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h1. {color:#807f83}Allen Brain Atlas API{color}

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|http://http://community.brain-map.org/display/hackathon/2012+Allen+Brain+Atlas+Hackathon] materials are made available to the community under the Allen Institute's [Terms of Use|http://www.alleninstitute.org/Media/policies/terms_of_use_content.html] in hopes of facilitating discovery.

h5. Available Data and Services

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

* [Mouse Brain|mousebrain:API]
* [Developing Mouse Brain|devmouse:API]
* [Mouse Connectivity|mouseconnectivity:API]
* [Human Brain|humanbrain:API]
* [Developing Human Brain (BrainSpan)|devhumanbrain:API]
* [Non-Human Primate|nhp:API]

h5. 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 |http://www.brain-map.org].

h6. Example Applications

The [example applications |http://www.brain-map.org/api/1.html] 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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h6. Accessing Data and Services

In the spirit of [REST|http://en.wikipedia.org/wiki/Representational_State_Transfer], 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)|api:RESTful Model Access (RMA)] for searching and retrieving data in JSON, XML and CSV
* [SectionImage, AtlasImage, and ProjectionImage download services|api:Downloading an Image] 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|api:Image-to-Image Synchronization] uses alignment results to find corresponding position between SectionDataSets, the 3-D reference model and structures
* [Structure Graph Download Service|api:Downloading an Ontology's Structure Graph] for downloading anatomic structure ontologies
* [3-D Expression Grid Data Service|api:Downloading 3-D Expression Grid Data] for a 3-D gene expression summary re-sampled to a canonical reference space
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