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Comment: Deprecating the SectionImage and ProjectionImage Download Services in favor of a unified Image Download Service.

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

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Image Download Service

The SectionImage 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/section_image_download/[SectionImageSubImage.id]?downsample=[#]&quality=[#]&expressionview=[true|falseexpression|projection|tumor_feature_annotation|tumor_feature_boundary]

Examples

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

No Format
http://api.brain-map.org/api/v2/section_image_download/69750516?downsample=4

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No Format
http://api.brain-map.org/api/v2/section_image_download/69750516?downsample=4&view=expression=true

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

No Format
http://api.brain-map.org/api/v2/section_image_download/69750516?left=6174&top=2282&width=1000&height=1000

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No Format
http://api.brain-map.org/api/v2/section_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/section_image_download/102146167?range=0,923,0,987,0,4095&downsample=4

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No Format
http://api.brain-map.org/api/v2/section_image_download/311175878?downsample=4&view=tumor_feature_annotation=true

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

Find the closest NISSL image to SectionImage 71592261 and download it:

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No Format
http://api.brain-map.org/api/v2/section_image_download/71592412

Download all of the sagittal images in the Mouse Brain Atlas for the gene Adora2a at full resolution.

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No Format
http://api.brain-map.org/api/v2/section_image_download/70679088

Parameters

filename

Integer

SectionImage.id identifying the image to download.

expression view

Boolean String (optional)

  • Set the value to
true
  • expression to retrieve the specified SectionImage's expression mask image.
  • Set the value to tumor_feature_annotation

Boolean (optional)

Set the value
  • to
true to
  • retrieve the color block image for a Glioblastoma SectionImage.
  • Set the value to tumor_feature_boundary

Boolean (optional)

Set the value
  • to
true 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.

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A jpeg file of the requested image.

ProjectionImage Download Service

The Projection Image download service serves whole and partial two-dimensional images with projection data presented on the Allen Brain Atlas Web site.

Prototype

No Format

http://api.brain-map.org/api/v2/projection_image_download/[SectionImage.id]?downsample=[#]&quality=[#]&projection=[true|false]

Example

Download the downsampled SectionImage 126862583 with projection:

No Format

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

Parameters

filename

Integer

SectionImage.id identifying the image to download.

projection

Boolean (optional)

Set the value to true 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.

Returns

A jpeg file of the requested image.