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Allen Brain Atlas API">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.

Learn about the API with these atlas and resource overviews:


Mouse Brain
Developing Mouse Brain
Mouse Connectivity
Human Brain
Developing Human Brain
Non-Human Primate


Atlas Drawings and Ontologies

Download colorized and labeled atlas images, histological images, SVG atlas graphics and the associated structure ontology.

Data Model

The data model includes entities from molecular biology, anatomic atlases, laboratory artifacts, experiments, and annotations.

Downloading 3-D Expression Grid Data

Download 3-D expression grid data packaged into a compressed archive file (.zip).

Downloading and Displaying SVG

The SVG download service returns annotations associated with the specified SectionImage as scalable vector graphics.

Downloading an Image

The image download services serves whole and partial two-dimensional images presented on the Allen Brain Atlas Web site.

Downloading an Ontology's Structure Graph

Download a hierarchical XML or JSON document containing each of the Structures in the requested StructureGraph.

Example Queries for Experiment Metadata

Commonly requested queries for experiment metadata.

Image-to-Image Synchronization

Image synchronization services based on the image alignment results.

Quantified Data by Structures

Gene expression and projection statistics.

RESTful Model Access (RMA)

An HTTP service designed along RESTful principles to allow access to data in the Allen Institute API.

Searching Annotated SectionDataSets

Search expert annotations of the Developing Mouse Brain Atlas' ISH data.

Searching a Specimen or Structure Tree

The Structure and Specimen Tree Search services return flat lists of ancestors and/or descendants for a specified structure or specimen.

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:

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  • Mouse Brain
  • Human Brain Microarray
  • Developing Mouse Brain
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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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