This package is similar to RegisterWorkerApertures, whose documentation you should consult for an overview. This package differs in that it is targeted at "whole experiment" rather than "stack-by-stack" registration. It writes the mismatch data to disk, and then RegisterOptimize is used to optimize a time-series of deformations.
However, because the temporal regularization enforces smoothness, and many real-world data sets have discontinuous movements, this approach is not currently recommended.