This repository contains the analysis pipeline used to generate Figures 4, 5, S6, S10, S11, S12, and S13 of the paper. The scripts process single-vesicle tracking data exported from TrackMate (two-channel fluorescence microscopy), converting intensity ratios to absolute pH values using a Hill function calibration anchored per track to an NH4Cl plateau. The pipeline quantifies light-evoked lysosomal acidification and alkalization kinetics, response amplitudes, and spatial distributions relative to the nucleus.