Representation of coordinate reference systems for the rodent brain in the INCF Digital Atlasing Infrastructure
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1
Radboud University, Netherlands
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2
MRC Human Genetics Unit and IGMM, United Kingdom
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3
Informed Minds, Inc., United States
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4
MRC Human Genetics Unit and Heriot-Watt University, United Kingdom
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5
Allen Institute for Brain Science, United States
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6
University of California at San Diego, United States
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7
University of California Los Angeles, United States
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8
Leiden University, Netherlands
Digital atlases of rodent brain contain large volumes of 2D and 3D imagery, gene expression, electrophysiological and other information. Federating these atlases is one of the goals of the INCF Digital Atlasing Infrastructure (INCF-DAI) Task Force. To enable such federation, we rely on a collection of spatial and semantic translations that convert location and structure name information, respectively, between atlas-specific coordinate systems and semantic conventions. Transforming coordinate information, in turn, requires that the spatial reference system (SRS) of each atlas is formally described. We present an initial specification of coordinate reference system that can be applied across different rodent brain atlases, which has been developed in the course of INCF-DAI work on infrastructure for brain atlas interoperability.
Construction of reference coordinate systems for the brain is not straightforward as we have to deal with variations in the anatomy (size/shape) of individual animals; not to mention dependency of the spatial-temporal pattern information on specific procedures for sample preparation. Existing atlases present brain information in either 2D or 3D, and often differ with respect to coordinate system origin and coordinate axis orientations, while metadata about metric units or neuroscience interpretation of coordinate dimensions is often scattered over various textual descriptions. In addition the assumption of a simple cartesian axes valid over the whole is an approximation for the adult brain but completely inappropriate for the developing brain where curvature of the posterior-anterior axis changes dramatically as the brain develops.
In geodesy, where thousands of coordinate systems for different parts of the world have been developed and systematized over centuries, the community came to a common treatment of spatial reference systems. Standard SRS metadata is cataloged in an authoritative registry (http://www.epsg-registry.org/): each SRS is assigned an identification code which is used by researchers and software developers to find coordinate system description and invoke coordinate transformations.
Our goal is to create a similar authoritative registry for the brain, containing standard descriptions of spatial reference systems used in neuroscience. We present a prototype of such registry, which at the time of writing contains formal descriptions of several SRS for the mouse brain, including those used in the Allen Brain Atlas, the reference Waxholm Space, the Paxinos and Watson stereotaxic system, and coordinate descriptions used in the Edinburgh Mouse Atlas Project. The prototype information model of rodent brain SRS includes the following components:
1) Key SRS metadata, in particular SRS origin, units, coordinate axes specified with respect to common directions in the brain (ventral, dorsal, anterior, posterior, left and right)
2) Anatomical structures segmented in 2D or 3D, including information about the ontology in which the structure is described and a pointer to respective spatial representation of the feature
3) Fiducials (landmarks): points or higher-dimensional features related to the segmented anatomical structures, which can be used to relate this SRS with other systems
4) Orientations: specification of coordinate axes when they do not align with common neuroscience orientations but can be presented as a function of the latter (e.g. for the developing brain)
5) Slices: list of plates in a 2D reference atlas with their characteristics (if the atlas represents a set of 2D plates)
We will demonstrate how such anatomical structure-based characterizations of mouse brain coordinate systems are catalogued and managed within the emerging INCF infrastructure for digital brain atlases. We also demonstrate how this information is used to support on demand coordinate transformations, when a researcher needs to discover and analyze information available for a given point of interest in various atlases.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Oral Presentation
Topic:
Digital atlasing
Citation:
Bakker
R,
Baldock
R,
Boline
J,
Burger
A,
Hawrylycz
M,
Larson
S,
Memon
A,
Ng
L,
Ruffins
S,
Verbeek
F and
Zaslavsky
I
(2010). Representation of coordinate reference systems for the rodent brain in the INCF Digital Atlasing Infrastructure.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00135
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Received:
18 Jun 2010;
Published Online:
18 Jun 2010.
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Correspondence:
Ilya Zaslavsky, University of California at San Diego, San Diego, United States, zaslavsk@sdsc.edu