Amazing pictures. But not really sure what I'm looking at here. Are those red spheres meant to be the nuclei of atoms? Are the bright hexagonal lines meant to be the path of electrons? If so, isn't the nucleus much too large in relation to the size of the whole atom? Isn't the proportion of the size of the nucleus to the whole atom akin to the size of a fly in a cathedral?
It's the size of the electrical field of the nucleus, which is about the size of an atom (well, as much as you can define a size for such a thing).
The size you are thinking of is the size of the strong force of the nucleus - a lot smaller.
Atomic particles don't actually have a size - at all. They are entirely empty space. The only "size" you can define for them is the size of the forces that act on them, but then you have to say which force you are talking about.
Electromagnetic force, strong force, weak force, gravity and quark force (gluons), are your choices.
Note that some forces have a distinct "edge", others just peter out - so there is no real good way of defining the size. Gravity is especially interesting, because measured by that force objects are huge. But of course gravity has no edge, so how do you define size?
Probably the best definition for forces without distinct edges is where does the signal from the force get lost among the noise from other objects? (For example, the other atoms in a molecule.) That's what you see here - each atom is visible until the next atom near it is closer.
They say the pictures were taken with a variant of Atomic Force Microscopy, so what you're seeing is most likely a false-colored representation (that is, they just chose some gradient of colors to use instead of grayscale) of the strength of the electrostatic forces acting on the probe tip at each location. So the whole thing is essentially just an image of the electron clouds.
