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Section
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:API] !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 !structure_level_expression.png|width=32! [api:Quantified Data by Structures] !voxel_level_expression.png|width=32! [Quantified Data as 3-D Grids|api:Downloading 3-D Expression Grid Data] !search.png|width=32! [Search Services|api:Connected Services and Pipes] !download_image.png|width=32! [Image Download|api:Downloading an Image] !image_sync.png|width=32! [Image Synchronization|api:Image-to-Image Synchronization] !atlas.png|width=32! [api:Atlas Drawings and Ontologies] h5. Documentation | [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: {table:border=0} {tr:valign=top} {td:width=400px} !mouse_brain.png|width=32! *Mouse Brain* !developing_mouse_brain.png|width=32! *Developing Mouse Brain* !human_brain.png|width=32! *Human Brain* {td}{td} !sunburst.png|thumbnail,width=100! {td} {table}

Atlases

Image Added Mouse Brain
Image Added Developing Mouse Brain
Image Added Mouse Connectivity
Image Added Human Brain
Image Added Developing Human Brain
Image Added Non-Human Primate

Resources

Image Added Quantified Data by Structures
Image Added Quantified Data as 3-D Grids
Image Added Search Services
Image Added Image Download
Image Added Image Synchronization
Image Added Atlas Drawings and Ontologies
Image Added Example Applications and Source Code

Documentation
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width800px
Wiki Markup

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 .

Column