A method and a system for calibrating a first coordinate system Rf of a robot unit with a second coordinate system Cf of an object identification unit, wherein the robot unit includes a robot arm with an end effector and the object identification unit includes a camera unit. The calibration is performed using a calibration marker on the end effector. The method determines the intrinsic and the extrinsic parameters of the camera unit in two steps, a first step where the intrinsic parameters and a rotational part of the extrinsic parameters are determined, and a second step where a translational part of the extrinsic parameters are determined.