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Resource:Whole Brain Catalog

Name: Resource:Whole Brain Catalog
Description: An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework.

This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing.

The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations.

Within the Catalog, researchers can view and contribute a wide range of data including:

  • 3D meshes of subcellular scenes or brain region territories
  • Large 2D image datasets from both electron and light level microscopy
  • NeuroML and Neurolucida neuronal reconstructions
  • Protein Database molecular structures

Users of the Whole Brain Catalog can:

  • Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the "Waxholm Space."
  • View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations
  • View data up close and at a high resolution
  • View their own data in the Whole Brain Catalog environment
  • View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org.
  • Contribute code and connect personal tools to the environment
  • Make new connections with related research and researchers

5 Easy Ways to Explore:

  • Explore the datasets across multiple scales.
  • View data closely at high resolution.
  • Observe accurately simulated neurons.
  • Readily search for content.
  • Contribute your own research.
Parent Organization: University of California at San Diego; California; USA
Supporting Agency: Resource:Waitt Family Foundation
Related to: Resource:NITRC, Resource:Biositemaps, Resource:NeuroLex, Resource:Cell Centered Database, Resource:Neuroscience Information Framework, Resource:INCF Software Center
Resource Type(s): Atlas, Simulation software, Data visualization software, Data repository, Image collection, 3D spatial image, Image repository
Keywords: Crowd sourcing, Mouse, Brain, Cell, Neuron, Simulation, Microscopy, Neuroscience, Electron microscopy, Light microscopy, Bioinformatics, neuroinformatics, computational biology, biology, visualization, animation, molecular structure, neuronal reconstruction, subcellular, annotation
Abbreviation: WBC
Resource: Resource
URL: http://www.wholebraincatalog.org/
Availability: GNU Lesser General Public License, The community can contribute to this resource
Id: nif-0000-23345
Organism: Mouse
Link to OWL / RDF: Download this content as OWL/RDF

Parts of Resource:Whole Brain Catalog

Curation status: Curated

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Notes

This page uses this default form:Resource

Alt. NITRC URL: http://www.nitrc.org/projects/incf_whole-brai/
Alt. INCF Software Center URL: http://software.incf.org/software/whole-brain-catalog

News

| Twitter Handle: @BrainCatalog

Contributors

Aarnaud, Ccdbuser, Nifbot2



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Facts about Resource:Whole Brain CatalogRDF feed
AbbrevWBC  +
AvailabilityGNU Lesser General Public License  +, and The community can contribute to this resource  +
CurationStatuscurated  +
DefiningCitationhttp://www.wholebraincatalog.org/  +
DefinitionAn open source, downloadable, 3d atlas of An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework.

This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing.

The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations.

Within the Catalog, researchers can view and contribute a wide range of data including:

  • 3D meshes of subcellular scenes or brain region territories
  • Large 2D image datasets from both electron and light level microscopy
  • NeuroML and Neurolucida neuronal reconstructions
  • Protein Database molecular structures

Users of the Whole Brain Catalog can:

  • Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the "Waxholm Space."
  • View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations
  • View data up close and at a high resolution
  • View their own data in the Whole Brain Catalog environment
  • View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org.
  • Contribute code and connect personal tools to the environment
  • Make new connections with related research and researchers

5 Easy Ways to Explore:

  • Explore the datasets across multiple scales.
  • View data closely at high resolution.
  • Observe accurately simulated neurons.
  • Readily search for content.
  • Contribute your own research. r content.
  • Contribute your own research.
ExampleImageWBC.PNG  +
Has default formThis property is a special property in this wiki.Resource  +
Has roleAtlas  +, Simulation software  +, Data visualization software  +, Data repository  +, Image collection  +, 3D spatial image  +, and Image repository  +
Idnif-0000-23345  +
Is part ofUniversity of California at San Diego; California; USA  +
KeywordsCrowd sourcing  +, Mouse  +, Brain  +, Cell  +, Neuron  +, Simulation  +, Microscopy  +, Neuroscience  +, Electron microscopy  +, Light microscopy  +, Bioinformatics  +, Neuroinformatics  +, Computational biology  +, Biology  +, Visualization  +, Animation  +, Molecular structure  +, Neuronal reconstruction  +, Subcellular  +, and Annotation  +
LabelResource:Whole Brain Catalog  +
ModifiedDate7 November 2013  +
Page has default formThis property is a special property in this wiki.Resource  +
RelatedToResource:NITRC  +, Resource:Biositemaps  +, Resource:NeuroLex  +, Resource:Cell Centered Database  +, Resource:Neuroscience Information Framework  +, and Resource:INCF Software Center  +
SpeciesMouse  +
SuperCategoryResource  +
Supporting AgencyResource:Waitt Family Foundation  +
TwitterBrainCatalog  +