An open Google Earth for neuroinformatics: The Whole Brain Catalog
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1
University of California, San Diego, Center for Research in Biological Systems, United States
The brain is a deeply intricate structure with important features of organization occurring at multiple spatial scales. Relevant data can be derived from subcellular junctional connectivity, cytoarchitectural local connectivity, and long-range topographical connectivity, just to name a few. This fact forces investigators to use a variety of different techniques to observe its structure, each of which tend to reveal only pieces of a vast puzzle. Because of this, neuroscience faces challenges to understanding the structure of the nervous system, including the problem of assembling structural data collected from the neuroscience community. To address this challenge, it would be useful to have a single system that is capable of the following functions: 1) upload data into a common data environment where it can be easily discovered and retrieved, 2) contextualize data by superimposing and combining related data from multiple scales, and 3) create hypothetical, synthetic views of structures of interest by stitching data together or generalizing patterns found in data. The framework would allow researchers to deal with their data both spatially, placing it in register in a common brain space, and semantically, annotating and tagging it with standard ontological terms. These two dimensions of data - spatial and semantic - create a key basis for organizing the heterogenous, scattered knowledge of the brain's structure into a cohesive whole. Inspired by Google Earth (an online virtual globe system that allows the superimposition of satellite and map imagery), we have created the Whole Brain Catalog (WBC; http://wholebraincatalog.org), an open source virtual brain system that allows the superimposition of multiple neuroscience imagery data, data sources and modalities. Goals of the Whole Brain Catalog include the ability to facilitate insight into data by putting it back within the context of the anatomy of the whole brain, and to allow investigators to make new connections between their data and other intersecting data sets and resources. The Whole Brain Catalog is composed of the following key elements 1) a 3D game engine that allows real-time rendering and interaction with 2D and 3D multi-scale data, 2) a user interface and a set of navigation controls that allow the user to make specific data sets visible, zoom to them, and manipulate them, 3) a spatial registry layer built in concert with services provided by the INCF Digital Atlasing Infrastructure task force that allows users to connect to additional data sources such as the Allen Brain Institute and the University of Edinburgh’s EMAP system via spatial query, 4) a semantics layer built in conjunction with the INCF Program on Ontologies of Neural structures task force that allows users to connect to additional data sources such as NeuroLex.org via semantic query, 5) a simulation service that allows users to upload models to a cluster running a parallel version of the NEURON simulation engine, retrieve results, and render them as an animation, and 6) back-end web services and a data management layer that tie these elements together. While the Whole Brain Catalog is still a beta system, it is currently available for use and evaluation. The Whole Brain Catalog displays data in forms such as 3D meshes of subcellular scenes and of brain region territories, 3D volumetric data from MRI, EM tomography, and serial section EM, large 2D image sets from both EM and light level microscopy, and NeuroML / Neurolucida 3D neuronal reconstructions. The 3D brain region atlas is taken from the Allen Institute’s mouse atlas, with the option to display the INCF Waxholm space brain regions, provided by the Duke Center for In Vivo Imaging, as an alternate atlas. We conclude that this platform takes a step forward to producing a shared knowledge environment for neuroscience that can handle the multiple scales and modalities of data within this complex domain.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Oral Presentation
Topic:
Spotlight presentations
Citation:
Larson
SD,
Aprea
C,
Martinez
J,
Little
D,
Astakhov
V,
Kim
HS,
Zaslavsky
I,
Martone
M and
Ellisman
M
(2010). An open Google Earth for neuroinformatics: The Whole Brain Catalog.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00137
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Received:
21 Jun 2010;
Published Online:
21 Jun 2010.
*
Correspondence:
Stephen D Larson, University of California, San Diego, Center for Research in Biological Systems, La Jolla, United States, stephen.larson@gmail.com