# New Consensus Whole Mouse Brain Taxonomy Available for Download and Programmatic Access

**URL:** <https://community.brain-map.org/t/new-consensus-whole-mouse-brain-taxonomy-available-for-download-and-programmatic-access/4754>\
**Category:** Technical\
**Created:** [November 11, 2025, 6:23pm UTC](https://community.brain-map.org/t/new-consensus-whole-mouse-brain-taxonomy-available-for-download-and-programmatic-access/4754 "2025-11-11T18:23:46Z")\
**Posts on this page:** 1\
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**Author:** ![Elysha-AIBS](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/elysha-aibs/32/828_2.png) [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)\
**Post date:** [November 11, 2025, 6:23pm UTC](https://community.brain-map.org/t/new-consensus-whole-mouse-brain-taxonomy-available-for-download-and-programmatic-access/4754/1 "2025-11-11T18:23:46Z")

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We are pleased to share a new Consensus, Whole Mouse Brain (WMB) integrated taxonomy. This new cell type taxonomy is built upon two publicly released transcriptionally defined WMB taxonomies: one derived from single-cell RNA sequencing (scRNA-seq) data and the other from single-nucleus RNA sequencing (snRNA-seq) data. It is available now on [GitHub](https://alleninstitute.github.io/abc_atlas_access/descriptions/Consensus-WMB-dataset.html) for download and programmatic access.

1. The [Allen Institute for Brain Science (AIBS) taxonomy](https://alleninstitute.github.io/abc_atlas_access/descriptions/WMB-taxonomy.html), based on over 4 million scRNA-seq profiles, defines 5,322 clusters organized hierarchically into 34 classes, 338 subclasses, and 1,201 supertypes. The set of data products for this release can be found [here](https://alleninstitute.github.io/abc_atlas_access/descriptions/WMB_dataset.html).
2. In parallel, the Broad Institute taxonomy, constructed from 4.4 million snRNA-seq profiles, defines 16 classes, 223 metaclusters, and 5,030 clusters. Integrating these two large-scale taxonomies into a unified framework represents a natural and impactful next step, enabling a consensus view of cell types across the entire mouse brain and benefiting the broader neuroscience community.

To generate this consensus taxonomy, we applied the AIBS Quality Control (QC) and post-integration QC pipelines, retaining 7,651,713 cells and nuclei. Integration of scRNA-seq and snRNA-seq data was performed using scVI, with subsampling by original clusters to mitigate sampling imbalance across cell types and brain regions, followed by projection of all remaining cells into a shared latent space. The same iterative clustering strategy used in the AIBS taxonomy was applied in a hierarchical manner—globally, at nine neighborhood levels, and across eight finer group levels.

The resulting comprehensive taxonomy comprises a hierarchically arranged set of cell types with 9 neighborhoods, 43 classes, 414 subclasses, 1,386 supertypes, and 6,721 clusters. A detailed cell type annotation table accompanies the taxonomy, including hierarchical membership, anatomical localization, and neurotransmitter identity.

Expression matrices and metadata for the two combined whole mouse brain datasets, [Allen Institute for Brain Science (AIBS), Whole Mouse Brain (WMB)](https://alleninstitute.github.io/abc_atlas_access/descriptions/WMB_dataset.html) and a release from the Broad Institute, Macosko lab. These two scRNA-seq and snRNA-seq datasets (AIBS WMB and Macosko respectively) are combined here into this Consensus Mouse release and [Consensus Mouse Taxonomy](https://alleninstitute.github.io/abc_atlas_access/descriptions/Consensus-WMB-taxonomy.html).

All associated metadata is publicly available as an AWS Public Dataset hosted on Amazon S3 and through the [Abc\_atlas\_access package](https://alleninstitute.github.io/abc_atlas_access/descriptions/Consensus-WMB-dataset.html) on GitHub.