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

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

Gene Expression Resources

Primary data, experiment metadata, and annotations for genome-wide atlases and studies involving gene expression include:

  • High resolution ISH and FISH images
  • Microarray and exon microarray summarized to exons and genes
  • RNA sequencing summarized to exons and genes
  • Grid-level gene expression values registered to reference atlas space
  • Manual annotations indicating gene expression characteristics
Anatomical Resources
  • High resolution Nissl and Ache images
  • Samples mapped to MNI space
  • Reference atlas ontologies, structure boundary drawings, and 3-D models
  • MRI and DTI files
Connectivity Resources
  • High resolution 2-D projectivity images
  • BDA vs. rAAV comparison
  • Transgenic characterization
Services
  • Image-to-Image Synchronization
  • Correlation
  • Differential Expression
  • NeuroBlast Search
  • Anatomic Gene Expression Atlas (AGEA)
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 .

Example Applications

The example applications demonstrate several features of the API for the following studies:

  • Mouse Brain
  • Human Brain Microarray
  • Developing Mouse Brain

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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
    
    
    h6. Studies
    
    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]
    
    h6. Gene Expression Resources
    
    Primary data, experiment metadata, and annotations for genome-wide atlases and studies involving gene expression include:
    
    * High resolution ISH and FISH images
    * Microarray and exon microarray summarized to exons and genes
    * RNA sequencing summarized to exons and genes
    * Grid-level gene expression values registered to reference atlas space
    * Manual annotations indicating gene expression characteristics
    
    h6. Anatomical Resources
    
    * High resolution Nissl and Ache images
    * Samples mapped to MNI space
    * Reference atlas ontologies, structure boundary drawings, and 3-D models
    * MRI and DTI files
    
    h6. Connectivity Resources
    
    * High resolution 2-D projectivity images
    * BDA vs. rAAV comparison
    * Transgenic characterization
    
    h6. Services
    
    * Image-to-Image Synchronization
    * Correlation
    * Differential Expression
    * NeuroBlast Search
    * Anatomic Gene Expression Atlas (AGEA)
    
    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://api.brain-map.org/doc/ExampleIndex.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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