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 PrScO3, 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.
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 ScO2 that is arranged as O-Sc-O. The fainter single spots are the other O nuclei that fill out the PrScO3 structure.