search

PrincetonUniversity / BrainPipe

GNU General Public License v3.0
18 stars 9 forks source link

Transform data to allen space #4

Open PolarBean opened 2 months ago

PolarBean commented 2 months ago

Hi, Is it possible to transform data which is registered to the Princeton Mouse Atlas into the Allen space? Thanks in advance.

tjp7rr commented 2 months ago

Yes, you could use elastix (https://elastix.dev/) by itself or via brainpipe to compute the transformation. Attached are the two step affine, then bpsline transformation files between going from Allen to Princeton Mouse Atlas spaces. I would ensure you are applying the transform in the correct direction. Sometimes it's best to do the registration yourself in both directions as you'll have more control.

ABA_to_PMA_Elastix_TransformParameters.0.txt ABA_to_PMA_Elastix_TransformParameters.1.txt

PolarBean commented 2 months ago

great, thanks! I am building a library to help others easily translate between brain atlases and plan on integrating the Princeton Atlas once I've replicated the transform. Thanks again for your help.

https://github.com/Neural-Systems-at-UIO/CCF_translator