An active texture-based digital atlas enables automated mapping of structures and markers across brains

Chen, Y., McElvain, L. E., Tolpygo, A. S., Ferrante, D., Friedman, B., Mitra, P. P., Karten, H. J., Freund, Y., Kleinfeld, D. (March 2019) An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nat Methods, 16 (4). pp. 341-350. ISSN 1548-7091

URL: https://www.ncbi.nlm.nih.gov/pubmed/30858600
DOI: 10.1038/s41592-019-0328-8

Abstract

Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.

Item Type: Paper
Subjects: Investigative techniques and equipment > brain atlas
CSHL Authors:
Communities: CSHL labs > Mitra lab
Depositing User: Matthew Dunn
Date: 11 March 2019
Date Deposited: 25 Mar 2019 19:47
Last Modified: 23 Apr 2019 14:35
Related URLs:
URI: http://repository.cshl.edu/id/eprint/37764

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