A substrate transport apparatus comprising: a transport chamber (125A-125D) with a substrate transport opening arranged for communication with a substrate station module; a drive section (200, 201) connected to the transport chamber, and having a motor defining at least one independent drive axis; a robot arm mounted inside the transport chamber, and having an end effector (210E-213E) at a distal end of the robot arm, configured to support a substrate thereon, the robot arm being operably connected to the drive section generating, with the at least one independent drive axis, at least arm motion in a radial direction extending and retracting the robot arm and moving the end effector, in the radial direction, from a retracted position to an extended position; an imaging system with a camera mounted in a predetermined location with respect to the transport chamber and disposed so as to image at least part of the robot arm; and a controller communicably connected to the imaging system and configured to image, with the camera, the at least part of the robot arm moving to or in a predetermined repeatable position (650, 650') defined by the at least one independent drive axis, the controller effecting capture of a first image of the at least part of the robot arm on registry of the robot arm proximate to or in the predetermined repeatable position decoupled from encoder data of the at least one drive axis, wherein the controller is configured to calculate a positional variance of the at least part of the robot arm from comparison of the first image with a calibration image of the at least part of the robot arm, and from the positional variance determine a motion compensation factor changing the extended position of the robot arm. a transport chamber (125A-125D) with a substrate transport opening arranged for communication with a substrate station module; a drive section (200, 201) connected to the transport chamber, and having a motor defining at least one independent drive axis; a robot arm mounted inside the transport chamber, and having an end effector (210E-213E) at a distal end of the robot arm, configured to support a substrate thereon, the robot arm being operably connected to the drive section generating, with the at least one independent drive axis, at least arm motion in a radial direction extending and retracting the robot arm and moving the end effector, in the radial direction, from a retracted position to an extended position; an imaging system with a camera mounted in a predetermined location with respect to the transport chamber and disposed so as to image at least part of the robot arm; and a controller communicably connected to the imaging system and configured to image, with the camera, the at least part of the robot arm moving to or in a predetermined repeatable position (650, 650') defined by the at least one independent drive axis, the controller effecting capture of a first image of the at least part of the robot arm on registry of the robot arm proximate to or in the predetermined repeatable position decoupled from encoder data of the at least one drive axis, wherein the controller is configured to calculate a positional variance of the at least part of the robot arm from comparison of the first image with a calibration image of the at least part of the robot arm, and from the positional variance determine a motion compensation factor changing the extended position of the robot arm.