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://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.

Learn about the API with these atlas and resource overviews:

h5. Atlases

!mouse_brain.png|width=32! [Mouse Brain|mousebrain:API]
!developing_mouse_brain.png|width=32! [Developing Mouse Brain|devmouse:API]
!mouse_connectivity.png|width=32! [Mouse Connectivity|mouseconnectivity]
!human_brain.png|width=32! [Human Brain|humanbrain:API]
﻿ !developing_human_brain.png|width=32! [Developing Human Brain|devhumanbrain:API]
!nhp.png|width=32! [Non-Human Primate|nhp:API]

h5. Resources

| [Atlas Drawings and Ontologies |api:Atlas Drawings and Ontologies] | Download colorized and labeled atlas images, histological images, SVG atlas graphics and the associated structure ontology. |
| [api:Data Model] | The data model includes entities from molecular biology, anatomic atlases, laboratory artifacts, experiments, and annotations. |
| [Downloading 3-D Expression Grid Data |api:Downloading 3-D Expression Grid Data] | Download 3-D gene expression summaries re-sampled to a canonical reference space. |
| [Downloading and Displaying SVG |api:Downloading and Displaying SVG] | The SVG download service returns annotations associated with the specified SectionImage as scalable vector graphics. |
| [api: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 |api: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 |api:Example Queries for Experiment Metadata] | Commonly requested queries for experiment metadata. |
| [Image-to-Image Synchronization|api: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 |api:Quantified Data by Structures] | Gene expression and projection statistics. |
| [RESTful Model Access (RMA) |api:RESTful Model Access (RMA)] | RESTful service for searching and retrieving data from the Allen Institute. |
| [api:Searching Annotated SectionDataSets] | Search expert annotations of the Developing Mouse Brain Atlas' ISH data. |
| [Searching a Specimen or Structure Tree |api: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 |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:


!mouse_brain.png|width=32! *Mouse Brain*
!developing_mouse_brain.png|width=32! *Developing Mouse Brain*
!human_brain.png|width=32! *Human Brain*