there are types of microscopes which can resolve even individual atoms.
In order to "see" something so inconceivably small, I have the imagination that we humans would have to shrink ourselves to the size of an entity that fits on the tip of a pin a million times over. What kind of device can do that? What idea do you have of an atom?
For me, it can only be a linguistic one, a translation of what we are able to understand with our senses. The science which deals with the microscopical realm has developed since the modern age into an abstract science. I experience that it argues reductionistically, speaks in metaphors, because the observable space remains very restricted, if not closed.