Imaging Data Archive (IDA) 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 imaging, database, data service, storage data transfer, anonymization Database; Data Management http://ida.loni.ucla.edu/ LONI License 3D Image volumes (raw data or models) in any planar or volumetric file format, plus clinically relevant subject information 3D Image volumes (raw data or models) in any planar or volumetric file format, plus clinically relevant subject information Web-service Database UCLA Laboratory of Neuro Imaging (LONI) 3 3/1/2006 Mature jViewbox A portable software framework for medical imaging research Jack C. Wei, Scott Neu, and Daniel J. Valentino A portable software framework for medical imaging research Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=1 CCB License 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format 2D or 3D Graphical Data Display Class Library / Toolkit UCLA Center for Computational Biology 2.0b1 3/1/2003 Development with public userbase LONI Pipeline Processing Environment Protocol Execution Environment Arash Payan, Jagadeeswaran Rajendiran, Arthur Toga Protocol Execution Environment Graphical e.g., HIVE Pipeline http://pipeline.loni.ucla.edu CCB License Various 2D/3D Brain Image volume type data Data Analysis Workflows in XML format and analysis results of different graphical and quantititive types Application UCLA Center for Computational Biology 1 2/28/2006 Beta 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. 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. Cortical Modeling http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=4 CCB License 3D Image volumes in ANALYZE/IMG format OBJ, DXF surface formats Application UCLA Center for Computational Biology 2.0a NA Development with public userbase Sub-Volume Thresholding Analysis A tool for Statistical Analysis of Stereotactic Functional Brain Data Ivo D. Dinov A tool for Statistical Analysis of Stereotactic Functional Brain Data Statistical Package http://www.loni.ucla.edu/~dinov/SVT.html CCB License Two populations of 3D PET/MRI Image volumes in ANALYZE/IMG format 3D Statistical Analysis volumes in ANALYZE/IMG format Application UCLA Center for Computational Biology 5.3 NA Development with public userbase Wavelet Analysis of Image Registration A tool for quantitative analysis of various n-dimensional (n-D) image registration techniques. Ivo D. Dinov A tool for quantitative analysis of various n-dimensional (n-D) image registration techniques. Wavelet Transform http://www.loni.ucla.edu/~dinov/WAIR.html CCB License 3D Brain Image volumes in ANALYZE/IMG format 3D Brain Image volumes in ANALYZE/IMG format and quantitative tables of warp classification data Application UCLA Center for Computational Biology 2 NA Development with public userbase LONI Visualization Tool An interactive tool for stereotaxic brain data visualization Ivo D. Dinov, Bae Cheol Shin, Fotios Konstantinidis and Arthur Toga An interactive tool for stereotaxic brain data visualization Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/~dinov/LONI_Vis.html CCB License 3D/4D PET/MRI/fMRI Image volumes in ANALYZE/IMG or MNC format 2D or 3D Graphical Data Display and stacks of UCF contours Application UCLA Center for Computational Biology 5.3 5/23/2006 Development with public userbase Automated Image Registration A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. Roger P. Woods A tool for automated registration of 3D and 2D images within and across subjects and across imaging modalities. Registration http://bishopw.loni.ucla.edu/AIR5/ CCB License 3D Brain Image volumes in ANALYZE/IMG format 3D Brain Image volumes in ANALYZE/IMG format or Displacement fiels in AIR/WARP file formats Application UCLA Center for Computational Biology 5.2.5 NA Mature LONI It's Close Enuf LONI ICE is a Java application that generates seed points for other image processing applications. Scott C. Neu LONI ICE is a Java application that generates seed points for other image processing applications. Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=40 CCB License 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format 2D or 3D Graphical Data Display Application UCLA Center for Computational Biology 1 11/1/2006 Development with public userbase Statistical Online Computational Resource The SOCR resource provides a hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. 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. Statistical Package http://www.SOCR.ucla.edu CCB License Tabular ASCII data (copy/paste) or human interface Tabular ASCII data (copy/paste) or human interface Application UCLA Center for Computational Biology 1 8/1/2003 Mature MultiTracer 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. 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. Manifold Viewers 2D, 3D, 4D, ND http://bishopw.loni.ucla.edu/MultiTracer/MultiTracer.html CCB License 3D Brain Image volumes in ANALYZE/IMG format 2D or 3D Graphical Data Display or stacks of UCF contours Application UCLA Center for Computational Biology 1 NA Development with public userbase LONI Debabeler 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. Data Transforms http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11 CCB License Various 2D/3D Brain Image volume type data Various 2D/3D Brain Image volume type data Application UCLA Center for Computational Biology 2.6 11/13/2006 Development with public userbase MultiPhase-SEG MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Igor Yanovskiy MultiPhase-SEG is a segmentation software that employs the implementation of the active contours without edges level set based segmentation model. Segmentation http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=16 CCB License 3D Brain Image volumes in ANALYZE/IMG format 3D Brain Image volumes in ANALYZE/IMG format Application UCLA Center for Computational Biology 1 3/1/2005 Development with public userbase Synchronized Histological Image Viewing Architecture The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. Heng Yuan, Allan MacKenzie-Graham, Eagle S. Jones, David W. Shattuck, Arthur W. Toga The Synchronized Histological Image Viewing Architecture (SHIVA) is a Java-based visualization and analysis application. Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12 CCB License Various 2D/3D Brain Image volume type data 2D or 3D Graphical Data Display Application UCLA Center for Computational Biology 1 10/16/2005 Development with public userbase Extract4DUcfAttributes The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file. Craig Schwartz The Extract4DUcfAttributes application extracts data attributes associated with each vertex of a Ucf file. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=32 CCB License 4D UCF contour File format Column of ASCII 1D float data Application UCLA Center for Computational Biology 1.1.0 5/10/2006 Development with public userbase ShapeCurvature 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. Bae Cheol Shin and Craig Schwartz 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. Shape Analysis http://www.loni.ucla.edu/Software/Features_Detail.jsp?software_id=33 CCB License Triangulated Surface Object (in various 3D surface formats) ASCII tables Application UCLA Center for Computational Biology 1.0.0 5/10/2006 Development with public userbase ShapeToDX 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 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." Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=34 CCB License OBJ surface or Stacks or UCF contours DXF Surface format Application UCLA Center for Computational Biology 1.0.0 5/10/2006 Development with public userbase Virtual File System Browser The Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols. Jeff Ma The Virtual File System Browser is an interoperable replacement for the Java JfileChooser that supports sFTP and ssh protocols. Data Transfer http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=35 CCB License URL, data server, host FTP or File download tunnel Class Library / Toolkit UCLA Center for Computational Biology 1.1.0 5/10/2006 Development with public userbase FFT Library An FFT library in Java Herbert Chang and Daniel Valentino An FFT library in Java Fourier Transform http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=36 CCB License 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format Class Library / Toolkit UCLA Center for Computational Biology 1.1 2/24/2005 Development with public userbase Charged Fluid Model for Vascular Segmentation A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model. Herbert Chang A computer-aided took for 3D vascular tree segmentation using an electrostatic charged fluid model. Segmentation http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=37 CCB License 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format Class Library / Toolkit UCLA Center for Computational Biology 1 5/30/2006 Development with public userbase Charged Fluid Model for Brain Image Segmentation 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. Segmentation http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=41 CCB License 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format 2D or 3D Image planes or volumes in ANALYZE/IMG or resterized format Class Library / Toolkit UCLA Center for Computational Biology 1.1 1/20/2007 Development with public userbase BLASTgres NA Stott Parker and Ruey-Lung Hsiao PostgreSQL, data management of biological sequences, sequence analysis, bioinformatics. Information retrieval, traversal and querying http://blastgres.cs.ucla.edu/ CCB License biological sequences Range, an integer interval, representing a segment in a sequence. Loc, a sequence location defined by a range and a sequence id, representing a specific segment in a specific sequence. Class Library / Toolkit UCLA Center for Computational Biology 1 Dec-06 Development with public userbase LONI Java Image I/O Plugins Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats. Scott C. Neu, Bryan Vann, Kejia Ma, and Craig Schwartz Decoders and encoders written in Java for the AFNI, ANALYZE, DICOM, ECAT, GE, MINC, NIFTI and other neuroimaging file formats. Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=17 CCB License Various 2D/3D Brain Image volume type data Various 2D/3D Brain Image volume type data Class Library / Toolkit UCLA Center for Computational Biology 1.2 11/13/2006 Development with public userbase 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. Jeff Q. Ma 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. Manifold Viewers 2D, 3D, 4D, ND http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=18 CCB License Varrious Surface and Contour file formats 2D or 3D Graphical Data Display Application UCLA Center for Computational Biology 1.1.0 5/10/2006 Development with public userbase BrainSuite2 BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. David W. Shattuck BrainSuite2 is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head. Image Processing http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=19 CCB License Various 2D/3D Brain Image volume type data 2D or 3D Graphical Data Display Application UCLA Center for Computational Biology 2 6/1/2005 Development with public userbase DualSurfaceMin 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. Jussi Tohka, Mikko Itäranta and Jouni Mykkänen 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. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=22 CCB License 3D Brain Image volumes in ANALYZE/IMG format 3D Brain Image volumes in ANALYZE/IMG format Application UCLA Center for Computational Biology 1.1 5/31/2005 Development with public userbase 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. Scott C. Neu and Karen Crawford A simple to use Java application for removing patient-identifying information (e.g., patient name and id) from medical image files. Data Transforms http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=11 CCB License Various 2D/3D Brain Image volume type data Various 2D/3D Brain Image volume type data Application UCLA Center for Computational Biology 1 10/13/2005 Development with public userbase InterpolateUcf InterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file. Craig Schwartz InterpolateUcf is a java based tool that interpolates contour vertices and data attributes in a Ucf file. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=24 CCB License Uniform Contour File Format (UCF) Uniform Contour File Format (UCF) Application UCLA Center for Computational Biology 1.1.0 10/10/2005 Development with public userbase LONI ShapeTools The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. Craig Schwartz The ShapeTools library is a collection of Java classes that enable Java programmers to model and manipulate geometric shapes and associated data values. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=25 CCB License Varrious Surface and Contour file formats Varrious Surface and Contour file formats Class Library / Toolkit UCLA Center for Computational Biology 1.2.0 5/10/2006 Development with public userbase LONI ShapeDistance A tool for calculating the distance between vertices of two shape files Craig Schwartz A tool for calculating the distance between vertices of two shape files Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=26 CCB License Varrious Surface and Contour file formats Floating point distance values Application UCLA Center for Computational Biology 1.0.0 10/31/2005 Development with public userbase DXJava The DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files. Craig Schwartz The DXJava is a collection of Java classes that enable Java programmers to read and write OpenDX general format files. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=31 CCB License Varrious Surface and Contour file formats Varrious Surface and Contour file formats Class Library / Toolkit UCLA Center for Computational Biology 1.0.0 5/1/2006 Development with public userbase Pygr Pygr is an open source software project used to develop graph database interfaces. Christopher Lee, Alexander Alekseyenko, Stott Parker, Zach Fierstadt Pygr is an open source software project used to develop graph database interfaces. BiologicalConcept http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=27 CCB License biological sequences Charts Class Library / Toolkit UCLA Center for Computational Biology 0.3 3/10/2006 Development with public userbase LONI ShapeViewerApplet The ShapeViewerApplet displays three dimensional shapes in a web page Jeff Q. Ma The ShapeViewerApplet displays three dimensional shapes in a web page Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=18 CCB License Varrious Surface and Contour file formats 2D or 3D Graphical Data Display Application UCLA Center for Computational Biology 1.1.0 10/28/2005 Development with public userbase ShapeTransform The ShapeTransform application facilitates the moveof a shape file from one coordinate system to another. Bae Cheol Shin and Craig Schwartz The ShapeTransform application facilitates the moveof a shape file from one coordinate system to another. Shape Analysis http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=30 CCB License Varrious Surface and Contour file formats Varrious Surface and Contour file formats Application UCLA Center for Computational Biology 1.1.0 5/3/2006 Development with public userbase ASAP 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 Christopher Lee, Alexander Alekseyenko, Stott Parker, Zach Fierstadt alternative splicing, biological process, alternatively spliced isoforms Information retrieval, traversal and querying http://bioinfo.mbi.ucla.edu/ASAP/ CCB License biological sequences Charts Web Service UCLA Center for Computational Biology 2.1 6/28/1905 Development with public userbase