A method determines axial alignment between the centroid of an end effector and the effective center of a specimen held by the end effector. The method is implemented with use of an end effector coupled to a robot arm and having a controllable supination angle. A condition in which two locations of the effective center of the specimen measured at 180.degree. displaced supination angles do not lie on the supination axis indicates that the centroid is offset from the actual effective center of the specimen.