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The registration of atmospheric emission in the near-UV range with high time resolution is perspective area of researches. UV emission is produced in the Earth's upper atmosphere and associates with internal thunderstorm activity and the influence of near-space factors. The UV registration with high time resolution allows one to observe the fine spatio-temporal structure of transient (flash) luminous events. Lomonosov Moscow State University implements projects of orbital high-sensitivity telescopes for measuring atmospheric radiation: Mini-EUSO and K-EUSO detectors for the International Space Station. One of the most important tasks in the development and creation of orbital telescopes is the calibration of the instrument. Multi-anode photomultiplier tubes (MAPMTs) are used as photo detectors to provide maximum sensitivity and time resolution. Each MAPMT is unique, because it has individual characteristics such as gain, photocathode quantum efficiency, etc. Moreover, the characteristics of pixels may differ from each other in a single MAPMT. Thus, pixel-by-pixel calibration is necessary to reconstruct accurately the intensity of the input light from the digital data obtained in the experiment. In this research the calibration of the K-EUSO orbital telescope module is presented. The photodetector of this device includes more than 105 channels, so the automatization of the calibration process is important. A special set-up in the laboratory and dedicated software were created. The software controls the calibration light intensity of the photodiode and the positioning system to place a photodiode precisely in front of each pixel. It also provides data collection from the power meter and the K-EUSO photo detector module. The calibration process includes 2 steps: finding the optimal threshold voltage on the PMT (to minimize noise level and increase photodetection efficiency) and plotting the calibration curve (the dependence of the digital signal of the channel on the intensity of the input light with a selected threshold). As a result, the optimal threshold voltages and calibration curves of each pixel were obtained. After calibration the photo detector module was tested in laboratory with the artificial discharges.