MERFISH spatial transcriptomics dataset of a single adult mouse brain#

A 4.0 million cell spatial transcriptomics dataset spanning a single adult mouse brain with a 500 gene panel and mapped to the whole mouse brain taxonomy. It was used in the creation of a high resolution transcriptomic and spatial atlas of cell types described in Yao et al..

The expression matrices and associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:


Current Version


Expression Matrices


14.2 GB



1.81 GB

Data is being share under the CC BY NC 4.0 license.

Related resources :

  • Whole mouse brain clustering (WMB-10X)

  • Whole mouse brain mouse taxonomy of cell types (WMB-taxonomy)

Associated notebooks:

  • Getting started: learn how to use the AbcProjectCache to facilitate data download and usage.

  • 10x scRNA-seq clustering analysis and annotation: learn about the whole mouse brain taxonomy through some example use cases and visualization.

    • MERFISH whole brain spatial transcriptomics

    • Part 1: learn about the MERFISH dataset through some example use cases and visualization for a single brain section.

    • Part 2a: learn to access data and prepare for whole brain example use cases in part 2b.

    • Part 2b: Explore the whole brain data through visualization and analyses of a set of genes of interest.