Virtual File System BrowserJeff Mahttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=351.1.05/10/2006Development with public userbaseThe Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols.CCB LicenseThe Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols.UCLA Center for Computational BiologyDevelopment with public userbaseNA5.3CCB LicenseUCLA Center for Computational BiologyIvo D. Dinovhttp://www.loni.ucla.edu/~dinov/SVT.htmlA tool for Statistical Analysis of Stereotactic Functional Brain DataSub-Volume Thresholding AnalysisA tool for Statistical Analysis of Stereotactic Functional Brain Data15/30/2006Development with public userbasehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=37A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model.UCLA Center for Computational BiologyHerbert ChangCCB LicenseCharged Fluid Model for Vascular SegmentationA computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model.Herbert Chang and Daniel Valentino1.12/24/2005Development with public userbasehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=36An FFT library in JavaAn FFT library in JavaFFT LibraryCCB LicenseUCLA Center for Computational BiologyLONI ShapeDistance1.0.010/31/2005Development with public userbaseUCLA Center for Computational Biologyhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=26A tool for calculating the distance between vertices of two shape filesCCB LicenseCraig SchwartzA tool for calculating the distance between vertices of two shape files
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The ShapeViewerApplet displays three dimensional shapes in a web page10/28/2005Development with public userbase1.1.0CCB LicenseThe ShapeViewerApplet displays three dimensional shapes in a web pageLONI ShapeViewerAppletJeff Q. Mahttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=18UCLA Center for Computational BiologyThe ShapeTransform application facilitates the moveof a shape file from one coordinate system to another.The ShapeTransform application facilitates the moveof a shape file from one coordinate system to another.ShapeTransformCCB LicenseUCLA Center for Computational Biology5/3/20061.1.0Development with public userbasehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=30Bae Cheol Shin and Craig Schwartz
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Extract4DUcfAttributesUCLA Center for Computational BiologyCCB License1.1.0Development with public userbase5/10/2006The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file.The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file.Craig Schwartzhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=32Synchronized Histological Image Viewing ArchitectureThe Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application.The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application.CCB LicenseHeng Yuan, Allan MacKenzie-Graham, Eagle S. Jones, David W. Shattuck, Arthur W. Togahttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12UCLA Center for Computational Biology1Development with public userbase10/16/2005CCB LicenseUCLA Center for Computational BiologyJeff Q. Ma5/10/2006Development with public userbase1.1.0The LONI ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java,it can run on a wide variety of computers.LONI ShapeViewerThe LONI ShapeViewer is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions. Since it is written in Java,it can run on a wide variety of computers.http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=18CCB LicenseASAPChristopher Lee, Alexander Alekseyenko, Stott Parker, Zach FierstadtUCLA Center for Computational BiologyAfter transcription of a gene, the resulting pre-mRNA is spliced before exiting the nucleus. Alternative splicing of a single pre-mRNA can give rise to different mRNA transcripts. Consequently, alternative splicing is an important mechanism for generating protein diversity from a single gene. It has been suggested that large numbers of human genes are alternatively spliced (1, 2, 3). Alternative splicing is observed all across metazoa, and has been implicated in various biological processes6/28/1905Development with public userbase2.1alternative splicing, biological process, alternatively spliced isoformshttp://bioinfo.mbi.ucla.edu/ASAP/UCLA Center for Computational BiologyThe DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files.http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=31Craig SchwartzDXJavaThe DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files.CCB LicenseDevelopment with public userbase1.0.05/1/2006Ivo D. Dinovhttp://www.loni.ucla.edu/~dinov/WAIR.htmlUCLA Center for Computational BiologyA tool for quantitative analysis of various n-dimensional (n-D) image registration techniques.CCB LicenseWavelet Analysis of Image RegistrationA tool for quantitative analysis of various n-dimensional (n-D) image registration techniques.Development with public userbase2NA
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- waveletstransformspectralregistrationevaluationvolumetricfrequencyspacehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=6
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UCLA Center for Computational BiologyCCB LicenseLONI ICE is a Java application that generates seed points for other image processing applications.LONI ICE is a Java application that generates seed points for other image processing applications.LONI It's Close Enufhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=40Scott C. NeuDevelopment with public userbase111/1/2006The ShapeToDX application is a Java application that translates data files
that can be read by the ShapeTools library into an OpenDX genreal format
data file.The ShapeToDX application is a Java application that translates data files
that can be read by the ShapeTools library into an OpenDX genreal format
data file.Craig SchwartzUCLA Center for Computational BiologyShapeToDXCCB Licensehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=341.0.0Development with public userbase5/10/2006Charged Fluid Model for Brain Image SegmentationUCLA Center for Computational BiologyCCFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model.Herbert Chang,Daniel Valentiino, Gary Duckwiler, and Arthur TogaCCFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model.Development with public userbase1.11/20/2007CCB Licensehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=41UCLA Center for Computational Biologyhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=1CCB LicenseDevelopment with public userbase2.0b13/1/2003Jack C. Wei, Scott Neu, and Daniel J. ValentinoA portable software framework for medical imaging researchA portable software framework for medical imaging researchjViewboxInterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file.CCB LicenseInterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file.InterpolateUcfCraig Schwartzhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=24UCLA Center for Computational Biology10/10/20051.1.0Development with public userbaseUCLA Center for Computational BiologyLONI De-identification DebabletA simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files.A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files.Scott C. Neu and Karen CrawfordCCB Licensehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11110/13/2005Development with public userbaseUCLA Center for Computational BiologyCCB Licensehttp://bishopw.loni.ucla.edu/AIR5/NA5.2.5MatureA tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities.Roger P. WoodsAutomated Image Registrationhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=19David W. ShattuckDevelopment with public userbase26/1/2005CCB LicenseBrainSuite2BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.UCLA Center for Computational Biology11/13/20061.2Development with public userbaseDecoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats.http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=17CCB LicenseUCLA Center for Computational BiologyLONI Java Image I/O PluginsScott C. Neu, Bryan Vann, Kejia Ma, and Craig Schwartzhttp://www.loni.ucla.edu/Software/Features_Detail.jsp?software_id=33The ShapeCurvature application allows researchers to calculate the curvature of a surface mesh that is stored in a shape file. These curvature values may be written to disk files in a variety of file formats.UCLA Center for Computational Biology5/10/2006Development with public userbase1.0.0The ShapeCurvature application allows researchers to calculate the curvature of a surface mesh that is stored in a shape file. These curvature values may be written to disk files in a variety of file formats.ShapeCurvatureBae Cheol Shin and Craig SchwartzCCB LicenseUCLA Center for Computational Biology13/1/2005Development with public userbasehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model.Igor YanovskiyCCB LicenseMultiPhase-SEGMultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model.I. Dinov, Juana Sanchez, Nicolas, Christou, Robert Gould, J. Ma, J. Hu, D. Ylvisaker, R. Gould, J. Landerman, H. Wang, P. Efstathopoulos, F. Konstantinidios, Arthur TogaThe SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications.CCB LicenseStatistical Online Computational ResourceUCLA Center for Computational Biologyhttp://www.SOCR.ucla.eduThe SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications.1Mature8/1/2003David Shattuck , Richard Leahy, Stephanie Sandor, Bijan TimsariBrain Surface Extraction: Designed to automatically extract the brain from a set of T1 weighted Magnetic Resonance (MR) images of the human head.Development with public userbase2.0aNACCB Licensehttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=4Brain Surface ExtractorBrain Surface Extraction: Designed to automatically extract the brain from a set of T1 weighted Magnetic Resonance (MR) images of the human head.UCLA Center for Computational BiologyThe ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values.CCB LicenseThe ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values.http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=25Craig SchwartzDevelopment with public userbase1.2.05/10/2006LONI ShapeToolsUCLA Center for Computational Biologyhttp://ida.loni.ucla.edu/The LONI Image Data Archive (IDA) provides a simple and effective means of securely storing, searching and organizing neuroimaging data on the LONI storage network. The easy-to-use web browser interface provides complete data de-identification, data transmission, search and download functionality. The LONI Image Data Archive System also provides a secure system for the archival of collaborator collected image data, ensuring confidentiality, and restricting access to authorized users (http://ida.loni.ucla.edu/LONI_IDA_User_Manual.pdf)Arthur W. Toga, Karen Crawford, Scott NeuUCLA Laboratory of Neuro Imaging (LONI)Imaging Data Archive (IDA)imaging, database, data service, storage data transfer, anonymization33/1/2006MatureLONI LicenseRoger P. WoodsTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.CCB Licensehttp://bishopw.loni.ucla.edu/MultiTracer/MultiTracer.htmlUCLA Center for Computational Biology1NADevelopment with public userbaseTracer is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.MultiTracerDevelopment with public userbase1.15/31/2005Jussi Tohka, Mikko Itäranta and Jouni MykkänenCCB LicenseThe dualsurfacemin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces [1]. The method is developed for automatic surface extraction from noisy volumetric images.DualSurfaceMinhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=22UCLA Center for Computational BiologyThe dualsurfacemin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces [1]. The method is developed for automatic surface extraction from noisy volumetric images.http://pipeline.loni.ucla.eduLONI Pipeline Processing Environment1Beta2/28/2006Protocol Execution EnvironmentCCB LicenseUCLA Center for Computational BiologyProtocol Execution EnvironmentArash Payan, Jagadeeswaran Rajendiran, Arthur TogaUCLA Center for Computational Biology0.3Development with public userbase3/10/2006Pygr is an open source software project used to develop graph database interfaces.Pygr is an open source software project used to develop graph database interfaces.http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=27CCB LicenseChristopher Lee, Alexander Alekseyenko, Stott Parker, Zach FierstadtPygrLONI Visualization ToolUCLA Center for Computational Biology5.35/23/2006Development with public userbaseAn interactive tool for stereotaxic brain data visualizationhttp://www.loni.ucla.edu/~dinov/LONI_Vis.htmlAn interactive tool for stereotaxic brain data visualizationIvo D. Dinov, Bae Cheol Shin, Fotios Konstantinidis and Arthur TogaCCB LicenseLONI DebabelerCCB License11/13/20062.6Development with public userbaseUCLA Center for Computational Biologyhttp://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11The LONI Debabeler enables researchers to manage the conversion of imaging data from one file format to another using a graphical user interface.Scott C Neu and Daniel J ValentinoThe LONI Debabeler enables researchers to manage the conversion of imaging data from one file format to another using a graphical user interface.NABLASTgresUCLA Center for Computational BiologyStott Parker and Ruey-Lung Hsiaohttp://blastgres.cs.ucla.edu/PostgreSQL, data management of biological sequences, sequence analysis, bioinformatics.CCB LicenseDec-061Development with public userbase