A substrate transport apparatus including a transport chamber, a drive section, a robot arm having an end effector at a distal end configured to support a substrate and being connected to the drive section generating at least arm motion in a radial direction extending and retracting the arm, an imaging system with a camera mounted in a predetermined location to image at least part of the robot arm, and a controller connected to the imaging system to image the arm moving to a predetermined repeatable position, the controller effecting capture of a first image of the robot arm proximate to the repeatable position decoupled from encoder data of the drive axis, wherein the controller calculates a positional variance of the robot arm from comparison of the first image with a calibration image, and from the positional variance determines a motion compensation factor changing the extended position of the robot arm.