HMSiR680-Me is a bright and stable fluorescent dye designed for multicolor, time-lapse, and super-resolution imaging to observe acidic organelles. It is suitable for overnight time-lapse experiments and rapid continuous super-resolution microscopy imaging, maintaining imaging quality for at least 1000 frames. HMSiR680-Me can also be used with silicon rhodamine dyes in multiplexed super-resolution microscopy experiments, enabling the visualization of interactions between the mitochondrial inner membrane and lysosomes using a single excitation laser and simultaneous depletion technique.