Downloading and Displaying SVG

filename	Integer	SectionImage.id identifying the SVG to download.
groups	list of Group.id (optional)	Filter the Groups to include in the SVG

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API

Atlas Drawing and Ontologies

Explore how brain atlases are created and organized through ontologies. Learn about anatomical structure hierarchies and classification systems.

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]

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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

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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]

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“Atlas - Developing Human” images for the “Human, 34 years, Cortex - Gyral” atlas

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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]

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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

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

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View the vector graphics for one “Human, 34 years, Cortex - Gyral” atlas image

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

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Download the vector graphics for one “Human, 34 years, Cortex - Gyral” atlas image

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

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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

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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]

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Download the “Mouse Brain Atlas” ontology as a hierarchically structured json file

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

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Download the “Developing Human Brain Atlas” ontology as a hierarchically structured json file

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

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API

Image-to-Image Synchronization

Master image-to-image synchronization for comparing brain atlas data. Navigate corresponding sections across multiple datasets simultaneously.

The following set of image synchronization services uses the image alignment results from the Informatics Data Processing Pipeline. Note: all locations on SectionImages are reported in pixel coordinates and all locations in 3-D ReferenceSpaces are reported in microns.

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Image-to_Atlas

For a specified Atlas, find the closest annotated SectionImage and (x,y) location as defined by a seed SectionImage and seed (x,y) location.

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Prototype

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http://api.brain-map.org/api/v2/image_to_atlas/[SectionImage.id].[xml|json]?x=[#]&y=[#]&z=[#]&atlas_id=[#]

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Example

For a seed location in SectionImage 68173101, locate the closest image and (x,y) position within the P56 coronal Atlas:

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http://api.brain-map.org/api/v2/image_to_atlas/68173101.xml?x=6208&y=2368&atlas_id=1

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Parameters

filename	Integer	Seed SectionImage for spatial sync.
file extension	String	XML or JSON format is specified as the file extension.
x	Float	x pixel coordinate of the seed location in the seed SectionImage.
y	Float	y pixel coordinate of the seed location in the seed SectionImage.
atlas_id	Integer	Target Atlas for image sync.

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Returns

XML or JSON document containing the following:

section_image_id	Closest annotated SectionImage to the seed SectionImage and pixel location.
section_number	Section number of the closest SectionImage.
x	Closest x pixel coordinate on the closest SectionImage.
y	Closest y pixel coordinate on the closest SectionImage.

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Image-to_Image

For a list of target SectionDataSets, find the closest SectionImage and (x,y) location as defined by a seed SectionImage and seed (x,y) pixel location.

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Prototype

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http://api.brain-map.org/api/v2/image_to_image/[SectionImage.id].[xml|json]?x=[#]&y=[#]&section_data_set_ids=[#,#,#...]

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Example

For seed location in SectionImage 68173101, locate the closest 3-D position in each input SectionDataSet.

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http://api.brain-map.org/api/v2/image_to_image/68173101.xml?x=6208&y=2368&section_data_set_ids=67810540,69782969

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Parameters

filename	Integer	Seed SectionImage for spatial sync.
file extension	String	XML or JSON format is specified as the file extension.
x	Float	x pixel coordinate of the seed location in the seed SectionImage.
y	Float	y pixel coordinate of the seed location in the seed SectionImage.
section_data_set_ids	Array	Comma delimited list of target SectionDataSet IDs for image sync.

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Returns

XML or JSON document containing the following for each SectionDataSet in the section_data_set_ids:

section_image_id	Closest SectionImage to the seed SectionImage and pixel location.
section_number	Section number of the closest SectionImage.
x	Closest x pixel coordinate on the closest SectionImage.
y	Closest y pixel coordinate on the closest SectionImage.

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Image-to-Image 2-D

For a list of target SectionImages, find the closest (x,y) location as defined by a seed SectionImage and seed (x,y) location.

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Prototype

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http://api.brain-map.org/api/v2/image_to_image_2d/[SectionImage.id].[xml|json]?x=[#]&y=[#]&section_image_ids=[#,#,#...]

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Example

For a seed location in SectionImage 68173101, locate the closest 2-D position in each input SectionImage:

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http://api.brain-map.org/api/v2/image_to_image_2d/68173101.xml?x=6208&y=2368&section_image_ids=68173103,68173105,68173107

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Parameters

filename	Integer	Seed SectionImage ID for image sync.
file extension	String	XML or JSON format is specified as the file extension.
x	Float	x pixel coordinate of the seed location in the seed SectionImage.
y	Float	y pixel coordinate of the seed location in the seed SectionImage.
section_image_ids	Array	Comma delimited list of target SectionImage IDs for image sync.

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Returns

XML or JSON document containing the following for each SectionImage in the section_image_ids:

x	Closest x pixel coordinate to the seed location.
y	Closest y pixel coordinate to the seed location.

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Reference-To-Image

For a list of target SectionDataSets, find the closest SectionImage and (x,y) location as defined by a (x,y,z) location in a specified ReferenceSpace.

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Prototype

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http://api.brain-map.org/api/v2/reference_to_image/[ReferenceSpace.id].[xml|json]?x=[#]&y=[#]&z=[#]&section_data_set_ids=[#,#,#...]

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Example

For a 3-D seed location in the P56 ReferenceSpace, locate the closest image and (x,y) location for each input SectionDataSet.

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http://api.brain-map.org/api/v2/reference_to_image/10.xml?x=6085&y=3670&z=4883&section_data_set_ids=68545324,67810540

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Parameters

filename	Integer	Seed ReferenceSpace for spatial sync.
file extension	String	XML or JSON format is specified as the file extension.
x	Float	x coordinate (in microns) of the seed location in the seed ReferenceSpace.
y	Float	y coordinate (in microns) of the seed location in the seed ReferenceSpace.
z	Float	z coordinate (in microns) of the seed location in the seed ReferenceSpace.
section_data_set_ids	Array	Comma delimited list of target SectionDataSets IDs for image sync.

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Returns

XML or JSON document containing the following for each SectionDataSet in the section_data_set_ids:

section_image_id	Closest SectionImage to the seed ReferenceSpace and location.
section_number	Section number of the closest SectionImage.
x	Closest x pixel coordinate to the seed location.
y	Closest y pixel coordinate to the closest SectionImage.

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Image-To-Reference

For a specified SectionImage and (x,y) location, return the (x,y,z) location in the ReferenceSpace of the associated SectionDataSet.

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Prototype

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http://api.brain-map.org/api/v2/image_to_reference/[SectionImage.id].[xml|json]?x=[#]&y=[#]

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Example

For a location in SectionImage 68173101, return the (x,y,z) position in the associated ReferenceSpace.

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http://api.brain-map.org/api/v2/image_to_reference/68173101.xml?x=6208&y=2368

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RMA query to return the associated ReferenceSpace:

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http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SubImage, rma::criteria,[id$eq68173101],
rma::include,data_set, 
rma::options[only$eq'data_sets.id,data_sets.reference_space_id,sub_images.id']

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Parameters

filename	Integer	SectionImage.id.
file extension	String	XML or JSON format is specified as the file extension.
x	Float	x pixel coordinate on the specified SectionImage.
y	Float	y pixel coordinate on the specified SectionImage.

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Returns

XML or JSON document containing the (x,y,z) location in the associated ReferenceSpace.

x	x coordinate (in microns) in the associated ReferenceSpace.
y	y coordinate (in microns) in the associated ReferenceSpace.
z	z coordinate (in microns) in the associated ReferenceSpace.

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Structure-To-Image

For a list of target structures, find the closest SectionImage and (x,y) location as defined by the centroid of each Structure.

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Prototype

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http://api.brain-map.org/api/v2/structure_to_image/[SectionDataSet.id].[xml|json]?structure_ids=[#,#,#...]

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Example

For each Structure in the input list, locate the closest image and (x,y) location in SectionDataSet 68545324:

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http://api.brain-map.org/api/v2/structure_to_image/68545324.xml?structure_ids=315,698,1089,703,477,803,512,549,1097,313,771,354

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Parameters

filename	Integer	ID of the closest SectionImage to the 3-D centroid of the structure.
file extension	String	XML or JSON format is specified as the file extension.
structure_ids	Array	List of target Structures for sync.

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Returns

XML or JSON document containing the following for each Structure in the structure_ids:

section_image_id	Closest SectionImage to the 3-D centroid of the structure.
section_number	Section number of the closest SectionImage.
x	Closest x pixel coordinate of the closest SectionImage.
y	Closest y pixel coordinate of the closest SectionImage.

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API

Downloading 3-D Expression Grid Data

Learn to download 3-D expression grid data as NRRD files. Access voxel-level gene expression values for computational brain analysis.

Downloading 3-D Expression Grid Data

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Download 3-D expression grid data packaged into a compressed archive file (.zip).

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Prototype

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http://api.brain-map.org/grid_data/download/[SectionDataSet.id]&include=[images]

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Examples

Download the 200um density volume for the Mouse Brain Atlas SectionDataSet 69816930:

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http://api.brain-map.org/grid_data/download/69816930

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Download the 200um energy and intensity volumes for Mouse Brain Atlas SectionDataSet 69816930:

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http://api.brain-map.org/grid_data/download/183282970?include=energy,intensity

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Download the energy volume for the Mouse Brain Atlas’ coronal Adora2a experiment.

First, search for relevant experiments’ IDs (SectionDataSets):

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http://api.brain-map.org/api/v2/data/query.xml?criteria= model::SectionDataSet, rma::criteria,[failed$eq'false'],products[abbreviation$eq'Mouse'],plane_of_section[name$eq'coronal'],genes[acronym$eq'Adora2a']

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Then, download the energy volume for each of the experiments’ IDs:

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http://api.brain-map.org/grid_data/download/72109410?include=energy

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Parameters

ID	Integer	ID of the desired SectionDataSet.
include	String (optional)	Explicitly choose the desired image volumes. Valid volumes are energy, density, and intensity. Supply multiple volumes in a comma-delimited list (e.g. “include=energy,density,intensity”). By default, only energy is returned.

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Response

Zip file (.zip) containing a folder filled with the default files (data_set.xml, energy.mhd, energy.raw) or the requested data volumes.

data_set.xml	XML file with details regarding the specimen and images that is only returned if the volumes parameter is null.
energy.mhd	A simple text header file in MetaImage format describing the volume. This file is returned by default if the volumes parameter is null.
energy.raw	A raw uncompressed float (32-bit) little-endian volume representing average expression energy per voxel. A value of “-1” represents no data. This file is returned by default if the volumes parameter is null.
density.mhd	A simple text header file in MetaImage format describing the volume.
density.raw	A raw uncompressed float (32-bit) little-endian volume representing average expression density per voxel. A value of “-1” represents no data.
intensity.mhd	A simple text header file in MetaImage format describing the volume.
intensity.raw	A raw uncompressed float (32-bit) little-endian volume representing average expression intensity per voxel. A value of “-1” represents no data.
injection.mhd	A simple text header file in MetaImage format describing the volume.
injection.raw	A raw uncompressed float (32-bit) little-endian volume representing the proportion of pixels within each voxel that were within the manually annotated injection site.

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Downloading 3-D Projection Grid Data

Download 3-D projection grid data packaged into a compressed .nrrd image.

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Prototype

http://api.brain-map.org/grid_data/download_file/[SectionDataSet.id]&image=[image]&resolution=[resolution]

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Examples

Download the 100um density volume for the Mouse Connectivity Atlas SectionDataSet 181777177:

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http://api.brain-map.org/grid_data/download_file/181777177

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Download the 25um injection_fraction volume for Mouse Connectivity Atlas SectionDataSet 181777177:

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http://api.brain-map.org/grid_data/download_file/181777177?image=injection_fraction&resolution=25

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Parameters

ID	Integer	ID of the desired SectionDataSet.
image	String (optional)	Explicitly choose the desired image volume. Valid volumes are projection_density, projection_energy, injection_fraction, injection_density, injection_energy, and data_mask.
resolution	Integer (optional)	Available resolutions for projection data are 10, 25, 50, and 100 (in microns).

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Response

The response will be a single 32-big floating point Nrrd image named for the requested image type and resolution. If no image is specified, the density volume is returned. If no resolution is specified, 100um resolution is assumed.

projection_density	Density of projecting signal (number of projecting pixels / volume)
projection_energy	Density of projecting signal multiplied by total signal intensity
injection_fraction	Fraction of pixels belonging to the injection site
injection_density	Density of projecting signal for pixels belonging to the injection site
injection_energy	Injection density multiplied by total signal intensity for pixels belonging to the injection site
data_mask	Binary image where a value of ‘1’ indicates that greater than 50% of a grid voxel contains valid data.

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