Extending the INCF digital atlasing infrastructure to include online image registration to atlas references spaces
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1
University of California San Diego, United States
The INCF digital atlasing infrastructure (DAI) is being developed to assist neuroscientists with discovery, access and integration of information from multiple atlases based on location in the brain. The backbone of the DAI service-oriented architecture is a collection of atlas web services, which provide access to location information including anatomic feature labels at a given point of interest, registered images, gene expression data, annotations, etc. A registry of formally defined atlas reference spaces for widely used atlases and coordinate transformation functions between them are the foundation for spatial integration. The atlas web service interface is an implementation of the Web Processing Service (WPS) standard, and the information exchanged via services is encoded in Waxholm Markup Language (WaxML) which is an application schema of ISO 19136 and provides standard constructs for representing coordinate systems, transformations, names and locations of brain structures, etc. Standard-compliance of atlas web services enables DAI to leverage a number of standard components developed elsewhere, including client libraries and online portal interfaces. The current operational system of services incorporates reference spaces for several mouse brain atlases (the ABA voxel space, ABA reference plates, Allen Gene Expression Atlas (AGEA), WHS, and Paxinos-Franklin atlas) as well as for atlases of the rat brain (the Paxinos-Watson atlas, WHSrat, and Wistar-Rat).
While the DAI framework enabled neuroscientists to access information from existing atlases, easy integration of user imagery into the system remained a challenge. To address it, we developed a workflow for spatial registration of 2D images and 2D image collections. The workflow can be invoked from the DAI atlas portal. In the current implementation, users upload their image collections to the INCF DataSpace, an online data grid environment for managing and sharing distributed data using iRODS. The uploaded images are processed to generate a number of derivate representations used in the registration process. Presented with a gallery of uploaded images, users then align image slices to reference spaces and establish fiducial reference points for thin plate spline computation using online software called Jibber. Coordinate system descriptions and coordinate transformation functions for the added image or image collection are then generated automatically based on the spline coefficients, using the workflow’s Jetsam component. As a result, users have the ability to immediately query available atlas hubs via atlas services using spatial locations on their own images to retrieve structure names, other registered images, gene expression and other data associated with user-defined points of interest.
This work was conducted within the DAI Task Force of the INCF Program on Digital Brain Atlasing.
Keywords:
digial atlasing,
image registration,
atlas services,
Waxholm Space,
data integration
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Digital atlasing
Citation:
Zaslavsky
I,
Lamont
S and
Memon
A
(2013). Extending the INCF digital atlasing infrastructure to include online image registration to atlas references spaces.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00012
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Received:
07 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Ilya Zaslavsky, University of California San Diego, San Diego, CA, MC 0505, United States, zaslavsk@sdsc.edu