Sagittal section registration to allen brain atlas

[cobioda]

Hi,

Thank you so much for this very useful tool! I managed to register merfish mouse brain coronal section to the 3D Allen Brain Atlas as described in this tutorial: https://jef.works/STalign/notebooks/merfish-allen3Datlas-alignment.html

I now need to do registration for sagittal sections, could you help point out the changes required?

vol,hdr = nrrd.read('aba_nissl.nrrd')
vol = np.swapaxes(vol, 0.2)

at the beginning of the script does not seem to be enough, and some changes need to be made after.

Thank you very much!

[mmganant]

Hello, apologies for the delayed response! Which step and what is the error you are encountering?