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:
Atlases
Mouse Brain
Developing Mouse Brain
Mouse Connectivity
Human Brain
Developing Human Brain
Non-Human Primate
Resources
Download colorized and labeled atlas images, histological images, SVG atlas graphics and the associated structure ontology. |
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The data model includes entities from molecular biology, anatomic atlases, laboratory artifacts, experiments, and annotations. |
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Download 3-D expression grid data packaged into a compressed archive file (.zip). |
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The SVG download service returns annotations associated with the specified SectionImage as scalable vector graphics. |
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The image download services serves whole and partial two-dimensional images presented on the Allen Brain Atlas Web site. |
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Download a hierarchical XML or JSON document containing each of the Structures in the requested StructureGraph. |
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Commonly requested queries for experiment metadata. |
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Image synchronization services based on the image alignment results. |
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Gene expression and projection statistics. |
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An HTTP service designed along RESTful principles to allow access to data in the Allen Institute API. |
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Search expert annotations of the Developing Mouse Brain Atlas' ISH data. |
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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:
- 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:
- RESTful Model Access (RMA) for searching and retrieving data in JSON, XML and CSV
- SectionImage, AtlasImage, and ProjectionImage download services for whole or partial images
- NeuroBlast Service for finding genes with a similar spatial expression profile to a seed gene when compared over a user-specified domain
- Differential Search Service for finding genes with higher expression in 1..n structures when compared to another 1..n structures
- Image-to-Image Synchronization Service uses alignment results to find corresponding position between SectionDataSets, the 3-D reference model and structures
- Structure Graph Download Service for downloading anatomic structure ontologies
- 3-D Expression Grid Data Service for a 3-D gene expression summary re-sampled to a canonical reference space