The Registry of Open Data on AWS is now available on AWS Data Exchange
All datasets on the Registry of Open Data are now discoverable on AWS Data Exchange alongside 3,000+ existing data products from category-leading data providers across industries. Explore the catalog to find open, free, and commercial data sets. Learn more about AWS Data Exchange

Allen Mouse Brain Atlas

biology gene expression genetic image processing imaging life sciences Mus musculus neurobiology transcriptomics


The Allen Mouse Brain Atlas is a genome-scale collection of cellular resolution gene expression profiles using in situ hybridization (ISH). Highly methodical data production methods and comprehensive anatomical coverage via dense, uniformly spaced sampling facilitate data consistency and comparability across >20,000 genes. The use of an inbred mouse strain with minimal animal-to-animal variance allows one to treat the brain essentially as a complex but highly reproducible three-dimensional tissue array. The entire Allen Mouse Brain Atlas dataset and associated tools are available through an unrestricted web-based viewing application ( The collection of > 650,000 images have been made available in this Open Data bucket to enable efficient access and analysis of the this dataset.

Update Frequency




Managed By

See all datasets managed by Allen Institute.


How to Cite

Allen Mouse Brain Atlas was accessed on DATE from

Usage Examples

Tools & Applications

Resources on AWS

  • Description
    Project data files in a public bucket
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    AWS Region
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://allen-mouse-brain-atlas/

Edit this dataset entry on GitHub

Tell us about your project