How to: Allen Human Brain Atlas

This is the online help for the Allen Human Brain Atlas web application.

The Dataset

The Allen Human Brain Atlas is a unique multi-modal atlas of the human brain, integrating anatomic and genomic information and coupled with a suite of visualization and data mining tools.


Microarray data providing an “all genes, all structures” survey in multiple adult control brains

  • Genome-wide coverage - over 62,000 gene probes per expression profile
  • Comprehensive anatomic coverage - approximately 500 samples per hemisphere across cerebral, cerebellar and brainstem structures
  • Mapped with histology into unified 3-D anatomic framework based on MRI
  • Anatomic and gene-based search with options for comparing among structures or donors
  • Heat map and other viewing options, as well as files available for download

In situ hybridization image data comprising multiple data sets from targeted studies covering selected genes in specific brain regions

  • Subcortex study examining 55 genes across subcortical regions and 10 additional genes in hypothalamus in one male and one female donor
  • Cortex Study surveying 1,000 genes in visual and temporal cortex in multiple adult control brains
  • Schizophrenia Study of 60 genes in dorsolateral prefrontal cortex of over 50 control and schizophrenia cases
  • Autism Study of 25 genes in frontal, temporal and occipital cortical regions of 11 control and 11 autism cases
  • Neurotransmitter Study characterizing expression of selected neurotransmitter system genes in major cortical and subcortical areas of adult human brain

MRI data for brains used for all microarray and some ISH analyses

  • Multi-planar viewer for structural MRI
  • T1, T2 and DTI files for download

Brain Explorer® 3-D viewer for interactive viewing of brain anatomy and gene expression distribution, including inflated cortical surface views

For complete details please see the Whole Brain Microarray and In situ hybridization white papers on our Documentation page.

Dear professor,
From ‘Interactive Atlas Viewer :: Atlas Viewer’, I could only find half of the brain. I want to define lateral septal nucleus as region of interest used in MRI studies. Is it possible for me to download the Allen Human Brain Atlat including the full brain? Could you kindly give me some help?
Thank you in advance.
Rubai Zhou, MD, PhD,
Psychiatrist, Shanghai Mental Health Center. 600 South Wan Ping Road, Shanghai 200030, China.
Tel: +86 15000038562. 73529. E-mail: