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Allen Brain Atlas API

The Allen Institute for Brain Science offers access to its published data through an application programming interface (API). The API, documentation, sample applications, and 2012 Allen Brain Atlas Hackathon materials are made available to the community under the Allen Institute's Terms of Use in hopes of facilitating discovery.

Available Data and Services

Examples of studies with data and services made available through the Allen Brain Atlas API include:

Gene Expression Resources

Primary data, experiment metadata, informatics and manual annotations from genome-wide atlases and studies involving gene expression include:

  • High resolution images, including ISH
  • Microarray, including exon microarray summarized to exons and genes
  • RNA sequencing
  • Manual annotations
  • Grid-level gene expression values registered to the Mouse Brain and Developing Mouse Brain reference atlas spaces
Anatomical Resources
  • High resolution images including Nissl
  • Samples mapped to MNI space
  • Reference atlas ontologies, SVG drawings, and 3-D models
  • MRI and DTI files
  • Image-to-Image Synchronization
  • Differential Expression
  • NeuroBlast Search
  • Anatomic Gene Expression Atlas (AGEA)
Getting Started

Familiarize yourself with the available data and methods, as well as how to take advantage of resources by reading these overviews:

  • Mouse Brain ISH Data: Informatics Data Processing Pipelines
  • Human Brain Microarray Survey

For more detailed information, please refer to the Allen Brain Atlas Data Portal .

Example Applications

The example applications demonstrate several features of the API for the following studies:

  • Mouse Brain
  • Human Brain Microarray
  • Developing Mouse Brain
Accessing Data and Services

In the spirit of REST, the Allen Institute publishes its data model as documents that can be requested using the standard HTTP method, GET. Use RESTful Model Access (RMA) with the following services for searching and downloading data:

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