Both Martian moons, Phobos and Deimos, have been observed during several imaging campaigns by the SRC on Mars Express. Several tens of images are obtained during mutual event observations - when the Martian moons are both observed or together with another solar system body. These observations provide new opportunities to determine the bodies' positions in their orbits. A method was sought to automate the observation of the positions of the imaged bodies. Within one image sequence a similarly accurate localization of the objects in all images should be possible. Shape models of Phobos and Deimos are applied to simulate the appearance of the bodies in the images. Matching the illuminated simulation against the observation provides a reliable determination of the bodies' location within the image. To enhance the matching confidence several corrections need to be applied to the simulation to closely reconstruct the observation. In total 884 relative positions between the different objects are provided.