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 j

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.