Register Virtual Stack Slices (real) user manual


Anyone knows where to find explanations of what the various options of Register Virtual Stack Slices plugin do? The “user manual” in Register Virtual Stack Slices - ImageJ is not helpful at all. In particular, I would be interested in understanding which option to pick for feature extraction model and registration model.

I find this a general issue with ImageJ documentation.


Can you clarify: are you unsure about the terms Rigid, Similarity, Affine etc., or would you like to know why you have to choose two (possibly different) models for feature extraction and for registration?

Thanks for asking.

As a biologist, I do not have the background to know which transformation to use, what I know is what I want to do with my image dataset. Similarity and Affine are synonyms to me, for example. Even worse, the tens of parameters to pick.

  1. How should they be tied to image size? If I have a 10k by 10k pixel image of a high res tissue section, and need registration at the cell level, I assume those parameters will need to be different from a 100x100 pixel image, at same res.

  2. What is the unit of measure of the parameters? Pixels? Pixel square? Microns? For example, max image size parameter seems something that could be pixel square, is it?

Hope this helps seeing the manuals issue from a different perspective!