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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, and annotations for genome-wide atlases and studies involving gene expression include:

  • High resolution ISH and FISH images
  • Microarray and exon microarray summarized to exons and genes
  • RNA sequencing summarized to exons and genes
  • Grid-level gene expression values registered to reference atlas space
  • Manual annotations indicating gene expression characteristics
Anatomical Resources
  • High resolution Nissl and Ache images
  • Samples mapped to MNI space
  • Reference atlas ontologies, structure boundary drawings, and 3-D models
  • MRI and DTI files
Connectivity Resources
  • High resolution 2-D projectivity images
  • BDA vs. rAAV comparison
  • Transgenic characterization
  • Image-to-Image Synchronization
  • Correlation
  • 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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