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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
The brighter spots are the nuclei of the Pr, Sc, and O atoms, which are reflecting the electrons of the scanning beams (because they're comparatively much heavier).
The space in between the nuclei is where the electrons from all of the atoms are. Because the atoms are bound as PrScO~3~, the electrons are shared and not really part of any one particular atom or other.
Technically all of it is "the atoms" because the electrons are part of the structure as much as the protons and neutrons.
This diagram in the article is helpful:
The drawing in the lower right shows how the atoms are arranged. The double spots are the nuclei of two Pr atoms very close together. The slightly fainter, elongated spots are actually ScO~2~ that is arranged as O-Sc-O. The fainter single spots are the other O nuclei that fill out the PrScO~3~ structure.
That is only sort of true - this image is not made of electrons reflected by the nuclei. These are results from TEM imaging, so Transmission Electron Microscopy. The electron detector is placed behind the sample.
What you are describing is SEM - Scanning Electron Microscopy - in that case, the detector can be placed above the sample, for example (but not limited to) circularly around the beam to measure the backscattered electrons
In TEM the samples are cut into very thin slices (in the picture you posted it is said to be between 0.8nm - 30nm) and the crystal lattice acts as a diffraction grating for the electron beam. The diffraction pattern can be then used to reconstruct the crystal lattice structure.
So the spots are the nuclei and not the electron cloud? Wow! This is waaaaay smaller imaging than i was thinking it was!
The yellow areas are the 'shades' of the nuclei, but do not reflect their actual size. The lattice constant of the crystal according to the figure is 59 pm = 59 e-12 m, which is the horizontal or vertical distance you see between two of the Pr couples. The actual size of a nucleus would be of order ~ 10 fm = ~ 10 e-15 m.