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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 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 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 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$eqall]
  • "Atlas - Developing Human" images for the "Human, 34 yrs" atlas 
    http://api.brain-map.org/api/v2/data/query.xml?criteria=model::AtlasImage,
rma::criteria,
[annotated$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 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 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 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

11

"Developing Human Brain Atlas"

16

Developing Human Brain

  • Reference Atlases
  • Annotation of Transcriptome 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

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
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