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!!! 

 

UPDATED AGAIN on October 16, 2026:

 

 Shinestacker does a better job when the *cr3 files from my Canon R7 are fed to it directly.  I don't think it does a perfect job at processing, but the stacks look better than when it is fed jpegs.  

 

For my use case (images, primarily, of histology slides) I think Helicon Focus does a better job, but I will continue to use this.  Shinestacker has been improved since I made these posts.  It shows a high level of sophisticated knowledge.