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; (b) imaging the array to generate image data; (c) analyzing the image data to identify locations of the sites of interest; (d) generating a mask based upon the locations of the sites of interest; 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.