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. 2014 Sep 12;8:74. doi: 10.3389/fninf.2014.00074

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Copyright © 2014 Zaslavsky, Baldock and Boline.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Main steps of the atlas registration workflow for collections of 2D images. The example images are from a study of innervation and genetic similarity in brainstem (Matthews, 2012). The images are segmented, packaged together and uploaded to INCF DataSpace. Subsequent steps include generation of an image gallery page, aligning individual images in the gallery with target reference plates (using Jibber), generating thin plain spline transformations, generating warped images (using Jetsam), generating and updating a new SRS description (called BrainStem) and forward and inverse transformations between the new SRS and the target reference atlas (in this case, the ABA reference atlas). Once the user has registered their data, they can identify areas of interest in their datasets and apply information from other Atlas Hubs to their data (e.g., what structure is found at this location in space in the Allen Brain Atlas). More analytic capabilities are also possible, but these are not currently offered by the INCF Digital Atlasing Program.