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
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: | bioinformatics Investigative techniques and equipment bioinformatics > computational biology > algorithms organism description > animal organs, tissues, organelles, cell types and functions > organs types and functions > brain Investigative techniques and equipment > brain atlas bioinformatics > computational biology bioinformatics > computational biology > algorithms > machine learning organism description > animal > mammal organism description > animal > mammal > rodent > mouse organs, tissues, organelles, cell types and functions > organs types and functions organs, tissues, organelles, cell types and functions organism description > animal > mammal > rodent |
| CSHL Authors: | |
| Communities: | CSHL labs > Mitra lab |
| Depositing User: | Matthew Dunn |
| Date: | 11 March 2019 |
| Date Deposited: | 25 Mar 2019 19:47 |
| Last Modified: | 01 Feb 2024 21:01 |
| PMCID: | PMC6736610 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/37764 |
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