This script creates an animation from ROIs added to the ROI Manager. It uses the associated image plane of each ROI, adjusted spatially such that the first (X, Y) coordinate of each ROI occupies the same location, as a "poor man's" registration technique. Each plane is then assembled into the final movie.
The command is: Plugins > LOCI > Tracking Movie.
To use, open your hyperstack and proceed to mark points using the point tool. Add each point to the ROI Manager by pressing T. Once you have marked all desired points, run the script to generate a movie consisting of all planes marked by those points, coregistered such that the points remain in a fixed location.