The image was generated by firing a beam of electrons through the crystal and noting how those electrons got deflected. Bigger atoms like Pr and Sc will deflect electrons a lot more than tiny atoms like O. The nucleus of any atom in the crystal has a positive charge, and the electron has a negative charge. Opposites attract, after all, so an electron gets tugged at by the nucleus of any atom it gets close to, and the bigger the atom, the greater the effect. If an electron zips by a nucleus really closely, it could even be thrown backward.
Praseodymium orthoscandate 3-D structure, with only atoms shown
Overlay of PrScO3 image with predicted crystal structure:
Article from Cornell University here.