Results of the first two experiments using semiconductor pixel detectors of the Medipix family for cosmic ray imaging in the stratospheric environment are presented. The original detecting device was based on the hybrid pixel detectors Medipix2 and Timepix developed at CERN with USB interface developed at the Institute of Experimental and Applied Physics of Czech Technical University in Prague. The detectors were used in tracking mode allowing them to operate as an "active nuclear emulsion". Extensive datasets of different types of cosmic ray tracks were acquired in the stratospheric radiation environment, sorted and analyzed. Detector performance was evaluated for further design implications of proposed usage on satellites.