ArticleCell2020
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas.
Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 959 papers.
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Who cites it
959 citing papers in PubMed.
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- SpatialZoomer: multi-scale feature analysis of spatial transcriptomics.Nature biomedical engineering · 2026Article
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- The lipidomic architecture of the mouse brain.Nature · 2026Article
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- Diffusion MRI reveals amyloid plaque-associated cellular signatures through spatial transcriptomic integration.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
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- Article
- Neonatal Sevoflurane Exposure Induces Long-Term Cognitive Impairment via Epigenetically Mediated MMP9 Activation and Perineuronal Net Disruption in the Hippocampal CA2.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Stroke drives glioma progression through the emergence of tumor-associated astrocytes with reduced CaNature cancer · 2026Article
- Real-time closed-loop feedback system for mouse mesoscale cortical signal and movement control.eLife · 2026Article
- Population geometries in frontal cortex coordinate value-based decisions.bioRxiv : the preprint server for biology · 2026Article
- Retrosplenial cortex maturation aligns with the transition from infant forgetting to persistent memory.Cell reports · 2026Article
- Paratenial thalamus engages in reciprocal and broadcast circuits with the prefrontal cortex.Cell reports · 2026Article
899 more citing papers are in PubMed but not listed here.
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Authors and funding
25 authors.
Funding
Abstract
Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).
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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.