Science.gov

Sample records for imaging workspace software

  1. Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.

    PubMed

    Prior, Fred W; Erickson, Bradley J; Tarbox, Lawrence

    2007-11-01

    The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research. PMID:17846835

  2. Teacher Workspaces

    ERIC Educational Resources Information Center

    Gordon, Douglas

    2010-01-01

    Well-designed and -equipped teacher workspaces provide the opportunity to improve student achievement at every step of their K-12 education. Shared workspace enhances communication among teachers as they evaluate student performance individually and collectively, and share insights with one another. This paper addresses the key elements found in…

  3. SAPHIRE 8 Volume 5 - Workspaces

    SciTech Connect

    C. L. Smith; J. K. Knudsen; D. O'Neal

    2011-03-01

    The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) Version 8 is a software application developed for performing a complete probabilistic risk assessment using a personal computer running the Microsoft Windows™ operating system. SAPHIRE 8 is funded by the U.S. Nuclear Regulatory Commission (NRC). The role of the Idaho National Laboratory (INL) in this project is that of software developer and tester. In older versions of SAPHIRE, the model creation and analysis functions were intermingled. However, in SAPHIRE 8, the act of creating a model has been separated from the analysis of that model in order to improve the quality of both the model (e.g., by avoiding inadvertent changes) and the analysis. Consequently, in SAPHIRE 8, the analysis of models is performed by using what are called Workspaces. Currently, there are Workspaces for three types of analyses: (1) the NRC’s Accident Sequence Precursor program, where the workspace is called “Events and Condition Assessment (ECA);” (2) the NRC’s Significance Determination Process (SDP); and (3) the General Analysis (GA) workspace. Workspaces for each type are created and saved separately from the base model which keeps the original database intact. Workspaces are independent of each other and modifications or calculations made within one workspace will not affect another. In addition, each workspace has a user interface and reports tailored for their intended uses.

  4. Cathodoluminescence Spectrum Imaging Software

    Energy Science and Technology Software Center (ESTSC)

    2011-04-07

    The software developed for spectrum imaging is applied to the analysis of the spectrum series generated by our cathodoluminescence instrumentation. This software provides advanced processing capabilities s such: reconstruction of photon intensity (resolved in energy) and photon energy maps, extraction of the spectrum from selected areas, quantitative imaging mode, pixel-to-pixel correlation spectrum line scans, ASCII, output, filling routines, drift correction, etc.

  5. Biological Imaging Software Tools

    PubMed Central

    Eliceiri, Kevin W.; Berthold, Michael R.; Goldberg, Ilya G.; Ibáñez, Luis; Manjunath, B.S.; Martone, Maryann E.; Murphy, Robert F.; Peng, Hanchuan; Plant, Anne L.; Roysam, Badrinath; Stuurman, Nico; Swedlow, Jason R.; Tomancak, Pavel; Carpenter, Anne E.

    2013-01-01

    Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options. PMID:22743775

  6. Image Processing Software

    NASA Technical Reports Server (NTRS)

    1992-01-01

    To convert raw data into environmental products, the National Weather Service and other organizations use the Global 9000 image processing system marketed by Global Imaging, Inc. The company's GAE software package is an enhanced version of the TAE, developed by Goddard Space Flight Center to support remote sensing and image processing applications. The system can be operated in three modes and is combined with HP Apollo workstation hardware.

  7. Flyover Animation of Phoenix Workspace

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation

    This animated 'flyover' of the workspace of NASA's Phoenix Mars Lander's was created from images taken by the Surface Stereo Imager on Sol 14 (June 8, 2008), or the 14th Martian day after landing.

    The visualization uses both of the camera's 'eyes' to provide depth perception and ranging. The camera is looking north over the workspace.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  8. Confined Space Imager (CSI) Software

    SciTech Connect

    Karelilz, David

    2013-07-03

    The software provides real-time image capture, enhancement, and display, and sensor control for the Confined Space Imager (CSI) sensor system The software captures images over a Cameralink connection and provides the following image enhancements: camera pixel to pixel non-uniformity correction, optical distortion correction, image registration and averaging, and illumination non-uniformity correction. The software communicates with the custom CSI hardware over USB to control sensor parameters and is capable of saving enhanced sensor images to an external USB drive. The software provides sensor control, image capture, enhancement, and display for the CSI sensor system. It is designed to work with the custom hardware.

  9. IMAGE Software Suite

    NASA Technical Reports Server (NTRS)

    Gallagher, Dennis L.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    The IMAGE Mission is generating a truely unique set of magnetospheric measurement through a first-of-its-kind complement of remote, global observations. These data are being distributed in the Universal Data Format (UDF), which consists of data, calibration, and documentation. This is an open dataset, available to all by request to the National Space Science Data Center (NSSDC) at NASA Goddard Space Flight Center. Browse data, which consists of summary observations, is also available through the NSSDC in the Common Data Format (CDF) and graphic representations of the browse data. Access to the browse data can be achieved through the NSSDC CDAWeb services or by use of NSSDC provided software tools. This presentation documents the software tools, being provided by the IMAGE team, for use in viewing and analyzing the UDF telemetry data. Like the IMAGE data, these tools are openly available. What these tools can do, how they can be obtained, and how they are expected to evolve will be discussed.

  10. Software thermal imager simulator

    NASA Astrophysics Data System (ADS)

    Le Noc, Loic; Pancrati, Ovidiu; Doucet, Michel; Dufour, Denis; Debaque, Benoit; Turbide, Simon; Berthiaume, Francois; Saint-Laurent, Louis; Marchese, Linda; Bolduc, Martin; Bergeron, Alain

    2014-10-01

    A software application, SIST, has been developed for the simulation of the video at the output of a thermal imager. The approach offers a more suitable representation than current identification (ID) range predictors do: the end user can evaluate the adequacy of a virtual camera as if he was using it in real operating conditions. In particular, the ambiguity in the interpretation of ID range is cancelled. The application also allows for a cost-efficient determination of the optimal design of an imager and of its subsystems without over- or under-specification: the performances are known early in the development cycle, for targets, scene and environmental conditions of interest. The simulated image is also a powerful method for testing processing algorithms. Finally, the display, which can be a severe system limitation, is also fully considered in the system by the use of real hardware components. The application consists in Matlabtm routines that simulate the effect of the subsystems atmosphere, optical lens, detector, and image processing algorithms. Calls to MODTRAN® for the atmosphere modeling and to Zemax for the optical modeling have been implemented. The realism of the simulation depends on the adequacy of the input scene for the application and on the accuracy of the subsystem parameters. For high accuracy results, measured imager characteristics such as noise can be used with SIST instead of less accurate models. The ID ranges of potential imagers were assessed for various targets, backgrounds and atmospheric conditions. The optimal specifications for an optical design were determined by varying the Seidel aberration coefficients to find the worst MTF that still respects the desired ID range.

  11. Confined Space Imager (CSI) Software

    Energy Science and Technology Software Center (ESTSC)

    2013-07-03

    The software provides real-time image capture, enhancement, and display, and sensor control for the Confined Space Imager (CSI) sensor system The software captures images over a Cameralink connection and provides the following image enhancements: camera pixel to pixel non-uniformity correction, optical distortion correction, image registration and averaging, and illumination non-uniformity correction. The software communicates with the custom CSI hardware over USB to control sensor parameters and is capable of saving enhanced sensor images to anmore » external USB drive. The software provides sensor control, image capture, enhancement, and display for the CSI sensor system. It is designed to work with the custom hardware.« less

  12. Image processing software for imaging spectrometry

    NASA Technical Reports Server (NTRS)

    Mazer, Alan S.; Martin, Miki; Lee, Meemong; Solomon, Jerry E.

    1988-01-01

    The paper presents a software system, Spectral Analysis Manager (SPAM), which has been specifically designed and implemented to provide the exploratory analysis tools necessary for imaging spectrometer data, using only modest computational resources. The basic design objectives are described as well as the major algorithms designed or adapted for high-dimensional images. Included in a discussion of system implementation are interactive data display, statistical analysis, image segmentation and spectral matching, and mixture analysis.

  13. Phoenix Robotic Arm's Workspace After 90 Sols

    NASA Technical Reports Server (NTRS)

    2008-01-01

    During the first 90 Martian days, or sols, after its May 25, 2008, landing on an arctic plain of Mars, NASA's Phoenix Mars Lander dug several trenches in the workspace reachable with the lander's robotic arm.

    The lander's Surface Stereo Imager camera recorded this view of the workspace on Sol 90, early afternoon local Mars time (overnight Aug. 25 to Aug. 26, 2008). The shadow of the the camera itself, atop its mast, is just left of the center of the image and roughly a third of a meter (one foot) wide.

    The workspace is on the north side of the lander. The trench just to the right of center is called 'Neverland.'

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  14. Spotlight-8 Image Analysis Software

    NASA Technical Reports Server (NTRS)

    Klimek, Robert; Wright, Ted

    2006-01-01

    Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

  15. Automatic AVHRR image navigation software

    NASA Technical Reports Server (NTRS)

    Baldwin, Dan; Emery, William

    1992-01-01

    This is the final report describing the work done on the project entitled Automatic AVHRR Image Navigation Software funded through NASA-Washington, award NAGW-3224, Account 153-7529. At the onset of this project, we had developed image navigation software capable of producing geo-registered images from AVHRR data. The registrations were highly accurate but required a priori knowledge of the spacecraft's axes alignment deviations, commonly known as attitude. The three angles needed to describe the attitude are called roll, pitch, and yaw, and are the components of the deviations in the along scan, along track and about center directions. The inclusion of the attitude corrections in the navigation software results in highly accurate georegistrations, however, the computation of the angles is very tedious and involves human interpretation for several steps. The technique also requires easily identifiable ground features which may not be available due to cloud cover or for ocean data. The current project was motivated by the need for a navigation system which was automatic and did not require human intervention or ground control points. The first step in creating such a system must be the ability to parameterize the spacecraft's attitude. The immediate goal of this project was to study the attitude fluctuations and determine if they displayed any systematic behavior which could be modeled or parameterized. We chose a period in 1991-1992 to study the attitude of the NOAA 11 spacecraft using data from the Tiros receiving station at the Colorado Center for Astrodynamic Research (CCAR) at the University of Colorado.

  16. Easy and Accessible Imaging Software

    NASA Technical Reports Server (NTRS)

    2003-01-01

    DATASTAR, Inc., of Picayune, Mississippi, has taken NASA s award-winning Earth Resources Laboratory Applications Software (ELAS) program and evolved it into a user-friendly desktop application and Internet service to perform processing, analysis, and manipulation of remotely sensed imagery data. NASA s Stennis Space Center developed ELAS in the early 1980s to process satellite and airborne sensor imagery data of the Earth s surface into readable and accessible information. Since then, ELAS information has been applied worldwide to determine soil content, rainfall levels, and numerous other variances of topographical information. However, end-users customarily had to depend on scientific or computer experts to provide the results, because the imaging processing system was intricate and labor intensive.

  17. Software for Automated Image-to-Image Co-registration

    NASA Technical Reports Server (NTRS)

    Benkelman, Cody A.; Hughes, Heidi

    2007-01-01

    The project objectives are: a) Develop software to fine-tune image-to-image co-registration, presuming images are orthorectified prior to input; b) Create a reusable software development kit (SDK) to enable incorporation of these tools into other software; d) provide automated testing for quantitative analysis; and e) Develop software that applies multiple techniques to achieve subpixel precision in the co-registration of image pairs.

  18. Workspaces that move people.

    PubMed

    Waber, Ben; Magnolfi, Jennifer; Lindsay, Greg

    2014-10-01

    Few companies measure whether the design of their workspaces helps or hurts performance, but they should. The authors have collected data that capture individuals' interactions, communications, and location information. They've learned that face-to-face interactions are by far the most important activity in an office; creating chance encounters between knowledge workers, both inside and outside the organization, improves performance. The Norwegian telecom company Telenor was ahead of its time in 2003, when it incorporated "hot desking" (no assigned seats) and spaces that could easily be reconfigured for different tasks and evolving teams. The CEO credits the design of the offices with helping Telenor shift from a state-run monopoly to a competitive multinational carrier with 150 million subscribers. In another example, data collected at one pharmaceuticals company showed that when a salesperson increased interactions with coworkers on other teams by 10%, his or her sales increased by 10%. To get the sales staff running into colleagues from other departments, management shifted from one coffee machine for every six employees to one for every 120 and created a new large cafeteria for everyone. Sales rose by 20%, or $200 million, afterjust one quarter, quickly justifying the capital investment in the redesign. PMID:25509577

  19. False Color Terrain Model of Phoenix Workspace

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is a terrain model of Phoenix's Robotic Arm workspace. It has been color coded by depth with a lander model for context. The model has been derived using images from the depth perception feature from Phoenix's Surface Stereo Imager (SSI). Red indicates low-lying areas that appear to be troughs. Blue indicates higher areas that appear to be polygons.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  20. Image analysis library software development

    NASA Technical Reports Server (NTRS)

    Guseman, L. F., Jr.; Bryant, J.

    1977-01-01

    The Image Analysis Library consists of a collection of general purpose mathematical/statistical routines and special purpose data analysis/pattern recognition routines basic to the development of image analysis techniques for support of current and future Earth Resources Programs. Work was done to provide a collection of computer routines and associated documentation which form a part of the Image Analysis Library.

  1. Software Operates On Bit-Map Images

    NASA Technical Reports Server (NTRS)

    Choi, Diana

    1992-01-01

    PIXTOOLS is software for Silicon Graphics IRIS consisting of thirteen programs plus library for operating on bit-map images. Enables user to create, edit, and save high-resolution images in forms in which displayed on video screens, resize them, and capture them. Eleven programs print information and read and write files. Two offer graphical interfaces. Menus enable manipulation of images and background color and saving of an image screen to file. Written in C.

  2. Infrared Imaging Data Reduction Software and Techniques

    NASA Astrophysics Data System (ADS)

    Sabbey, C. N.; McMahon, R. G.; Lewis, J. R.; Irwin, M. J.

    Developed to satisfy certain design requirements not met in existing packages (e.g., full weight map handling) and to optimize the software for large data sets (non-interactive tasks that are CPU and disk efficient), the InfraRed Data Reduction software package is a small ANSI C library of fast image processing routines for automated pipeline reduction of infrared (dithered) observations. The software includes stand-alone C programs for tasks such as running sky frame subtraction with object masking, image registration and co-addition with weight maps, dither offset measurement using cross-correlation, and object mask dilation. Although currently used for near-IR mosaic images, the modular software is concise and readily adaptable for reuse in other work. IRDR, available via anonymous ftp at ftp.ast.cam.ac.uk in pub/sabbey

  3. Software for Simulation of Hyperspectral Images

    NASA Technical Reports Server (NTRS)

    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.

  4. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center,atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image stabilization and Registration (VISAR), which is illustrated in this Quick Time movie. VISAR is a computer algorithm that stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. VISAR could also have applications in law enforcement, medical, and meteorological imaging. The software can be used for defense application by improving reconnaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  5. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center, atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image Stabilization and Registration (VISAR), which is illustrated in this Quick Time movie. VISAR is a computer algorithm that stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. VISAR could also have applications in law enforcement, medical, and meteorological imaging. The software can be used for defense application by improving reconnaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  6. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center,atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image Stabilization and Registration (VISAR). VISAR may help law enforcement agencies catch criminals by improving the quality of video recorded at crime scenes. In this photograph, the single frame at left, taken at night, was brightened in order to enhance details and reduce noise or snow. To further overcome the video defects in one frame, Law enforcement officials can use VISAR software to add information from multiple frames to reveal a person. Images from less than a second of videotape were added together to create the clarified image at right. VISAR stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. VISAR could also have applications in medical and meteorological imaging. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. The software can be used for defense application by improving recornaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  7. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA Marshall Space Flight Center, atmospheric scientist Paul Meyer (left) and solar physicist Dr. David Hathaway, have developed promising new software, called Video Image Stabilization and Registration (VISAR), that may help law enforcement agencies to catch criminals by improving the quality of video recorded at crime scenes, VISAR stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects; produces clearer images of moving objects; smoothes jagged edges; enhances still images; and reduces video noise of snow. VISAR could also have applications in medical and meteorological imaging. It could steady images of Ultrasounds which are infamous for their grainy, blurred quality. It would be especially useful for tornadoes, tracking whirling objects and helping to determine the tornado's wind speed. This image shows two scientists reviewing an enhanced video image of a license plate taken from a moving automobile.

  8. Product review: lucis image processing software.

    PubMed

    Johnson, J E

    1999-04-01

    Lucis is a software program that allows the manipulation of images through the process of selective contrast pattern emphasis. Using an image-processing algorithm called Differential Hysteresis Processing (DHP), Lucis extracts and highlights patterns based on variations in image intensity (luminance). The result is that details can be seen that would otherwise be hidden in deep shadow or excessive brightness. The software is contained on a single floppy disk, is easy to install on a PC, simple to use, and runs on Windows 95, Windows 98, and Windows NT operating systems. The cost is $8,500 for a license, but is estimated to save a great deal of money in photographic materials, time, and labor that would have otherwise been spent in the darkroom. Superb images are easily obtained from unstained (no lead or uranium) sections, and stored image files sent to laser printers are of publication quality. The software can be used not only for all types of microscopy, including color fluorescence light microscopy, biological and materials science electron microscopy (TEM and SEM), but will be beneficial in medicine, such as X-ray films (pending approval by the FDA), and in the arts. PMID:10206154

  9. SUPRIM: easily modified image processing software.

    PubMed

    Schroeter, J P; Bretaudiere, J P

    1996-01-01

    A flexible, modular software package intended for the processing of electron microscopy images is presented. The system consists of a set of image processing tools or filters, written in the C programming language, and a command line style user interface based on the UNIX shell. The pipe and filter structure of UNIX and the availability of command files in the form of shell scripts eases the construction of complex image processing procedures from the simpler tools. Implementation of a new image processing algorithm in SUPRIM may often be performed by construction of a new shell script, using already existing tools. Currently, the package has been used for two- and three-dimensional image processing and reconstruction of macromolecules and other structures of biological interest. PMID:8742734

  10. Salvo: Seismic imaging software for complex geologies

    SciTech Connect

    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.

  11. Objective facial photograph analysis using imaging software.

    PubMed

    Pham, Annette M; Tollefson, Travis T

    2010-05-01

    Facial analysis is an integral part of the surgical planning process. Clinical photography has long been an invaluable tool in the surgeon's practice not only for accurate facial analysis but also for enhancing communication between the patient and surgeon, for evaluating postoperative results, for medicolegal documentation, and for educational and teaching opportunities. From 35-mm slide film to the digital technology of today, clinical photography has benefited greatly from technological advances. With the development of computer imaging software, objective facial analysis becomes easier to perform and less time consuming. Thus, while the original purpose of facial analysis remains the same, the process becomes much more efficient and allows for some objectivity. Although clinical judgment and artistry of technique is never compromised, the ability to perform objective facial photograph analysis using imaging software may become the standard in facial plastic surgery practices in the future. PMID:20511080

  12. Imaging Sensor Flight and Test Equipment Software

    NASA Technical Reports Server (NTRS)

    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

  13. User questionnaire to evaluate the radiological workspace.

    PubMed

    van Ooijen, Peter M A; Koesoema, Allya P; Oudkerk, Matthijs

    2006-01-01

    Over the past few years, an increase in digitalization of radiology departments can be seen, which has a large impact on the work of the radiologists. This impact is not only demonstrated by the increased use of digital images but also by changing demands on the whole reading environment. In this study, we evaluated the satisfaction of our radiologists with our digital Picture Archival and Communication System environment and their workspace. This evaluation was performed by distribution of a questionnaire consisting of a score sheet and some open questions to all radiologists and residents. Out of 25 questionnaires, 12 were adequately answered and returned. Results clearly showed that most problems were present in the area of reading room design and layout and comfort and ergonomics. Based on the results from this study, adaptations were made and the results were also used in the planning of the redesign of the entire department of radiology. PMID:16767350

  14. ICER-3D Hyperspectral Image Compression Software

    NASA Technical Reports Server (NTRS)

    Xie, Hua; Kiely, Aaron; Klimesh, matthew; Aranki, Nazeeh

    2010-01-01

    Software has been developed to implement the ICER-3D algorithm. ICER-3D effects progressive, three-dimensional (3D), wavelet-based compression of hyperspectral images. If a compressed data stream is truncated, the progressive nature of the algorithm enables reconstruction of hyperspectral data at fidelity commensurate with the given data volume. The ICER-3D software is capable of providing either lossless or lossy compression, and incorporates an error-containment scheme to limit the effects of data loss during transmission. The compression algorithm, which was derived from the ICER image compression algorithm, includes wavelet-transform, context-modeling, and entropy coding subalgorithms. The 3D wavelet decomposition structure used by ICER-3D exploits correlations in all three dimensions of sets of hyperspectral image data, while facilitating elimination of spectral ringing artifacts, using a technique summarized in "Improving 3D Wavelet-Based Compression of Spectral Images" (NPO-41381), NASA Tech Briefs, Vol. 33, No. 3 (March 2009), page 7a. Correlation is further exploited by a context-modeling subalgorithm, which exploits spectral dependencies in the wavelet-transformed hyperspectral data, using an algorithm that is summarized in "Context Modeler for Wavelet Compression of Hyperspectral Images" (NPO-43239), which follows this article. An important feature of ICER-3D is a scheme for limiting the adverse effects of loss of data during transmission. In this scheme, as in the similar scheme used by ICER, the spatial-frequency domain is partitioned into rectangular error-containment regions. In ICER-3D, the partitions extend through all the wavelength bands. The data in each partition are compressed independently of those in the other partitions, so that loss or corruption of data from any partition does not affect the other partitions. Furthermore, because compression is progressive within each partition, when data are lost, any data from that partition received

  15. Workspaces in the Semantic Web

    NASA Technical Reports Server (NTRS)

    Wolfe, Shawn R.; Keller, RIchard M.

    2005-01-01

    Due to the recency and relatively limited adoption of Semantic Web technologies. practical issues related to technology scaling have received less attention than foundational issues. Nonetheless, these issues must be addressed if the Semantic Web is to realize its full potential. In particular, we concentrate on the lack of scoping methods that reduce the size of semantic information spaces so they are more efficient to work with and more relevant to an agent's needs. We provide some intuition to motivate the need for such reduced information spaces, called workspaces, give a formal definition, and suggest possible methods of deriving them.

  16. Image processing software for imaging spectrometry data analysis

    NASA Technical Reports Server (NTRS)

    Mazer, Alan; Martin, Miki; Lee, Meemong; Solomon, Jerry E.

    1988-01-01

    Imaging spectrometers simultaneously collect image data in hundreds of spectral channels, from the near-UV to the IR, and can thereby provide direct surface materials identification by means resembling laboratory reflectance spectroscopy. Attention is presently given to a software system, the Spectral Analysis Manager (SPAM) for the analysis of imaging spectrometer data. SPAM requires only modest computational resources and is composed of one main routine and a set of subroutine libraries. Additions and modifications are relatively easy, and special-purpose algorithms have been incorporated that are tailored to geological applications.

  17. IMCAT: Image and Catalogue Manipulation Software

    NASA Astrophysics Data System (ADS)

    Kaiser, Nick

    2011-08-01

    The IMCAT software was developed initially to do faint galaxy photometry for weak lensing studies, and provides a fairly complete set of tools for this kind of work. Unlike most packages for doing data analysis, the tools are standalone unix commands which you can invoke from the shell, via shell scripts or from perl scripts. The tools are arranges in a tree of directories. One main branch is the 'imtools'. These deal only with fits files. The most important imtool is the 'image calculator' 'ic' which allows one to do rather general operations on fits images. A second branch is the 'catools' which operate only on catalogues. The key cattool is 'lc'; this effectively defines the format of IMCAT catalogues, and allows one to do very general operations on and filtering of such catalogues. A third branch is the 'imcattools'. These tend to be much more specialised than the cattools and imcattools and are focussed on faint galaxy photometry.

  18. Collaborative workspace for multimedia medical conferencing.

    PubMed

    Kim, H J; Park, E S; Lee, S G; Shin, Y G

    1998-01-01

    We propose an approach for collaborative workspace management in medical conferencing. A collaborative workspace is a virtual data space shared between medical experts for working out solutions collaboratively while conferencing. Our approach provides medical users with an integrated view of various kinds of multimedia patient data and a unified control over the workspace. For data navigation and conferencing, a tree-like navigation tool, which we named the patient record tree, is provided. And we classify patient data, which is the object of medical collaborative works, into six basic types, and provide a view template for displaying each of these types. PMID:10384472

  19. A Global Workspace perspective on mental disorders

    PubMed Central

    Wallace, Rodrick

    2005-01-01

    Background Recent developments in Global Workspace theory suggest that human consciousness can suffer interpenetrating dysfunctions of mutual and reciprocal interaction with embedding environments which will have early onset and often insidious staged developmental progression, possibly according to a cancer model, in which a set of long-evolved control strategies progressively fails. Methods and results A rate distortion argument implies that, if an external information source carries a damaging 'message', then sufficient exposure to it, particularly during critical developmental periods, is sure to write a sufficiently accurate image of it on mind and body in a punctuated manner so as to initiate or promote similarly progressively punctuated developmental disorder, in essence either a staged failure affecting large-scale brain connectivity, which is the sine qua non of human consciousness, or else damaging the ability of embedding goal contexts to contain conscious dynamics. Conclusion The key intervention, at the population level, is clearly to limit exposure to factors triggering developmental disorders, a question of proper environmental sanitation, in a large sense, primarily a matter of social justice which has long been known to be determined almost entirely by the interactions of cultural trajectory, group power relations, and economic structure, with public policy. Intervention at the individual level appears limited to triggering or extending periods of remission, representing reestablishment of an extensive, but largely unexplored, spectrum of evolved control strategies, in contrast with the far better-understood case of cancer. PMID:16371149

  20. Metamodels for Planar 3R Workspace Optimization.

    SciTech Connect

    Turner, C. J.

    2002-01-01

    Robotic workspace optimization is a central element of robot system design. To formulate the optimization problem, the complex relationships between design variables, tuning parameters, and performance indices need to be accurately and efficiently represented. The nature of the relationships suggests that metamodels, or models of the models, should be used to derive suitable objective functions. A comparison of two metamodeling techniques for robotic workspace optimization problems for several trial cases suggests that non-uniform rational B-spline models, derived from computer graphics and computer-aided design techniques, are as suitable as response surface models to solve planar 3R workspace optimization problems. Promising nonlinear modeling results with B-spline models suggest future work is justified and performance gains can be realized.

  1. Prototype for remotely shared textual workspaces

    SciTech Connect

    Abdel-Wahab, H.M.; Guan, S.U.; Nievergelt, J.

    1987-01-01

    Computer-based collaboration between geographically dispersed users is still limited primarily to electronic mail and file transfer, but there is increasing interest in computer support for real-time interaction between remote users. The problem of implementing remotely shared workspaces, which allow users to operate simultaneously on the same objects, is of broad interest. Our objective is to show textual workspaces that allow real-time collaboration can be implemented efficiently by using existing operating systems and communications primitives. This paper documents our experiences in implementing a prototype under Berkeley UNIX, using the programming language C, and Berkeley Interprocess Communication facilities. The authors describe design alternatives that take into account the communications bandwidth between the different sites of the network, and they introduce an efficient protocol that regulates user access to the shared workspace.

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

    SciTech Connect

    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.

  3. Using Shared Workspaces in Higher Education.

    ERIC Educational Resources Information Center

    Sikkel, Klaas; Gommer, Lisa; Veen, Jan van der

    2002-01-01

    Evaluates use of BSCW (a groupware system) shared workspaces in higher education by means of a comparison of seven courses in which this environment was used. Identifies different functions for which the BSCW environment has been used and discusses the relative success of these functions across the cases. (AEF)

  4. Earth Observation Services (Image Processing Software)

    NASA Technical Reports Server (NTRS)

    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.

  5. Software Helps Extract Information From Astronomical Images

    NASA Technical Reports Server (NTRS)

    Hartley, Booth; Ebert, Rick; Laughlin, Gaylin

    1995-01-01

    PAC Skyview 2.0 is interactive program for display and analysis of astronomical images. Includes large set of functions for display, analysis and manipulation of images. "Man" pages with descriptions of functions and examples of usage included. Skyview used interactively or in "server" mode, in which another program calls Skyview and executes commands itself. Skyview capable of reading image data files of four types, including those in FITS, S, IRAF, and Z formats. Written in C.

  6. Development and implementation of software systems for imaging spectroscopy

    USGS Publications Warehouse

    Boardman, J.W.; Clark, R.N.; Mazer, A.S.; Biehl, L.L.; Kruse, F.A.; Torson, J.; Staenz, K.

    2006-01-01

    Specialized software systems have played a crucial role throughout the twenty-five year course of the development of the new technology of imaging spectroscopy, or hyperspectral remote sensing. By their very nature, hyperspectral data place unique and demanding requirements on the computer software used to visualize, analyze, process and interpret them. Often described as a marriage of the two technologies of reflectance spectroscopy and airborne/spaceborne remote sensing, imaging spectroscopy, in fact, produces data sets with unique qualities, unlike previous remote sensing or spectrometer data. Because of these unique spatial and spectral properties hyperspectral data are not readily processed or exploited with legacy software systems inherited from either of the two parent fields of study. This paper provides brief reviews of seven important software systems developed specifically for imaging spectroscopy.

  7. MaZda--a software package for image texture analysis.

    PubMed

    Szczypiński, Piotr M; Strzelecki, Michał; Materka, Andrzej; Klepaczko, Artur

    2009-04-01

    MaZda, a software package for 2D and 3D image texture analysis is presented. It provides a complete path for quantitative analysis of image textures, including computation of texture features, procedures for feature selection and extraction, algorithms for data classification, various data visualization and image segmentation tools. Initially, MaZda was aimed at analysis of magnetic resonance image textures. However, it revealed its effectiveness in analysis of other types of textured images, including X-ray and camera images. The software was utilized by numerous researchers in diverse applications. It was proven to be an efficient and reliable tool for quantitative image analysis, even in more accurate and objective medical diagnosis. MaZda was also successfully used in food industry to assess food product quality. MaZda can be downloaded for public use from the Institute of Electronics, Technical University of Lodz webpage. PMID:18922598

  8. Software for Viewing Landsat Mosaic Images

    NASA Technical Reports Server (NTRS)

    Watts, Jack; Farve, Catherine L.; Harvey, Craig

    2002-01-01

    A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of 5 in latitude by approximately equal to 6 degrees in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bit-map file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

  9. Software for Viewing Landsat Mosaic Images

    NASA Technical Reports Server (NTRS)

    2002-01-01

    A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of approx. 5 in latitude by approx. 6 deg in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bit-map file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

  10. Software for Viewing Landsat Mosaic Images

    NASA Technical Reports Server (NTRS)

    Watts, Zack; Farve, Catharine L.; Harvey, Craig

    2003-01-01

    A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of .5 in latitude by .6 in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bitmap file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

  11. The image related services of the HELIOS software engineering environment.

    PubMed

    Engelmann, U; Meinzer, H P; Schröter, A; Günnel, U; Demiris, A M; Makabe, M; Evers, H; Jean, F C; Degoulet, P

    1995-01-01

    This paper describes the approach of the European HELIOS project to integrate image processing tools into ward information systems. The image processing tools are the result of the basic research in image analysis in the Department Medical and Biological Informatics at the German Cancer Research Center. These tools for the analysis of two-dimensional images and three-dimensional data volumes with 3D reconstruction and visualization ae part of the Image Related Services of HELIOS. The HELIOS software engineering environment allows to use the image processing functionality in integrated applications. PMID:7743775

  12. Software Graphical User Interface For Analysis Of Images

    NASA Technical Reports Server (NTRS)

    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.

  13. FITSH: Software Package for Image Processing

    NASA Astrophysics Data System (ADS)

    Pál, András

    2011-11-01

    FITSH provides a standalone environment for analysis of data acquired by imaging astronomical detectors. The package provides utilities both for the full pipeline of subsequent related data processing steps (including image calibration, astrometry, source identification, photometry, differential analysis, low-level arithmetic operations, multiple image combinations, spatial transformations and interpolations, etc.) and for aiding the interpretation of the (mainly photometric and/or astrometric) results. The package also features a consistent implementation of photometry based on image subtraction, point spread function fitting and aperture photometry and provides easy-to-use interfaces for comparisons and for picking the most suitable method for a particular problem. The utilities in the package are built on the top of the commonly used UNIX/POSIX shells (hence the name of the package), therefore both frequently used and well-documented tools for such environments can be exploited and managing massive amount of data is rather convenient.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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 0.5Tesla 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 500kHz 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. PMID:27394165

  16. MOSAIC: Software for creating mosaics from collections of images

    NASA Technical Reports Server (NTRS)

    Varosi, F.; Gezari, D. Y.

    1992-01-01

    We have developed a powerful, versatile image processing and analysis software package called MOSAIC, designed specifically for the manipulation of digital astronomical image data obtained with (but not limited to) two-dimensional array detectors. The software package is implemented using the Interactive Data Language (IDL), and incorporates new methods for processing, calibration, analysis, and visualization of astronomical image data, stressing effective methods for the creation of mosaic images from collections of individual exposures, while at the same time preserving the photometric integrity of the original data. Since IDL is available on many computers, the MOSAIC software runs on most UNIX and VAX workstations with the X-Windows or Sun View graphics interface.

  17. MOPEX: a software package for astronomical image processing and visualization

    NASA Astrophysics Data System (ADS)

    Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

    2006-06-01

    We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software

  18. Image-Processing Software For A Hypercube Computer

    NASA Technical Reports Server (NTRS)

    Lee, Meemong; Mazer, Alan S.; Groom, Steven L.; Williams, Winifred I.

    1992-01-01

    Concurrent Image Processing Executive (CIPE) is software system intended to develop and use image-processing application programs on concurrent computing environment. Designed to shield programmer from complexities of concurrent-system architecture, it provides interactive image-processing environment for end user. CIPE utilizes architectural characteristics of particular concurrent system to maximize efficiency while preserving architectural independence from user and programmer. CIPE runs on Mark-IIIfp 8-node hypercube computer and associated SUN-4 host computer.

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

    NASA Astrophysics Data System (ADS)

    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.

  20. NASA's MERBoard: An Interactive Collaborative Workspace Platform. Chapter 4

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Wales, Roxana; Gossweiler, Rich

    2003-01-01

    This chapter describes the ongoing process by which a multidisciplinary group at NASA's Ames Research Center is designing and implementing a large interactive work surface called the MERBoard Collaborative Workspace. A MERBoard system involves several distributed, large, touch-enabled, plasma display systems with custom MERBoard software. A centralized server and database back the system. We are continually tuning MERBoard to support over two hundred scientists and engineers during the surface operations of the Mars Exploration Rover Missions. These scientists and engineers come from various disciplines and are working both in small and large groups over a span of space and time. We describe the multidisciplinary, human-centered process by which this h4ERBoard system is being designed, the usage patterns and social interactions that we have observed, and issues we are currently facing.

  1. Single-molecule localization software applied to photon counting imaging.

    PubMed

    Hirvonen, Liisa M; Kilfeather, Tiffany; Suhling, Klaus

    2015-06-01

    Centroiding in photon counting imaging has traditionally been accomplished by a single-step, noniterative algorithm, often implemented in hardware. Single-molecule localization techniques in superresolution fluorescence microscopy are conceptually similar, but use more sophisticated iterative software-based fitting algorithms to localize the fluorophore. Here, we discuss common features and differences between single-molecule localization and photon counting imaging and investigate the suitability of single-molecule localization software for photon event localization. We find that single-molecule localization software packages designed for superresolution microscopy-QuickPALM, rapidSTORM, and ThunderSTORM-can work well when applied to photon counting imaging with a microchannel-plate-based intensified camera system: photon event recognition can be excellent, fixed pattern noise can be low, and the microchannel plate pores can easily be resolved. PMID:26192667

  2. Performance of Personal Workspace Controls Final Report

    SciTech Connect

    Rubinstein, Francis; Kiliccote, Sila; Loffeld, John; Pettler,Pete; Snook, Joel

    2004-12-01

    One of the key deliverables for the DOE-funded controls research at LBNL for FY04 was the development of a prototype Personal Workspace Control system. The successful development of this system is a critical milestone for the LBNL Lighting Controls Research effort because this system demonstrates how IBECS can add value to today's Task Ambient lighting systems. LBNL has argued that by providing both the occupant and the facilities manager with the ability to precisely control the operation of overhead lighting and all task lighting in a coordinated manner, that task ambient lighting can optimize energy performance and occupant comfort simultaneously [Reference Task Ambient Foundation Document]. The Personal Workspace Control system is the application of IBECS to this important lighting problem. This report discusses the development of the Personal Workspace Control to date including descriptions of the different fixture types that have been converted to IBECS operation and a detailed description of the operation of PWC Scene Controller, which provides the end user with precise control of his task ambient lighting system. The objective, from the Annual Plan, is to demonstrate improvements in efficiency, lighting quality and occupant comfort realized using Personal Workspace Controls (PWC) designed to optimize the delivery of lighting to the individual's workstation regardless of which task-ambient lighting solution is chosen. The PWC will be capable of controlling floor-mounted, desk lamps, furniture-mounted and overhead lighting fixtures from a personal computer and handheld remote. The PWC will use an environmental sensor to automatically monitor illuminance, temperature and occupancy and to appropriately modulate ambient lighting according to daylight availability and to switch off task lighting according to local occupancy. [Adding occupancy control to the system would blunt the historical criticism of occupant-controlled lighting - the tendency of the occupant

  3. Modified control software for imaging ultracold atomic clouds

    NASA Astrophysics Data System (ADS)

    Whitaker, D. L.; Sharma, A.; Brown, J. M.

    2006-12-01

    A charge-coupled device (CCD) camera capable of taking high-quality images of ultracold atomic samples can often represent a significant portion of the equipment costs in atom trapping experiment. We have modified the commercial control software of a CCD camera designed for astronomical imaging to take absorption images of ultracold rubidium clouds. This camera is sensitive at 780 nm and has been modified to take three successive 16-bit images at full resolution. The control software can be integrated into a Matlab graphical user interface with fitting routines written as Matlab functions. This camera is capable of recording high-quality images at a fraction of the cost of similar cameras typically used in atom trapping experiments.

  4. Parallel algorithm for computing 3-D reachable workspaces

    NASA Astrophysics Data System (ADS)

    Alameldin, Tarek K.; Sobh, Tarek M.

    1992-03-01

    The problem of computing the 3-D workspace for redundant articulated chains has applications in a variety of fields such as robotics, computer aided design, and computer graphics. The computational complexity of the workspace problem is at least NP-hard. The recent advent of parallel computers has made practical solutions for the workspace problem possible. Parallel algorithms for computing the 3-D workspace for redundant articulated chains with joint limits are presented. The first phase of these algorithms computes workspace points in parallel. The second phase uses workspace points that are computed in the first phase and fits a 3-D surface around the volume that encompasses the workspace points. The second phase also maps the 3- D points into slices, uses region filling to detect the holes and voids in the workspace, extracts the workspace boundary points by testing the neighboring cells, and tiles the consecutive contours with triangles. The proposed algorithms are efficient for computing the 3-D reachable workspace for articulated linkages, not only those with redundant degrees of freedom but also those with joint limits.

  5. Analyzing huge pathology images with open source software

    PubMed Central

    2013-01-01

    Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http

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

    NASA Technical Reports Server (NTRS)

    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.

  7. Software development for a Ring Imaging Detector

    NASA Astrophysics Data System (ADS)

    Torisky, Benjamin; Benmokhtar, Fatiha

    2015-04-01

    Jefferson Lab (Jlab) is performing a large-scale upgrade to their Continuous Electron Beam Accelerator Facility (CEBAF) up to 12 GeV beam. The Large Acceptance Spectrometer (CLAS12) in Hall B is being upgraded and a new Ring Imaging CHerenkov (RICH) detector is being developed to provide better kaon - pion separation throughout the 3 to 12 GeV range. With this addition, when the electron beam hits the target, the resulting pions, kaons, and other particles will pass through a wall of translucent aerogel tiles and create Cherenkov radiation. This light can then be accurately detected by a large array of Multi-Anode PhotoMultiplier Tubes (MA-PMT). I am presenting my work on the implementation of Java based reconstruction programs for the RICH in the CLAS12 main analysis package.

  8. Software Development for Ring Imaging Detector

    NASA Astrophysics Data System (ADS)

    Torisky, Benjamin

    2016-03-01

    Jefferson Lab (Jlab) is performing a large-scale upgrade to their Continuous Electron Beam Accelerator Facility (CEBAF) up to 12GeV beam. The Large Acceptance Spectrometer (CLAS12) in Hall B is being upgraded and a new Ring Imaging Cherenkov (RICH) detector is being developed to provide better kaon - pion separation throughout the 3 to 12 GeV range. With this addition, when the electron beam hits the target, the resulting pions, kaons, and other particles will pass through a wall of translucent aerogel tiles and create Cherenkov radiation. This light can then be accurately detected by a large array of Multi-Anode PhotoMultiplier Tubes (MA-PMT). I am presenting an update on my work on the implementation of Java based reconstruction programs for the RICH in the CLAS12 main analysis package.

  9. Software to model AXAF image quality

    NASA Technical Reports Server (NTRS)

    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

  10. Open environment for image processing and software development

    NASA Astrophysics Data System (ADS)

    Rasure, John R.; Young, Mark

    1992-04-01

    The main goal of the Khoros software project is to create and provide an integrated software development environment for information processing and data visualization. The Khoros software system is now being used as a foundation to improve productivity and promote software reuse in a wide variety of application domain. A powerful feature of the Khoros system is the high-level, abstract visual language that can be employed to significantly boost the productivity of the researcher. Central to the Khoros system is the need for a consistent yet flexible user interface development system that provides cohesiveness to the vast number of programs that make up the Khoros system. Automated tools assist in maintenance as well as development of programs. The software structure that embodies this system provides for extensibility and portability, and allows for easy tailoring to target specific application domains and processing environments. First, an overview of the Khoros software environment is given. Then this paper presents the abstract applications programmer interface, API, the data services that are provided in Khoros to support it, and the Khoros visualization and image file format. The authors contend that Khoros is an excellent environment for the exploration and implementation of imaging standards.

  11. Non-Imaging Software/Data Analysis Requirements

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The analysis software needs of the non-imaging planetary data user are discussed. Assumptions as to the nature of the planetary science data centers where the data are physically stored are advanced, the scope of the non-imaging data is outlined, and facilities that users are likely to need to define and access data are identified. Data manipulation and analysis needs and display graphics are discussed.

  12. Software to model AXAF-I image quality

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed Central

    Kaifosh, Patrick; Zaremba, Jeffrey D.; Danielson, Nathan B.; Losonczy, Attila

    2014-01-01

    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/. PMID:25295002

  14. The Khoros software development environment for image and signal processing.

    PubMed

    Konstantinides, K; Rasure, J R

    1994-01-01

    Data flow visual language systems allow users to graphically create a block diagram of their applications and interactively control input, output, and system variables. Khoros is an integrated software development environment for information processing and visualization. It is particularly attractive for image processing because of its rich collection of tools for image and digital signal processing. This paper presents a general overview of Khoros with emphasis on its image processing and DSP tools. Various examples are presented and the future direction of Khoros is discussed. PMID:18291923

  15. Stromatoporoid biometrics using image analysis software: A first order approach

    NASA Astrophysics Data System (ADS)

    Wolniewicz, Pawel

    2010-04-01

    Strommetric is a new image analysis computer program that performs morphometric measurements of stromatoporoid sponges. The program measures 15 features of skeletal elements (pillars and laminae) visible in both longitudinal and transverse thin sections. The software is implemented in C++, using the Open Computer Vision (OpenCV) library. The image analysis system distinguishes skeletal elements from sparry calcite using Otsu's method for image thresholding. More than 150 photos of thin sections were used as a test set, from which 36,159 measurements were obtained. The software provided about one hundred times more data than the current method applied until now. The data obtained are reproducible, even if the work is repeated by different workers. Thus the method makes the biometric studies of stromatoporoids objective.

  16. [Utility of noise addition image made by using water phantom and image addition and subtraction software].

    PubMed

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

    2010-08-20

    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 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. PMID:20953102

  17. Image Fusion Software in the Clearpem-Sonic Project

    NASA Astrophysics Data System (ADS)

    Pizzichemi, M.; di Vara, N.; Cucciati, G.; Ghezzi, A.; Paganoni, M.; Farina, F.; Frisch, B.; Bugalho, R.

    2012-08-01

    ClearPEM-Sonic is a mammography scanner that combines Positron Emission Tomography with 3D ultrasound echographic and elastographic imaging. It has been developed to improve early stage detection of breast cancer by combining metabolic and anatomical information. The PET system has been developed by the Crystal Clear Collaboration, while the 3D ultrasound probe has been provided by SuperSonic Imagine. In this framework, the visualization and fusion software is an essential tool for the radiologists in the diagnostic process. This contribution discusses the design choices, the issues faced during the implementation, and the commissioning of the software tools developed for ClearPEM-Sonic.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Software for visualization, analysis, and manipulation of laser scan images

    NASA Astrophysics Data System (ADS)

    Burnsides, Dennis B.

    1997-03-01

    The recent introduction of laser surface scanning to scientific applications presents a challenge to computer scientists and engineers. Full utilization of this two- dimensional (2-D) and three-dimensional (3-D) data requires advances in techniques and methods for data processing and visualization. This paper explores the development of software to support the visualization, analysis and manipulation of laser scan images. Specific examples presented are from on-going efforts at the Air Force Computerized Anthropometric Research and Design (CARD) Laboratory.

  20. Towards a cognitive neuroscience of consciousness: basic evidence and a workspace framework.

    PubMed

    Dehaene, S; Naccache, L

    2001-04-01

    brain-imaging data strongly argue for a major role of prefrontal cortex, anterior cingulate, and the areas that connect to them, in creating the postulated brain-scale workspace. PMID:11164022

  1. Parallel-Processing Software for Creating Mosaic Images

    NASA Technical Reports Server (NTRS)

    Klimeck, Gerhard; Deen, Robert; McCauley, Michael; DeJong, Eric

    2008-01-01

    A computer program implements parallel processing for nearly real-time creation of panoramic mosaics of images of terrain acquired by video cameras on an exploratory robotic vehicle (e.g., a Mars rover). Because the original images are typically acquired at various camera positions and orientations, it is necessary to warp the images into the reference frame of the mosaic before stitching them together to create the mosaic. [Also see "Parallel-Processing Software for Correlating Stereo Images," Software Supplement to NASA Tech Briefs, Vol. 31, No. 9 (September 2007) page 26.] The warping algorithm in this computer program reflects the considerations that (1) for every pixel in the desired final mosaic, a good corresponding point must be found in one or more of the original images and (2) for this purpose, one needs a good mathematical model of the cameras and a good correlation of individual pixels with respect to their positions in three dimensions. The desired mosaic is divided into slices, each of which is assigned to one of a number of central processing units (CPUs) operating simultaneously. The results from the CPUs are gathered and placed into the final mosaic. The time taken to create the mosaic depends upon the number of CPUs, the speed of each CPU, and whether a local or a remote data-staging mechanism is used.

  2. Designing multistatic ultrasound imaging systems using software analysis

    NASA Astrophysics Data System (ADS)

    Lee, Michael; Singh, Rahul S.; Culjat, Martin O.; Stubbs, Scott; Natarajan, Shyam; Brown, Elliott R.; Grundfest, Warren S.; Lee, Hua

    2010-03-01

    This paper describes the method of using the finite-element analysis software, PZFlex, to direct the design of a novel ultrasound imaging system which uses conformal transducer arrays. Current challenges in ultrasound array technology, including 2D array processing, have motivated exploration into new data acquisition and reconstruction techniques. Ultimately, these efforts encourage a broader examination of the processes used to effectively validate new array configurations and image formation procedures. Commercial software available today is capable of efficiently and accurately modeling detailed operational aspects of customized arrays. Combining quality simulated data with prototyped reconstruction techniques presents a valuable tool for testing novel schemes before committing more costly resources. To investigate this practice, we modeled three 1D ultrasound arrays operating multistatically instead of by the conventional phased-array approach. They are: a simple linear array, a half-circle array with 180-degree coverage, and a full circular array for inward imaging. We present the process used to create unique array models in PZFlex, simulate operation and obtain data, and subsequently generate images by inputting data into a reconstruction algorithm in MATLAB. Further discussion describes the tested reconstruction algorithm and includes resulting images.

  3. Software components for medical image visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    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

  4. Woods Hole Image Processing System Software implementation; using NetCDF as a software interface for image processing

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    The Branch of Atlantic Marine Geology has been involved in the collection, processing and digital mosaicking of high, medium and low-resolution side-scan sonar data during the past 6 years. In the past, processing and digital mosaicking has been accomplished with a dedicated, shore-based computer system. With the need to process sidescan data in the field with increased power and reduced cost of major workstations, a need to have an image processing package on a UNIX based computer system which could be utilized in the field as well as be more generally available to Branch personnel was identified. This report describes the initial development of that package referred to as the Woods Hole Image Processing System (WHIPS). The software was developed using the Unidata NetCDF software interface to allow data to be more readily portable between different computer operating systems.

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

    NASA Technical Reports Server (NTRS)

    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.

  6. Software for Verifying Image-Correlation Tie Points

    NASA Technical Reports Server (NTRS)

    Klimeck, Gerhard; Yagi, Gary

    2008-01-01

    A computer program enables assessment of the quality of tie points in the image-correlation processes of the software described in the immediately preceding article. Tie points are computed in mappings between corresponding pixels in the left and right images of a stereoscopic pair. The mappings are sometimes not perfect because image data can be noisy and parallax can cause some points to appear in one image but not the other. The present computer program relies on the availability of a left- right correlation map in addition to the usual right left correlation map. The additional map must be generated, which doubles the processing time. Such increased time can now be afforded in the data-processing pipeline, since the time for map generation is now reduced from about 60 to 3 minutes by the parallelization discussed in the previous article. Parallel cluster processing time, therefore, enabled this better science result. The first mapping is typically from a point (denoted by coordinates x,y) in the left image to a point (x',y') in the right image. The second mapping is from (x',y') in the right image to some point (x",y") in the left image. If (x,y) and(x",y") are identical, then the mapping is considered perfect. The perfect-match criterion can be relaxed by introducing an error window that admits of round-off error and a small amount of noise. The mapping procedure can be repeated until all points in each image not connected to points in the other image are eliminated, so that what remains are verified correlation data.

  7. Reachable Workspace in Facioscapulohumeral muscular dystrophy (FSHD) by Kinect

    PubMed Central

    Han, Jay J.; Kurillo, Gregorij; Abresch, Richard T.; de Bie, Evan; Nicorici, Alina; Bajcsy, Ruzena

    2014-01-01

    Introduction A depth-ranging sensor (Kinect) based upper extremity motion analysis system was applied to determine the spectrum of reachable workspace encountered in facioscapulohumeral muscular dystrophy (FSHD). Methods Reachable workspaces were obtained from 22 individuals with FSHD and 24 age- and height-matched healthy controls. To allow comparison, total and quadrant reachable workspace relative surface areas (RSA) were obtained by normalizing the acquired reachable workspace by each individual’s arm length. Results Significantly contracted reachable workspace and reduced RSAs were noted for the FSHD cohort compared to controls (0.473±0.188 vs. 0.747±0.082; P<0.0001). With worsening upper extremity function as categorized by the FSHD evaluation subscale II+III, the upper quadrant RSAs decreased progressively, while the lower quadrant RSAs were relatively preserved. There were no side-to-side differences in reachable workspace based on hand-dominance. Discussion This study demonstrates the feasibility and potential of using an innovative Kinect-based reachable workspace outcome measure in FSHD. PMID:24828906

  8. Reducing depth uncertainty in large surgical workspaces, with applications to veterinary medicine

    NASA Astrophysics Data System (ADS)

    Audette, Michel A.; Kolahi, Ahmad; Enquobahrie, Andinet; Gatti, Claudio; Cleary, Kevin

    2010-02-01

    This paper presents on-going research that addresses uncertainty along the Z-axis in image-guided surgery, for applications to large surgical workspaces, including those found in veterinary medicine. Veterinary medicine lags human medicine in using image guidance, despite MR and CT data scanning of animals. The positional uncertainty of a surgical tracking device can be modeled as an octahedron with one long axis coinciding with the depth axis of the sensor, where the short axes are determined by pixel resolution and workspace dimensions. The further a 3D point is from this device, the more elongated is this long axis, and the greater the uncertainty along Z of this point's position, in relation to its components along X and Y. Moreover, for a triangulation-based tracker, its position error degrades with the square of distance. Our approach is to use two or more Micron Trackers to communicate with each other, and combine this feature with flexible positioning. Prior knowledge of the type of surgical procedure, and if applicable, the species of animal that determines the scale of the workspace, would allow the surgeon to pre-operatively configure the trackers in the OR for optimal accuracy. Our research also leverages the open-source Image-guided Surgery Toolkit (IGSTK).

  9. Software and Algorithms for Biomedical Image Data Processing and Visualization

    NASA Technical Reports Server (NTRS)

    Talukder, Ashit; Lambert, James; Lam, Raymond

    2004-01-01

    A new software equipped with novel image processing algorithms and graphical-user-interface (GUI) tools has been designed for automated analysis and processing of large amounts of biomedical image data. The software, called PlaqTrak, has been specifically used for analysis of plaque on teeth of patients. New algorithms have been developed and implemented to segment teeth of interest from surrounding gum, and a real-time image-based morphing procedure is used to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The PlaqTrak system integrates these components into a single software suite with an easy-to-use GUI (see Figure 1) that allows users to do an end-to-end run of a patient s record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image. The automated and accurate processing of the captured images to segment each tooth [see Figure 2(a)] and then detect plaque on a tooth-by-tooth basis is a critical component of the PlaqTrak system to do clinical trials and analysis with minimal human intervention. These features offer distinct advantages over other competing systems that analyze groups of teeth or synthetic teeth. PlaqTrak divides each segmented tooth into eight regions using an advanced graphics morphing procedure [see results on a chipped tooth in Figure 2(b)], and a pattern recognition classifier is then used to locate plaque [red regions in Figure 2(d)] and enamel regions. The morphing allows analysis within regions of teeth, thereby facilitating detailed statistical analysis such as the amount of plaque present on the biting surfaces on teeth. This software system is applicable to a host of biomedical applications, such as cell analysis and life detection, or robotic applications, such

  10. Special Software for Planetary Image Processing and Research

    NASA Astrophysics Data System (ADS)

    Zubarev, A. E.; Nadezhdina, I. E.; Kozlova, N. A.; Brusnikin, E. S.; Karachevtseva, I. P.

    2016-06-01

    The special modules of photogrammetric processing of remote sensing data that provide the opportunity to effectively organize and optimize the planetary studies were developed. As basic application the commercial software package PHOTOMOD™ is used. Special modules were created to perform various types of data processing: calculation of preliminary navigation parameters, calculation of shape parameters of celestial body, global view image orthorectification, estimation of Sun illumination and Earth visibilities from planetary surface. For photogrammetric processing the different types of data have been used, including images of the Moon, Mars, Mercury, Phobos, Galilean satellites and Enceladus obtained by frame or push-broom cameras. We used modern planetary data and images that were taken over the years, shooting from orbit flight path with various illumination and resolution as well as obtained by planetary rovers from surface. Planetary data image processing is a complex task, and as usual it can take from few months to years. We present our efficient pipeline procedure that provides the possibilities to obtain different data products and supports a long way from planetary images to celestial body maps. The obtained data - new three-dimensional control point networks, elevation models, orthomosaics - provided accurate maps production: a new Phobos atlas (Karachevtseva et al., 2015) and various thematic maps that derived from studies of planetary surface (Karachevtseva et al., 2016a).

  11. Validity, Reliability, and Sensitivity of a 3D Vision Sensor-based Upper Extremity Reachable Workspace Evaluation in Neuromuscular Diseases

    PubMed Central

    Han, Jay J.; Kurillo, Gregorij; Abresch, R. Ted; Nicorici, Alina; Bajcsy, Ruzena

    2013-01-01

    Introduction: One of the major challenges in the neuromuscular field has been lack of upper extremity outcome measures that can be useful for clinical therapeutic efficacy studies. Using vision-based sensor system and customized software, 3-dimensional (3D) upper extremity motion analysis can reconstruct a reachable workspace as a valid, reliable and sensitive outcome measure in various neuromuscular conditions where proximal upper extremity range of motion and function is impaired. Methods: Using a stereo-camera sensor system, 3D reachable workspace envelope surface area normalized to an individual’s arm length (relative surface area: RSA) to allow comparison between subjects was determined for 20 healthy controls and 9 individuals with varying degrees of upper extremity dysfunction due to neuromuscular conditions. All study subjects were classified based on Brooke upper extremity function scale. Right and left upper extremity reachable workspaces were determined based on three repeated measures. The RSAs for each frontal hemi-sphere quadrant and total reachable workspaces were determined with and without loading condition (500 gram wrist weight). Data were analyzed for assessment of the developed system and validity, reliability, and sensitivity to change of the reachable workspace outcome. Results: The mean total RSAs of the reachable workspace for the healthy controls and individuals with NMD were significantly different (0.586 ± 0.085 and 0.299 ± 0.198 respectively; p<0.001). All quadrant RSAs were reduced for individuals with NMDs compared to the healthy controls and these reductions correlated with reduced upper limb function as measured by Brooke grade. The upper quadrants of reachable workspace (above the shoulder level) demonstrated greatest reductions in RSA among subjects with progressive severity in upper extremity impairment. Evaluation of the developed outcomes system with the Bland-Altman method demonstrated narrow 95% limits of agreement (LOA

  12. Software considerations in the design of an image archive

    NASA Astrophysics Data System (ADS)

    Seshadri, Sridhar B.; Kishore, Sheel; Khalsa, Satjeet S.; Stevens, John F.; Arenson, Ronald L.

    1990-08-01

    The Radiology Department at the Hospital of the University of Pennsylvania is currently expanding its prototype Picture Archiving and Communications System (PACS) into a fully functional clinical system. The first phase of this expansion involves three major efforts: the upgrade of the 10-Mbit token-ring to an 80-Mbit backbone with associated sub-nets, the implementation of a large-scale image archive, and, an interface between the PACS and the Department's Radiology Information System. Upon the completion of this phase, the PACS will serve the storage and display needs of four MRI scanners and four of the Hospital's Intensive Care Units. This paper addresses the implementation of a software suite designed to duplicate and enhance conventional Film Library functions on a PACS. The structure of an electronic 'folder' based upon the ACR/NEMA Digital Imaging and Communication Standard is also introduced.

  13. 'Face value': new medical imaging software in commercial view.

    PubMed

    Coopmans, Catelijne

    2011-04-01

    Based on three ethnographic vignettes describing the engagements of a small start-up company with prospective competitors, partners and customers, this paper shows how commercial considerations are folded into the ways visual images become 'seeable'. When company members mount demonstrations of prototype mammography software, they seek to generate interest but also to protect their intellectual property. Pivotal to these efforts to manage revelation and concealment is the visual interface, which is variously performed as obstacle and ally in the development of a profitable product. Using the concept of 'face value', the paper seeks to develop further insight into contemporary dynamics of seeing and showing by tracing the way techno-visual presentations and commercial considerations become entangled in practice. It also draws attention to the salience and significance of enactments of surface and depth in image-based practices. PMID:21998921

  14. Automatic Image Registration Using Free and Open Source Software

    NASA Astrophysics Data System (ADS)

    Giri Babu, D.; Raja Shekhar, S. S.; Chandrasekar, K.; Sesha Sai, M. V. R.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Image registration is the most critical operation in remote sensing applications to enable location based referencing and analysis of earth features. This is the first step for any process involving identification, time series analysis or change detection using a large set of imagery over a region. Most of the reliable procedures involve time consuming and laborious manual methods of finding the corresponding matching features of the input image with respect to reference. Also the process, as it involves human interaction, does not converge with multiple operations at different times. Automated procedures rely on accurately determining the matching locations or points from both the images under comparison and the procedures are robust and consistent over time. Different algorithms are available to achieve this, based on pattern recognition, feature based detection, similarity techniques etc. In the present study and implementation, Correlation based methods have been used with a improvement over newly developed technique of identifying and pruning the false points of match. Free and Open Source Software (FOSS) have been used to develop the methodology to reach a wider audience, without any dependency on COTS (Commercially off the shelf) software. Standard deviation from foci of the ellipse of correlated points, is a statistical means of ensuring the best match of the points of interest based on both intensity values and location correspondence. The methodology is developed and standardised by enhancements to meet the registration requirements of remote sensing imagery. Results have shown a performance improvement, nearly matching the visual techniques and have been implemented in remote sensing operational projects. The main advantage of the proposed methodology is its viability in production mode environment. This paper also shows that the visualization capabilities of MapWinGIS, GDAL's image handling abilities and OSSIM's correlation facility can be efficiently

  15. Image Settings Affecting Nuchal Translucency Measurement Using Volume NT™ Software

    PubMed Central

    Cho, Hee Young; Kim, Young Han; Park, Yong Won; Kim, Sung Yoon; Lee, Kwang Hee; Yoo, Joon Sang

    2015-01-01

    Purpose To evaluate the effects of the deviation from the mid-sagittal plane, fetal image size, tissue harmonic imaging (THI), and speckle reduction filter (SRF) on the measurement of the nuchal translucency (NT) thickness using Volume NT™ software. Materials and Methods In 79 pregnant women, NT was measured using Volume NT™. Firstly, the three-dimensional volumes were categorized based on the angle of deviation in 10° intervals from the mid-sagittal plane. Secondly, the operator downsized the fetal image to less than 50% of the screen (Method A) and by magnifying the image (Method B). Next, the image was magnified until the fetal head and thorax occupied 75% of the screen, and the NT was measured (Method C). Lastly, NT values were acquired with THI and SRF functions on, with each function alternately on, and with both functions off. Results The mean differences in NT measurements were -0.09 mm (p<0.01) between two-dimensional (2D) and a deviation of 31-40° and -0.10 mm (p<0.01) between 2D and 41-50°. The intraclass correlation coefficients (ICC) for 2D-NT and NT according to image size were 0.858, 0.923, and 0.928 for methods A, B, and C, respectively. The ICC for 2D-NT and NT with respect to the THI and SRF were 0.786, 0.761, 0.740, and 0.731 with both functions on, THI only, SRF only, and with both functions off, respectively. Conclusion NT measurements made using Volume NT™ are affected by angle deviation from the mid-sagittal plane and fetal image size. Additionally, the highest correlation with 2D-NT was achieved when THI and SRF functions were used. PMID:26256978

  16. Workspace zone differentiation and visualization for virtual humans.

    PubMed

    Yang, J; Sinokrot, T; Abdel-Malek, K; Beck, S; Nebel, K

    2008-03-01

    Human performance measures such as discomfort and joint displacement play an important role in product design. The virtual human Santos, a new generation of virtual humans developed at the University of Iowa, goes directly to the computer-aided design model to evaluate a design, saving time and money. This paper presents an optimization-based workspace zone differentiation and visualization. Around the workspace of virtual humans, a volume is discretized to small zones and the posture prediction on each central point of the zone will determine whether the points are outside the workspace as well as the values of different objective functions. Visualization of zone differentiation is accomplished by showing different colours based on values of human performance measures on points that are located inside the workspace. The proposed method can subsequently help ergonomic design. For example, in a vehicle's interior, the controls should not only lie inside the workspace, but also in the zone that encloses the most comfortable points. Using the palette of colours inside the workspace as a visual guide, a designer can obtain a reading of the discomfort level of product users. PMID:18311614

  17. How to Frame Universal Workspace Lighting.

    PubMed

    Mathiasen, Nanet; Frandsen, Anne Kathrine

    2016-01-01

    In 2012 the headquarters for the umbrella organisation 'Disabled people's organisation Denmark' opened, an office building that offers workspace for the administrations of all the member organisations. The ambition for the building was to be the most accessible office building in the world; regardless of disability everybody should be able to move around in the house and work in any of the offices. One, of many ambitions, was to design a functional and effective lighting scheme using as much daylight as possible, and integrating the artificial lighting design and daylight design. The lighting was intended to support all work stations in both one-man offices and open-plan offices with a functional and comfortable visual environment, fit for all users, regardless of disability. Based on a post occupancy evaluation conducted 2 years after the organisations moved in, the present paper evaluates the lighting design in the offices. It reveals that not all the people working in the offices have the same needs and preferences of lighting conditions; these differ even among users with the same disability. Accordingly the findings lead to a discussion on how to understand the concept of Universal Design. Based on the lighting theory of Peter Boyce, the paper discusses the idea of encompassing everyone in the same solution. PMID:27534330

  18. Development of image-processing software for automatic segmentation of brain tumors in MR images

    PubMed Central

    Vijayakumar, C.; Gharpure, Damayanti Chandrashekhar

    2011-01-01

    Most of the commercially available software for brain tumor segmentation have limited functionality and frequently lack the careful validation that is required for clinical studies. We have developed an image-analysis software package called ‘Prometheus,’ which performs neural system–based segmentation operations on MR images using pre-trained information. The software also has the capability to improve its segmentation performance by using the training module of the neural system. The aim of this article is to present the design and modules of this software. The segmentation module of Prometheus can be used primarily for image analysis in MR images. Prometheus was validated against manual segmentation by a radiologist and its mean sensitivity and specificity was found to be 85.71±4.89% and 93.2±2.87%, respectively. Similarly, the mean segmentation accuracy and mean correspondence ratio was found to be 92.35±3.37% and 0.78±0.046, respectively. PMID:21897560

  19. WorkstationJ: workstation emulation software for medical image perception and technology evaluation research

    NASA Astrophysics Data System (ADS)

    Schartz, Kevin M.; Berbaum, Kevin S.; Caldwell, Robert T.; Madsen, Mark T.

    2007-03-01

    We developed image presentation software that mimics the functionality available in the clinic, but also records time-stamped, observer-display interactions and is readily deployable on diverse workstations making it possible to collect comparable observer data at multiple sites. Commercial image presentation software for clinical use has limited application for research on image perception, ergonomics, computer-aids and informatics because it does not collect observer responses, or other information on observer-display interactions, in real time. It is also very difficult to collect observer data from multiple institutions unless the same commercial software is available at different sites. Our software not only records observer reports of abnormalities and their locations, but also inspection time until report, inspection time for each computed radiograph and for each slice of tomographic studies, window/level, and magnification settings used by the observer. The software is a modified version of the open source ImageJ software available from the National Institutes of Health. Our software involves changes to the base code and extensive new plugin code. Our free software is currently capable of displaying computed tomography and computed radiography images. The software is packaged as Java class files and can be used on Windows, Linux, or Mac systems. By deploying our software together with experiment-specific script files that administer experimental procedures and image file handling, multi-institutional studies can be conducted that increase reader and/or case sample sizes or add experimental conditions.

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

    PubMed Central

    2010-01-01

    Background 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. Results 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

  1. 49. TILE PACKING AREA AND APPRENTICE WORKSPACE, SECOND FLOOR, SOUTH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    49. TILE PACKING AREA AND APPRENTICE WORKSPACE, SECOND FLOOR, SOUTH END OF EAST WING. THE SKYLIGHT, ADDED IN 1976. COVERS A ROOF OPENING LEFT FOR THE CHIMNEY OF A POSSIBLE THIRD BISCUIT KILN. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  2. Toward an Information Visualization Workspace: Combining Multiple Means of Expression.

    ERIC Educational Resources Information Center

    Roth, Steven F.; Chuah, Mei C.; Kerpedjiev, Stephan; Kolojejchick, John A.; Lucas, Peter

    1997-01-01

    Presents an information visualization workspace in which users are able to explore data presented in diverse but coordinated formats using related systems called Visage, SAGE, and selective dynamic manipulation (SDM). Discusses four dimensions for analyzing user interfaces that reveal the combination of design approaches needed for visualizations…

  3. Random issues in workspace analysis for a mobile robot

    NASA Astrophysics Data System (ADS)

    Stǎnescu, Tony; Dolga, Valer; Mondoc, Alina

    2014-12-01

    Evolution of the mobile robot is currently characterized by multiple applications in dynamic workspaces and low initial knowledge. In this paper presents aspects of approaching random processes of evolution of a mobile robot in an unstructured environment . The experimental results are used for modeling an infrared sensor (integrated in the mobile robot structure) and to assess the probability of locating obstacles in the environment.

  4. Appropriation of a Shared Workspace: Organizing Principles and Their Application

    ERIC Educational Resources Information Center

    Overdijk, Maarten; van Diggelen, Wouter

    2008-01-01

    The use and effects of a CSCL-tool are not always predictable from the properties of the tool alone, but depend on how that tool is appropriated. This paper presents the findings from a case study about the appropriation of a graphical shared workspace. When students are presented with a new tool they may encounter competing constraints and…

  5. NEIGHBOUR-IN: Image processing software for spatial analysis of animal grouping

    PubMed Central

    Caubet, Yves; Richard, Freddie-Jeanne

    2015-01-01

    Abstract Animal grouping is a very complex process that occurs in many species, involving many individuals under the influence of different mechanisms. To investigate this process, we have created an image processing software, called NEIGHBOUR-IN, designed to analyse individuals’ coordinates belonging to up to three different groups. The software also includes statistical analysis and indexes to discriminate aggregates based on spatial localisation of individuals and their neighbours. After the description of the software, the indexes computed by the software are illustrated using both artificial patterns and case studies using the spatial distribution of woodlice. The added strengths of this software and methods are also discussed. PMID:26261448

  6. Platform-independent software for medical image processing on the Internet

    NASA Astrophysics Data System (ADS)

    Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

    1997-05-01

    We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

  7. IMAGE information monitoring and applied graphics software environment. Volume 1. Executive overview

    SciTech Connect

    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).

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

    SciTech Connect

    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).

  9. IMAGE information monitoring and applied graphics software environment. Volume 3. User's guide

    SciTech Connect

    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 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).

  10. GILDAS: Grenoble Image and Line Data Analysis Software

    NASA Astrophysics Data System (ADS)

    Gildas Team

    2013-05-01

    GILDAS is a collection of software oriented toward (sub-)millimeter radioastronomical applications (either single-dish or interferometer). It has been adopted as the IRAM standard data reduction package and is jointly maintained by IRAM & CNRS. GILDAS contains many facilities, most of which are oriented towards spectral line mapping and many kinds of 3-dimensional data. The code, written in Fortran-90 with a few parts in C/C++ (mainly keyboard interaction, plotting, widgets), is easily extensible.

  11. ESO C Library for an Image Processing Software Environment (eclipse)

    NASA Astrophysics Data System (ADS)

    Devillard, N.

    Written in ANSI C, eclipse is a library offering numerous services related to astronomical image processing: FITS data access, various image and cube loading methods, binary image handling and filtering (including convolution and morphological filters), 2-D cross-correlation, connected components, cube and image arithmetic, dead pixel detection and correction, object detection, data extraction, flat-fielding with robust fit, image generation, statistics, photometry, image-space resampling, image combination, and cube stacking. It also contains support for mathematical tools like random number generation, FFT, curve fitting, matrices, fast median computation, and point-pattern matching. The main feature of this library is its ability to handle large amounts of input data (up to 2 GB in the current version) regardless of the amount of memory and swap available on the local machine. Another feature is the very high speed allowed by optimized C, making it an ideal base tool for programming efficient number-crunching applications, e.g., on parallel (Beowulf) systems. Running on all Unix-like platforms, eclipse is portable. A high-level interface to Python is foreseen that would allow programmers to prototype their applications much faster than through C programs.

  12. Eclipse: ESO C Library for an Image Processing Software Environment

    NASA Astrophysics Data System (ADS)

    Devillard, Nicolas

    2011-12-01

    Written in ANSI C, eclipse is a library offering numerous services related to astronomical image processing: FITS data access, various image and cube loading methods, binary image handling and filtering (including convolution and morphological filters), 2-D cross-correlation, connected components, cube and image arithmetic, dead pixel detection and correction, object detection, data extraction, flat-fielding with robust fit, image generation, statistics, photometry, image-space resampling, image combination, and cube stacking. It also contains support for mathematical tools like random number generation, FFT, curve fitting, matrices, fast median computation, and point-pattern matching. The main feature of this library is its ability to handle large amounts of input data (up to 2GB in the current version) regardless of the amount of memory and swap available on the local machine. Another feature is the very high speed allowed by optimized C, making it an ideal base tool for programming efficient number-crunching applications, e.g., on parallel (Beowulf) systems.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. BIRP: Software for interactive search and retrieval of image engineering data

    NASA Technical Reports Server (NTRS)

    Arvidson, R. E.; Bolef, L. K.; Guinness, E. A.; Norberg, P.

    1980-01-01

    Better Image Retrieval Programs (BIRP), a set of programs to interactively sort through and to display a database, such as engineering data for images acquired by spacecraft is described. An overview of the philosophy of BIRP design, the structure of BIRP data files, and examples that illustrate the capabilities of the software are provided.

  15. Software for Analyzing Sequences of Flow-Related Images

    NASA Technical Reports Server (NTRS)

    Klimek, Robert; Wright, Ted

    2004-01-01

    Spotlight is a computer program for analysis of sequences of images generated in combustion and fluid physics experiments. Spotlight can perform analysis of a single image in an interactive mode or a sequence of images in an automated fashion. The primary type of analysis is tracking of positions of objects over sequences of frames. Features and objects that are typically tracked include flame fronts, particles, droplets, and fluid interfaces. Spotlight automates the analysis of object parameters, such as centroid position, velocity, acceleration, size, shape, intensity, and color. Images can be processed to enhance them before statistical and measurement operations are performed. An unlimited number of objects can be analyzed simultaneously. Spotlight saves results of analyses in a text file that can be exported to other programs for graphing or further analysis. Spotlight is a graphical-user-interface-based program that at present can be executed on Microsoft Windows and Linux operating systems. A version that runs on Macintosh computers is being considered.

  16. A Review of Diffusion Tensor Magnetic Resonance Imaging Computational Methods and Software Tools

    PubMed Central

    Hasan, Khader M.; Walimuni, Indika S.; Abid, Humaira; Hahn, Klaus R.

    2010-01-01

    In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766

  17. A review of diffusion tensor magnetic resonance imaging computational methods and software tools.

    PubMed

    Hasan, Khader M; Walimuni, Indika S; Abid, Humaira; Hahn, Klaus R

    2011-12-01

    In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766

  18. Spatial data software integration - Merging CAD/CAM/mapping with GIS and image processing

    NASA Technical Reports Server (NTRS)

    Logan, Thomas L.; Bryant, Nevin A.

    1987-01-01

    The integration of CAD/CAM/mapping with image processing using geographic information systems (GISs) as the interface is examined. Particular emphasis is given to the development of software interfaces between JPL's Video Image Communication and Retrieval (VICAR)/Imaged Based Information System (IBIS) raster-based GIS and the CAD/CAM/mapping system. The design and functions of the VICAR and IBIS are described. Vector data capture and editing are studied. Various software programs for interfacing between the VICAR/IBIS and CAD/CAM/mapping are presented and analyzed.

  19. The design of real time infrared image generation software based on Creator and Vega

    NASA Astrophysics Data System (ADS)

    Wang, Rui-feng; Wu, Wei-dong; Huo, Jun-xiu

    2013-09-01

    Considering the requirement of high reality and real-time quality dynamic infrared image of an infrared image simulation, a method to design real-time infrared image simulation application on the platform of VC++ is proposed. This is based on visual simulation software Creator and Vega. The functions of Creator are introduced simply, and the main features of Vega developing environment are analyzed. The methods of infrared modeling and background are offered, the designing flow chart of the developing process of IR image real-time generation software and the functions of TMM Tool and MAT Tool and sensor module are explained, at the same time, the real-time of software is designed.

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

    NASA Technical Reports Server (NTRS)

    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.

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

    SciTech Connect

    Bogdanov, G.; Ludwig, R.; Wiggins, J.; Bertagnolli, K.

    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.

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

    SciTech Connect

    Lehman, S.

    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.

  3. Workspace Analysis and Optimization of 3-PUU Parallel Mechanism in Medicine Base on Genetic Algorithm.

    PubMed

    Hou, Yongchao; Zhao, Yang

    2015-01-01

    A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients. PMID:26628930

  4. Workspace Analysis and Optimization of 3-PUU Parallel Mechanism in Medicine Base on Genetic Algorithm

    PubMed Central

    Hou, Yongchao; Zhao, Yang

    2015-01-01

    A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients. PMID:26628930

  5. Image analysis software for following progression of peripheral neuropathy

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  7. Validated novel software to measure the conspicuity index of lesions in DICOM images

    NASA Astrophysics Data System (ADS)

    Szczepura, K. R.; Manning, D. J.

    2016-03-01

    A novel software programme and associated Excel spreadsheet has been developed to provide an objective measure of the expected visual detectability of focal abnormalities within DICOM images. ROIs are drawn around the abnormality, the software then fits the lesion using a least squares method to recognize the edges of the lesion based on the full width half maximum. 180 line profiles are then plotted around the lesion, giving 360 edge profiles.

  8. Assessment of using Imaging software Image J to determine percentage woody cover from half meter resolution satellite images

    NASA Astrophysics Data System (ADS)

    Mace, W. D.; Cerling, T. E.

    2010-12-01

    The percentage of woody cover over a landscape has been shown to be related to the d13C in soil organic matter because of the difference in carbon isotope discrimination between plants using C3 and C4 photosynthetic pathways. Woody plants such as those found in dense forests predominantly use the C3 pathway; whereas plants that are found to grow in arid grasslands are predominantly using the C4 pathway. Therefore it has also been shown that it is possible to determine the vegetation of current and past ecosystems using d13C in soil organic matter. With the introduction of very high resolution remote sensing it is becoming possible to make detailed maps based on d13C and estimate percentage woody cover. Using these maps it may be possible to create large scale representations of prehistoric ecosystems. Here we asses the use of a widely available imaging software, Image J to survey the percentage of woody cover of tropical ecosystems in East Africa. These results are compared with canopy gap fraction that has been calculated from in-situ ground-up circular fisheye images. We find that in areas where the percentage woody cover is less than 0.5, Image J is an effective method of analysis; however as the percentage cover becomes greater than 0.5 it becomes difficult to distinguish between true canopy and shadows.

  9. Parallel-Processing Software for Correlating Stereo Images

    NASA Technical Reports Server (NTRS)

    Klimeck, Gerhard; Deen, Robert; Mcauley, Michael; DeJong, Eric

    2007-01-01

    A computer program implements parallel- processing algorithms for cor relating images of terrain acquired by stereoscopic pairs of digital stereo cameras on an exploratory robotic vehicle (e.g., a Mars rove r). Such correlations are used to create three-dimensional computatio nal models of the terrain for navigation. In this program, the scene viewed by the cameras is segmented into subimages. Each subimage is assigned to one of a number of central processing units (CPUs) opera ting simultaneously.

  10. DEIReconstructor: a software for diffraction enhanced imaging processing and tomography reconstruction

    NASA Astrophysics Data System (ADS)

    Zhang, Kai; Yuan, Qing-Xi; Huang, Wan-Xia; Zhu, Pei-Ping; Wu, Zi-Yu

    2014-10-01

    Diffraction enhanced imaging (DEI) has been widely applied in many fields, especially when imaging low-Z samples or when the difference in the attenuation coefficient between different regions in the sample is too small to be detected. Recent developments of this technique have presented a need for a new software package for data analysis. Here, the Diffraction Enhanced Image Reconstructor (DEIReconstructor), developed in Matlab, is presented. DEIReconstructor has a user-friendly graphical user interface and runs under any of the 32-bit or 64-bit Microsoft Windows operating systems including XP and Win7. Many of its features are integrated to support imaging preprocessing, extract absorption, refractive and scattering information of diffraction enhanced imaging and allow for parallel-beam tomography reconstruction for DEI-CT. Furthermore, many other useful functions are also implemented in order to simplify the data analysis and the presentation of results. The compiled software package is freely available.

  11. Image processing software for providing radiometric inputs to land surface climatology models

    NASA Technical Reports Server (NTRS)

    Newcomer, Jeffrey A.; Goetz, Scott J.; Strebel, Donald E.; Hall, Forrest G.

    1989-01-01

    During the First International Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE), 80 gigabytes of image data were generated from a variety of satellite and airborne sensors in a multidisciplinary attempt to study energy and mass exchange between the land surface and the atmosphere. To make these data readily available to researchers with a range of image data handling experience and capabilities, unique image-processing software was designed to perform a variety of nonstandard image-processing manipulations and to derive a set of standard-format image products. The nonconventional features of the software include: (1) adding new layers of geographic coordinates, and solar and viewing conditions to existing data; (2) providing image polygon extraction and calibration of data to at-sensor radiances; and, (3) generating standard-format derived image products that can be easily incorporated into radiometric or climatology models. The derived image products consist of easily handled ASCII descriptor files, byte image data files, and additional per-pixel integer data files (e.g., geographic coordinates, and sun and viewing conditions). Details of the solutions to the image-processing problems, the conventions adopted for handling a variety of satellite and aircraft image data, and the applicability of the output products to quantitative modeling are presented. They should be of general interest to future experiment and data-handling design considerations.

  12. An image-processing software package: UU and Fig for optical metrology applications

    NASA Astrophysics Data System (ADS)

    Chen, Lujie

    2013-06-01

    Modern optical metrology applications are largely supported by computational methods, such as phase shifting [1], Fourier Transform [2], digital image correlation [3], camera calibration [4], etc, in which image processing is a critical and indispensable component. While it is not too difficult to obtain a wide variety of image-processing programs from the internet; few are catered for the relatively special area of optical metrology. This paper introduces an image-processing software package: UU (data processing) and Fig (data rendering) that incorporates many useful functions to process optical metrological data. The cross-platform programs UU and Fig are developed based on wxWidgets. At the time of writing, it has been tested on Windows, Linux and Mac OS. The userinterface is designed to offer precise control of the underline processing procedures in a scientific manner. The data input/output mechanism is designed to accommodate diverse file formats and to facilitate the interaction with other independent programs. In terms of robustness, although the software was initially developed for personal use, it is comparably stable and accurate to most of the commercial software of similar nature. In addition to functions for optical metrology, the software package has a rich collection of useful tools in the following areas: real-time image streaming from USB and GigE cameras, computational geometry, computer vision, fitting of data, 3D image processing, vector image processing, precision device control (rotary stage, PZT stage, etc), point cloud to surface reconstruction, volume rendering, batch processing, etc. The software package is currently used in a number of universities for teaching and research.

  13. Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience

    PubMed Central

    Enquobahrie, Andinet; Gobbi, David; Turek, Matt; Cheng, Patrick; Yaniv, Ziv; Lindseth, Frank; Cleary, Kevin

    2009-01-01

    Objective Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. Methods IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. Results The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. Conclusion With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community. PMID:20037671

  14. Pore Size Distribution Estimates Compared: Available software applied to soil CT and synthetic images.

    NASA Astrophysics Data System (ADS)

    Houston, Alasdair N.; Falconer, Ruth E.; Otten, Wilfred; Hapca, Simona M.

    2015-04-01

    The Pore Size Distribution (PSD) has been widely used as a means of characterising porous media and, in conjunction with knowledge of pore space connectivity, has been used to infer hydrological properties. There exist various strategies to estimate PSD from a segmented image and each strategy typically involves a sequence of algorithms that transform image information. Some of these algorithms may be explicitly parameterised, requiring decisions by a knowledgeable operator. As a result PSD estimates may be quite variable between software applications and operators. In order to better understand these differences, a constrained boolean model was used to construct synthetic images whose pore structure is without ambiguity and whose properties can be analytically determined. Applying to such images a selection of analysis procedures in the form of readily available software applications, reveals differences between PSD estimates and analytic information. In some cases it is possible to attribute these differences to artifacts visible within map images generated by the analysis procedures, permitting correction procedures to be devised. In the case of soil CT images which exhibit complex interconnected pore structure, differences in the PSD estimate between analysis procedures are very great in some cases. Inspection of map images can again help in identifying the cause of such problems, but this may result from a fundamental property of the procedure with respect to complex pore structure. Based on the evidence presented, we conclude that some readily available software will produce PSD estimates that can usefully characterise geomaterials.

  15. Monte Carlo PENRADIO software for dose calculation in medical imaging

    NASA Astrophysics Data System (ADS)

    Adrien, Camille; Lòpez Noriega, Mercedes; Bonniaud, Guillaume; Bordy, Jean-Marc; Le Loirec, Cindy; Poumarede, Bénédicte

    2014-06-01

    The increase on the collective radiation dose due to the large number of medical imaging exams has led the medical physics community to deeply consider the amount of dose delivered and its associated risks in these exams. For this purpose we have developed a Monte Carlo tool, PENRADIO, based on a modified version of PENELOPE code 2006 release, to obtain an accurate individualized radiation dose in conventional and interventional radiography and in computed tomography (CT). This tool has been validated showing excellent agreement between the measured and simulated organ doses in the case of a hip conventional radiography and a coronography. We expect the same accuracy in further results for other localizations and CT examinations.

  16. Web-based interactive 2D/3D medical image processing and visualization software.

    PubMed

    Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

    2010-05-01

    There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies. PMID:20022133

  17. Comparison of two academic software packages for analyzing two-dimensional gel images.

    PubMed

    Wu, Yukun; Zhang, Le

    2011-12-01

    One of the key limitations for proteomic studies using two-dimensional (2D) gel is the lack of automatic, fast, robust, and reliable methods for detecting, matching, and quantifying protein spots. Although there are commercial software packages for 2D gel image analysis, extensive human intervention is still needed for spot detection and matching, which is time-consuming and error-prone. Moreover, the commercial software packages are usually expensive and non-open source. Thus, it is very beneficial for researchers to have free software that is fast, fully automatic, and robust. In this paper, we review and compare two recently developed and publicly available software packages, RegStatGel and Pinnacle, for analyzing 2D gel images. These two software packages share some common features and also have some fundamental difference in the aspects of spot detection and quantification. Based on our experience, RegStatGel is much better in terms of spot detection and matching. It also contains more advanced statistical tools and is more user-friendly. In contrast, Pinnacle is quite sensitive to background noise and relies on external statistical software packages for statistical analysis. PMID:22084013

  18. MMX-I: data-processing software for multimodal X-ray imaging and tomography.

    PubMed

    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. PMID:27140159

  19. MMX-I: data-processing software for multimodal X-ray imaging and tomography

    PubMed Central

    Bergamaschi, Antoine; Medjoubi, Kadda; Messaoudi, Cédric; Marco, Sergio; Somogyi, Andrea

    2016-01-01

    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. PMID:27140159

  20. Development of HydroImage, A User Friendly Hydrogeophysical Characterization Software

    SciTech Connect

    Mok, Chin Man; Hubbard, Susan; Chen, Jinsong; Suribhatla, Raghu; Kaback, Dawn Samara

    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.

  1. The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.

    PubMed

    Enquobahrie, Andinet; Cheng, Patrick; Gary, Kevin; Ibanez, Luis; Gobbi, David; Lindseth, Frank; Yaniv, Ziv; Aylward, Stephen; Jomier, Julien; Cleary, Kevin

    2007-11-01

    This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences. PMID:17703338

  2. A User Assessment of Workspaces in Selected Music Education Computer Laboratories.

    ERIC Educational Resources Information Center

    Badolato, Michael Jeremy

    A study of 120 students selected from the user populations of four music education computer laboratories was conducted to determine the applicability of current ergonomic and environmental design guidelines in satisfying the needs of users of educational computing workspaces. Eleven categories of workspace factors were organized into a…

  3. Shadow netWorkspace: An Open Source Intranet for Learning Communities

    ERIC Educational Resources Information Center

    Laffey, James M.; Musser, Dale

    2006-01-01

    Shadow netWorkspace (SNS) is a web application system that allows a school or any type of community to establish an intranet with network workspaces for all members and groups. The goal of SNS has been to make it easy for schools and other educational organizations to provide network services in support of implementing a learning community. SNS is…

  4. Digital processing of side-scan sonar data with the Woods Hole image processing system software

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    Since 1985, the Branch of Atlantic Marine Geology has been involved in collecting, processing and digitally mosaicking high and low-resolution side-scan sonar data. Recent development of a UNIX-based image-processing software system includes a series of task specific programs for processing side-scan sonar data. This report describes the steps required to process the collected data and to produce an image that has equal along- and across-track resol

  5. Digital image measurement of specimen deformation based on CCD cameras and Image J software: an application to human pelvic biomechanics

    NASA Astrophysics Data System (ADS)

    Jia, Yongwei; Cheng, Liming; Yu, Guangrong; Lou, Yongjian; Yu, Yan; Chen, Bo; Ding, Zuquan

    2008-03-01

    A method of digital image measurement of specimen deformation based on CCD cameras and Image J software was developed. This method was used to measure the biomechanics behavior of human pelvis. Six cadaveric specimens from the third lumbar vertebra to the proximal 1/3 part of femur were tested. The specimens without any structural abnormalities were dissected of all soft tissue, sparing the hip joint capsules and the ligaments of the pelvic ring and floor. Markers with black dot on white background were affixed to the key regions of the pelvis. Axial loading from the proximal lumbar was applied by MTS in the gradient of 0N to 500N, which simulated the double feet standing stance. The anterior and lateral images of the specimen were obtained through two CCD cameras. Based on Image J software, digital image processing software, which can be freely downloaded from the National Institutes of Health, digital 8-bit images were processed. The procedure includes the recognition of digital marker, image invert, sub-pixel reconstruction, image segmentation, center of mass algorithm based on weighted average of pixel gray values. Vertical displacements of S1 (the first sacral vertebrae) in front view and micro-angular rotation of sacroiliac joint in lateral view were calculated according to the marker movement. The results of digital image measurement showed as following: marker image correlation before and after deformation was excellent. The average correlation coefficient was about 0.983. According to the 768 × 576 pixels image (pixel size 0.68mm × 0.68mm), the precision of the displacement detected in our experiment was about 0.018 pixels and the comparatively error could achieve 1.11\\perthou. The average vertical displacement of S1 of the pelvis was 0.8356+/-0.2830mm under vertical load of 500 Newtons and the average micro-angular rotation of sacroiliac joint in lateral view was 0.584+/-0.221°. The load-displacement curves obtained from our optical measure system

  6. Onboard utilization of ground control points for image correction. Volume 4: Correlation analysis software design

    NASA Technical Reports Server (NTRS)

    1981-01-01

    The software utilized for image correction accuracy measurement is described. The correlation analysis program is written to allow the user various tools to analyze different correlation algorithms. The algorithms were tested using LANDSAT imagery in two different spectral bands. Three classification algorithms are implemented.

  7. 3-dimensional root phenotyping with a novel imaging and software platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel imaging and software platform was developed for the high-throughput phenotyping of 3-dimensional root traits during seedling development. To demonstrate the platform’s capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and ...

  8. WHIPPET: a collaborative software environment for medical image processing and analysis

    NASA Astrophysics Data System (ADS)

    Hu, Yangqiu; Haynor, David R.; Maravilla, Kenneth R.

    2007-03-01

    While there are many publicly available software packages for medical image processing, making them available to end users in clinical and research labs remains non-trivial. An even more challenging task is to mix these packages to form pipelines that meet specific needs seamlessly, because each piece of software usually has its own input/output formats, parameter sets, and so on. To address these issues, we are building WHIPPET (Washington Heterogeneous Image Processing Pipeline EnvironmenT), a collaborative platform for integrating image analysis tools from different sources. The central idea is to develop a set of Python scripts which glue the different packages together and make it possible to connect them in processing pipelines. To achieve this, an analysis is carried out for each candidate package for WHIPPET, describing input/output formats, parameters, ROI description methods, scripting and extensibility and classifying its compatibility with other WHIPPET components as image file level, scripting level, function extension level, or source code level. We then identify components that can be connected in a pipeline directly via image format conversion. We set up a TWiki server for web-based collaboration so that component analysis and task request can be performed online, as well as project tracking, knowledge base management, and technical support. Currently WHIPPET includes the FSL, MIPAV, FreeSurfer, BrainSuite, Measure, DTIQuery, and 3D Slicer software packages, and is expanding. Users have identified several needed task modules and we report on their implementation.

  9. CellProfiler Analyst: data exploration and analysis software for complex image-based screens

    PubMed Central

    Jones, Thouis R; Kang, In Han; Wheeler, Douglas B; Lindquist, Robert A; Papallo, Adam; Sabatini, David M; Golland, Polina; Carpenter, Anne E

    2008-01-01

    Background Image-based screens can produce hundreds of measured features for each of hundreds of millions of individual cells in a single experiment. Results Here, we describe CellProfiler Analyst, open-source software for the interactive exploration and analysis of multidimensional data, particularly data from high-throughput, image-based experiments. Conclusion The system enables interactive data exploration for image-based screens and automated scoring of complex phenotypes that require combinations of multiple measured features per cell. PMID:19014601

  10. New Software Developments for Quality Mesh Generation and Optimization from Biomedical Imaging Data

    PubMed Central

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

    2013-01-01

    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. PMID:24252469

  11. Capturing a failure of an ASIC in-situ, using infrared radiometry and image processing software

    NASA Technical Reports Server (NTRS)

    Ruiz, Ronald P.

    2003-01-01

    Failures in electronic devices can sometimes be tricky to locate-especially if they are buried inside radiation-shielded containers designed to work in outer space. Such was the case with a malfunctioning ASIC (Application Specific Integrated Circuit) that was drawing excessive power at a specific temperature during temperature cycle testing. To analyze the failure, infrared radiometry (thermography) was used in combination with image processing software to locate precisely where the power was being dissipated at the moment the failure took place. The IR imaging software was used to make the image of the target and background, appear as unity. As testing proceeded and the failure mode was reached, temperature changes revealed the precise location of the fault. The results gave the design engineers the information they needed to fix the problem. This paper describes the techniques and equipment used to accomplish this failure analysis.

  12. Software for MR image overlay guided needle insertions: the clinical translation process

    NASA Astrophysics Data System (ADS)

    Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

    2013-03-01

    PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

  13. IHE cross-enterprise document sharing for imaging: interoperability testing software

    PubMed Central

    2010-01-01

    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. PMID:20858241

  14. A software to digital image processing to be used in the voxel phantom development.

    PubMed

    Vieira, J W; Lima, F R A

    2009-01-01

    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

  15. A near-infrared fluorescence-based surgical navigation system imaging software for sentinel lymph node detection

    NASA Astrophysics Data System (ADS)

    Ye, Jinzuo; Chi, Chongwei; Zhang, Shuang; Ma, Xibo; Tian, Jie

    2014-02-01

    Sentinel lymph node (SLN) in vivo detection is vital in breast cancer surgery. A new near-infrared fluorescence-based surgical navigation system (SNS) imaging software, which has been developed by our research group, is presented for SLN detection surgery in this paper. The software is based on the fluorescence-based surgical navigation hardware system (SNHS) which has been developed in our lab, and is designed specifically for intraoperative imaging and postoperative data analysis. The surgical navigation imaging software consists of the following software modules, which mainly include the control module, the image grabbing module, the real-time display module, the data saving module and the image processing module. And some algorithms have been designed to achieve the performance of the software, for example, the image registration algorithm based on correlation matching. Some of the key features of the software include: setting the control parameters of the SNS; acquiring, display and storing the intraoperative imaging data in real-time automatically; analysis and processing of the saved image data. The developed software has been used to successfully detect the SLNs in 21 cases of breast cancer patients. In the near future, we plan to improve the software performance and it will be extensively used for clinical purpose.

  16. OsiriX: an open-source software for navigating in multidimensional DICOM images.

    PubMed

    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. PMID:15534753

  17. Applying Workspace Limitations in a Velocity-Controlled Robotic Mechanism

    NASA Technical Reports Server (NTRS)

    Abdallah, Muhammad E. (Inventor); Hargrave, Brian (Inventor); Platt, Robert J., Jr. (Inventor)

    2014-01-01

    A robotic system includes a robotic mechanism responsive to velocity control signals, and a permissible workspace defined by a convex-polygon boundary. A host machine determines a position of a reference point on the mechanism with respect to the boundary, and includes an algorithm for enforcing the boundary by automatically shaping the velocity control signals as a function of the position, thereby providing smooth and unperturbed operation of the mechanism along the edges and corners of the boundary. The algorithm is suited for application with higher speeds and/or external forces. A host machine includes an algorithm for enforcing the boundary by shaping the velocity control signals as a function of the reference point position, and a hardware module for executing the algorithm. A method for enforcing the convex-polygon boundary is also provided that shapes a velocity control signal via a host machine as a function of the reference point position.

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

    PubMed Central

    2014-01-01

    Background 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. Methods 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. Results 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). Conclusion 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. PMID:25223399

  19. The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

    PubMed Central

    Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin

    2015-01-01

    The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research. PMID:25332403

  20. The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes.

    PubMed

    Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin

    2015-01-01

    The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research. PMID:25332403

  1. An open-source deconvolution software package for 3-D quantitative fluorescence microscopy imaging

    PubMed Central

    SUN, Y.; DAVIS, P.; KOSMACEK, E. A.; IANZINI, F.; MACKEY, M. A.

    2010-01-01

    Summary Deconvolution techniques have been widely used for restoring the 3-D quantitative information of an unknown specimen observed using a wide-field fluorescence microscope. Deconv, an open-source deconvolution software package, was developed for 3-D quantitative fluorescence microscopy imaging and was released under the GNU Public License. Deconv provides numerical routines for simulation of a 3-D point spread function and deconvolution routines implemented three constrained iterative deconvolution algorithms: one based on a Poisson noise model and two others based on a Gaussian noise model. These algorithms are presented and evaluated using synthetic images and experimentally obtained microscope images, and the use of the library is explained. Deconv allows users to assess the utility of these deconvolution algorithms and to determine which are suited for a particular imaging application. The design of Deconv makes it easy for deconvolution capabilities to be incorporated into existing imaging applications. PMID:19941558

  2. Determination of 6D workspaces of Gough-type parallel manipulator and comparison between different geometries

    SciTech Connect

    Merlet, J.P.

    1999-09-01

    The author considers in this paper a Gough-type parallel robot whose leg length values are constrained to lie within some fixed ranges and for which there may be mechanical limits for the motion of the passive joints. The purpose of this paper is to present algorithms to determine: the constant orientation workspace; all the possible locations of the center of the platform that can be reached with a fixed orientation; the total orientation workspace: all the possible locations of the center of the platform that can be reached with any orientation in a set defined by three ranges for the orientation angles; the inclusive orientation workspace: all the possible locations of the center of the platform that can be reached with at least one orientation among a set defined by three ranges for the orientation angles. Most of these algorithms are based on a basic methods: approximation of the results by a set of 3D or 6D boxes obtained from an initial estimation through a bisection process. The boxes in the result will either fully or partially lie inside the workspace: the bisection stops as soon as all the boxes that do not lie fully inside the workspace have a size that is lower than a fixed threshold. The paper includes a comparison between the workspace volumes of four different robot geometries, which shows that for robots of similar dimensions the joints layout has a large influence on the workspace volume.

  3. Upper Extremity 3D Reachable Workspace Assessment in ALS by Kinect sensor

    PubMed Central

    Oskarsson, Bjorn; Joyce, Nanette C.; de Bie, Evan; Nicorici, Alina; Bajcsy, Ruzena; Kurillo, Gregorij; Han, Jay J.

    2016-01-01

    Introduction Reachable workspace is a measure that provides clinically meaningful information regarding arm function. In this study, a Kinect sensor was used to determine the spectrum of 3D reachable workspace encountered in a cross-sectional cohort of individuals with ALS. Method Bilateral 3D reachable workspace was recorded from 10 subjects with ALS and 23 healthy controls. The data were normalized by each individual's arm length to obtain a reachable workspace relative surface area (RSA). Concurrent validity was assessed by correlation with ALSFRSr scores. Results The Kinect-measured reachable workspace RSA differed significantly between the ALS and control subjects (0.579±0.226 vs. 0.786±0.069; P<0.001). The RSA demonstrated correlation with ALSFRSr upper extremity items (Spearman correlation ρ=0.569; P=0.009). With worsening upper extremity function as categorized by the ALSFRSr, the reachable workspace also decreased progressively. Conclusions This study demonstrates the feasibility and potential of using a novel Kinect-based reachable workspace outcome measure in ALS. PMID:25965847

  4. MedXViewer: an extensible web-enabled software package for medical imaging

    NASA Astrophysics Data System (ADS)

    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).

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

    NASA Astrophysics Data System (ADS)

    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

  6. Higher-order continuation for the determination of robot workspace boundaries

    NASA Astrophysics Data System (ADS)

    Hentz, Gauthier; Charpentier, Isabelle; Renaud, Pierre

    2016-02-01

    In the medical and surgical fields, robotics may be of great interest for safer and more accurate procedures. Space constraints for a robotic assistant are however strict. Therefore, roboticists study non-conventional mechanisms with advantageous size/workspace ratios. The determination of mechanism workspace, and primarily its boundaries, is thus of major importance. This Note builds on boundary equation definition, continuation and automatic differentiation to propose a general, accurate, fast and automated method for the determination of mechanism workspace. The method is illustrated with a planar RRR mechanism and a three-dimensional Orthoglide parallel mechanism.

  7. Despeckle filtering software toolbox for ultrasound imaging of the common carotid artery.

    PubMed

    Loizou, Christos P; Theofanous, Charoula; Pantziaris, Marios; Kasparis, Takis

    2014-04-01

    Ultrasound imaging of the common carotid artery (CCA) is a non-invasive tool used in medicine to assess the severity of atherosclerosis and monitor its progression through time. It is also used in border detection and texture characterization of the atherosclerotic carotid plaque in the CCA, the identification and measurement of the intima-media thickness (IMT) and the lumen diameter that all are very important in the assessment of cardiovascular disease (CVD). Visual perception, however, is hindered by speckle, a multiplicative noise, that degrades the quality of ultrasound B-mode imaging. Noise reduction is therefore essential for improving the visual observation quality or as a pre-processing step for further automated analysis, such as image segmentation of the IMT and the atherosclerotic carotid plaque in ultrasound images. In order to facilitate this preprocessing step, we have developed in MATLAB(®) a unified toolbox that integrates image despeckle filtering (IDF), texture analysis and image quality evaluation techniques to automate the pre-processing and complement the disease evaluation in ultrasound CCA images. The proposed software, is based on a graphical user interface (GUI) and incorporates image normalization, 10 different despeckle filtering techniques (DsFlsmv, DsFwiener, DsFlsminsc, DsFkuwahara, DsFgf, DsFmedian, DsFhmedian, DsFad, DsFnldif, DsFsrad), image intensity normalization, 65 texture features, 15 quantitative image quality metrics and objective image quality evaluation. The software is publicly available in an executable form, which can be downloaded from http://www.cs.ucy.ac.cy/medinfo/. It was validated on 100 ultrasound images of the CCA, by comparing its results with quantitative visual analysis performed by a medical expert. It was observed that the despeckle filters DsFlsmv, and DsFhmedian improved image quality perception (based on the expert's assessment and the image texture and quality metrics). It is anticipated that the

  8. The Spectral Image Processing System (SIPS): Software for integrated analysis of AVIRIS data

    NASA Technical Reports Server (NTRS)

    Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

    1992-01-01

    The Spectral Image Processing System (SIPS) is a software package developed by the Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, in response to a perceived need to provide integrated tools for analysis of imaging spectrometer data both spectrally and spatially. SIPS was specifically designed to deal with data from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and the High Resolution Imaging Spectrometer (HIRIS), but was tested with other datasets including the Geophysical and Environmental Research Imaging Spectrometer (GERIS), GEOSCAN images, and Landsat TM. SIPS was developed using the 'Interactive Data Language' (IDL). It takes advantage of high speed disk access and fast processors running under the UNIX operating system to provide rapid analysis of entire imaging spectrometer datasets. SIPS allows analysis of single or multiple imaging spectrometer data segments at full spatial and spectral resolution. It also allows visualization and interactive analysis of image cubes derived from quantitative analysis procedures such as absorption band characterization and spectral unmixing. SIPS consists of three modules: SIPS Utilities, SIPS_View, and SIPS Analysis. SIPS version 1.1 is described below.

  9. Oxygen octahedra picker: A software tool to extract quantitative information from STEM images.

    PubMed

    Wang, Yi; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y; van Aken, Peter A

    2016-09-01

    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 BO6 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. PMID:27344044

  10. The Image-Guided Surgery ToolKit IGSTK: an open source C++ software toolkit

    NASA Astrophysics Data System (ADS)

    Cheng, Peng; Ibanez, Luis; Gobbi, David; Gary, Kevin; Aylward, Stephen; Jomier, Julien; Enquobahrie, Andinet; Zhang, Hui; Kim, Hee-su; Blake, M. Brian; Cleary, Kevin

    2007-03-01

    The Image-Guided Surgery Toolkit (IGSTK) is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. The focus of the toolkit is on robustness using a state machine architecture. This paper presents an overview of the project based on a recent book which can be downloaded from igstk.org. The paper includes an introduction to open source projects, a discussion of our software development process and the best practices that were developed, and an overview of requirements. The paper also presents the architecture framework and main components. This presentation is followed by a discussion of the state machine model that was incorporated and the associated rationale. The paper concludes with an example application.

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

    PubMed Central

    2011-01-01

    Background 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. Methods 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. Results 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

  12. Development of a software based automatic exposure control system for use in image guided radiation therapy

    NASA Astrophysics Data System (ADS)

    Morton, Daniel R.

    Modern image guided radiation therapy involves the use of an isocentrically mounted imaging system to take radiographs of a patient's position before the start of each treatment. Image guidance helps to minimize errors associated with a patients setup, but the radiation dose received by patients from imaging must be managed to ensure no additional risks. The Varian On-Board Imager (OBI) (Varian Medical Systems, Inc., Palo Alto, CA) does not have an automatic exposure control system and therefore requires exposure factors to be manually selected. Without patient specific exposure factors, images may become saturated and require multiple unnecessary exposures. A software based automatic exposure control system has been developed to predict optimal, patient specific exposure factors. The OBI system was modelled in terms of the x-ray tube output and detector response in order to calculate the level of detector saturation for any exposure situation. Digitally reconstructed radiographs are produced via ray-tracing through the patients' volumetric datasets that are acquired for treatment planning. The ray-trace determines the attenuation of the patient and subsequent x-ray spectra incident on the imaging detector. The resulting spectra are used in the detector response model to determine the exposure levels required to minimize detector saturation. Images calculated for various phantoms showed good agreement with the images that were acquired on the OBI. Overall, regions of detector saturation were accurately predicted and the detector response for non-saturated regions in images of an anthropomorphic phantom were calculated to generally be within 5 to 10 % of the measured values. Calculations were performed on patient data and found similar results as the phantom images, with the calculated images being able to determine detector saturation with close agreement to images that were acquired during treatment. Overall, it was shown that the system model and calculation

  13. Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions

    PubMed Central

    Shenoy, Shailesh M.

    2016-01-01

    A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software’s support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity. PMID:27516727

  14. TiLIA: a software package for image analysis of firefly flash patterns.

    PubMed

    Konno, Junsuke; Hatta-Ohashi, Yoko; Akiyoshi, Ryutaro; Thancharoen, Anchana; Silalom, Somyot; Sakchoowong, Watana; Yiu, Vor; Ohba, Nobuyoshi; Suzuki, Hirobumi

    2016-05-01

    As flash signaling patterns of fireflies are species specific, signal-pattern analysis is important for understanding this system of communication. Here, we present time-lapse image analysis (TiLIA), a free open-source software package for signal and flight pattern analyses of fireflies that uses video-recorded image data. TiLIA enables flight path tracing of individual fireflies and provides frame-by-frame coordinates and light intensity data. As an example of TiLIA capabilities, we demonstrate flash pattern analysis of the fireflies Luciola cruciata and L. lateralis during courtship behavior. PMID:27069594

  15. 2D-CELL: image processing software for extraction and analysis of 2-dimensional cellular structures

    NASA Astrophysics Data System (ADS)

    Righetti, F.; Telley, H.; Leibling, Th. M.; Mocellin, A.

    1992-01-01

    2D-CELL is a software package for the processing and analyzing of photographic images of cellular structures in a largely interactive way. Starting from a binary digitized image, the programs extract the line network (skeleton) of the structure and determine the graph representation that best models it. Provision is made for manually correcting defects such as incorrect node positions or dangling bonds. Then a suitable algorithm retrieves polygonal contours which define individual cells — local boundary curvatures are neglected for simplicity. Using elementary analytical geometry relations, a range of metric and topological parameters describing the population are then computed, organized into statistical distributions and graphically displayed.

  16. Vobi One: a data processing software package for functional optical imaging

    PubMed Central

    Takerkart, Sylvain; Katz, Philippe; Garcia, Flavien; Roux, Sébastien; Reynaud, Alexandre; Chavane, Frédéric

    2014-01-01

    Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10–20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one. PMID:24478623

  17. Vobi One: a data processing software package for functional optical imaging.

    PubMed

    Takerkart, Sylvain; Katz, Philippe; Garcia, Flavien; Roux, Sébastien; Reynaud, Alexandre; Chavane, Frédéric

    2014-01-01

    Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10-20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one. PMID:24478623

  18. SOFI Simulation Tool: A Software Package for Simulating and Testing Super-Resolution Optical Fluctuation Imaging.

    PubMed

    Girsault, Arik; Lukes, Tomas; Sharipov, Azat; Geissbuehler, Stefan; Leutenegger, Marcel; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Lasser, Theo

    2016-01-01

    Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data. PMID:27583365

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    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.

  20. AIRS: The Medical Imaging Software for Segmentation and Registration in SPECT/CT

    NASA Astrophysics Data System (ADS)

    Widita, R.; Kurniadi, R.; Haryanto, F.; Darma, Y.; Perkasa, Y. S.; Zasneda, S. S.

    2010-06-01

    We have been successfully developed a new software, Automated Image Registration and Segmentation (AIRS), to fuse the CT and SPECT images. It is designed to solve different registration and segmentation problems that arises in tomographic data sets. AIRS is addressed to obtain anatomic information to be applied to NanoSpect system which is imaging for nano-tissues or small animals. It will be demonstrated that the information obtained by SPECT/CT is more accurate in evaluating patients/objects than that obtained from either SPECT or CT alone. The registration methods developed here are for both two-dimensional and three-dimensional registration. We used normalized mutual information (NMI) which is amenable for images produced by different modalities and having unclear boundaries between tissues. The segmentation components used in this software is region growing algorithms which have proven to be an effective approach for image segmentation. The implementations of region growing developed here are connected threshold and neighborhood connected. Our method is designed to perform with clinically acceptable speed, using accelerated techniques (multiresolution).

  1. Image 100 procedures manual development: Applications system library definition and Image 100 software definition

    NASA Technical Reports Server (NTRS)

    Guseman, L. F., Jr.; Decell, H. P., Jr.

    1975-01-01

    An outline for an Image 100 procedures manual for Earth Resources Program image analysis was developed which sets forth guidelines that provide a basis for the preparation and updating of an Image 100 Procedures Manual. The scope of the outline was limited to definition of general features of a procedures manual together with special features of an interactive system. Computer programs were identified which should be implemented as part of an applications oriented library for the system.

  2. [Development of DICOM image viewing software for efficient image reading and evaluation of distributed server system for diagnostic environment].

    PubMed

    Ishikawa, K

    2000-12-01

    To construct an efficient diagnostic environment using computer displays, the author investigated the time of network transmission using clinical images. In our hospital, we introduced optical-fiber 100Base-Fx Ethernet connections between 22 HIS-segments and one RIS-segment. Although Ethernet architecture is inexpensive, the speed of image transmission becomes 2371 KB/sec. (4.6 CT-slice/sec.) in the RIS-segment and 996 KB/sec. (1.9 CT-slice/sec.) from the RIS-segment to HIS-segments. Because one examination is transmitted in one minute, it does not disturb image reading. Otherwise, a distributed server system using inexpensive personal computers helps in constructing an efficient system. This investigation showed that commercially based Digital Imaging and Communications in Medicine(DICOM) servers and RSNA Central Test Node servers are not so different in transmission speed. The author programmed and developed DICOM transmission and viewing software for Macintosh computers. This viewer includes two inventions, dynamic tiling window system (DTWS) and window binding mode(WBM). On DTWS, windows, tiles, and images are independent objects, which are movable and resizable. The tile-matrix is changeable by mouse dragging, which realizes suitable tile rectangles for wide-low or narrow-high images. The arranging window tool prevents windows from scattering. Using WBM, any operation affects each window similarly. This means that the relationship of compared images is always equivalent. DTWS and WBM contribute greatly to a filmless diagnostic environment. PMID:11197836

  3. BAMS2 Workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections

    PubMed Central

    Bota, Mihail; Talpalaru, Ştefan; Hintiryan, Houri; Dong, Hong-Wei; Swanson, Larry W.

    2014-01-01

    We present in this paper a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information about gray matter region axonal connections. This de novo constructed module allows registered users to directly collate their data by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats, and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail, and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions. PMID:24668342

  4. CPG-inspired workspace trajectory generation and adaptive locomotion control for quadruped robots.

    PubMed

    Liu, Chengju; Chen, Qijun; Wang, Danwei

    2011-06-01

    This paper deals with the locomotion control of quadruped robots inspired by the biological concept of central pattern generator (CPG). A control architecture is proposed with a 3-D workspace trajectory generator and a motion engine. The workspace trajectory generator generates adaptive workspace trajectories based on CPGs, and the motion engine realizes joint motion imputes. The proposed architecture is able to generate adaptive workspace trajectories online by tuning the parameters of the CPG network to adapt to various terrains. With feedback information, a quadruped robot can walk through various terrains with adaptive joint control signals. A quadruped platform AIBO is used to validate the proposed locomotion control system. The experimental results confirm the effectiveness of the proposed control architecture. A comparison by experiments shows the superiority of the proposed method against the traditional CPG-joint-space control method. PMID:21216715

  5. BAMS2 workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections.

    PubMed

    Bota, Mihail; Talpalaru, Stefan; Hintiryan, Houri; Dong, Hong-Wei; Swanson, Larry W

    2014-10-01

    We describe a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information on gray matter region axonal connections. This de novo constructed module allows registered users to collate their data directly by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third-party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions. PMID:24668342

  6. A collaborative resource management workspace and project management application for data collection, analysis and visualization: OpenNRM

    NASA Astrophysics Data System (ADS)

    Osti, A.

    2013-12-01

    During the process of research and design for OpenNRM, we imagined a place where diverse groups of people and communities could effectively and efficiently collaborate to manage large-scale environmental problems and projects. Our research revealed the need to combine a variety of software components. Users can explore and analyze a topic while simultaneously develop stories and solve problems in a way that the end result is consumable by their colleagues and the general public. To do this we brought together software modules that are typically separate: Document and Asset Management, GIS and Interactive Mapping, WIKI and Information Libraries, Data Catalogs and Services, Project Management Tools and Storytelling templates. These components, along with others are supported by extensive data catalogs (NWIS, Storet, CDEC, Cuahsi), data analysis tools and web services for a turn-key workspace that will allow you to quickly build project communities and data stories. In this presentation we will show you how our investigation into these collaborative efforts are implemented and working for some of our clients, including the State of California's Sacramento San Joaquin Bay-Delta and San Joaquin River Basin. The case study will display the use of the OpenNRM workspace for real time environmental conditions management, data visualization, project operations, environmental restoration, high frequency monitoring and data reporting. We will demonstrate how scientists and policy makers are working together to tell the story of this complicated and divisive system and how they are becoming better managers of that system. Using the genius of web services, we will show you how OpenNRM was designed to allow you to build your own community while easily sharing data stories, project data, monitoring results, document libraries, interactive maps and datasets with others. We will get into more technical detail by presenting how our data interpolation tools can show high frequency

  7. A Survey of DICOM Viewer Software to Integrate Clinical Research and Medical Imaging.

    PubMed

    Haak, Daniel; Page, Charles-E; Deserno, Thomas M

    2016-04-01

    The digital imaging and communications in medicine (DICOM) protocol is the leading standard for image data management in healthcare. Imaging biomarkers and image-based surrogate endpoints in clinical trials and medical registries require DICOM viewer software with advanced functionality for visualization and interfaces for integration. In this paper, a comprehensive evaluation of 28 DICOM viewers is performed. The evaluation criteria are obtained from application scenarios in clinical research rather than patient care. They include (i) platform, (ii) interface, (iii) support, (iv) two-dimensional (2D), and (v) three-dimensional (3D) viewing. On the average, 4.48 and 1.43 of overall 8 2D and 5 3D image viewing criteria are satisfied, respectively. Suitable DICOM interfaces for central viewing in hospitals are provided by GingkoCADx, MIPAV, and OsiriX Lite. The viewers ImageJ, MicroView, MIPAV, and OsiriX Lite offer all included 3D-rendering features for advanced viewing. Interfaces needed for decentral viewing in web-based systems are offered by Oviyam, Weasis, and Xero. Focusing on open source components, MIPAV is the best candidate for 3D imaging as well as DICOM communication. Weasis is superior for workflow optimization in clinical trials. Our evaluation shows that advanced visualization and suitable interfaces can also be found in the open source field and not only in commercial products. PMID:26482912

  8. Upper extremity 3D reachable workspace analysis in dystrophinopathy using Kinect

    PubMed Central

    Han, Jay J.; Kurillo, Gregorij; Abresch, Richard T.; de Bie, Evan; Nicorici, Alina; Bajcsy, Ruzena

    2015-01-01

    Introduction An innovative upper extremity 3D reachable workspace outcome measure acquired using Kinect sensor is applied towards Duchenne/Becker muscular dystrophy (DMD/BMD). The validity, sensitivity, and clinical meaningfulness of the novel outcome is examined. Methods Upper extremity function assessment (Brooke scale, NeuroQOL questionnaire) and Kinect-based reachable workspace analyses were conducted in 43 individuals with dystrophinopathy (30-DMD, 13-BMD; ages 7–60) and 46 controls (ages 6–68). Results The reachable workspace measure reliably captured a wide-range of upper extremity impairments encountered in both pediatric and adult, as well as ambulatory and non-ambulatory individuals with dystrophinopathy. Reduced reachable workspaces were noted for the dystrophinopathy cohort compared to controls, and they correlated with Brooke grades. Additionally, progressive reduction in reachable workspace directly correlated with worsening ability to perform activities of daily living, as self-reported on the NeuroQOL. Discussion This study demonstrates the utility and potential of the novel sensor-acquired reachable workspace outcome measure in dystrophinopathy. PMID:25597487

  9. Optimal Design of a 3-Leg 6-DOF Parallel Manipulator for a Specific Workspace

    NASA Astrophysics Data System (ADS)

    Fu, Jianxun; Gao, Feng

    2016-04-01

    Researchers seldom study optimum design of a six-degree-of-freedom(DOF) parallel manipulator with three legs based upon the given workspace. An optimal design method of a novel three-leg six-DOF parallel manipulator(TLPM) is presented. The mechanical structure of this robot is introduced, with this structure the kinematic constrain equations is decoupled. Analytical solutions of the forward kinematics are worked out, one configuration of this robot, including position and orientation of the end-effector are graphically displayed. Then, on the basis of several extreme positions of the kinematic performances, the task workspace is given. An algorithm of optimal designing is introduced to find the smallest dimensional parameters of the proposed robot. Examples illustrate the design results, and a design stability index is introduced, which ensures that the robot remains a safe distance from the boundary of sits actual workspace. Finally, one prototype of the robot is developed based on this method. This method can easily find appropriate kinematic parameters that can size a robot having the smallest workspace enclosing a predefined task workspace. It improves the design efficiency, ensures that the robot has a small mechanical size possesses a large given workspace volume, and meets the lightweight design requirements.

  10. Software and hardware integration of a microprogrammable state machine for NMR imaging.

    PubMed

    Stewart, B K; Pratt, R G; Thomas, S R; Dieckman, S L; Ridgway, T H

    1991-01-01

    We have integrated a commercially available microprogrammable state machine (Tecmag PULSkit) for use as a magnetic resonance pulse programmer. Providing the capability for active research environment imaging protocols, it features timing resolution of 100 nsec, ten 16-bit loop counters, and individually addressable look-up tables. This integration involved hardware and software integration with a VAX 11/750 at several levels. Hardware: Each of the three gradient channels employs three digital-to-analog converters (DACs). An 8-bit, 4-quadrant, multiplying DAC generates the gradient waveform shape. A 12-bit DAC generates the multiplying DAC scaling voltage, controlling gradient amplitude and sign. A third 12-bit DAC produces a gradient offset (shim) voltage. An eddy current compensation network is present for each gradient channel. Software: The software design philosophy was to create a flexible interface (interactive window environment), while not constraining complex manipulation of the hardware (direct use of the pulse-sequence compiler primitives and microprogramming). The software levels include (a) pulse-sequence microprogramming, (b) pulse-sequence compiler, (c) interactive parameter specification, and (d) canned pulse-sequence microcode library. PMID:1779734

  11. Development of an Open Source Image-Based Flow Modeling Software - SimVascular

    NASA Astrophysics Data System (ADS)

    Updegrove, Adam; Merkow, Jameson; Schiavazzi, Daniele; Wilson, Nathan; Marsden, Alison; Shadden, Shawn

    2014-11-01

    SimVascular (www.simvascular.org) is currently the only comprehensive software package that provides a complete pipeline from medical image data segmentation to patient specific blood flow simulation. This software and its derivatives have been used in hundreds of conference abstracts and peer-reviewed journal articles, as well as the foundation of medical startups. SimVascular was initially released in August 2007, yet major challenges and deterrents for new adopters were the requirement of licensing three expensive commercial libraries utilized by the software, a complicated build process, and a lack of documentation, support and organized maintenance. In the past year, the SimVascular team has made significant progress to integrate open source alternatives for the linear solver, solid modeling, and mesh generation commercial libraries required by the original public release. In addition, the build system, available distributions, and graphical user interface have been significantly enhanced. Finally, the software has been updated to enable users to directly run simulations using models and boundary condition values, included in the Vascular Model Repository (vascularmodel.org). In this presentation we will briefly overview the capabilities of the new SimVascular 2.0 release. National Science Foundation.

  12. CONRAD—A software framework for cone-beam imaging in radiology

    SciTech Connect

    Maier, Andreas; Choi, Jang-Hwan; Riess, Christian; Keil, Andreas; Fahrig, Rebecca; Hofmann, Hannes G.; Berger, Martin; Fischer, Peter; Schwemmer, Chris; Wu, Haibo; Müller, Kerstin; Hornegger, Joachim

    2013-11-15

    Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform with extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and

  13. CAVASS: a computer-assisted visualization and analysis software system - image processing aspects

    NASA Astrophysics Data System (ADS)

    Udupa, Jayaram K.; Grevera, George J.; Odhner, Dewey; Zhuge, Ying; Souza, Andre; Mishra, Shipra; Iwanaga, Tad

    2007-03-01

    The development of the concepts within 3DVIEWNIX and of the software system 3DVIEWNIX itself dates back to the 1970s. Since then, a series of software packages for Computer Assisted Visualization and Analysis (CAVA) of images came out from our group, 3DVIEWNIX released in 1993, being the most recent, and all were distributed with source code. CAVASS, an open source system, is the latest in this series, and represents the next major incarnation of 3DVIEWNIX. It incorporates four groups of operations: IMAGE PROCESSING (including ROI, interpolation, filtering, segmentation, registration, morphological, and algebraic operations), VISUALIZATION (including slice display, reslicing, MIP, surface rendering, and volume rendering), MANIPULATION (for modifying structures and surgery simulation), ANALYSIS (various ways of extracting quantitative information). CAVASS is designed to work on all platforms. Its key features are: (1) most major CAVA operations incorporated; (2) very efficient algorithms and their highly efficient implementations; (3) parallelized algorithms for computationally intensive operations; (4) parallel implementation via distributed computing on a cluster of PCs; (5) interface to other systems such as CAD/CAM software, ITK, and statistical packages; (6) easy to use GUI. In this paper, we focus on the image processing operations and compare the performance of CAVASS with that of ITK. Our conclusions based on assessing performance by utilizing a regular (6 MB), large (241 MB), and a super (873 MB) 3D image data set are as follows: CAVASS is considerably more efficient than ITK, especially in those operations which are computationally intensive. It can handle considerably larger data sets than ITK. It is easy and ready to use in applications since it provides an easy to use GUI. The users can easily build a cluster from ordinary inexpensive PCs and reap the full power of CAVASS inexpensively compared to expensive multiprocessing systems which are less

  14. 76 FR 43724 - In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Commission...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-21

    ... Cupertino, California (``Apple''). 75 FR 28058 (May 19, 2010). The complaint alleged ] violations of section... COMMISSION In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Commission... related software by reason of infringement of various claims of United States Patent Nos. 6,031,964 and...

  15. The role of camera-bundled image management software in the consumer digital imaging value chain

    NASA Astrophysics Data System (ADS)

    Mueller, Milton; Mundkur, Anuradha; Balasubramanian, Ashok; Chirania, Virat

    2005-02-01

    This research was undertaken by the Convergence Center at the Syracuse University School of Information Studies (www.digital-convergence.info). Project ICONICA, the name for the research, focuses on the strategic implications of digital Images and the CONvergence of Image management and image CApture. Consumer imaging - the activity that we once called "photography" - is now recognized as in the throes of a digital transformation. At the end of 2003, market researchers estimated that about 30% of the households in the U.S. and 40% of the households in Japan owned digital cameras. In 2004, of the 86 million new cameras sold (excluding one-time use cameras), a majority (56%) were estimated to be digital cameras. Sales of photographic film, while still profitable, are declining precipitously.

  16. Creation of 4D imaging data using open source image registration software

    NASA Astrophysics Data System (ADS)

    Wong, Kenneth H.; Ibanez, Luis; Popa, Teo; Cleary, Kevin

    2006-03-01

    4D images (3 spatial dimensions plus time) using CT or MRI will play a key role in radiation medicine as techniques for respiratory motion compensation become more widely available. Advance knowledge of the motion of a tumor and its surrounding anatomy will allow the creation of highly conformal dose distributions in organs such as the lung, liver, and pancreas. However, many of the current investigations into 4D imaging rely on synchronizing the image acquisition with an external respiratory signal such as skin motion, tidal flow, or lung volume, which typically requires specialized hardware and modifications to the scanner. We propose a novel method for 4D image acquisition that does not require any specific gating equipment and is based solely on open source image registration algorithms. Specifically, we use the Insight Toolkit (ITK) to compute the normalized mutual information (NMI) between images taken at different times and use that value as an index of respiratory phase. This method has the advantages of (1) being able to be implemented without any hardware modification to the scanner, and (2) basing the respiratory phase on changes in internal anatomy rather than external signal. We have demonstrated the capabilities of this method with CT fluoroscopy data acquired from a swine model.

  17. Comparison of Perfusion- and Diffusion-weighted Imaging Parameters in Brain Tumor Studies Processed Using Different Software Platforms

    PubMed Central

    Milchenko, Mikhail V.; Rajderkar, Dhanashree; LaMontagne, Pamela; Massoumzadeh, Parinaz; Bogdasarian, Ronald; Schweitzer, Gordon; Benzinger, Tammie; Marcus, Dan; Shimony, Joshua S.; Fouke, Sarah Jost

    2015-01-01

    Rationale and Objectives To compare quantitative imaging parameter measures from diffusion- and perfusion-weighted imaging magnetic resonance imaging (MRI) sequences in subjects with brain tumors that have been processed with different software platforms. Materials and Methods Scans from 20 subjects with primary brain tumors were selected from the Comprehensive Neuro-oncology Data Repository at Washington University School of Medicine (WUSM) and the Swedish Neuroscience Institute. MR images were coregistered, and each subject's data set was processed by three software packages: 1) vendor-specific scanner software, 2) research software developed at WUSM, and 3) a commercially available, Food and Drug Administration–approved, processing platform (Nordic Ice). Regions of interest (ROIs) were chosen within the brain tumor and normal nontumor tissue. The results obtained using these methods were compared. Results For diffusion parameters, including mean diffusivity and fractional anisotropy, concordance was high when comparing different processing methods. For perfusion-imaging parameters, a significant variance in cerebral blood volume, cerebral blood flow, and mean transit time (MTT) values was seen when comparing the same raw data processed using different software platforms. Correlation was better with larger ROIs (radii ≥ 5 mm). Greatest variance was observed in MTT. Conclusions Diffusion parameter values were consistent across different software processing platforms. Perfusion parameter values were more variable and were influenced by the software used. Variation in the MTT was especially large suggesting that MTT estimation may be unreliable in tumor tissues using current MRI perfusion methods. PMID:25088833

  18. Mississippi Company Using NASA Software Program to Provide Unique Imaging Service: DATASTAR Success Story

    NASA Technical Reports Server (NTRS)

    2001-01-01

    DATASTAR, Inc., of Picayune, Miss., has taken NASA's award-winning Earth Resources Laboratory Applications (ELAS) software program and evolved it to the point that the company is now providing a unique, spatial imagery service over the Internet. ELAS was developed in the early 80's to process satellite and airborne sensor imagery data of the Earth's surface into readable and useable information. While there are several software packages on the market that allow the manipulation of spatial data into useable products, this is usually a laborious task. The new program, called the DATASTAR Image Processing Exploitation, or DIPX, Delivery Service, is a subscription service available over the Internet that takes the work out of the equation and provides normalized geo-spatial data in the form of decision products.

  19. A comprehensive software system for image processing and programming. Final report

    SciTech Connect

    Rasure, J.; Hallett, S.; Jordan, R.

    1994-12-31

    XVision is an example of a comprehensive software system dedicated to the processing of multidimensional scientific data. Because it is comprehensive it is necessarily complex. This design complexity is dealt with by considering XVision as nine overlapping software systems, their components and the required standards. The complexity seen by a user of XVision is minimized by the different interfaces providing access to the image processing routines as well as an interface to ease the incorporation of new routines. The XVision project has stressed the importance of having: (1) interfaces to accommodate users with differing preferences and backgrounds and (2) tools to support the programmer and the scientist. The result is a system that provides a framework for building a powerful research, education and development tool.

  20. Advances in hardware, software, and automation for 193nm aerial image measurement systems

    NASA Astrophysics Data System (ADS)

    Zibold, Axel M.; Schmid, R.; Seyfarth, A.; Waechter, M.; Harnisch, W.; Doornmalen, H. v.

    2005-05-01

    A new, second generation AIMS fab 193 system has been developed which is capable of emulating lithographic imaging of any type of reticles such as binary and phase shift masks (PSM) including resolution enhancement technologies (RET) such as optical proximity correction (OPC) or scatter bars. The system emulates the imaging process by adjustment of the lithography equivalent illumination and imaging conditions of 193nm wafer steppers including circular, annular, dipole and quadrupole type illumination modes. The AIMS fab 193 allows a rapid prediction of wafer printability of critical mask features, including dense patterns and contacts, defects or repairs by acquiring through-focus image stacks by means of a CCD camera followed by quantitative image analysis. Moreover the technology can be readily applied to directly determine the process window of a given mask under stepper imaging conditions. Since data acquisition is performed electronically, AIMS in many applications replaces the need for costly and time consuming wafer prints using a wafer stepper/ scanner followed by CD SEM resist or wafer analysis. The AIMS fab 193 second generation system is designed for 193nm lithography mask printing predictability down to the 65nm node. In addition to hardware improvements a new modular AIMS software is introduced allowing for a fully automated operation mode. Multiple pre-defined points can be visited and through-focus AIMS measurements can be executed automatically in a recipe based mode. To increase the effectiveness of the automated operation mode, the throughput of the system to locate the area of interest, and to acquire the through-focus images is increased by almost a factor of two in comparison with the first generation AIMS systems. In addition a new software plug-in concept is realised for the tools. One new feature has been successfully introduced as "Global CD Map", enabling automated investigation of global mask quality based on the local determination of

  1. Real-time telemedicine using shared three-dimensional workspaces over ATM

    NASA Astrophysics Data System (ADS)

    Cahoon, Peter; Forsey, David R.; Hutchison, Susan

    1999-03-01

    During the past five years a high speed ATM network has been developed at UBC that provides a campus testbed, a local testbed to the hospitals, and a National testbed between here and the BADLAB in Ottawa. This testbed has been developed to combine a commercial shared audio/video/whiteboard environment coupled with a shared interactive 3-dimensional solid model. This solid model ranges from a skull reconstructed from a CT scan with muscles and an overlying skin, to a model of the ventricle system of the human brain. Typical interactions among surgeon, radiologist and modeler consist of having image slices of the original scan shared by all and the ability to adjust the surface of the model to conform to each individuals perception of what the final object should look like. The purpose of this interaction can range from forensic reconstruction from partial remains to pre-maxillofacial surgery. A joint project with the forensic unit of the R.C.M.P. in Ottawa using the BADLAB is now in the stages of testing this methodology on a real case beginning with a CT scan of partial remains. A second study underway with the department of Maxiofacial reconstruction at Dalhousie University in Halifax Nova Scotia and concerns a subject who is about to undergo orthognathic surgery, in particular a mandibular advancement. This subject has been MRI scanned, a solid model constructed of the mandible and the virtual surgery constructed on the model. This model and the procedure have been discussed and modified by the modeler and the maxillofacial specialist using these shared workspaces. The procedure will be repeated after the actual surgery to verify the modeled procedure. The advantage of this technique is that none of the specialists need be in the same room, or city. Given the scarcity of time and specialists this methodology shows great promise. In November of this last year a shared live demonstration of this facial modeler was done between Vancouver and Dalhousie University in

  2. Features of the Upgraded Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) Software

    NASA Technical Reports Server (NTRS)

    Mason, Michelle L.; Rufer, Shann J.

    2016-01-01

    The Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) software is used at the NASA Langley Research Center to analyze global aeroheating data on wind tunnel models tested in the Langley Aerothermodynamics Laboratory. One-dimensional, semi-infinite heating data derived from IHEAT are used in the design of thermal protection systems for hypersonic vehicles that are exposed to severe aeroheating loads, such as reentry vehicles during descent and landing procedures. This software program originally was written in the PV-WAVE(Registered Trademark) programming language to analyze phosphor thermography data from the two-color, relative-intensity system developed at Langley. To increase the efficiency, functionality, and reliability of IHEAT, the program was migrated to MATLAB(Registered Trademark) syntax and compiled as a stand-alone executable file labeled version 4.0. New features of IHEAT 4.0 include the options to perform diagnostic checks of the accuracy of the acquired data during a wind tunnel test, to extract data along a specified multi-segment line following a feature such as a leading edge or a streamline, and to batch process all of the temporal frame data from a wind tunnel run. Results from IHEAT 4.0 were compared on a pixel level to the output images from the legacy software to validate the program. The absolute differences between the heat transfer data output from the two programs were on the order of 10(exp -5) to 10(exp -7). IHEAT 4.0 replaces the PV-WAVE(Registered Trademark) version as the production software for aeroheating experiments conducted in the hypersonic facilities at NASA Langley.

  3. Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

    PubMed Central

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

    2013-01-01

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803

  4. Digital map and situation surface: a team-oriented multidisplay workspace for network enabled situation analysis

    NASA Astrophysics Data System (ADS)

    Peinsipp-Byma, E.; Geisler, Jürgen; Bader, Thomas

    2009-05-01

    System concepts for network enabled image-based ISR (intelligence, surveillance, reconnaissance) is the major mission of Fraunhofer IITB's applied research in the area of defence and security solutions. For the TechDemo08 as part of the NATO CNAD POW Defence against terrorism Fraunhofer IITB advanced a new multi display concept to handle the shear amount and high complexity of ISR data acquired by networked, distributed surveillance systems with the objective to support the generation of a common situation picture. Amount and Complexity of ISR data demands an innovative man-machine interface concept for humans to deal with it. The IITB's concept is the Digital Map & Situation Surface. This concept offers to the user a coherent multi display environment combining a horizontal surface for the situation overview from the bird's eye view, an attached vertical display for collateral information and so-called foveatablets as personalized magic lenses in order to obtain high resolved and role-specific information about a focused areaof- interest and to interact with it. In the context of TechDemo08 the Digital Map & Situation Surface served as workspace for team-based situation visualization and analysis. Multiple sea- and landside surveillance components were connected to the system.

  5. A complete software application for automatic registration of x-ray mammography and magnetic resonance images

    SciTech Connect

    Solves-Llorens, J. A.; Rupérez, M. J. Monserrat, C.; Lloret, M.

    2014-08-15

    Purpose: This work presents a complete and automatic software application to aid radiologists in breast cancer diagnosis. The application is a fully automated method that performs a complete registration of magnetic resonance (MR) images and x-ray (XR) images in both directions (from MR to XR and from XR to MR) and for both x-ray mammograms, craniocaudal (CC), and mediolateral oblique (MLO). This new approximation allows radiologists to mark points in the MR images and, without any manual intervention, it provides their corresponding points in both types of XR mammograms and vice versa. Methods: The application automatically segments magnetic resonance images and x-ray images using the C-Means method and the Otsu method, respectively. It compresses the magnetic resonance images in both directions, CC and MLO, using a biomechanical model of the breast that distinguishes the specific biomechanical behavior of each one of its three tissues (skin, fat, and glandular tissue) separately. It makes a projection of both compressions and registers them with the original XR images using affine transformations and nonrigid registration methods. Results: The application has been validated by two expert radiologists. This was carried out through a quantitative validation on 14 data sets in which the Euclidean distance between points marked by the radiologists and the corresponding points obtained by the application were measured. The results showed a mean error of 4.2 ± 1.9 mm for the MRI to CC registration, 4.8 ± 1.3 mm for the MRI to MLO registration, and 4.1 ± 1.3 mm for the CC and MLO to MRI registration. Conclusions: A complete software application that automatically registers XR and MR images of the breast has been implemented. The application permits radiologists to estimate the position of a lesion that is suspected of being a tumor in an imaging modality based on its position in another different modality with a clinically acceptable error. The results show that the

  6. Gemini planet imager integration to the Gemini South telescope software environment

    NASA Astrophysics Data System (ADS)

    Rantakyrö, Fredrik T.; Cardwell, Andrew; Chilcote, Jeffrey; Dunn, Jennifer; Goodsell, Stephen; Hibon, Pascale; Macintosh, Bruce; Quiroz, Carlos; Perrin, Marshall D.; Sadakuni, Naru; Saddlemyer, Leslie; Savransky, Dmitry; Serio, Andrew; Winge, Claudia; Galvez, Ramon; Gausachs, Gaston; Hardie, Kayla; Hartung, Markus; Luhrs, Javier; Poyneer, Lisa; Thomas, Sandrine

    2014-08-01

    The Gemini Planet Imager is an extreme AO instrument with an integral field spectrograph (IFS) operating in Y, J, H, and K bands. Both the Gemini telescope and the GPI instrument are very complex systems. Our goal is that the combined telescope and instrument system may be run by one observer operating the instrument, and one operator controlling the telescope and the acquisition of light to the instrument. This requires a smooth integration between the two systems and easily operated control interfaces. We discuss the definition of the software and hardware interfaces, their implementation and testing, and the integration of the instrument with the telescope environment.

  7. Multithreaded real-time 3D image processing software architecture and implementation

    NASA Astrophysics Data System (ADS)

    Ramachandra, Vikas; Atanassov, Kalin; Aleksic, Milivoje; Goma, Sergio R.

    2011-03-01

    Recently, 3D displays and videos have generated a lot of interest in the consumer electronics industry. To make 3D capture and playback popular and practical, a user friendly playback interface is desirable. Towards this end, we built a real time software 3D video player. The 3D video player displays user captured 3D videos, provides for various 3D specific image processing functions and ensures a pleasant viewing experience. Moreover, the player enables user interactivity by providing digital zoom and pan functionalities. This real time 3D player was implemented on the GPU using CUDA and OpenGL. The player provides user interactive 3D video playback. Stereo images are first read by the player from a fast drive and rectified. Further processing of the images determines the optimal convergence point in the 3D scene to reduce eye strain. The rationale for this convergence point selection takes into account scene depth and display geometry. The first step in this processing chain is identifying keypoints by detecting vertical edges within the left image. Regions surrounding reliable keypoints are then located on the right image through the use of block matching. The difference in the positions between the corresponding regions in the left and right images are then used to calculate disparity. The extrema of the disparity histogram gives the scene disparity range. The left and right images are shifted based upon the calculated range, in order to place the desired region of the 3D scene at convergence. All the above computations are performed on one CPU thread which calls CUDA functions. Image upsampling and shifting is performed in response to user zoom and pan. The player also consists of a CPU display thread, which uses OpenGL rendering (quad buffers). This also gathers user input for digital zoom and pan and sends them to the processing thread.

  8. Position, singularity and workspace analysis of 3-PSR-O spatial parallel manipulator

    NASA Astrophysics Data System (ADS)

    Shao, Jiejie; Chen, Wenyu; Fu, Xin

    2015-04-01

    Although the parallel mechanisms have the advantages of high accuracy, velocity, stiffness, and payload capacity, the shortcomings of the space utilization and workspace limit the applications in the confined space. A novel 3 degrees of freedom spatial parallel manipulator 3-PSR-O (prismatic-spherical-revolute) is proposed, which possesses a compact architecture and extended workspace while maintaining the inherent advantages of the parallel mechanisms. The direct-inverse position, singularity and workspace are investigated. The mapping method is adopted in the position analysis, and the closed form solution is derived in the form of a six order equation. The singularity analysis of the mechanism is also carried out based on the geometrical constraints, including six singularity boundaries. A feature boundary, which is independent of the prismatic joints' stroke limit, is obtained by integrating the six singularity boundaries. According to the formation of the reachable workspace, a concept of basic workspace is also introduced and presented in the analytical way. By demarcating the basic workspace along the central height with the feature boundary, the reachable workspace can be derived and analyzed more efficiently. Finally, a comparative study on the space utilization between the 3-PSP parallel mechanism and the new mechanism is also presented. The area of feature boundary of the new mechanism is about 140% of the 3-PSP parallel mechanism, while its installation radius is only 1/2 of the 3-PSP parallel mechanism. The proposed parallel mechanism shows great space utilization, and is ideally suited for applications in confined space occasions such as immersion lithography, nano-imprint etc.

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

    PubMed

    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. PMID:25359577

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

    PubMed Central

    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 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. Results 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

  11. Software-Assisted Depth Analysis of Optic Nerve Stereoscopic Images in Telemedicine

    PubMed Central

    Xia, Tian; Patel, Shriji N.; Szirth, Ben C.

    2016-01-01

    Background. Software guided optic nerve assessment can assist in process automation and reduce interobserver disagreement. We tested depth analysis software (DAS) in assessing optic nerve cup-to-disc ratio (VCD) from stereoscopic optic nerve images (SONI) of normal eyes. Methods. In a prospective study, simultaneous SONI from normal subjects were collected during telemedicine screenings using a Kowa 3Wx nonmydriatic simultaneous stereoscopic retinal camera (Tokyo, Japan). VCD was determined from SONI pairs and proprietary pixel DAS (Kowa Inc., Tokyo, Japan) after disc and cup contour line placement. A nonstereoscopic VCD was determined using the right channel of a stereo pair. Mean, standard deviation, t-test, and the intraclass correlation coefficient (ICCC) were calculated. Results. 32 patients had mean age of 40 ± 14 years. Mean VCD on SONI was 0.36 ± 0.09, with DAS 0.38 ± 0.08, and with nonstereoscopic 0.29 ± 0.12. The difference between stereoscopic and DAS assisted was not significant (p = 0.45). ICCC showed agreement between stereoscopic and software VCD assessment. Mean VCD difference was significant between nonstereoscopic and stereoscopic (p < 0.05) and nonstereoscopic and DAS (p < 0.005) recordings. Conclusions. DAS successfully assessed SONI and showed a high degree of correlation to physician-determined stereoscopic VCD. PMID:27190507

  12. Software-Assisted Depth Analysis of Optic Nerve Stereoscopic Images in Telemedicine.

    PubMed

    Xia, Tian; Patel, Shriji N; Szirth, Ben C; Kolomeyer, Anton M; Khouri, Albert S

    2016-01-01

    Background. Software guided optic nerve assessment can assist in process automation and reduce interobserver disagreement. We tested depth analysis software (DAS) in assessing optic nerve cup-to-disc ratio (VCD) from stereoscopic optic nerve images (SONI) of normal eyes. Methods. In a prospective study, simultaneous SONI from normal subjects were collected during telemedicine screenings using a Kowa 3Wx nonmydriatic simultaneous stereoscopic retinal camera (Tokyo, Japan). VCD was determined from SONI pairs and proprietary pixel DAS (Kowa Inc., Tokyo, Japan) after disc and cup contour line placement. A nonstereoscopic VCD was determined using the right channel of a stereo pair. Mean, standard deviation, t-test, and the intraclass correlation coefficient (ICCC) were calculated. Results. 32 patients had mean age of 40 ± 14 years. Mean VCD on SONI was 0.36 ± 0.09, with DAS 0.38 ± 0.08, and with nonstereoscopic 0.29 ± 0.12. The difference between stereoscopic and DAS assisted was not significant (p = 0.45). ICCC showed agreement between stereoscopic and software VCD assessment. Mean VCD difference was significant between nonstereoscopic and stereoscopic (p < 0.05) and nonstereoscopic and DAS (p < 0.005) recordings. Conclusions. DAS successfully assessed SONI and showed a high degree of correlation to physician-determined stereoscopic VCD. PMID:27190507

  13. Software development for ACR-approved phantom-based nuclear medicine tomographic image quality control with cross-platform compatibility

    NASA Astrophysics Data System (ADS)

    Oh, Jungsu S.; Choi, Jae Min; Nam, Ki Pyo; Chae, Sun Young; Ryu, Jin-Sook; Moon, Dae Hyuk; Kim, Jae Seung

    2015-07-01

    Quality control and quality assurance (QC/QA) have been two of the most important issues in modern nuclear medicine (NM) imaging for both clinical practices and academic research. Whereas quantitative QC analysis software is common to modern positron emission tomography (PET) scanners, the QC of gamma cameras and/or single-photon-emission computed tomography (SPECT) scanners has not been sufficiently addressed. Although a thorough standard operating process (SOP) for mechanical and software maintenance may help the QC/QA of a gamma camera and SPECT-computed tomography (CT), no previous study has addressed a unified platform or process to decipher or analyze SPECT phantom images acquired from various scanners thus far. In addition, a few approaches have established cross-platform software to enable the technologists and physicists to assess the variety of SPECT scanners from different manufacturers. To resolve these issues, we have developed Interactive Data Language (IDL)-based in-house software for crossplatform (in terms of not only operating systems (OS) but also manufacturers) analyses of the QC data on an ACR SPECT phantom, which is essential for assessing and assuring the tomographical image quality of SPECT. We applied our devised software to our routine quarterly QC of ACR SPECT phantom images acquired from a number of platforms (OS/manufacturers). Based on our experience, we suggest that our devised software can offer a unified platform that allows images acquired from various types of scanners to be analyzed with great precision and accuracy.

  14. Holistic approach to design and implementation of a medical teleconsultation workspace.

    PubMed

    Czekierda, Łukasz; Malawski, Filip; Wyszkowski, Przemysław

    2015-10-01

    While there are many state-of-the-art approaches to introducing telemedical services in the area of medical imaging, it is hard to point to studies which would address all relevant aspects in a complete and comprehensive manner. In this paper we describe our approach to design and implementation of a universal platform for imaging medicine which is based on our longstanding experience in this area. We claim it is holistic, because, contrary to most of the available studies it addresses all aspects related to creation and utilization of a medical teleconsultation workspace. We present an extensive analysis of requirements, including possible usage scenarios, user needs, organizational and security issues and infrastructure components. We enumerate and analyze multiple usage scenarios related to medical imaging data in treatment, research and educational applications - with typical teleconsultations treated as just one of many possible options. Certain phases common to all these scenarios have been identified, with the resulting classification distinguishing several modes of operation (local vs. remote, collaborative vs. non-interactive etc.). On this basis we propose a system architecture which addresses all of the identified requirements, applying two key concepts: Service Oriented Architecture (SOA) and Virtual Organizations (VO). The SOA paradigm allows us to decompose the functionality of the system into several distinct building blocks, ensuring flexibility and reliability. The VO paradigm defines the cooperation model for all participating healthcare institutions. Our approach is validated by an ICT platform called TeleDICOM II which implements the proposed architecture. All of its main elements are described in detail and cross-checked against the listed requirements. A case study presents the role and usage of the platform in a specific scenario. Finally, our platform is compared with similar systems described into-date studies and available on the market

  15. Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

    NASA Technical Reports Server (NTRS)

    Tilton, James C.

    2003-01-01

    A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic

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

    PubMed

    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. PMID:26612079

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

    PubMed

    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. PMID:21384268

  18. AnaSP: a software suite for automatic image analysis of multicellular spheroids.

    PubMed

    Piccinini, Filippo

    2015-04-01

    Today, more and more biological laboratories use 3D cell cultures and tissues grown in vitro as a 3D model of in vivo tumours and metastases. In the last decades, it has been extensively established that multicellular spheroids represent an efficient model to validate effects of drugs and treatments for human care applications. However, a lack of methods for quantitative analysis limits the usage of spheroids as models for routine experiments. Several methods have been proposed in literature to perform high throughput experiments employing spheroids by automatically computing different morphological parameters, such as diameter, volume and sphericity. Nevertheless, these systems are typically grounded on expensive automated technologies, that make the suggested solutions affordable only for a limited subset of laboratories, frequently performing high content screening analysis. In this work we propose AnaSP, an open source software suitable for automatically estimating several morphological parameters of spheroids, by simply analyzing brightfield images acquired with a standard widefield microscope, also not endowed with a motorized stage. The experiments performed proved sensitivity and precision of the segmentation method proposed, and excellent reliability of AnaSP to compute several morphological parameters of spheroids imaged in different conditions. AnaSP is distributed as an open source software tool. Its modular architecture and graphical user interface make it attractive also for researchers who do not work in areas of computer vision and suitable for both high content screenings and occasional spheroid-based experiments. PMID:25737369

  19. SNARK09 - a software package for reconstruction of 2D images from 1D projections.

    PubMed

    Klukowska, Joanna; Davidi, Ran; Herman, Gabor T

    2013-06-01

    The problem of reconstruction of slices and volumes from 1D and 2D projections has arisen in a large number of scientific fields (including computerized tomography, electron microscopy, X-ray microscopy, radiology, radio astronomy and holography). Many different methods (algorithms) have been suggested for its solution. In this paper we present a software package, SNARK09, for reconstruction of 2D images from their 1D projections. In the area of image reconstruction, researchers often desire to compare two or more reconstruction techniques and assess their relative merits. SNARK09 provides a uniform framework to implement algorithms and evaluate their performance. It has been designed to treat both parallel and divergent projection geometries and can either create test data (with or without noise) for use by reconstruction algorithms or use data collected by another software or a physical device. A number of frequently-used classical reconstruction algorithms are incorporated. The package provides a means for easy incorporation of new algorithms for their testing, comparison and evaluation. It comes with tools for statistical analysis of the results and ten worked examples. PMID:23414602

  20. Imaging C. elegans Embryos using an Epifluorescent Microscope and Open Source Software

    PubMed Central

    Verbrugghe, Koen J. C.; Chan, Raymond C.

    2011-01-01

    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 samples1,2. 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 lineage3, thus providing an ideal experiment model for studying questions in cell biology4,5and development6-9. C. elegans is amendable to genetic manipulation by forward genetics (based on random mutagenesis10,11) and reverse genetics to target specific genes (based on RNAi-mediated interference and targeted mutagenesis12-15). In addition, transgenic animals can be readily created to express fluorescently tagged proteins or reporters16,17. These traits combine to make it easy to identify the genetic pathways regulating fundamental cellular and developmental processes in vivo18-21. 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. PMID:21490567

  1. Measuring the Pain Area: An Intra- and Inter-Rater Reliability Study Using Image Analysis Software.

    PubMed

    Dos Reis, Felipe Jose Jandre; de Barros E Silva, Veronica; de Lucena, Raphaela Nunes; Mendes Cardoso, Bruno Alexandre; Nogueira, Leandro Calazans

    2016-01-01

    Pain drawings have frequently been used for clinical information and research. The aim of this study was to investigate intra- and inter-rater reliability of area measurements performed on pain drawings. Our secondary objective was to verify the reliability when using computers with different screen sizes, both with and without mouse hardware. Pain drawings were completed by patients with chronic neck pain or neck-shoulder-arm pain. Four independent examiners participated in the study. Examiners A and B used the same computer with a 16-inch screen and wired mouse hardware. Examiner C used a notebook with a 16-inch screen and no mouse hardware, and Examiner D used a computer with an 11.6-inch screen and a wireless mouse. Image measurements were obtained using GIMP and NIH ImageJ computer programs. The length of all the images was measured using GIMP software to a set scale in ImageJ. Thus, each marked area was encircled and the total surface area (cm(2) ) was calculated for each pain drawing measurement. A total of 117 areas were identified and 52 pain drawings were analyzed. The intrarater reliability between all examiners was high (ICC = 0.989). The inter-rater reliability was also high. No significant differences were observed when using different screen sizes or when using or not using the mouse hardware. This suggests that the precision of these measurements is acceptable for the use of this method as a measurement tool in clinical practice and research. PMID:25490926

  2. Image pixel guided tours: a software platform for non-destructive x-ray imaging

    NASA Astrophysics Data System (ADS)

    Lam, K. P.; Emery, R.

    2009-02-01

    Multivariate analysis seeks to describe the relationship between an arbitrary number of variables. To explore highdimensional data sets, projections are often used for data visualisation to aid discovering structure or patterns that lead to the formation of statistical hypothesis. The basic concept necessitates a systematic search for lower-dimensional representations of the data that might show interesting structure(s). Motivated by the recent research on the Image Grand Tour (IGT), which can be adapted to view guided projections by using objective indexes that are capable of revealing latent structures of the data, this paper presents a signal processing perspective on constructing such indexes under the unifying exploratory frameworks of Independent Component Analysis (ICA) and Projection Pursuit (PP). Our investigation begins with an overview of dimension reduction techniques by means of orthogonal transforms, including the classical procedure of Principal Component Analysis (PCA), and extends to an application of the more powerful techniques of ICA in the context of our recent work on non-destructive testing technology by element specific x-ray imaging.

  3. RegStatGel: proteomic software for identifying differentially expressed proteins based on 2D gel images

    PubMed Central

    Li, Feng; Seillier-Moiseiwitsch, Françoise

    2011-01-01

    Image analysis of two-dimensional gel electrophoresis is a key step in proteomic workflow for identifying proteins that change under different experimental conditions. Since there are usually large amount of proteins and variations shown in the gel images, the use of software for analysis of 2D gel images is inevitable. We developed open-source software with graphical user interface for differential analysis of 2D gel images. The user-friendly software, RegStatGel, contains fully automated as well as interactive procedures. It was developed and has been tested under Matlab 7.01. Availability The database is available for free at http://www.mediafire.com/FengLi/2DGelsoftware PMID:21904427

  4. New AIRS: The medical imaging software for segmentation and registration of elastic organs in SPECT/CT

    NASA Astrophysics Data System (ADS)

    Widita, R.; Kurniadi, R.; Darma, Y.; Perkasa, Y. S.; Trianti, N.

    2012-06-01

    We have been successfully improved our software, Automated Image Registration and Segmentation (AIRS), to fuse the CT and SPECT images of elastic organs. Segmentation and registration of elastic organs presents many challenges. Many artifacts can arise in SPECT/CT scans. Also, different organs and tissues have very similar gray levels, which consign thresholding to limited utility. We have been developed a new software to solve different registration and segmentation problems that arises in tomographic data sets. It will be demonstrated that the information obtained by SPECT/CT is more accurate in evaluating patients/objects than that obtained from either SPECT or CT alone. We used multi-modality registration which is amenable for images produced by different modalities and having unclear boundaries between tissues. The segmentation components used in this software is region growing algorithms which have proven to be an effective approach for image segmentation. Our method is designed to perform with clinically acceptable speed, using accelerated techniques (multiresolution).

  5. An Effective On-line Polymer Characterization Technique by Using SALS Image Processing Software and Wavelet Analysis

    PubMed Central

    Xian, Guang-ming; Qu, Jin-ping; Zeng, Bi-qing

    2008-01-01

    This paper describes an effective on-line polymer characterization technique by using small-angle light-scattering (SALS) image processing software and wavelet analysis. The phenomenon of small-angle light scattering has been applied to give information about transparent structures on morphology. Real-time visualization of various scattered light image and light intensity matrices is performed by the optical image real-time processing software for SALS. The software can measure the signal intensity of light scattering images, draw the frequency-intensity curves and the amplitude-intensity curves to indicate the variation of the intensity of scattered light in different processing conditions, and estimate the parameters. The current study utilizes a one-dimensional wavelet to delete noise from the original SALS signal and estimate the variation trend of maximum intensity area of the scattered light. So, the system brought the qualitative analysis of the structural information of transparent film success. PMID:19229343

  6. NeuronMetrics: Software for Semi-Automated Processing of Cultured-Neuron Images

    PubMed Central

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

    2007-01-01

    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 ~60 2D images is 1.0–2.5 hours, 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. PMID:17270152

  7. An image-based software tool for screening retinal fundus images using vascular morphology and network transport analysis

    NASA Astrophysics Data System (ADS)

    Clark, Richard D.; Dickrell, Daniel J.; Meadows, David L.

    2014-03-01

    As the number of digital retinal fundus images taken each year grows at an increasing rate, there exists a similarly increasing need for automatic eye disease detection through image-based analysis. A new method has been developed for classifying standard color fundus photographs into both healthy and diseased categories. This classification was based on the calculated network fluid conductance, a function of the geometry and connectivity of the vascular segments. To evaluate the network resistance, the retinal vasculature was first manually separated from the background to ensure an accurate representation of the geometry and connectivity. The arterial and venous networks were then semi-automatically separated into two separate binary images. The connectivity of the arterial network was then determined through a series of morphological image operations. The network comprised of segments of vasculature and points of bifurcation, with each segment having a characteristic geometric and fluid properties. Based on the connectivity and fluid resistance of each vascular segment, an arterial network flow conductance was calculated, which described the ease with which blood can pass through a vascular system. In this work, 27 eyes (13 healthy and 14 diabetic) from patients roughly 65 years in age were evaluated using this methodology. Healthy arterial networks exhibited an average fluid conductance of 419 ± 89 μm3/mPa-s while the average network fluid conductance of the diabetic set was 165 ± 87 μm3/mPa-s (p < 0.001). The results of this new image-based software demonstrated an ability to automatically, quantitatively and efficiently screen diseased eyes from color fundus imagery.

  8. Software-based high-level synthesis design of FPGA beamformers for synthetic aperture imaging.

    PubMed

    Amaro, Joao; Yiu, Billy Y S; Falcao, Gabriel; Gomes, Marco A C; Yu, Alfred C H

    2015-05-01

    Field-programmable gate arrays (FPGAs) can potentially be configured as beamforming platforms for ultrasound imaging, but a long design time and skilled expertise in hardware programming are typically required. In this article, we present a novel approach to the efficient design of FPGA beamformers for synthetic aperture (SA) imaging via the use of software-based high-level synthesis techniques. Software kernels (coded in OpenCL) were first developed to stage-wise handle SA beamforming operations, and their corresponding FPGA logic circuitry was emulated through a high-level synthesis framework. After design space analysis, the fine-tuned OpenCL kernels were compiled into register transfer level descriptions to configure an FPGA as a beamformer module. The processing performance of this beamformer was assessed through a series of offline emulation experiments that sought to derive beamformed images from SA channel-domain raw data (40-MHz sampling rate, 12 bit resolution). With 128 channels, our FPGA-based SA beamformer can achieve 41 frames per second (fps) processing throughput (3.44 × 10(8) pixels per second for frame size of 256 × 256 pixels) at 31.5 W power consumption (1.30 fps/W power efficiency). It utilized 86.9% of the FPGA fabric and operated at a 196.5 MHz clock frequency (after optimization). Based on these findings, we anticipate that FPGA and high-level synthesis can together foster rapid prototyping of real-time ultrasound processor modules at low power consumption budgets. PMID:25965680

  9. Workspace Safe Operation of a Force- or Impedance-Controlled Robot

    NASA Technical Reports Server (NTRS)

    Abdallah, Muhammad E. (Inventor); Hargrave, Brian (Inventor); Yamokoski, John D. (Inventor); Strawser, Philip A. (Inventor)

    2013-01-01

    A method of controlling a robotic manipulator of a force- or impedance-controlled robot within an unstructured workspace includes imposing a saturation limit on a static force applied by the manipulator to its surrounding environment, and may include determining a contact force between the manipulator and an object in the unstructured workspace, and executing a dynamic reflex when the contact force exceeds a threshold to thereby alleviate an inertial impulse not addressed by the saturation limited static force. The method may include calculating a required reflex torque to be imparted by a joint actuator to a robotic joint. A robotic system includes a robotic manipulator having an unstructured workspace and a controller that is electrically connected to the manipulator, and which controls the manipulator using force- or impedance-based commands. The controller, which is also disclosed herein, automatically imposes the saturation limit and may execute the dynamic reflex noted above.

  10. Creating the optimal workspace for hospital staff using human centred design.

    PubMed

    Cawood, T; Saunders, E; Drennan, C; Cross, N; Nicholl, D; Kenny, A; Meates, D; Laing, R

    2016-07-01

    We were tasked with creating best possible non-clinical workspace solutions for approximately 450 hospital staff across 11 departments encompassing medical, nursing, allied health, administrative and other support staff. We used a Human-Centred Design process, involving 'Hear, Create and Deliver' stages. We used observations, contextual enquiry and role-specific workshops to understand needs, key interactions and drivers of behaviour. Co-design workshops were then used to explore and prototype-test concepts for the final design. With extensive employee engagement and design process expertise, an innovative solution was created that focussed on meeting the functional workspace needs of a diverse group of staff requiring a range of different spaces, incorporating space constraints and equity. This project demonstrated the strength of engaging employees in an expert-led Human-Centred Design process. We believe this is a successful blueprint process for other institutions to embrace when facing similar workspace design challenges. PMID:27405891

  11. Pre-Hardware Optimization of Spacecraft Image Processing Software Algorithms and Hardware Implementation

    NASA Technical Reports Server (NTRS)

    Kizhner, Semion; Flatley, Thomas P.; Hestnes, Phyllis; Jentoft-Nilsen, Marit; Petrick, David J.; Day, John H. (Technical Monitor)

    2001-01-01

    Spacecraft telemetry rates have steadily increased over the last decade presenting a problem for real-time processing by ground facilities. This paper proposes a solution to a related problem for the Geostationary Operational Environmental Spacecraft (GOES-8) image processing application. Although large super-computer facilities are the obvious heritage solution, they are very costly, making it imperative to seek a feasible alternative engineering solution at a fraction of the cost. The solution is based on a Personal Computer (PC) platform and synergy of optimized software algorithms and re-configurable computing hardware technologies, such as Field Programmable Gate Arrays (FPGA) and Digital Signal Processing (DSP). It has been shown in [1] and [2] that this configuration can provide superior inexpensive performance for a chosen application on the ground station or on-board a spacecraft. However, since this technology is still maturing, intensive pre-hardware steps are necessary to achieve the benefits of hardware implementation. This paper describes these steps for the GOES-8 application, a software project developed using Interactive Data Language (IDL) (Trademark of Research Systems, Inc.) on a Workstation/UNIX platform. The solution involves converting the application to a PC/Windows/RC platform, selected mainly by the availability of low cost, adaptable high-speed RC hardware. In order for the hybrid system to run, the IDL software was modified to account for platform differences. It was interesting to examine the gains and losses in performance on the new platform, as well as unexpected observations before implementing hardware. After substantial pre-hardware optimization steps, the necessity of hardware implementation for bottleneck code in the PC environment became evident and solvable beginning with the methodology described in [1], [2], and implementing a novel methodology for this specific application [6]. The PC-RC interface bandwidth problem for the

  12. HydroImage: A New Software for HydroGeophysical and BioGeophysical Data Integration

    NASA Astrophysics Data System (ADS)

    Suribhatla, R. M.; Mok, C. M.; Kaback, D.; Chen, J.; Hubbard, S. S.

    2011-12-01

    Hydrogeophysical and biogeophysical data integration have recently emerged as cost-effective and rapid techniques for improving subsurface characterization and monitoring. In a Bayesian framework for integration, borehole based data provide prior distribution and geophysical information serve as data to update the prior through likelihood functions obtained from petrophysical models between borehole and cross-well data. We present the application of a Windows-based software called HydroImage that uses this Bayesian framework for data integration and visualization. HydroImage can be used for geostatistical estimation, geophysical tomographic inversion, petrophysical model development, and Bayesian integration. We demonstrate HydroImage using three different field datasets to estimate different subsurface states or parameters. The first example combines wellbore flowmeter test data and crosshole seismic and ground penetrating radar (GPR) data to estimate hydraulic conductivity at the DOE Bacterial Transport Site in Oyster, Virginia. The second example focuses on using time-lapse radar data to estimate moisture content dynamics associated with a desiccation test performed to remediate the deep vadose zone in Hanford, Washington. The third example demonstrates the use of spectral induced polarization data to estimate the spatial and temporal distribution of geochemical parameters that are indicative of the redox state of a contaminated aquifer.

  13. JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age (Invited)

    NASA Astrophysics Data System (ADS)

    Mueller, D.; Dimitoglou, G.; Langenberg, M.; Pagel, S.; Dau, A.; Nuhn, M.; Garcia Ortiz, J. P.; Dietert, H.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

    2010-12-01

    The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is bound to be accessible only from a few repositories and users will have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community.

  14. Measuring the area of tear film break-up by image analysis software

    NASA Astrophysics Data System (ADS)

    Pena-Verdeal, Hugo; García-Resúa, Carlos; Ramos, Lucía.; Mosquera, Antonio; Yebra-Pimentel, Eva; Giráldez, María. Jesús

    2013-11-01

    Tear film breakup time (BUT) test only examines the first break in the tear film, but subsequent tear film events are not monitored. We present a method of measuring the area of breakup after the appearance of the first breakup by using open source software. Furthermore, the speed of the rupture was determined. 84 subjects participated in the study. 2 μl volume of 2% sodium fluorescein was instilled using a micropipette. The subject was seated behind a slit-lamp using a cobalt blue filter together with a Wratten 12 yellow filter. Then, the tear film was recorded by a camera attached to the slit lamp. 4 frames of each video was extracted, the first rupture (BUT_0), breakup after 1 second (BUT_1), rupture after 2 seconds (BUT_2) and breakup before the last blink (BUT_F). Open source software of measurement based on Java (NIH ImageJ) was used to measure the number of pixels in areas of breakup. These areas were divided by the area of exposed cornea to obtain the percentage of ruptures. Instantaneous breakup speed was calculated for second 1 as the difference between BUT_1 - BUT_0, whereas instant speed for second 2 was BUT_2 - BUT_1. Mean area of breakup obtained was: BUT_0 = 0.26%, BUT_1 = 0.48%, BUT_2 = 0.79% and BUT_F = 1.61%. Break speed was 0.22 area/sec for second 1 and 0.31 area/sec for second 2, showing a statistical difference between them (p = 0.007). Post BUT analysis may be easily monitoring with the aid of this software.

  15. Quantitative Neuroimaging Software for Clinical Assessment of Hippocampal Volumes on MR Imaging

    PubMed Central

    Ahdidan, Jamila; Raji, Cyrus A.; DeYoe, Edgar A.; Mathis, Jedidiah; Noe, Karsten Ø.; Rimestad, Jens; Kjeldsen, Thomas K.; Mosegaard, Jesper; Becker, James T.; Lopez, Oscar

    2015-01-01

    Background: Multiple neurological disorders including Alzheimer’s disease (AD), mesial temporal sclerosis, and mild traumatic brain injury manifest with volume loss on brain MRI. Subtle volume loss is particularly seen early in AD. While prior research has demonstrated the value of this additional information from quantitative neuroimaging, very few applications have been approved for clinical use. Here we describe a US FDA cleared software program, NeuroreaderTM, for assessment of clinical hippocampal volume on brain MRI. Objective: To present the validation of hippocampal volumetrics on a clinical software program. Method: Subjects were drawn (n = 99) from the Alzheimer Disease Neuroimaging Initiative study. Volumetric brain MR imaging was acquired in both 1.5 T (n = 59) and 3.0 T (n = 40) scanners in participants with manual hippocampal segmentation. Fully automated hippocampal segmentation and measurement was done using a multiple atlas approach. The Dice Similarity Coefficient (DSC) measured the level of spatial overlap between NeuroreaderTM and gold standard manual segmentation from 0 to 1 with 0 denoting no overlap and 1 representing complete agreement. DSC comparisons between 1.5 T and 3.0 T scanners were done using standard independent samples T-tests. Results: In the bilateral hippocampus, mean DSC was 0.87 with a range of 0.78–0.91 (right hippocampus) and 0.76–0.91 (left hippocampus). Automated segmentation agreement with manual segmentation was essentially equivalent at 1.5 T (DSC = 0.879) versus 3.0 T (DSC = 0.872). Conclusion: This work provides a description and validation of a software program that can be applied in measuring hippocampal volume, a biomarker that is frequently abnormal in AD and other neurological disorders. PMID:26484924

  16. Computation of robot configuration and workspaces via the Fourier transform on the discrete-motion group

    SciTech Connect

    Kyatkin, A.B.; Chirikjian, G.S.

    1999-06-01

    The authors apply the Fourier transform on the discrete-motion group to the problem of computing the configuration-space obstacles of mobile robots which move among static obstacles, the problem of finding the workspace density of binary manipulators with many actuators, and the problem of determining workspace boundaries of manipulators with continuous-motion actuators. They develop and implement Fourier transforms for the discrete-motion group of the plane. These transforms allow them to apply fast Fourier transform methods to the computation of convolution-like integrals that arise in robot kinematics and motion planning. The results of the implementation are discussed for particular examples.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Digital mapping of side-scan sonar data with the Woods Hole Image Processing System software

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    Since 1985, the Branch of Atlantic Marine Geology has been involved in collecting, processing and digitally mosaicking high and low resolution sidescan sonar data. In the past, processing and digital mosaicking has been accomplished with a dedicated, shore-based computer system. Recent development of a UNIX-based image-processing software system includes a series of task specific programs for pre-processing sidescan sonar data. To extend the capabilities of the UNIX-based programs, development of digital mapping techniques have been developed. This report describes the initial development of an automated digital mapping procedure. Included is a description of the programs and steps required to complete the digital mosaicking on a UNIXbased computer system, and a comparison of techniques that the user may wish to select.

  19. SU-E-J-264: Comparison of Two Commercially Available Software Platforms for Deformable Image Registration

    SciTech Connect

    Tuohy, R; Stathakis, S; Mavroidis, P; Bosse, C; Papanikolaou, N

    2014-06-01

    Purpose: To evaluate and compare the deformable image registration algorithms available in the Velocity (Velocity Medical Solutions, Atlanta, GA) and RayStation (RaySearch Americas, Inc., Garden city NY). Methods: Ten consecutive patient cone beam CTs (CBCT) for each fraction were collected. The CBCTs along with the simulation CT were exported to the Velocity and the RayStation software. Each CBCT was registered using deformable image registration to the simulation CT and the resulting deformable vector matrix was generated. Each registration was visually inspected by a physicist and the prescribing physician. The volumes of the critical organs were calculated for each deformable CT and used for comparison. Results: The resulting deformable registrations revealed differences between the two algorithms. These differences were realized when the organs at risk were contoured on each deformed CBCT. Differences in the order of 10% ±30% in volume were observed for bladder, 17 ±21% for rectum and 16±10% for sigmoid. The prostate and PTV volume differences were in the order of 3±5%. The volumetric differences observed had a respective impact on the DVHs of all organs at risk. Differences of 8–10% in the mean dose were observed for all organs above. Conclusion: Deformable registration is a powerful tool that aids in the definition of critical structures and is often used for the evaluation of daily dose delivered to the patient. It should be noted that extended QA should be performed before clinical implementation of the software and the users should be aware of advantages and limitations of the methods.

  20. Comparison between three methods to value lower tear meniscus measured by image software

    NASA Astrophysics Data System (ADS)

    García-Resúa, Carlos; Pena-Verdeal, Hugo; Lira, Madalena; Oliveira, M. Elisabete Real; Giráldez, María. Jesús; Yebra-Pimentel, Eva

    2013-11-01

    To measure different parameters of lower tear meniscus height (TMH) by using photography with open software of measurement. TMH was addressed from lower eyelid to the top of the meniscus (absolute TMH) and to the brightest meniscus reflex (reflex TMH). 121 young healthy subjects were included in the study. The lower tear meniscus was videotaped by a digital camera attached to a slit lamp. Three videos were recorded in central meniscus portion on three different methods: slit lamp without fluorescein instillation, slit lamp with fluorescein instillation and TearscopeTM without fluorescein instillation. Then, a masked observed obtained an image from each video and measured TMH by using open source software of measurement based on Java (NIH ImageJ). Absolute central (TMH-CA), absolute with fluorescein (TMH-F) and absolute using the Tearscope (TMH-Tc) were compared each other as well as reflex central (TMH-CR) and reflex Tearscope (TMH-TcR). Mean +/- S.D. values of TMH-CA, TMH-CR, TMH-F, TMH-Tc and TMH-TcR of 0.209 +/- 0.049, 0.139 +/- 0.031, 0.222 +/- 0.058, 0.175 +/- 0.045 and 0.109 +/- 0.029 mm, respectively were found. Paired t-test was performed for the relationship between TMH-CA - TMH-CR, TMH-CA - TMH-F, TMH-CA - TMH-Tc, TMH-F - TMH-Tc, TMH-Tc - TMH-TcR and TMH-CR - TMH-TcR. In all cases, it was found a significant difference between both variables (all p < 0.008). This study showed a useful tool to objectively measure TMH by photography. Eye care professionals should maintain the same TMH parameter in the follow-up visits, due to the difference between them.

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

    NASA Astrophysics Data System (ADS)

    Yang, Bang-Hung; Tsai, Sung-Yi; Wang, Shyh-Jen; Su, Tung-Ping; Chou, Yuan-Hwa; Chen, Chia-Chieh; Chen, Jyh-Cheng

    2011-08-01

    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 123I-ADAM. The image matrix size was 128×128 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 123I-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 α of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2 analysis. This finding might help us

  2. A flexible software architecture for scalable real-time image and video processing applications

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    Real-time image and video processing applications require skilled architects, and recent trends in the hardware platform make the design and implementation of these applications increasingly complex. Many frameworks and libraries have been proposed or commercialized to simplify the design and tuning of real-time image processing applications. However, they tend to lack flexibility because they are normally oriented towards particular types of applications, or they impose specific data processing models such as the pipeline. Other issues include large memory footprints, difficulty for reuse and inefficient execution on multicore processors. This paper presents a novel software architecture for real-time image and video processing applications which addresses these issues. The architecture is divided into three layers: the platform abstraction layer, the messaging layer, and the application layer. The platform abstraction layer provides a high level application programming interface for the rest of the architecture. The messaging layer provides a message passing interface based on a dynamic publish/subscribe pattern. A topic-based filtering in which messages are published to topics is used to route the messages from the publishers to the subscribers interested in a particular type of messages. The application layer provides a repository for reusable application modules designed for real-time image and video processing applications. These modules, which include acquisition, visualization, communication, user interface and data processing modules, take advantage of the power of other well-known libraries such as OpenCV, Intel IPP, or CUDA. Finally, we present different prototypes and applications to show the possibilities of the proposed architecture.

  3. Global workspace dynamics: cortical "binding and propagation" enables conscious contents.

    PubMed

    Baars, Bernard J; Franklin, Stan; Ramsoy, Thomas Zoega

    2013-01-01

    A global workspace (GW) is a functional hub of binding and propagation in a population of loosely coupled signaling elements. In computational applications, GW architectures recruit many distributed, specialized agents to cooperate in resolving focal ambiguities. In the brain, conscious experiences may reflect a GW function. For animals, the natural world is full of unpredictable dangers and opportunities, suggesting a general adaptive pressure for brains to resolve focal ambiguities quickly and accurately. GW theory aims to understand the differences between conscious and unconscious brain events. In humans and related species the cortico-thalamic (C-T) core is believed to underlie conscious aspects of perception, thinking, learning, feelings of knowing (FOK), felt emotions, visual imagery, working memory, and executive control. Alternative theoretical perspectives are also discussed. The C-T core has many anatomical hubs, but conscious percepts are unitary and internally consistent at any given moment. Over time, conscious contents constitute a very large, open set. This suggests that a brain-based GW capacity cannot be localized in a single anatomical hub. Rather, it should be sought in a functional hub - a dynamic capacity for binding and propagation of neural signals over multiple task-related networks, a kind of neuronal cloud computing. In this view, conscious contents can arise in any region of the C-T core when multiple input streams settle on a winner-take-all equilibrium. The resulting conscious gestalt may ignite an any-to-many broadcast, lasting ∼100-200 ms, and trigger widespread adaptation in previously established networks. To account for the great range of conscious contents over time, the theory suggests an open repertoire of binding coalitions that can broadcast via theta/gamma or alpha/gamma phase coupling, like radio channels competing for a narrow frequency band. Conscious moments are thought to hold only 1-4 unrelated items; this small

  4. Software for Collaborative Use of Large Interactive Displays

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Shab, Thodore; Wales, Roxana; Vera, Alonso; Tollinger, Irene; McCurdy, Michael; Lyubimov, Dmitriy

    2006-01-01

    The MERBoard Collaborative Workspace, which is currently being deployed to support the Mars Exploration Rover (MER) Missions, is the first instantiation of a new computing architecture designed to support collaborative and group computing using computing devices situated in NASA mission operations room. It is a software system for generation of large-screen interactive displays by multiple users

  5. SU-E-I-13: Evaluation of Metal Artifact Reduction (MAR) Software On Computed Tomography (CT) Images

    SciTech Connect

    Huang, V; Kohli, K

    2015-06-15

    Purpose: A new commercially available metal artifact reduction (MAR) software in computed tomography (CT) imaging was evaluated with phantoms in the presence of metals. The goal was to assess the ability of the software to restore the CT number in the vicinity of the metals without impacting the image quality. Methods: A Catphan 504 was scanned with a GE Optima RT 580 CT scanner (GE Healthcare, Milwaukee, WI) and the images were reconstructed with and without the MAR software. Both datasets were analyzed with Image Owl QA software (Image Owl Inc, Greenwich, NY). CT number sensitometry, MTF, low contrast, uniformity, noise and spatial accuracy were compared for scans with and without MAR software. In addition, an in-house made phantom was scanned with and without a stainless steel insert at three different locations. The accuracy of the CT number and metal insert dimension were investigated as well. Results: Comparisons between scans with and without MAR algorithm on the Catphan phantom demonstrate similar results for image quality. However, noise was slightly higher for the MAR algorithm. Evaluation of the CT number at various locations of the in-house made phantom was also performed. The baseline HU, obtained from the scan without metal insert, was compared to scans with the stainless steel insert at 3 different locations. The HU difference between the baseline scan versus metal scan was improved when the MAR algorithm was applied. In addition, the physical diameter of the stainless steel rod was over-estimated by the MAR algorithm by 0.9 mm. Conclusion: This work indicates with the presence of metal in CT scans, the MAR algorithm is capable of providing a more accurate CT number without compromising the overall image quality. Future work will include the dosimetric impact on the MAR algorithm.

  6. Fostering Collaborative Knowledge Construction in a Video-Based Learning Setting: Effects of a Shared Workspace and a Content-Specific Graphical Representation

    ERIC Educational Resources Information Center

    Hron, Aemilian; Cress, Ulrike; Hammer, Karsten; Friedrich, Helmut-Felix

    2007-01-01

    This study examined means of fostering videoconference-based collaborative learning. An experiment was conducted with 15 learning dyads divided into three conditions of videoconference-based learning: without shared workspace, with shared workspace and with shared workspace plus a content-specific graphical representation. Compared with those with…

  7. Xmipp 3.0: an improved software suite for image processing in electron microscopy.

    PubMed

    de la Rosa-Trevín, J M; Otón, J; Marabini, R; Zaldívar, A; Vargas, J; Carazo, J M; Sorzano, C O S

    2013-11-01

    Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter "wizards" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es. PMID:24075951

  8. An adaptive workspace hypothesis about the neural correlates of consciousness: insights from neuroscience and meditation studies.

    PubMed

    Raffone, Antonino; Srinivasan, Narayanan

    2009-01-01

    While enormous progress has been made to identify neural correlates of consciousness (NCC), crucial NCC aspects are still very controversial. A major hurdle is the lack of an adequate definition and characterization of different aspects of conscious experience and also its relationship to attention and metacognitive processes like monitoring. In this paper, we therefore attempt to develop a unitary theoretical framework for NCC, with an interdependent characterization of endogenous attention, access consciousness, phenomenal awareness, metacognitive consciousness, and a non-referential form of unified consciousness. We advance an adaptive workspace hypothesis about the NCC based on the global workspace model emphasizing transient resonant neurodynamics and prefrontal cortex function, as well as meditation-related characterizations of conscious experiences. In this hypothesis, transient dynamic links within an adaptive coding net in prefrontal cortex, especially in anterior prefrontal cortex, and between it and the rest of the brain, in terms of ongoing intrinsic and long-range signal exchanges, flexibly regulate the interplay between endogenous attention, access consciousness, phenomenal awareness, and metacognitive consciousness processes. Such processes are established in terms of complementary aspects of an ongoing transition between context-sensitive global workspace assemblies, modulated moment-to-moment by body and environment states. Brain regions associated to momentary interoceptive and exteroceptive self-awareness, or first-person experiential perspective as emphasized in open monitoring meditation, play an important modulatory role in adaptive workspace transitions. PMID:19733756

  9. Revolute manipulator workspace optimization using a modified bacteria foraging algorithm: A comparative study

    NASA Astrophysics Data System (ADS)

    Panda, S.; Mishra, D.; Biswal, B. B.; Tripathy, M.

    2014-02-01

    Robotic manipulators with three-revolute (3R) motions to attain desired positional configurations are very common in industrial robots. The capability of these robots depends largely on the workspace of the manipulator in addition to other parameters. In this study, an evolutionary optimization algorithm based on the foraging behaviour of the Escherichia coli bacteria present in the human intestine is utilized to optimize the workspace volume of a 3R manipulator. The new optimization method is modified from the original algorithm for faster convergence. This method is also useful for optimization problems in a highly constrained environment, such as robot workspace optimization. The new approach for workspace optimization of 3R manipulators is tested using three cases. The test results are compared with standard results available using other optimization algorithms, i.e. the differential evolution algorithm, the genetic algorithm and the particle swarm optimization algorithm. The present method is found to be superior to the other methods in terms of computational efficiency.

  10. A Neuro-genetic Control Scheme Application for Industrial R 3 Workspaces

    NASA Astrophysics Data System (ADS)

    Irigoyen, E.; Larrea, M.; Valera, J.; Gómez, V.; Artaza, F.

    This work presents a neuro-genetic control scheme for a R 3 workspace application. The solution is based on a Multi Objective Genetic Algorithm reference generator and an Adaptive Predictive Neural Network Controller. Crane position control is presented as an application of the proposed control scheme.