Systems and methods are described that may be applied to scanning biological materials in or on probe arrays. For example, a system is described that includes a scanner that has one or more excitation sources and an emission receiving element, such as an objective lens, that receives from locations of the probe array an emission signal responsive to the excitation sources. The scanner also has a radial position generator that generates radial positions of the emission receiving element. Also included in the system is a computer memory having stored therein a plurality of position data, each representing a radial position of the emission receiving element. Also stored in the computer memory unit is a set of comparator instructions that generate a clock signal based, at least in part, on comparing one or more of the plurality of radial positions with one or more of the plurality of position data.