Affine alignment on just a few slices

Hi all,

So, I have a stack of about 10,000 EM images that need to be registered. A SIFT align with just translations performs quite well, except on just a few (~25) slices which to me look like they need an affine transformation to be lined up with the rest of the stack. (I’m using FIJI but open to other tools as well.)

Maybe it’s silly, but I feel like it’s overkill to run an affine alignment on the whole stack – ideally, I’d like to align most of the stack with translations, and just special case these few slices to be aligned with an affine transformation.

I’m thinking about just manually taking those slices and re-aligning them by affine transform with the translation-aligned version of the stack, but I think this could cause continuity errors and it’s also a bit of a pain. Is there a better way to attack this problem?