Use with different atlases

[mvesser]

Hi,
I notice a version of this question was already asked in 2019 but I'm wondering if anyone has made any further progress since then. I'm interested in using this tool to analyze some rat histology slices that I have and identify them to a location on a rat atlas. I have a rat atlas as a volumetric file (nifty/.nii); do you know of a way that I could get SHARP-Track to work with this instead of the Allen CCF mouse brain? Or, alternatively, a rat atlas that's already in a good format for this?
Thanks

[philshams]

Hi, I'm not personally aware of any progress on this. The Allen Institute's mouse atlas is in this form:

1. 3D (averaged) image of the mouse brain. This is a 1320x800x1140 array, where each element corresponds to the brightness of the voxel. (The exact size of the array will likely be different for the rat atlas, of course)
2. 3D array of the exact same size, but instead of brightness, each element is a number-identifier. This number can be searched in a lookup to find the identity of the brain region at that particular voxel.
3. A lookup table connecting number-identifiers with brain regions.

Would it be possible to create these three things from what you have? If so, SHARP-Track should be able to work with your data.