Atomic bond types discernible in images

Isn't all solid matter surface form just the high probability areas of the electron clouds?

The tip atom would be oxygen, as CO adsorbs to metal surfaces via carbon-metal bonding.

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.

I believe the red areas are more or less "empty" space. The edges are bonds and the nodes would be the nucleus.

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.