Atoms are almost entirely empty space. And electrons themselves don't really occupy a specific dot in space, they're more of a blur that fuzzes out in a "large" region of space around the nucleus. So what's shown here is most likely a visualization of the area that the electrons occupy.
But I'm no physicist and i didn't read the article, so take this with a big grain of salt
EDIT
Another person here said the round things are actually the nuclei, and they sound like they know what they're talking about. So while the informational stuff i said is right, it might not actually be a description of the image we're looking at
