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Resource:LONI Visualization Tool

Name: Resource:LONI Visualization Tool
Description: A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. 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). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture.

LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest.

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
    [1]
Other Name(s): LOVE, LONI Viz environment, LONI Visualization Environment
Parent Organization: Resource:Laboratory of Neuro Imaging
Supporting Agency: NIA, NLM, NCRR, NIMH, NSF, Resource:National Centers for Biomedical Computing
Related to: Resource:NITRC, Resource:Biositemaps
Resource Type(s): Data visualization software
Keywords: brain, atlas, visualization, gene mapping, Atlas Application, Magnetic resonance, Surface Analysis
Grant: P50 AG16570, K08 AG100784, R01 2R01 LM05639-06, 2 P41 RR13642, 5 P01 MN52176, DUE 0442992, U52 RR021813
Abbreviation: LONI Viz, LONI_Viz, LOVE
Resource: Resource
URL: http://www.loni.ucla.edu/Software/LOVE
PMID: PMID 16598642
Publication link: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045182
Availability: GNU General Public License, For educational and research purposes only
Id: nif-0000-23313
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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References

  1. Dinov ID et al. (2006) LONI visualization environment. J Digit Imaging 19: 148-58 PubMed

Notes

This page uses this default form:Resource

Alt. NITRC URL: http://www.nitrc.org/projects/incf_loni-viz
Alt. URL: http://www.loni.ucla.edu/~dinov/LONI_Vis.html



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Facts about Resource:LONI Visualization ToolRDF feed
AbbrevLONI Viz, LONI_Viz, LOVE  +
AvailabilityGNU General Public License  +, and For educational and research purposes only  +
CurationStatuscurated  +
DefiningCitationhttp://www.loni.ucla.edu/Software/LOVE  +
DefinitionA versatile 1D, 2D and 3D data viewer gear A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. 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). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture.

LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest.

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
    _Vis.dir/doc/LONI_Viz_Java_Docs.html
ExampleImageLONI Viz.PNG  +
GrantCategory:P50 AG16570   +, Category:K08 AG100784   +, Category:R01 2R01 LM05639-06   +, Category:2 P41 RR13642   +, Category:5 P01 MN52176   +, Category:DUE 0442992   +, and Category:U52 RR021813   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleData visualization software  +
Idnif-0000-23313  +
Is part ofResource:Laboratory of Neuro Imaging  +
KeywordsBrain  +, Atlas  +, Visualization  +, Gene mapping  +, Atlas Application  +, Magnetic resonance  +, and Surface Analysis  +
LabelResource:LONI Visualization Tool  +
ModifiedDate7 November 2013  +
PMID16598642  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3045182  +
RelatedToResource:NITRC  +, and Resource:Biositemaps  +
SuperCategoryResource  +
Supporting AgencyNIA  +, NLM  +, NCRR  +, NIMH  +, NSF  +, and Resource:National Centers for Biomedical Computing  +
SynonymLOVE  +, LONI Viz environment  +, and LONI Visualization Environment  +