Aligning image stack using MultiStackReg to reference stack

Consider 2 channels of the same set of FOVs.We try to align the second channel’s image stack to the first.Using MultiStackReg translation for this, using ch1 as reference and ch2 aligned to ch1, gives strange output.We do not expect any major changes such as rotation between the 2 image stacks.
Please see reference ch1 image and aligned ouput image of ch2 below.

I’d like to know why there is so much difference in the alignment and what this means.Is it possible to align the ch2 stack using ch1 as reference?
Thanks

@imageproc

I don’t have much experience in using that tool myself… what parameters are you using? Perhaps you need to constrict them a bit?

Have you taken a look at other plugins for aligning stacks in ImageJ? We have a list here: https://imagej.net/Registration

In particular - I’d point you to Linear Stack Alignment with SIFT or Register Virtual Stack Slices.

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