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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.

SUBMITTER: Chen Y

PROVIDER: S-EPMC6736610 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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

Chen Yuncong Y McElvain Lauren E LE Tolpygo Alexander S AS Ferrante Daniel D Friedman Beth B Mitra Partha P PP Karten Harvey J HJ Freund Yoav Y Kleinfeld David D

Nature methods 20190311 4

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 deriv ...[more]

PMID: 30858600

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Project description:BackgroundIncreasing physical activity, improving diet, and performing brain training exercises are associated with reduced cognitive decline in older adults.ObjectiveIn this paper, we describe a feasibility trial of the Active Brains intervention, a web-based digital intervention developed to support older adults to make these 3 healthy behavior changes associated with improved cognitive health. The Active Brains trial is a randomized feasibility trial that will test how accessible, acceptable, and feasible the Active Brains intervention is and the effectiveness of the study procedures that we intend to use in the larger, main trial.MethodsIn the randomized controlled trial (RCT), we use a parallel design. We will be conducting the intervention with 2 populations recruited through GP practices (family practices) in England from 2018 to 2019: older adults with signs of cognitive decline and older adults without any cognitive decline. Trial participants were randomly allocated to 1 of 3 study groups: usual care, the Active Brains intervention, or the Active Brains website plus brief support from a trained coach (over the phone or by email). The main outcomes are performance on cognitive tasks, quality of life (using EuroQol-5D 5 level), Instrumental Activities of Daily Living, and diagnoses of dementia. Secondary outcomes (including depression, enablement, and health care costs) and process measures (including qualitative interviews with participants and supporters) will also be collected. The trial has been approved by the National Health Service Research Ethics Committee (reference 17/SC/0463).ResultsResults will be published in peer-reviewed journals, presented at conferences, and shared at public engagement events. Data collection was completed in May 2020, and the results will be reported in 2021.ConclusionsThe findings of this study will help us to identify and make important changes to the website, the support received, or the study procedures before we progress to our main randomized phase III trial.Trial registrationInternational Standard Randomized Controlled Trial Number 23758980; http://www.isrctn.com/ISRCTN23758980.International registered report identifier (irrid)DERR1-10.2196/18929.

Dataset Information

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

Publications

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

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