I may be over looking some complexity here, but to me the least obvious part in the process is the coloring.
The rest just makes sense. If you want a total average, mix everything together.
To distinguish between neurons and glia, Herculano-
Houzel injected the vials with a chemical dye that
would make all nuclei fluoresce blue under ultraviolet
light, and then with another dye to make the nuclei of
neurons glow red.
You mean that part? It’s about differentiating support infrastructure from the actual cellular operators responsible for cognitive brain function.