Question regarding Section position within specimen in Human Brain

Technical
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#1

Hi,

I would like to use the ISH data from Allen Brain for a project specifically I am looking at CALB1 in the visual cortex.

When I click on a specimen I am taken to the following page for example:
http://human.brain-map.org/ish/specimen/show/706127?gene=789

Towards the bottom of the screen it states “Section position within the specimen” and each of the 10 images in the stamp images have a different position.

My question is, how have these images been ordered? From anterior to posterior?
How are the section number labels been given to the images?

I have searched all the help documents and white papers available on the Allen Brain website and I could not find an answer.

Any help is appreciated!
Thanks!

#2

Hi @lintek ,
Thanks for your question about image sequence. There is a section on this topic in the help section here, and the experimental design is explained in the technical whitepapers. You are correct that precise information on image sequence is not addressed directly; basically the images were processed in ‘series’ which, for human brain specimens, does not always align in a precise anterior-to-posterior configuration as was done for our Mouse Brain Atlas image series. The images are sequentially presented (and numbered), within each subdivided coronal slab. The thumbnail view is to help orient where the sections (hence images) are located in a whole brain specimen, but each subdivided area does not have precise stereotaxic coordinates in reference to the whole brain, but ‘section position within a subspecimen’. The series referred to as ‘within specimen’ means serially within the sub-dissected tissue slab, with every effort made to present images in sequence of section from the caudal/posterior to the rostral/anterior direction. The numbering of the sections reflects that within-subspecimen sequence, and an arbitrary barcode specimen ID (example 706127, for your question on CALB1) lets you view all data generated from a given subdivided tissue piece. We hope this information helps, but recognize that if you are looking for very accurate information about A/P section sequence brain-wide, this reference resource doesn’t provide that level of resolution. It is intended to provide a ‘local snapshot’ of gene expression in a given anatomical region of the brain.

#3

Hi @brain,

Thank you for your reply!
I had thought as much but wanted to double check.

Thanks again.