ArticleScientific reports2021
Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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9 citing papers in PubMed, 1 synthesis or guideline pooled it, 16 citations in OpenAlex.
- Where do we stand on fMRI in awake mice?Cerebral cortex (New York, N.Y. : 1991) · 2024Pooled it
- NeuroCarta: An automated and quantitative approach to mapping cellular networks in the mouse brain.Network neuroscience (Cambridge, Mass.) · 2025Article
- Neurogenesis-independent mechanisms of MRI-detectable hippocampal volume increase following electroconvulsive stimulation.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024Article
- Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model.Communications biology · 2024Article
- Shared GABA transmission pathology in dopamine agonist- and antagonist-induced dyskinesia.Cell reports. Medicine · 2023Article
- Detecting the effect of genetic diversity on brain composition in an Alzheimer's disease mouse model.bioRxiv : the preprint server for biology · 2023Article
- Comprehensive Volumetric Analysis ofFrontiers in neuroscience · 2022Article
- Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain.Frontiers in neuroanatomy · 2021Review
- Chd8 mutation in oligodendrocytes alters microstructure and functional connectivity in the mouse brain.Molecular brain · 2020Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher's necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.
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