1. A scanning system, comprising: one or more optical elements constructed and arranged to direct a excitation beam at a probe array; one or more detectors constructed and arranged to receive reflected intensity data responsive to the excitation beam, wherein the reflected intensity data is responsive, at least in part, to a focusing distance between an optical element and the probe array; a transport frame constructed and arranged to adjust the focusing distance in a first direction with respect to the probe array; an auto-focuser constructed and arranged to determine a best plane of focus based, at least in part, upon one or more characteristics of the reflected intensity data as received at two or more focusing distances, wherein the one or more characteristics includes a slope value, and the best plane of focus is based, at least in part, upon a maximum value of the slope value; and wherein: the one or more detectors are further constructed and arranged to receive a plurality of pixel intensity values based, at least in part, upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus; and the system further comprises an image generator constructed and arranged to associate each of the pixel intensity values with one or more image pixel positions of a probe array based, at least in part, upon one or more position correction values.