Biomolecules assemble into membraneless structures called biomolecular condensates via phase separation. Little is known how condensates behave within a unique physicochemical environment in the cell: the mitochondrion. Here, we develop quantitative image analysis pipelines using Python to study the phase behavior of optogenetically-induced condensates within live mitochondria at super-resolution. We show that these opto-droplets are relatively small, ~200 nm, and have signatures of non-equilibrium fluctuations, which sheds light on the behavior of endogenous mitochondrial condensates.