It is not very useful to discriminate between "seeing with your eyes" and "seeing with the aid of scientific instruments". Vast amounts of information processing occurs between light landing on your retina and an image forming in your brain, so if you are happy to call looking through glasses, or a microscope, or a telescope, "seeing with your eyes" then I see no reason to make a distinction when the information-carrying particle switches from photons to electrons. Especially since we mostly use digital microscopes etc. these days.