These aren’t plaques in the figure, it’s an experiment to show autophagy induction. The structure in panel G’’ in the figure that also appears as a red dot in the colour images, is associated with autophagy, a process of removing and recycling cell waste. The red shows where one of the autophagy proteins is. Here, an Endophilin A1 mutant is used that doesn’t need a calcium signal to turn it on. So they’ve shown that this ‘on’ state makes autophagic structures form.

Later in the paper they show that a different mutation of Endophilin A1 associated with Parkinson’s is an ‘off’ state mutation, and inhibits autophagy. So you’d see fewer of those autophagic structures, and since autophagy helps clear the stuff that causes plaques, this PD associated mutant could lead to plaque formation.

alpha-synuclein is believes to be part of the mechanism of pathology in PD. Beta-amyloid plaques is associated with Alzheimer's, but so is tau.