As with OptimumCS-Pro and TrueDoF-Pro, there’s a great deal of lovely optical science behind FocusStacker. And, yet again, you may feel free to ignore it, without fear that your creativity might suffer. If you’re interested, though, here’s the briefest of discussions.
How key outputs are calculated
At its heart, FocusStacker uses the optimisation algorithm originally developed for OptimumCS-Pro, so you may wish to review how that app functions—see OptimumCS-Pro Optical Science. For a full understanding, you will need to consult the references that are cited on that webpage.
In FocusStacker, that optimization algorithm is adapted to the taking of multiple shots. You will recall that one of the outputs of OptimumCS-Pro is blur spot diameter, a measure of how sharp the image will be (smaller blurs mean sharper images). In FocusStacker, the user specifies a target blur spot diameter, and the app calculates if a single shot (taken at the optimum settings) will meet that target. If it does not, the app calculates how many shots would be required (and, using OptimumCS-Pro methods, calculates what the optimum settings are for those shots) in order to meet the target.
A simplified, non-technical discussion of what goes on in focus stacking (at the shooting end rather than the image processing end) is presented in the article Focus Stacking in Landscape and Architectural Photography.
Focus Stacker Optical Science