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

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.

journal_name

Nat Methods

journal_title

Nature methods

authors

Chen Y,McElvain LE,Tolpygo AS,Ferrante D,Friedman B,Mitra PP,Karten HJ,Freund Y,Kleinfeld D

doi

10.1038/s41592-019-0328-8

subject

Has Abstract

pub_date

2019-04-01 00:00:00

pages

341-350

issue

4

eissn

1548-7091

issn

1548-7105

pii

10.1038/s41592-019-0328-8

journal_volume

16

pub_type

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