In a method for calibrating a stage-camera system, a travel distance of a stage is determined in a first coordinate system and an object displacement distance of at least one object is determined in a second coordinate system. A calibration measure for calibrating the coordinate systems is computed from the travel distance and the object displacement distance. The object displacement distance is determined by registering a calibration image with a reference image based on the at least one object. The method enables an automatic and accurate calibration of the stage-camera system.