I had itchy scalp off and on for most of my life and except for two episodes of head lice it seems to have been caused by my being sensitive to gluten - mild form of Dermatitis Herpetaformis. The areas would sometimes become infected. This comes back whenever I eat any gluten but it is a very delayed reaction occuring sometimes weeks after gluten exposure which starts the autoimmune reaction. For me the autoimmune reaction goes on for about 5 months until the antibody producing cells die off and soon after that the itchiness goes away.
I did years of microbiology and don't recall seeing colored bacterial cells unless they were stained so that would be my first thought but then these came form a pure culture so unless the stain was in the media it is not likely. My next thought would be a aerobic spore forming rod. Maybe a yeast but they are rather small if this is high magnification. I did see colored colonies of bacteria from areas where was lots of outside contamination but doubt I would have looked at them microscopicly without staining them.