I've been aware of atomic force microscopy for a while now, but it never ceases to amaze me. These pictures are incredible compared to the ones from some of the earlier experiments.
Am I interpreting these images correctly that the atoms themselves aren't truly visible and the hexagonal lines trace the outline of the bonds between them? (in which case the atoms would be located at the intersections of those lines). Which would be interesting if that were the case, because in some of those images there are curved "bubbles" that bend outwards to locations where there should be additional atoms but nothing is actually there. It would be even more interesting to see a new atom or molecule fall into that slot and watch how the structure changes as the energy levels rearrange themselves.
One of the things they are trying to investigate is why those bonds aren't always straight lines. Fascinating stuff. There is the world we see, and then the strange, alien world that exists at the molecular/atomic/quantum level.
Hate to pitch a total crackpot theory, but WSM (Wave Structure of Matter) would postulate that the funky shape of those bounds has to do with the enclosed regions between them, the blue (or red) bubbles outlined by the bonds. In WSM theory, covalent bonds are formed by "shade cones," fields of force radiating from atomic nuclei like little tractor beams that have the ability to capture electrons. The path of those cones can actually be deformed by regions of higher energy density (the colored regions) since in WSM, it's the incoming energy of radiation pressure that forms those force fields in the first place.