Image parameters for Nissl sections used for the atlases

I was wondering if it would be possible to share the image headers (size; micron/pixel; etc) for the images of the Nissl stained sections used in the standard adult and developing atlases (shared as .jpg). As important is section thickness and distance between sections. I wanted to use the Cavalieri estimator to assess volume of particular brain regions. The Brain Explorer has not proven useful for this (crashes on opening and does not report volumes).


Just wanted to confirm if you were looking to access (1) the high resolution images and SVG graphic (as you see in Interactive Atlas Viewer :: Atlas Viewer) or (2) as 3D reconstructed volumes (as you see in the upper panels of AGEA :: Allen Brain Atlas: Mouse Brain (

The first. The interactive atlas viewer, as well as these resources:

Take a look at the API documentation page
Atlas Drawings and Ontologies - Allen Brain Atlas API (

In the section “Downloading Atlas Images and Graphics” there is an example query,

For each atlas-image there is data for image-height, image-width, resolution, section-number

This second query provides information about section-thickness, which together with section-number provide you with the spacing between the atlas plates

Refer to the table at the top of the documentation to obtain the id and substitute into the queries above.

OK. This makes sense for the Atlas data for which I can find ID#s, but there are coronal, developmental Nissl series that would like to have:
P7: 100098039
P14: 100014118
P28: 100024848
For which there are no similar ID numbers and I can’t call up data by substituting in the sample query. Is there an alternative query that I can use to find the metadata for these datasets?

Since these are Nissl images and not Atlas we need to use a different query for SectionDataSet,rma::criteria,[id$eq100098039],rma::include,section_images

Reference: Downloading an Image - Allen Brain Atlas API (

Thank you!