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The Whole Brain Catalog is a ground-breaking, open-source, 3-D virtual environment developed by a team of researchers from UC San Diego under the Whole Brain Project. The Catalog aims to connect members of the international neuroscience community to facilitate solutions for today’s intractable challenges in brain research through cooperation and crowd sourcing.

Despite rapid progress in the development of new experimental methods, our ability to simultaneously study the brain across all scales remains quite limited.

Cutting-edge experimental technologies and new microscopy methods are now able to reveal new aspects of organization within these scales, yet the development of software tools to synthesize these data into more coherent models of brain structure and function has lagged behind. The Whole Brain Catalog is a client-server platform that 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.

The Whole Brain Project team demonstrated and released to the public the Whole Brain Catalog beta version 0.7 at Neuroscience 2009, the annual meeting of the Society for Neuroscience held October 17-21 in Chicago, Illinois.

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

The Whole Brain Catalog draws from resources such as the Cell Centered Database (CCDB) and the Neuroscience Information Framework (NIF), as well as many other important efforts in neuroscience, computational neuroscience, and open source development. 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

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