The Whole Brain Catalog: Platform for neuroscientific data integration

Stephen Larson (Whole Brain Project, UC San Diego), Jesus Martinez (Whole Brain Project, UC San Diego), Vadim Astakhov (Whole Brain Project, UC San Diego), Chris Aprea (Whole Brain Project, UC San Diego), David Little (Whole Brain Project, UC San Diego), Richard Stoner (Whole Brain Project, UC San Diego), Sid Vijay (Whole Brain Project, UC San Diego), Maryann Martone (Whole Brain Project, UC San Diego), Mark Ellisman (Whole Brain Project, UC San Diego)

Understanding the structure of the nervous system requires neuroscience to manage knowledge about the identity and location of a diverse collection of pieces and parts that occur across at least nine orders of magnitude of spatial scale.  Therefore at the heart of the problem of understanding the nervous system is a difficult problem of information management.  To address this problem, we have created the Whole Brain Catalog, a graphical three-dimensional browser interface like Google Earth, but for the Brain.  This interface allows a user to access a framework for representing nervous system structure that allows integration and synthesis of images, three dimensional geometries, three dimensional volumes, and other data types all within the same space, regardless of its format and its spatial scale.  In addition, these data can be tagged with terminologies derived from the Neuroscience Information Framework, enabling indexing and querying these data via the biological content it is representing.  The Whole Brain Catalog makes use of the Allen Institute’s Mouse Brain Atlas coordinate system as well as the INCF’s Waxholm space coordinate system, in order to allow data that is registered within it to be reused in other systems (Hawrylycz, et al. 2011).  It also is one of the first interfaces that makes use of the INCF’s Digital Atlasing Infrastructure web service API (  Lastly, it allows the integration of nervous system network models expressed in NeuroML (, allowing such models to be situated in their anatomical context.

Recently, the Whole Brain Catalog interface has been updated to operate through a web browser, rather than through a stand-alone downloadable interface.  Additionally a mobile version has been released for iPhone and iPad which allows browsing of a limited collection of multi-scale 2D images of nervous system tissue (  

Here we present a case study of the use of the Whole Brain Catalog to enable a structural analysis of mitral neurons extending from the olfactory bulb (Ghosh et al, 2011).  To accomplish this, a 3-week old mouse reference brain was constructed, a Neurolucida import feature was added, and handles allowing easy three dimensional manipulation of objects with space where integrated.  In addition, a Python interface was added that allows scripts to be written using Whole Brain Catalog queries for information that make use of popular Python-based scientific computing libraries.  This investigation provides a useful case study of how the Whole Brain Catalog can be used to fill in current gaps in neuroscience understanding.


Ghosh, S., Larson, S. D., Hefzi, H., Marnoy, Z., Cutforth, T., Dokka, K., et al. (2011). Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons. Nature, 1-6. Nature Publishing Group. doi: 10.1038/nature09945.

Hawrylycz, M., Baldock, R. a, Burger, A., Hashikawa, T., Johnson, G. A., Martone, M., et al. (2011). Digital Atlasing and Standardization in the Mouse Brain. (L. J. Graham, Ed.)PLoS Computational Biology, 7(2), e1001065. doi: 10.1371/journal.pcbi.1001065.

Preferred presentation format: Poster
Topic: General neuroinformatics

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