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This tool was invented in 80's and it is an amazing tool that enables sounding matter in nanoscale! :o Remember that in nanoscale the macroscopic laws don't apply to this order of magnitude. Quantum mechanics rules in this "new" very tiny, tiny world, ;) and common sense is, completely, not welcome in this world. ;)

I wonder if this tool could be used in flies on special structures, exempli gratia in ommatidia, ocelli and so on to discern very peculiar differences.
I mean I think that it is possible to use this microscope to distinguish among different species that are hard to split.