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DOWNLOADING AN IMAGE

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Download whole or partial two-dimensional images from the Allen Institute with the Image and AtlasImage Download Services.

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The Image download service serves whole and partial two-dimensional images presented on the Allen Brain Atlas Web site. Some images can be downloaded with expression or projection data. Glioblastoma images' color block and boundary data can also be downloaded.

Prototype

No Format

http://api.brain-map.org/api/v2/image_download/[SubImage.id]?downsample=[#]&quality=[#]&view=[expression|projection|tumor_feature_annotation|tumor_feature_boundary]

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Download a downsampled SectionImage of one sagittal section from the Mouse Brain Pdyn SectionDataSet:

No Format

http://api.brain-map.org/api/v2/image_download/69750516?downsample=4

Download a downsampled expression mask for a SectionImage of one sagittal section from the Mouse Brain Pdyn SectionDataSet:

No Format

http://api.brain-map.org/api/v2/image_download/69750516?downsample=4&view=expression

Download a region of interest at full resolution from the same sagittal SectionImage:

No Format

http://api.brain-map.org/api/v2/image_download/69750516?left=6174&top=2282&width=1000&height=1000

Download SectionImage 71592261 downsampled 3 times with 50% image quality:

No Format

http://api.brain-map.org/api/v2/image_download/71592261&downsample=3&quality=50

Download the downsampled SectionImage 126862583 with projection:

Code Block

http://api.brain-map.org/api/v2/projection_image_download/126862583?downsample=4&view=projection

Determine the default range values for a Mouse Connectivity Projection experiment by referring to its associated Equalization model (red_lower=0, red_upper=923, green_lower=0, green_upper=987, blue_lower=0, blue_upper=4095), then download one of its downsampled SectionImages:

No Format

http://api.brain-map.org/api/v2/data/SectionDataSet/100141599.xml?include=equalization,section_images

http://api.brain-map.org/api/v2/image_download/102146167?range=0,923,0,987,0,4095&downsample=4

Download the color block or color boundary image designating tissue features of Glioblastoma tumor:

No Format

http://api.brain-map.org/api/v2/image_download/311175878?downsample=4&view=tumor_feature_annotation

http://api.brain-map.org/api/v2/image_download/311174547?downsample=4&view=tumor_feature_boundary

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    First, search for the closest NISSL image:

No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionImage,
rma::criteria,[id$eq71592261],
rma::include,associates(data_set(treatments[name$eq'NISSL']))

    Second, download the NISSL image using the Associate.id:

No Format

http://api.brain-map.org/api/v2/image_download/71592412

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

No Format

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$eq'sagittal'],genes[acronym$eq'Adora2a']

    Second, retrieve a list of all images for one of the experiments (SectionImages):

No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::SectionImage,
rma::criteria,[data_set_id$eq70813257]

    Finally, iterate through the list of images and call the SectionImage Download Service with their IDs:

No Format

http://api.brain-map.org/api/v2/image_download/70679088

Parameters

filename

Integer

SectionImage.id identifying the image to download.

view

String (optional)

  • Set the value to expression to retrieve the specified SectionImage's expression mask image.
  • Set the value to tumor_feature_annotation to retrieve the color block image for a Glioblastoma SectionImage.
  • Set the value to tumor_feature_boundary to retrieve the color boundary image for a Glioblastoma SectionImage.
  • Set the value to projection to retrieve the specified SectionImage with projection.

downsample

Integer (optional)

The number of times to downsample the original image. For example, 'downsample=1' halves the number of pixels of the original image both horizontally and vertically. Specifying 'downsample=2' quarters the height and width values.

quality

Integer (optional)

The jpeg quality of the returned image. This must be an integer from 0, for the lowest quality, up to as high as 100. If it is not specified, it defaults to the highest quality.

left

Integer (optional)

Index of the leftmost column of the region of interest, specified in full-resolution (largest tier) pixel coordinates. SectionImage.x is the default value.

top

Integer (optional)

Index of the topmost row of the region of interest, specified in full-resolution (largest tier) pixel coordinates. SectionImage.y is the default value.

width

Integer (optional)

Number of columns in the output image, specified in tier-resolution (desired tier) pixel coordinates. SectionImage.width is the default value. It is automatically adjusted when downsampled.

height

Integer (optional)

Number of rows in the output image, specified in tier-resolution (desired tier) pixel coordinates. SectionImage.height is the default value. It is automatically adjusted when downsampled.

range

Array (optional)

Filter to specify the RGB channels. The range parameter consists of 6 comma delimited integers that define the lower (0) and upper (255) bound for each channel in red-green-blue order (i.e. "range=0,1500,0,1000,0,4095"). The default range values can be determined by referring to the following fields on the Equalization model associated with the SectionDataSet: red_lower, red_uppper, green_lower, green_upper, blue_lower, blue_upper. For more information, see the "Image Controls" section of the Allen Mouse Brain Connectivity Atlas: Projection Dataset help topic.

Returns

A jpeg file of the requested image.

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The AtlasImage download service serves whole and partial two-dimensional images with annotations presented on the Allen Brain Atlas Web site.

Prototype

No Format

http://api.brain-map.org/api/v2/atlas_image_download/[AtlasImage.id]?downsample=[#]&quality=[#]&annotation=[true|false]&atlas=[#]

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Download the downsampled AtlasImage 100883869 with annotations:

No Format

http://api.brain-map.org/api/v2/atlas_image_download/100883869?downsample=4&annotation=true

Request P56 Mouse Brain Atlas' annotations:

No Format

http://api.brain-map.org/api/v2/atlas_image_download/100883869?downsample=4&annotation=true&atlas=2

Request P56 Developing Mouse Brain Atlas' annotations:

No Format

http://api.brain-map.org/api/v2/atlas_image_download/100883869?downsample=4&annotation=true&atlas=181276165

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    Second, retrieve a list of the Mouse, P56 Sagittal Atlas' Nissl images (Atlas id=2):

No Format

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Atlas,
rma::criteria,[id$eq2],
rma::include,atlas_data_sets(atlas_images(treatments))

    Finally, iterate through the list of AtlasImages and call the AtlasImage Download Service to download the Nissl images:

No Format

http://api.brain-map.org/api/v2/atlas_image_download/100883771

Parameters

filename

Integer

AtlasImage.id identifying the image to download.

annotation

Boolean (optional)

Set the value to true to retrieve the specified AtlasImage with annotations.

atlas

Integer (optional)

Specify the desired Atlas.ID for the annotations. The P56 Adult Mouse Brain Atlas and Developing Mouse Brain Atlas share a common AtlasDataSet, so the Atlas.ID should be specified. 

downsample

Integer (optional)

The number of times to downsample the original image. For example, 'downsample=1' halves the number of pixels of the original image both horizontally and vertically. Specifying 'downsample=2' quarters the height and width values.

quality

Integer (optional)

The jpeg quality of the returned image. This must be an integer from 0, for the lowest quality, up to as high as 100. If it is not specified, it defaults to the highest quality.

left

Integer (optional)

Index of the leftmost column of the region of interest, specified in full-resolution (largest tier) pixel coordinates. SectionImage.x is the default value.

top

Integer (optional)

Index of the topmost row of the region of interest, specified in full-resolution (largest tier) pixel coordinates. SectionImage.y is the default value.

width

Integer (optional)

Number of columns in the output image, specified in tier-resolution (desired tier) pixel coordinates. SectionImage.width is the default value. It is automatically adjusted when downsampled.

height

Integer (optional)

Number of rows in the output image, specified in tier-resolution (desired tier) pixel coordinates. SectionImage.height is the default value. It is automatically adjusted when downsampled.

Returns

A jpeg file of the requested image.