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ATLAS DRAWINGS AND ONTOLOGIES

A set of high resolution digital reference atlases have been created to provide neuroanatomical context to in situ hybridization, microarray, RNA-sequencing and axonal projection data.

From the API, you can:

• Download the colorized and labeled atlas images
• Download atlas graphics in SVG (scalable vector graphics) format
• Download the underlying high resolution histological images
• Download the associated structural ontology

The following Atlases are available through the API (click on Atlas ID to launch the interactive atlas viewer):

Downloading Atlas Images And Graphics

The sections for each Atlas come from a single AtlasDataSet (child class of SectionDataSet) and single Specimen. Typically, only a subset of AtlasImages (child class of SectionImage) is used for the reference atlas. An "annotated" image is identified by the SubImage "annotated" attribute and the corresponding image type. Please note that multiple line example RMA queries on this page use the "+" character to represent spaces for browser compatibility.

Examples:

• "Atlas - Adult Mouse" images for the "Mouse, P56  Coronal" atlas

  http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AtlasImage,
  rma::criteria,
  [annotated$eqtrue],
  atlas_data_set(atlases[id$eq1]),
  alternate_images[image_type$eq'Atlas+-+Adult+Mouse'],
  rma::options[order$eq'sub_images.section_number'][num_rows$eqall]
  

• "Atlas - Developing Human" images for the "Human, 34 years, Cortex - Gyral" atlas

  http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AtlasImage,
  rma::criteria,
  [annotated$eqtrue],
  atlas_data_set(atlases[id$eq138322605]),
  alternate_images[image_type$eq'Atlas+-+Developing+Human'],
  rma::options[order$eq'sub_images.section_number'][num_rows$eqall]
  

Once the annotated images have been identified, the image ID can be used to download the colorized and labeled images using the Image Download Service and the vector graphics using the SVG Download Service.

Examples:

• Download colorized and labeled image for one "Mouse, P56  Coronal" atlas image

  http://api.brain-map.org/api/v2/atlas_image_download/100960248?downsample=4&annotation=true
  

• View the vector graphics for one "Human, 34 years, Cortex - Gyral" atlas image

  http://api.brain-map.org/api/v2/svg/112360908?groups=31,113753815,113753816,141667008&downsample=8
  

• Download the vector graphics for one "Human, 34 years, Cortex - Gyral" atlas image

  http://api.brain-map.org/api/v2/svg_download/112360908?groups=31,113753815,113753816,141667008&downsample=8
  

Structures And Ontologies

In the API, a Structure represents a neuroanatomical region of interest. Structures are grouped into Ontologies and organized in a hierarchy or StructureGraph. With the exception of the "root" structure, each Structure has one parent and denotes a "part-of" relationship. Structures are assigned a color to visually emphasize their hierarchical position in the brain. See the Structure model page for listing of attributes and associations.

Major structural ontologies used in the Allen Brain Atlas Data Portal:

From the API, Structure and Ontology information can be downloaded in various formats.

Examples:

• Download the "Human Brain Atlas" ontology as a CSV file

  http://api.brain-map.org/api/v2/data/query.csv?criteria=model::Structure,
  rma::criteria,[ontology_id$eq7],
  rma::options[order$eq%27structures.graph_order%27][num_rows$eqall]
  

• Download the "Mouse Brain Atlas" ontology as a hierarchically structured json file

  http://api.brain-map.org/api/v2/structure_graph_download/1.json
  

• Download the "Developing Human Brain Atlas" ontology as a hierarchically structured json file

  http://api.brain-map.org/api/v2/structure_graph_download/16.json