Virtual File System Browser Jeff Ma http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=35 1.1.0 5/10/2006 Development with public userbase The Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols. CCB License The Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols. UCLA Center for Computational Biology Development with public userbase NA 5.3 CCB License UCLA Center for Computational Biology Ivo D. Dinov http://www.loni.ucla.edu/~dinov/SVT.html A tool for Statistical Analysis of Stereotactic Functional Brain Data Sub-Volume Thresholding Analysis A tool for Statistical Analysis of Stereotactic Functional Brain Data 1 5/30/2006 Development with public userbase http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=37 A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model. UCLA Center for Computational Biology Herbert Chang CCB License Charged Fluid Model for Vascular Segmentation A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model. Herbert Chang and Daniel Valentino 1.1 2/24/2005 Development with public userbase http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=36 An FFT library in Java An FFT library in Java FFT Library CCB License UCLA Center for Computational Biology LONI ShapeDistance 1.0.0 10/31/2005 Development with public userbase UCLA Center for Computational Biology http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=26 A tool for calculating the distance between vertices of two shape files CCB License Craig Schwartz A tool for calculating the distance between vertices of two shape files The ShapeViewerApplet displays three dimensional shapes in a web page 10/28/2005 Development with public userbase 1.1.0 CCB License The ShapeViewerApplet displays three dimensional shapes in a web page LONI ShapeViewerApplet Jeff Q. Ma http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=18 UCLA Center for Computational Biology The 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. ShapeTransform CCB License UCLA Center for Computational Biology 5/3/2006 1.1.0 Development with public userbase http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=30 Bae Cheol Shin and Craig Schwartz Extract4DUcfAttributes UCLA Center for Computational Biology CCB License 1.1.0 Development with public userbase 5/10/2006 The 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 Schwartz http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=32 Synchronized Histological Image Viewing Architecture The 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 License Heng Yuan, Allan MacKenzie-Graham, Eagle S. Jones, David W. Shattuck, Arthur W. Toga http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12 UCLA Center for Computational Biology 1 Development with public userbase 10/16/2005 CCB License UCLA Center for Computational Biology Jeff Q. Ma 5/10/2006 Development with public userbase 1.1.0 The 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 ShapeViewer The 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=18 CCB License ASAP Christopher Lee, Alexander Alekseyenko, Stott Parker, Zach Fierstadt UCLA Center for Computational Biology After 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 processes 6/28/1905 Development with public userbase 2.1 alternative splicing, biological process, alternatively spliced isoforms http://bioinfo.mbi.ucla.edu/ASAP/ UCLA Center for Computational Biology The 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=31 Craig Schwartz DXJava The DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files. CCB License Development with public userbase 1.0.0 5/1/2006 Ivo D. Dinov http://www.loni.ucla.edu/~dinov/WAIR.html UCLA Center for Computational Biology A tool for quantitative analysis of various n-dimensional (n-D) image registration techniques. CCB License Wavelet Analysis of Image Registration A tool for quantitative analysis of various n-dimensional (n-D) image registration techniques. Development with public userbase 2 NA UCLA Center for Computational Biology CCB License LONI 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 Enuf http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=40 Scott C. Neu Development with public userbase 1 11/1/2006 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. 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 Schwartz UCLA Center for Computational Biology ShapeToDX CCB License http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=34 1.0.0 Development with public userbase 5/10/2006 Charged Fluid Model for Brain Image Segmentation UCLA Center for Computational Biology CCFMBIS 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 Toga CCFMBIS is a computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. Development with public userbase 1.1 1/20/2007 CCB License http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=41 UCLA Center for Computational Biology http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=1 CCB License Development with public userbase 2.0b1 3/1/2003 Jack C. Wei, Scott Neu, and Daniel J. Valentino A portable software framework for medical imaging research A portable software framework for medical imaging research jViewbox InterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file. CCB License InterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file. InterpolateUcf Craig Schwartz http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=24 UCLA Center for Computational Biology 10/10/2005 1.1.0 Development with public userbase UCLA Center for Computational Biology LONI De-identification Debablet A 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 Crawford CCB License http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11 1 10/13/2005 Development with public userbase UCLA Center for Computational Biology CCB License http://bishopw.loni.ucla.edu/AIR5/ NA 5.2.5 Mature A 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. Woods Automated Image Registration http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=19 David W. Shattuck Development with public userbase 2 6/1/2005 CCB License BrainSuite2 BrainSuite2 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 Biology 11/13/2006 1.2 Development with public userbase Decoders 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=17 CCB License UCLA Center for Computational Biology LONI Java Image I/O Plugins Scott C. Neu, Bryan Vann, Kejia Ma, and Craig Schwartz http://www.loni.ucla.edu/Software/Features_Detail.jsp?software_id=33 The 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 Biology 5/10/2006 Development with public userbase 1.0.0 The 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. ShapeCurvature Bae Cheol Shin and Craig Schwartz CCB License UCLA Center for Computational Biology 1 3/1/2005 Development with public userbase http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Igor Yanovskiy CCB License MultiPhase-SEG MultiPhase-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 Toga The SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. CCB License Statistical Online Computational Resource UCLA Center for Computational Biology http://www.SOCR.ucla.edu The SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. 1 Mature 8/1/2003 David Shattuck , Richard Leahy, Stephanie Sandor, Bijan Timsari Brain 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 userbase 2.0a NA CCB License http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=4 Brain Surface Extractor Brain 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 Biology The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. CCB License The 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=25 Craig Schwartz Development with public userbase 1.2.0 5/10/2006 LONI ShapeTools UCLA Center for Computational Biology http://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 Neu UCLA Laboratory of Neuro Imaging (LONI) Imaging Data Archive (IDA) imaging, database, data service, storage data transfer, anonymization 3 3/1/2006 Mature LONI License Roger P. Woods Tracer 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 License http://bishopw.loni.ucla.edu/MultiTracer/MultiTracer.html UCLA Center for Computational Biology 1 NA Development with public userbase Tracer 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. MultiTracer Development with public userbase 1.1 5/31/2005 Jussi Tohka, Mikko Itäranta and Jouni Mykkänen CCB License The 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. DualSurfaceMin http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=22 UCLA Center for Computational Biology The 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.edu LONI Pipeline Processing Environment 1 Beta 2/28/2006 Protocol Execution Environment CCB License UCLA Center for Computational Biology Protocol Execution Environment Arash Payan, Jagadeeswaran Rajendiran, Arthur Toga UCLA Center for Computational Biology 0.3 Development with public userbase 3/10/2006 Pygr 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=27 CCB License Christopher Lee, Alexander Alekseyenko, Stott Parker, Zach Fierstadt Pygr LONI Visualization Tool UCLA Center for Computational Biology 5.3 5/23/2006 Development with public userbase An interactive tool for stereotaxic brain data visualization http://www.loni.ucla.edu/~dinov/LONI_Vis.html An interactive tool for stereotaxic brain data visualization Ivo D. Dinov, Bae Cheol Shin, Fotios Konstantinidis and Arthur Toga CCB License LONI Debabeler CCB License 11/13/2006 2.6 Development with public userbase UCLA Center for Computational Biology http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11 The 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 Valentino The LONI Debabeler enables researchers to manage the conversion of imaging data from one file format to another using a graphical user interface. NA BLASTgres UCLA Center for Computational Biology Stott Parker and Ruey-Lung Hsiao http://blastgres.cs.ucla.edu/ PostgreSQL, data management of biological sequences, sequence analysis, bioinformatics. CCB License Dec-06 1 Development with public userbase