Finding Region Areas of ABA Plates

[jdknguyen]

Hi everyone,

I am looking to find the 2D areas of individual brain regions on mouse ABA plates. I believe this can be done via Fiji, but I am wondering if anyone else has found this data anywhere online. Any tips would be greatly appreciated!

Best,
Joseph

[brain]

Hi @jdknguyen,

When you say ‘2D areas’ are you referring to coordinates? Or anatomical tags in planar space? Have you reviewed other threads related to analysis of the reference atlas plates? Here’s one:

Mouse brain reference atlases & mapping your own data

How do I map my data to your reference atlas? We have been hearing this question (or variants of it) for as long as the Allen Mouse Brain Atlas has been online. The short answer is, We do not have a tool for this - but we have provided some resources to help, and many other researchers (and even companies!) have developed their own solutions. Some of those are shared here, and we welcome your additions to this list - either as publications, references to software or comments from other scie…

[jdknguyen]

Hi @brain,

Thank you very much for the response. When I say 2D areas, I mean the area of each brain region delineated for the mouse CCF on an image like the one below:

coronal_pic|430x359

I have looked at many other threads, but haven’t been able to find the data I’m looking for. I am able to find the 3D volume of each ABA brain region, but I am looking for the 2D area of every region on every coronal plate of the atlas at: Atlas Thumbnails :: Allen Brain Atlas: Mouse Brain.

Thanks,
Joseph