Compare 2 stacks in different resolution and position

Hello everyone,

I have 2 stacks from microCT (each containing over two thousand images). They present same bone in different resolution (60 and 30um) and position (scans were made at different times). I need to find identical fragments of those. Are there any metods to auto rotate these 2 stacks to same position or determine the rotation angle between them ? Or can I use Registration plugin to compare 2 stacks without need of rotation? I just don’t know if I can do something like this on such big stacks because very often program showed commend „out of memory” when I was performing minor activities.

I’m just beginning my journey with ImageJ so I would really really appreciate any small tips. So sorry if this is an absurd question for you.

Thank you very much in advance for your time & help.