Atlas Drawings and Ontologies
A set of high resolution digital reference atlases have been created to provide neuroanatomical context to the in situ hybridization and axonal projection data.
From the API, you can:
- Download the colorized and label 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 view in interactive atlas viewer):
Atlas ID |
|
Atlas Name |
Image Type |
Ontology |
StructureGraph ID |
GraphicGroupLabels |
||||
|---|---|---|---|---|---|---|---|---|---|---|
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[1 |
http://atlas.brain-map.org/atlas?atlas=1] |
!P56_Coronal.png |
width=32! |
"Mouse, P56 Coronal" |
"Atlas - Adult Mouse" |
"Mouse Brain Atlas" |
1 |
[28,159226751] |
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[2 |
http://atlas.brain-map.org/atlas?atlas=2] |
!P56_Sagittal.png |
width=32! |
"Mouse, P56 Sagittal" |
"Atlas - Adult Mouse" |
"Mouse Brain Atlas" |
1 |
[28] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276165 |
http://atlas.brain-map.org/atlas?atlas=181276165] |
!DevMouse_P56.jpg |
width=32! |
"Developing Mouse, P56" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276164 |
http://atlas.brain-map.org/atlas?atlas=181276164] |
!DevMouse_P14.jpg |
width=32! |
"Developing Mouse, P14" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32,167675952] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276162 |
http://atlas.brain-map.org/atlas?atlas=181276162] |
!DevMouse_P4.jpg |
width=32! |
"Developing Mouse, P4" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276160 |
http://atlas.brain-map.org/atlas?atlas=181276160] |
!DevMouse_E18pt5.jpg |
width=32! |
"Developing Mouse, E18.5" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276151 |
http://atlas.brain-map.org/atlas?atlas=181276151] |
!DevMouse_E15pt5.jpg |
width=32! |
"Developing Mouse, E15.5" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181276130 |
http://atlas.brain-map.org/atlas?atlas=181276130] |
!DevMouse_E13pt5.jpg |
width=32! |
"Developing Mouse, E13.5" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32] |
]]></ac:plain-text-body></ac:structured-macro> |
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[181275741 |
http://atlas.brain-map.org/atlas?atlas=181275741] |
!DevMouse_E11pt5.jpg |
width=32! |
"Developing Mouse, E11.5" |
"Atlas - Developing Mouse" |
"Developing Mouse Brain Atlas" |
17 |
[32,126768961] |
]]></ac:plain-text-body></ac:structured-macro> |
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[138322605 |
http://atlas.brain-map.org/atlas?atlas=138322605] |
!Human_34y.jpg |
width=32! |
"Human, 34 yrs" |
"Atlas - Developing Human" |
"Developing Human Brain Atlas" |
17 |
[31,113753815,113753816] |
]]></ac:plain-text-body></ac:structured-macro> |
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[3 |
http://atlas.brain-map.org/atlas?atlas=3] |
!Human_21pcw.jpg |
width=25! |
"Human, 21 pcw" |
"Atlas - Developing Human" |
"Developing Human Brain Atlas" |
16 |
[31] |
]]></ac:plain-text-body></ac:structured-macro> |
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[138322603 |
http://atlas.brain-map.org/atlas?atlas=138322603] |
!Human_15pcw.jpg |
width=20! |
"Human, 15 pcw" |
"Atlas - Developing Human" |
"Developing Human Brain Atlas" |
16 |
[31] |
]]></ac:plain-text-body></ac:structured-macro> |
Downloading Atlas Images and Graphics
The sections for each Atlas comes 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.
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$eqall]
- "Atlas - Developing Human" images for the "Human, 34 yrs" atlas
http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AtlasImage, rma::criteria, [annotated$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 label images using the Image Download Service and the vector graphics using the SVG Download Service.
Examples:
- Download colorized and label 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 yrs" atlas image
http://api.brain-map.org/api/v2/svg/112360908?groups=31,113753815,113753816&downsample=8
- Download the vector graphics for one "Human, 34 yrs" atlas image
http://api.brain-map.org/api/v2/svg_download/112360908?groups=31,113753815,113753816&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 using in the Allen Brain Atlas Data Portal: