ArticleNature methods2019
An active texture-based digital atlas enables automated mapping of structures and markers across brains.
Article in Nature methods, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
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- Chemoarchitectural studies of the rat hypothalamus and zona incerta.bioRxiv : the preprint server for biology · 2025Article
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- An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain.Imaging neuroscience (Cambridge, Mass.) · 2025Article
- Developmental mouse brain common coordinate framework.Nature communications · 2024Article
- A flowchart for adequate controls in virus-based monosynaptic tracing experiments identified Cre-independent leakage of the TVA receptor in RΦGT mice.BMC neuroscience · 2024Article
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- Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes.National science review · 2024Article
- Developmental Mouse Brain Common Coordinate Framework.bioRxiv : the preprint server for biology · 2023Article
- Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System.Neuroinformatics · 2023Article
- An interactive image segmentation method for the anatomical structures of the main olfactory bulb with micro-level resolution.Frontiers in neuroinformatics · 2023Article
- giRAff: an automated atlas segmentation tool adapted to single histological slices.Frontiers in neuroscience · 2023Article
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- Constructing the rodent stereotaxic brain atlas: a survey.Science China. Life sciences · 2022Review
- Artificial Intelligence Supports Decision Making during Open-Chest Surgery of Rare Congenital Heart Defects.Journal of clinical medicine · 2021Article
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- Connectivity characterization of the mouse basolateral amygdalar complex.Nature communications · 2021Article
- Graphical-model framework for automated annotation of cell identities in dense cellular images.eLife · 2021Article
- Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain.eLife · 2021Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.