Pixel size of mouse brain images in Allen Brain Atlas

Science
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1

Hello!
I am working on a project related to spatio-molecular methods and for that, I’d need to know the pixel size (i.e. which real world length one pixel represents) of the images present in the URL below:

https://mouse.brain-map.org/experiment/siv?id=100142143&imageId=102162042&imageType=atlas&initImage=atlas&showSubImage=y&contrast=0.5,0.5,0,255,4

(At the top-right, select “Other” instead of “Annotated” and the images are – number 11, 12, 13 and 14 (out of 132 images) whose pixel size is required)

Thanks in advance!

2

Hi Jaspreet,

The real-world scale of each pixel depends on the current zoom. In the bottom left of the viewer is a dynamic scale, and in the bottom center of the viewer is dynamic text which shows the zoom level.

image
image1002×201 55.1 KB

Tyler

3

Thanks for your answer Tyler!

But I wanted to know the pixel size of the “downloaded” images (not the images in the interactive atlas viewer).

An example of a pixel size would be: 1 micron/pixel or 1.5 micron/pixel (or any other similar to these sizes)

4

Hi Jaspreet,

This information is available through the related API, which is documented here:
https://help.brain-map.org/display/mousebrain/API

To retrieve metadata about the image series you asked for, you can use this query. In the XML response, the resolution is reported for each image, with units of microns per pixel.
http://api.brain-map.org/api/v2/data/query.xml?criteria=model::SectionDataSet,rma::criteria,[id$eq100142143],rma::include,section_images

Tyler

5

This is exactly what I required!
Thanks a lot Tyler!