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Just for curiosity. We can dive even more to the atomic level with the amazing Scanning tunneling microscopy (STM). Tunneling's concept came through quantum mechanics. Of course, it would be useless for the purposes of ID. :)

I think it is possible to "see" in AFM those peculiar structures with relevant interest for dipterans. At least there are some works like this one - Raman-atomic force microscopy of the ommatidial surfaces of Dipteran compound eyes