Can someone explain what the various parts of this picture of atoms are?

They say it's a picture of atoms, but what are the atoms: the glowing yellow balls or the entire meatball including the darker red? If it's the meatballs, then why do some have apparently two nuclei?

Here's the public press release: https://news.cornell.edu/stories/2021/05/cornell-researchers-see-atoms-record-resolution

Here's the actual scientific article: https://www.science.org/doi/10.1126/science.abg2533