I was wondering if there is a way to have access to and download horizontal plates of p56 mouse brain.
They are not there in the reference atlas (as far as I know), but in the connectivity atlas - spatial search I see what I need when selecting “horizontal” and moving along the D-V axis in a coronal section.
I hope I have made myself clear…
I would still be curious about how to get them, but I have found a workaround by reslicing in fiji (just in case anyone happens to run through the same issue)
There are not physical ‘horizontal plates’ for the Allen Mouse Brain Reference Atlas. The planes of view are virtually rendered, based on data gathered from coronal images that are averaged to a non-physical reference volume. Refer to the Documentation or technical whitepapers for the Allen Mouse Brain Connectivity Atlas to learn more about the creation of the common coordinate reference atlas framework or CCF. They can be downloaded directly here.
There are some recent publications describing reference atlas utilities from scientific teams not affiliated with the Allen Institute that you may be interested in. A publication by Xiong et al gives some nice use case examples for mapping that can be done without 3D reconstruction. Another publication by Puchades et al. describes the creation of a tool for reference mapping.
The P56 mouse brain is different from the Nissl volume of the Allen Brain Atlas (ABA), but you can slice any slice you want from the Nissl volume of the ABA by first downloading the full volume as instructed from the Allen website (clicking help and then API), and then you can use Fiji or if you are more comfortable with MATLAB, you can download my tool from https://sites.google.com/view/brain-mapping. The link has a Nissl volume saved in the .mat file and a function called “rotate_atlas.m”, the first input is the volume’s variable name, the second input is the rotation angle around the superior-interior axis in degrees, and the third input is the rotation angle around the horizontal axis in degrees.
You can manually find the best rotation angles, or find the best cutting angles using my tool.
So cool to have input directly from the authors of that paper - thanks Jing!
There is another tool that’s been created for use with coronal brain datasets, called SMART, for Semi-manual alignment to reference templates. Learn more about that from the creators on their GitHub page here: https://mjin1812.github.io/SMART/index.html
Nice documentation and demos!