In one embodiment a method for reducing variation in a plurality of scanners is described. The method comprises directing an excitation beam at a calibration standard in each of the plurality of scanners, where one of the plurality of scanners is a designated scanner; detecting emission data for each of the plurality of scanners from a plurality of fluorescent molecules disposed on the calibration standard, where the emission data is responsive to the excitation beam; determining variation in the emission data of one or more of the plurality of scanners based, at least in part, upon the emission data of the designated scanner; and adjusting one or more parameters in one or more of the plurality of scanners based, at least in part, upon the determined variation.