1. A method for calibrating a biological instrument comprising: executing a pre-scan calibration comprising: acquiring an image of at least one biological sample array; evaluating the image to determine fluorescence levels; modifying the fluorescence levels by adjusting an excitation source with an exposure time and a duty cycle to provide strong fluorescence levels without saturation; determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.