Instead of writing the counting tool he could have used the Multi-Point Tool in ImageJ [1] [2]. I used it just this morning for counting some embryos I collected.
It sounds like this may have been one of the pieces of software the author intentionally chose not to use:
> There are some clunky old Windows programs, niche scientific tools, and image analysis software that assumes you’re trying to count cells under a microscope...
"Sentences that flashbang people not in biology"