Currently operating optical superconducting tunnel junction (STJ) detectors, developed at the European Space Agency (ESA), can simultaneously measure the wavelength (?? = 50 nm at 500 nm) and arrival time (to within ~5?s) of individual photons in the range 310 to 720 nm with an efficiency of ~70%, and with count rates of the order of 5000 photons s~1 per junction. A number of STJs placed in an array format generates 4-D data: photon arrival time, energy, and array element (X,Y). Such STJ cameras are ideally suited for, e.g., high-time- resolution spectrally resolved monitoring of variable sources or low- resolution spectroscopy of faint extragalactic objects. The reduction of STJ data involves detector efficiency correction, atmospheric extinction correction, sky background subtraction, and, unlike that of data from CCD-based systems, a more complex energy calibration, barycentric arrival time correction, energy range selection, and time binning; these steps are, in many respects, analogous to procedures followed in high- energy astrophysics. We discuss these calibration steps in detail using a representative observation of the cataclysmic variable UZ Fornacis; these data were obtained with ESA's S-Cam2 6x6-pixel device. We furthermore discuss issues related to telescope pointing and guiding, differential atmospheric refraction, and atmosphere-induced image motion and image smearing ("seeing") in the focal plane. We also present a simple and effective recipe for extracting the evolution of atmospheric seeing with time from any science exposure and discuss a number of caveats in the interpretation of STJ-based time-binned data, such as light curves and hardness ratio plots.