How can I register/align shifted image stacks?

It’s a whole suite of tools. You asked about the displacement field, which is implemented and documented in RegisterDeformation. The other packages are built on top of that, and optimize the displacement field to approximately minimize the mean-square mismatch. The order in this list is roughly the “stacking order”: RegisterOptimize is the top-level package which minimizes the mismatch as a function of the displacement field.

Just step your way through the demo in the BlockRegistration documentation, I think it will become far clearer then.

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