Update Notes - Sept 12, 2023

The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data, features and improvements!

New Data

We are pleased to bring you updated whole-mouse-brain data with improvements to the cell types taxonomy. This cell type taxonomy is an updated version from bioRxiv preprint https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1. We are also excited to introduce a new data collection from Xiaowei Zhuang, Harvard University. Data downloads and notebooks with tutorials and examples for both data collections are available on GitHub.

Mouse Whole-Brain Transcriptomic Cell Type Atlas
Hongkui Zeng, Allen Institute for Brain Science

The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. The integrated transcriptomic taxonomy contains 5,322 clusters that are organized in a hierarchical manner with nested groupings of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 types/clusters. The scRNA-seq data reveal transcriptome-wide gene expression and co-expression patterns for each cell type. The anatomical location of each cell type has been annotated using a comprehensive brain-wide MERFISH dataset with a total of ~4 million segmented and QC-passed cells, probed with a 500-gene panel and registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3). The MERFISH data not only provide accurate spatial annotation of cell types at subclass, supertype and cluster levels, but also reveal fine-resolution spatial distinctions or gradients for cell types. The combination of scRNA-seq and MERFISH data reveals a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type, as well as unique features of cell type organization in different brain regions. A detailed cell type annotation table is also provided along with data downloads detailing information about the hierarchical membership, anatomical annotation, neurotransmitter type, cell type marker genes, transcription factor and neuropeptide markers, and other metadata types for each cluster. Learn more…

Xiaowei Zhuang, Harvard University

This spatially resolved cell atlas of the whole mouse brain provides a systematic characterization of the spatial organization of transcriptomically defined cell types across the entire adult mouses brain using in situ, single-cell transcriptomic profiling with multiplexed error-robust fluorescence in situ hybridization (MERFISH). We imaged ~9 million cells with a ~1,100-gene panel using MERFISH and performed spatially resolved, single-cell expression profiling at the whole-transcriptome scale by integrating our MERFISH data with the whole-brain single-cell RNA-sequencing (scRNA-seq) dataset generated by the Allen Institute. This allowed us to generate a comprehensive cell atlas of >5,000 transcriptionally distinct cell clusters, belonging to ∼300 major cell types (subclasses), in the whole mouse brain with high molecular and spatial resolution. The cell atlas was further registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3), which allows systematic quantifications of the cell composition and organization in individual brain regions as anatomically delineated in the CCF v3. This cell atlas also reveals molecularly defined brain regions characterized by distinct cell-type compositions, spatial gradients featuring gradual changes in the gene-expression profiles of cells, as well as cell-type-specific cell-cell interactions and the molecular basis and functional implications of these cell-cell interactions. Learn more…

New Features

Tool tips for cell color
Hovering your mouse over a cell will now display details of the cell’s color. For example, if your visualization is colored by Class, hovering over a cell will show which class the cell belongs to. If multiple cells overlap, the most common cell in the area will be shown.


Collapsible Control Panel
The Control Panel on the left of the page can now be collapsed and resized.

  • To minimize the panel and hide it from view, click the image icon.
  • To expand the panel, hover your mouse over the right edge of the panel until it becomes a double-sided arrow and drag the border to resize it.

Bug Fixes and Performance Improvements

For complete user guide documentation see Introducing the Allen Brain Cell Atlas! .

As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.

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