ABC Atlas User Guide: Mouse Whole-Brain Transcriptomic Cell Type Atlas Data and Dimensions

How To Allen Brain Cell (ABC) Atlas
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Mouse Whole-Brain Transcriptomic Cell Type Atlas - Data & Dimensions

For more detail and to download full datasets see the Project Page or GitHub for an overview of all the data including notebooks with examples.

Common Features

  • Gene Expression
    • Expand the Gene Expression feature to change the selected gene and view the gene expression distribution histogram.
    • To change genes, click the magnifying glass and enter the name of the gene you wish to see. Please note, not all genes are included in every dataset. Click the gene name in the search results to select it and click the droplet icon to apply color to the active frame.
  • If multiple cell points overlap (e.g. when zoomed out), the highest expression cell will appear “on top” of other cells. This is done to improve visibility of expression patterns.

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  • Cell Types (with 4 layers of subclassification)
    • Class: The top level of cell type definition in the mouse whole brain taxonomy. It is primarily determined by broad brain region and neurotransmitter type. All cells within a subclass belong to the same class. Class provides a broader categorization of cell types.
    • Subclass: The coarse level of cell type definition in the mouse whole brain taxonomy. All cells within a supertype belong to the same subclass. Subclass groups together related supertypes.
    • Supertype: The second finest level of cell type definition in the mouse whole brain taxonomy. All cells within a cluster belong to the same supertype. Supertype groups together similar clusters.
    • Cluster: The finest level of cell type definition in the mouse whole brain taxonomy. Cells within a cluster share similar characteristics and belong to the same supertype.

For a more detailed treatment of cell types explorable in this atlas see: A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain | Nature

Dataset Visualizations

MERSCOPE (Spatial slices)

  • Gene expression (500 genes)
  • Cell Types (with 4 layers of subclassification)
    *Neurotransmitter Type
    *Anatomical Division

10x scRNAseq (Whole brain UMAP embedding)

  • Gene expression (32,285 genes)
  • Cell Types (with 4 layers of subclassification)
  • Neurotransmitter type
  • Dissection Region
  • Donor ID
  • Platform
  • Sex
  • Genotype

See Introducing the Allen Brain Cell Atlas! for an overview of the tool.

Give us your feedback and suggest new features here: Allen Institute - Feedback

1 Like
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Hi there! This is a really exciting and cool new dataset to explore. Quick question - do you have any information about age/sex/strain of the mice used in the MERSCOPE/MERFISH data? And will there be slices without holes in them?

For the 10X scRNAseq, what do the names of the classes represent? Is there a list of that available, or would I be able to find that information in the preprint.

Thanks/Merci Beaucoup :slight_smile:

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Hi @Elysha-AIBS ,

I am trying to retrieve the data from the amazon web services bucket, I noticed that when I’m running the retrieval code in the python notebook from GitHub, my code runs for retrieval, however I notice the runtime is 0.0 seconds, and when I check my destination folder, I can’t locate the files from the AWS bucket. Is there any assistance to this end?

Thanks,
MP

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Hi @MPanday,

Can you paste a screenshot of your notebook here of these 2 cells?

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