ArticleNature communications2019
Enhanced and unified anatomical labeling for a common mouse brain atlas.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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Who cites it
105 citing papers in PubMed.
- Real-time closed-loop feedback system for mouse mesoscale cortical signal and movement control.eLife · 2026Article
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- Computational Model for Synthesizing Auditory Brainstem Responses to Assess Neuronal Alterations in Aging and Autistic Animal Models.Journal of the Association for Research in Otolaryngology : JARO · 2026Article
- A corticostriatal circuit updates subjective beliefs about latent task states.bioRxiv : the preprint server for biology · 2026Article
- Drug-induced changes in connectivity to midbrain dopamine cells revealed by rabies monosynaptic tracing.eLife · 2026Article
- Prefrontal modulation of striatal engagement: a hierarchical framework for goal-directed behavior.Communications biology · 2026Review
- Genoarchitecture and input-output organization of the mouse basal ganglia and thalamic parafascicular nucleus.Nature neuroscience · 2026Article
- Central amygdalar PKCδ neurons mediate fentanyl withdrawal.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- SynAPSeg: A novel dataset and image analysis framework for deep learning-based synapse detection and quantification.bioRxiv : the preprint server for biology · 2026Article
- LFP-LOC: an LFP power-based method for validating the anatomical placement of high-density neural probes in rodents.Frontiers in neuroscience · 2026Article
- A mouse brain atlas based on dendritic microenvironments.Nature neuroscience · 2026Article
- Dendritome mapping reveals the spatial organization of striatal neuron morphology.Nature neuroscience · 2025Article
- The ANTsX ecosystem for mapping the mouse brain.Nature communications · 2025Article
- VTA dopamine neuron activity produces spatially organized value representations.bioRxiv : the preprint server for biology · 2025Article
- ST-GCP: a graph convolutional network model with contrastive consistency and permutation for spatial transcriptomics.Briefings in bioinformatics · 2025Article
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45 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.
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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.