1. A method for determining motion of an eye relative to a beam of optical radiation, said beam being generated by a light source and directed to the eye via a scanner, said method comprising: directing imaging light to a region of the eye and collecting reflected image data to generate a partial image, wherein the imaging light is independent from the beam of radiation and wherein a two-dimensional image can be generated by scanning imaging light over a plurality of regions and combining the resulting partial images; comparing the partial image to a reference image to identify a substantially matching image portion; determining a displacement between the partial image and the location of the substantially matching image portion, said displacement corresponding to the motion of the eye; and using the determined displacement for one of: a) correcting the alignment of the beam of radiation with respect to the eye, b) adjusting the scan range of the imaging light, and c) correcting collected measurement data.