1. A method for calibrating a biological instrument with at least one biological sample array comprising: acquiring an image of at least one biological the sample array using an excitation source, the excitation source configured to generate the image of the sample array using one channel in a plurality of channels, each channel in the plurality comprising a combination of both an emission filter and an excitation filter; evaluating the acquired image; modifying at least one of an exposure time and a duty cycle of the excitation source in response to the acquired image, the exposure time and duty cycle being modified from a set of default parameters for the exposure time and duty cycle, the set of default parameters being determined during manufacture of the instrument; determining a first plurality of locations of interest on the sample array; and identifying a plurality of image elements, each image element being associated with a location from the first plurality of locations on the sample array.