Shinestacker for focus stacking: Hurray!!

 This is the first image I processed using Shinestacker.  It's a remarkable and technically advanced piece of open source software.    This software is beyond my skill level, but works incredibly well with defaults.  

 

Sufficeth to say it was very simple, after a somewhat convoluted---but not difficult---installation on CachyOS, to process this stack of 40 images.  I have a CPU with 27 or 28 processors; and this software even took advantage of my aging Nvidia GTX-1050 video card with a mere 3GB of video ram.  25X objective, mounted in UV-curing glass glue from a hardware store.  Too bad about the detritus.  Processing took a few seconds.  

 

Ossicles of sea cucumber Holothuria atra, mounted in UV-curing glass glue.

 UPDATE (2026 May 18)

  Updated Shinestacker this week,  Incredibly, it can accept Canon EOS *.cr3 raw files.  Neither Fiji (unless by trickery), or Helicon Focus can open these files.  The developer of Shinestacker stated that tiff files work better on SS, which apparentely was a major impetus for accepting cr3 files.  It works well, but required more resources.  My 26 core intel i7 cpu, with 32G of ram, and 128G of swap space, works well; shinestacker utilizes all cores, I believe.

 

Some images have shown blotchiness.  In one case, even using .cr3 files did not solve this.  These are microscope images, which may be a factor.  The focus stack of images of ossicles, above, used very few shots, a rather coarse Z sampling.  

The ease of using this software is a huge upside.   Some experimentation will be required to figure out advanced settings, ie, what kind of images do well with pyramid stacking, and which work best with depth masks.  I had some problems on some images; it seemed, perhaps, that turning off balancing may have helped.  These images are fairly consistent in illumination.

 

Hurray for  this software!!! 

 

 

Actually, Wayland is usable. I am leaning on Sway on my laptop.

 Just to bring the conversation up to date.  It is easier to use sway on this laptop---a Lenovo X1 Carbon gen. 9---because it has a HiDPI display.  I3/X11 are problematic, requiring numerous configuration tweaks.  Hyprland is easier, but less compatible.  

 

My personal customizations for i3 are not completely compatible with Sway.  For one thing, I have adopted dropdown windows for a number of applications on i3, which is sometimes problematic, but usually works.  Kitty works ok in this way on Sway.  Emacs, not so much.  The following applications have bindings in my i3 configuration, and work well: orage (calendar); xephem; R).  Emacs is ok, but tricky.  Kitty too can be tricky.  This manner of using i3wm is fantastic for my workflow.  I also have had kmag on a dropdown keybinding, which is useful.   

 I have, as of May, 2026, not made much effort to get all of these utilities working on Sway.  Dropbox's hot icon does not work on i3, so far, for me; on Sway it does work with swaybar, an excellent bar.  

 Tiling WMs work for me.  I3 is easy to configure.  Sway can run ok using the i3 config files, except for edge cases.

 

 

 

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