Hi @ylcnkzy ,
Thanks for tagging me, 3-D registration is something I would be super interested in as well, for example for the (fixed) cells I was showing in my CZI importer thread. The idea here (if I understood correctly) is to reimage the beads with different tagged markers and then somehow apply 3-D registration to show marker colocalization.
I don’t have stacks to register yet, so thank you for sharing yours!
Just to be sure, are your two timepoints called “original” and “crop”? Are these the two stacks you want to register together?
In my project, I was thinking of determining the centroids of each cells / nuclei and register my stacks based on a deformation field from point cloud 1 to point cloud 2.
PS: 3-D volumetric visualisation is quite hard for microscopy images, possibly due to the presence of background noise which creates some kind of “haze” between the observer and the object being observed… Working out some default values in the “Volume rendering” tab is on my TODO list 
Cheers,
Egor