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Whole Brain Catalog

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.

URL: http://www.wholebraincatalog.org/

Resource ID: nif-0000-23345     Resource Type: Resource     Version: Latest Version


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

Additional Resource Types

Atlas, Simulation Software, Data Visualization Software, Data Repository, Image Collection, D Spatial Image, Image Repository


GNU Lesser General Public License, The community can contribute to this resource



Related To

NeuroLex, Cell Centered Database, Neuroscience Information Framework, INCF Software Center



Parent Organization

Funding Information

Waitt Family Foundation,

Listed By

NITRC, Biositemaps



Original Submitter


Version Status


Submitted On

12:00am October 19, 2010

Originated From


Changes from Previous Version

    No Changes

    Version 4

    Created 1 month ago by Christie Wang

    Version 3

    Created 2 months ago by Christie Wang

    Version 2

    Created 2 months ago by Christie Wang

    Version 1

    Created 5 years ago by Anonymous