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

Data

• High resolution images
• Primary microarray results
• Exon microarray summarized to exons and genes
• Samples mapped to MNI space
• Grid-level gene expression values registered to a reference atlas space
• Reference atlas ontologies and 3-D models

Services

• Image-to-Image Synchronization Service
• Differential Expression Service
• NeuroBlast Search Service

Studies

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

• Mouse Brain
• Developing Mouse Brain
• Mouse Connectivity
• Human Brain
• Developing Human Brain (BrainSpan)

Getting Started

Resources

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:

• 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