1. A method for sequencing a plurality of nucleic acids, comprising: (a) performing a cycle of a sequencing procedure for an array comprising a plurality of nucleic acids at sites of interest on the array; (b) imaging the array to generate image data; (c) analyzing the image data to identify locations of the sites of interest on the array; (d) generating a mask based upon the locations of the sites of interest on the array, wherein the mask corresponds to a plurality of sites of interest for which image data acquired during subsequent cycles of the sequencing procedure is filtered; and (e) processing the image data based upon the mask to derive sequence data from the image data, the sequence data indicative of nucleotide species present at the sites of interest on the array; wherein steps (a), (b) and (e) are repeated, and wherein in subsequent repetitions of step (e), image data corresponding to locations of the sites of interest is processed differently from image data corresponding to other locations as defined by the mask.