Image parameters for Nissl sections used for the atlases

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1

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).

2

@Deanna

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 (brain-map.org).

3

The first. The interactive atlas viewer, as well as these resources:
http://developingmouse.brain-map.org/static/atlas
Thanks.

4

Take a look at the API documentation page
Atlas Drawings and Ontologies - Allen Brain Atlas API (brain-map.org)

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

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]

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

http://api.brain-map.org/api/v2/data/query.xml?criteria=
model::Atlas
,
rma::criteria,
[id$eq1],
rma::include,
atlas_data_sets

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

5

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?
Thanks.

6

Since these are Nissl images and not Atlas we need to use a different query for SectionDataSet

http://api.brain-map.org/api/v2/data/query.xml?criteria=model::SectionDataSet,rma::criteria,[id$eq100098039],rma::include,section_images

Reference: Downloading an Image - Allen Brain Atlas API (brain-map.org)

7

Thank you!