LONI Visualization Tool (LONI_Viz)®
What Is LONI_Viz?

• General:
  LONI_Viz is a versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). A semi-intelligent tool (BrainMapper) provides the real interaction between the anatomical (voxel/world) atlas coordinates, the brain-tree (region hierarchical labeling nomenclature), the region description data-base and the moleculo-genetic data-base. This allows the user to synchronously query these sources of information and continuously map results between these different entities.
  The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes.
  The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer.
  A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (10⁹ bytes) in size.
  The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc.
  
  
• Specific Features:
  
  • Region description DataBase
  • Moleculo-genetic database
  • Brain anatomical data viewer
  • BrainMapper tool
  • Surface (LightWave objects/scenes) and Volume rendering tools
  • Interactive Contour Drawing tool
  
  
  
• Implementation Issues:
  
  • Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software
  • Extendable object-oriented code (Java), computer architecture independent
  • Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html
  
  
  
• Computer Requirements:
  
  • RAM 128MB+,
  • OpenGL (SGI) or DirectX (Microsoft) graphics library,
  • Java virtual machine (Java 1.2+, JDK+JRE),
  • Java3D
  
  
  
• Future Goals:
  
  • Link the planar (axial/sagittal/coronal) projection coordinate system with the local coordinate systems in the SurfaceViewer and VolumeRenderer - these should be co-dependent.
  • Optimization of loading, reslicing, display of the data
  • Convert all corrdinates from voxel to world
  • More ...

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