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In this protocol, we describe the procedures for visualizing light-evoked calcium changes in fly visual neurons using two-photon microscopy. Before starting the imaging, the visual stimulation system should be set up properly. To facilitate later data analysis, we recommend synchronizing (or time-stamping) imaging and visual stimuli during experiments. Depending on the scientific question and experimental design, the visual stimuli can be modified. Here we provide an example protocol for measuring the intensity–response function in fly ultraviolet (UV)-sensing photoreceptors using UV illumination. For this purpose, precise time-stamping or synchronization is not required.