensions are described [fr

  1. Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

    Science.gov (United States)

    Wang, Chunliang; Ritter, Felix; Smedby, Orjan

    2010-07-01

    To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

  2. Mvox: Interactive 2-4D medical image and graphics visualization software

    DEFF Research Database (Denmark)

    Bro-Nielsen, Morten

    1996-01-01

    Mvox is a new tool for visualization, segmentation and manipulation of a wide range of 2-4D grey level and colour images, and 3D surface graphics, which has been developed at the Department of Mathematical Modelling, Technical University of Denmark. The principal idea behind the software has been...... to provide a flexible tool that is able to handle all the kinds of data that are typically used in a research environment for medical imaging and visualization. At the same time the software should be easy to use and have a consistent interface providing locally only the functions relevant to the context....... This has been achieved by using Unix standards such as X/Motif/OpenGL and conforming to modern standards of interactive windowed programs...

  3. Using CASE Software to Teach Undergraduates Systems Analysis and Design.

    Science.gov (United States)

    Wilcox, Russell E.

    1988-01-01

    Describes the design and delivery of a college course for information system students utilizing a Computer-Aided Software Engineering program. Discusses class assignments, cooperative learning, student attitudes, and the advantages of using this software in the course. (CW)

  4. ATLAS tile calorimeter cesium calibration control and analysis software

    International Nuclear Information System (INIS)

    Solovyanov, O; Solodkov, A; Starchenko, E; Karyukhin, A; Isaev, A; Shalanda, N

    2008-01-01

    An online control system to calibrate and monitor ATLAS Barrel hadronic calorimeter (TileCal) with a movable radioactive source, driven by liquid flow, is described. To read out and control the system an online software has been developed, using ATLAS TDAQ components like DVS (Diagnostic and Verification System) to verify the hardware before running, IS (Information Server) for data and status exchange between networked computers, and other components like DDC (DCS to DAQ Connection), to connect to PVSS-based slow control systems of Tile Calorimeter, high voltage and low voltage. A system of scripting facilities, based on Python language, is used to handle all the calibration and monitoring processes from hardware perspective to final data storage, including various abnormal situations. A QT based graphical user interface to display the status of the calibration system during the cesium source scan is described. The software for analysis of the detector response, using online data, is discussed. Performance of the system and first experience from the ATLAS pit are presented

  5. Phenomenology and Qualitative Data