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)
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 (http://j.mp/kQ1889).
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.
References
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.