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Online registration workflows for atlases of rodent brain and accuracy assessment of spatial translation

Filed under:

Ilya Zaslavsky (San Diego Supercomputer Center, UCSD), Asif Memon (University of California, San Diego), Stephan Lamont (University of California, San Diego), David Valentine (San Diego Supercomputer Center, UCSD), Luis Ibanez (Kitware, Inc.), Gang Song (University of Pennsylvania), Brian Avants (University of Pennsylvania), James Gee (University of Pennsylvania), Yang Liu (University of Pennsylvania), Jyl Boline (Informed Minds)

Registration of diverse sources of brain atlas data to standard coordinate spaces, managing coordinate transformations between reference spaces, and assessing the degree of certainty of spatial location descriptions and coordinate transformations, are the key issues in enabling atlas data integration based on spatial location in the brain. The problem is complex, because: a) different atlases and image stacks present different reference models of rodent brain; b) different image modalities result in different delineations of features and functional areas; c) there are a number of coordinate systems developed for the brain, each with different spatial properties and associated error models; d) coordinate transformations computed between 2D and 3D brain atlases have different error models, with degrees of distortion depending on the transformation technique; and e) the “true” deformation is usually unknown. This issue becomes more challenging as we move to atlas data integration across species, where transformations based on brain coordinates are likely to be meaningless.

To address this problem, the INCF Program on digital brain atlasing has developed a common reference space for mouse brain (Waxholm Space, or WHS), and a collection of atlas services, which support on-demand coordinate system description, coordinate transformations, and a range of requests based on point-of-interest queries. The atlas services have been deployed at several atlas hubs, initially supporting coordinate translation between WHS, reference plates and volume representations of the Allen Mouse Brain atlas, and the Paxinos-Watson atlas of the mouse brain. In addition, a mechanism has been developed to register additional image collections to the system of atlas hubs within INCF Digital Atlasing Infrastructure (INCF-DAI) and derive additional spatial reference system descriptions and transformations.

This poster focuses on two extensions of the INCF-DAI work: (a) standardization of online spatial registration workflows and (b) addition of coordinate transformation and registration accuracy measures to atlas services. We demonstrate registration workflow steps, show derivation of certainty fields for transformations between known coordinate systems, and present methodology for reporting transformation accuracy derived over the course of spatial registration.

This work was conducted within the Digital Atlasing Infrastructure Task Force of the INCF Program on Digital Brain Atlasing.
Preferred presentation format: Poster
Topic: Digital atlasing

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