a microscope system that shifts a plurality of observation locations that are set upon an observation subject in order onto an optical axis of an objective optical system , and for each of the observation locations , performs photography with an image - capturing device of an observation image of the observation subject a plurality of times as time elapses , includes : a drive unit that drives a stage upon which the observation subject is mounted , and the objective optical system , relative to one another two dimensionally in directions orthogonal to the optical axis ; a position detection unit that detects at least one of positions of the stage and the objective optical system ; and a correction unit that , based upon position information detected by the position detection unit , performs trimming correction upon a plurality of photographic images that have been photographed at each observation location as time elapses , so that the plurality of photographic images become images of a same observation region that includes the observation location .