1. A method, comprising: generating a predictive reference image that represents expected locations of emission spots as if said spots had been acquired in measurement from a layout design or portion thereof; correlating the predictive reference image to a measured image obtained from a device having a corresponding structure for the layout design or the portion thereof; computing a best match transformation between the predictive reference image and the measured image that corresponds to a highest quality correlation between the predictive reference image and the measured image; correlating the layout design or portion thereof with the measured image based upon the best match transformation; and applying the best match transformation directly to the layout design.