Focus Stacking to 2D plot and surface analysis

plot
extended-focus
3d
plugin
imagej
fiji
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#1

Hello colleagues, academics, experts…
Consider I did a depth of field extension, stacking of 50 images into something like the object attached. And I need to do analysis. A couple of questions please:

  1. I found Picolay good and fast, (compared to EPFL Extended Depth of Field in ImageJ which took me at least an hour), which good/fast program do you use?
  2. Once the object image is generated, how may I obtain a general Y function of X, to know the depth (in micrometers) as a function of position on surface? How to automate it and compare in case I have 10 other stacks (objects) to analyse?
  3. Any plugin/program to analyse the surface texture and give values I can plot? What to feed that program (specially if image/data comes from a different software).
  4. Plz let me know if any useful plugins in general for analysis related to any of the above.

Kind regards