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):
| Atlas ID | … | Atlas Name | Image Type | Ontology | StructureGraph ID | GraphicGroupLabels |
|---|---|---|---|---|---|---|
| 602630314 |  |
“Adult Mouse, 3D Coronal” | “Atlas - Adult Mouse” | “Mouse Brain Atlas” | 1 | [28] |
| 1 |  |
“Mouse, P56, Coronal” | “Atlas - Adult Mouse” | “Mouse Brain Atlas” | 1 | [28,159226751] |
| 2 |  |
“Mouse, P56, Sagittal” | “Atlas - Adult Mouse” | “Mouse Brain Atlas” | 1 | [28,159226751] |
| 181276165 |  |
“Developing Mouse, P56” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32,167675952] |
| 181276164 |  |
“Developing Mouse, P14” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32] |
| 181276162 |  |
“Developing Mouse, P4” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32] |
| 181276160 |  |
“Developing Mouse, E18.5” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32] |
| 181276151 |  |
“Developing Mouse, E15.5” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32] |
| 181276130 |  |
“Developing Mouse, E13.5” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32] |
| 181275741 |  |
“Developing Mouse, E11.5” | “Atlas - Developing Mouse” | “Developing Mouse Brain Atlas” | 17 | [32,126768961] |
| 138322605 |  |
“Human, 34 years, Cortex - Gyral” | “Atlas - Developing Human” | “Developing Human Brain Atlas” | 16 | [31,113753815,113753816,141667008] |
| 265297126 |  |
“Human, 34 years, Cortex - Mod. Brodmann” | “Atlas - Developing Human Brodmann” | “Developing Human Brain Atlas” | 16 | [31,113753816,141667008,265297118] |
| 3 |  |
“Human, 21 pcw” | “Atlas - Developing Human” | “Developing Human Brain Atlas” | 16 | [31,113753816,141667008] |
| 287730656 |  |
“Human, 21 pcw - Brainstem” | “Atlas - Developing Human” | “Developing Human Brain Atlas” | 16 | [31,141667008] |
| 138322603 |  |
“Human, 15 pcw” | “Atlas - Developing Human” | “Developing Human Brain Atlas” | 16 | [31,141667008] |
| 265297125 |  |
"Human Brain Atlas Guide " | “Atlas - Human” | “Human Brain Atlas” | 10 | [265297119,266932194,266932196,266932197] |
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:
| Ontology ID | Ontology Name | StructureGraph ID | Uses |
|---|---|---|---|
| 1 | “Mouse Brain Atlas” | 1 | Mouse Brain, Mouse Connectivity Reference Atlases, Brain Explorer, AGEA, Informatics quantification of ISH data, Informatics quantification of projection data, Search services |
| 12 | “Developing Mouse Brain Atlas” | 17 | Developing Mouse Brain, Reference Atlases, Brain Explorer, AGEA, Informatics quantification of ISH data, Search services |
| 7 | “Human Brain Atlas” | 10 | Human Brain, Annotation of microarray Sampling Sites, Brain Explorer, Heatmap and search services, “Hot spot” annotation of ISH data, Human Brain Atlas Guide |
| 11 | “Developing Human Brain Atlas” | 16 | Developing Human Brain, Reference Atlases, Annotation of RNA-sequencing and microarray Sampling Sites, Heatmap and search services, “Hot spot” annotation of ISH data |
| 4 | “Non-Human Primate Brain Atlas” | 8 | Non-Human Primate, Annotation of microarray Sampling Sites, Heatmap and search services, “Hot spot” annotation of ISH data |
| 10 | “Glioblastoma” | 15 | Glioblastoma, Human Glioblastoma RNASeq, Annotation of tumor features on H&E and ISH data, Annotation of RNA-Seq sampling sites |
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