How to translate quickNII coordinate system into distance from bregma?

Technical
1

Hi all,
I am using the QuickNII workflow in order to register mouse brain slices into the Allen CCFv3 mouse brain atlas.

The output from the program is in terms of: (Ox, Oy, Oz,), (Ux, Uy, Uz), (Vx, Vy, Vz), and I would like to transform it into distance from bregma in terms of mm.

I can see that if I will load the registration file (.XML) output again to the QuickNII I can see the values in presentation table. But, since I need it for many brains, it must be automatically - therefore I need to understand how to translate it.

Is there available tool?
Does anyone knows what is the needed calculation?

Thanks in advance,
Sivan

2

Hi @SivanSchwartz,

Have you checked out the related thread from GTMeijer?

How to transform CCF (x, y, z) coordinates into stereotactic coordinates - Technical - Allen Brain Map Community Forum (brain-map.org)

3

How is this relates to the coordinates of QuickNII where there are:

Ox, Oy, Oz, Ux, Uy, Uz, Vx, Vy, Vz

What is the transformation from this to the CCF? maybe this step will be more helpful

Thanks