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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
Cell Types


Quantified Data by Structures
Quantified Data as 3-D Grids
Search Services
Image Download
Image Synchronization
Atlas Drawings and Ontologies


Example Applications and Source Code
Example RMA Queries for Experiment Metadata


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 gene expression summaries re-sampled to a canonical reference space.
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 an Ontology.
Example Queries for Experiment Metadata Commonly requested queries for experiment metadata.
Image-to-Image Synchronization Image synchronization services use alignment results to find corresponding position between SectionDataSets, the 3-D reference model and structures.
Quantified Data by Structures Gene expression and projection statistics.
RESTful Model Access (RMA) RESTful service for searching and retrieving data from the Allen Institute.
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 .

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