How to: Allen Mouse Brain Atlas

This is the online help for the ALLEN Mouse Brain Atlas web application.

The Allen Mouse Brain Atlas is a genome-wide, cellular-resolution atlas of gene expression throughout the adult mouse brain.


In situ hybridization data

  • Genome-wide coverage
  • Comprehensive anatomic coverage
  • Microscopic resolution down to the cellular level
  • Differential search for enhanced gene expression by structure
  • Correlation search for genes with similar spatial expression patterns

AGEA tool for exploring transcriptome-based brain architecture and gene discovery

Brain Explorer® 3-D viewer

Anatomic reference atlases

  • Coronal and sagittal plates
  • High-resolution Nissl images
  • Structure ontology