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During longtime space fights and interplanetary missions among numerous outboard risks, the crew faces onboard microbiological intruders as well. There is no way to send biological tests for the analysis to the Earth in such missions, so special onboard system of methods and activities must solve two different problems: sampling different types of bacteria and fungus and perform independent analysis of collected material without professional microbiologist among the crew and any help from the Earth. So we meet an interesting task to create system that would minimize human factor and rely mostly on computing machinery. In order to use pattern recognition method, we need to perform proper tests sampling and prepare them for the machine analysis. Stereoscopy and spectrometry is the only way to achieve our goal. Apart from tests sampling it is necessary to develop modified mathematical model for pattern recognition of bacteria and fungus, which were found during the flight. For that reason we are making mathematical model, describing microbiological samples. Still, we have a lot of work to do but the result of our research could become common use not only in space sector, but also in clinical medicine as well.