Mouse reference atlas areas volume

Technical
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1

Hello,

I am wondering how to access the data of brain areas volumes (or number of cell) for the adult mouse reference atlas ? I would need it to normalize some quantifications I am doing.

Thanks in advance !

2

Hi aldupin,

I think I might have the same Problem. I’m currently using the 25 µm Atlas and was wondering if you figured out how great the different regions are.

Kind Regards!

3

You should be able to calculate them by counting the number of voxels per structure from the 3D reference download. This link should get you started. Even though it is part of the developing mouse brain atlas API, I think it also applies to the main atlas.

This page might also help.

Finally, I put this information together many years ago, so it may or may not still be accurate:

Downloading CCF annotations:

Download and unzip this: http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/P56_Mouse_gridAnnotation.zip

To read in these data in R, use the following:

fn2 = (folder where you unzipped grid annotation data)**
annot = readBin(fn2,what="int",n=159326,size=4)"/energy.raw"), what="double",n=159326,size=4)

I think this is the same as the “template” from here: mouse_connectivity