For optical coherence tomography engines a method for eliminating the effects of the movement of the eye on the optical coherence tomography scan calculates the motion of the eye from an image from an auxiliary scanning system and compares a reference region to a corresponding region in the image associated with the next frame, with the change in position sensing the motion of the eye. This is followed by utilizing this sensed motion to generate accurate offsets for the scanning mirror patterns of the OCT engine. Additionally, scan skipping is utilized to obviate the effects of rapid eye movement that occur at rates faster than the image acquisition rate.
