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.
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| 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!!!
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