I am looking for a plugin or solution to align a z-stack of images across time. Normally, I use StackReg on a z-projection and that works great. In this case however, I want to have all slices of the stack registered across time (the image is eventually going to Imaris, which uses the z-stack information). For example, I have a 13 z-step by 30 timepoint z-stack, where I want to correct for drift across time in all slices. Doing stackreg on each z-slice independently probably isn’t a great idea as there won’t be much structural information to use toward the edges of the stack. Note that I don’t need something to align slices in z at one time point; essentially what I want is to apply StackReg of the z-projection to each z-level of the stack across time (or some better computational method).Some things I’ve come across so far include:
-correct_3d_drift plugin, which I think theoretically does what I want, though the results on my stack weren’t great for xy drift correction. I may have included too many of the edge z-slices.
-multistackreg. I think this will do what I want as it’s essentially stackreg that saves out the transform, so I could write a macro that uses MultiStackReg on the z-projection to get the transform, then makes substacks at each z-slice of the original z-stack, applies the transform to each one, then re-stacks the slices.
-Poorman3DReg, looks like an old plugin and when I tried it it wouldn’t work on my computer, but theoretically this does what I’ve described with StackReg + apply to each z level.
Any input for existing solutions that would work better (or faster!) than this would be appreciated. Thanks.