1. A method of tracking the location of features of a specimen across a set of images of the specimen captured at different reference points, wherein said specimen comprises at least one tile comprising an array of molecules, wherein said array of molecules comprises a plurality of features, wherein a feature of said plurality of features comprises multiple copies of a molecule of said array of molecules, wherein said molecule comprises a nucleic acid, said method comprising the steps of: (a) providing a labeled nucleotide base to said array of molecules, thereby extending a primer hybridized to a nucleic acid within a feature so as to produce a signal corresponding to a feature comprising said nucleic acid, wherein each image in said set of images includes colors signals, wherein a different color corresponds to a different nucleotide base, wherein each image of the set of images comprises signals having a single color selected from four different colors, wherein four different labeled nucleotide bases are provided to said array of molecules so as to produce four different images, each image comprising signals having a single color, wherein the signal color is different for each of the four different images, thereby producing a cycle of four color images that corresponds to the four possible nucleotides present at a particular position in said nucleic acid; (b) providing additional labeled nucleotide bases to said array of molecules, thereby producing a plurality of cycles of color images; (c) selecting a subset of images, wherein the images of the subset depict signals corresponding to features of the specimen, and wherein the images of the subset are captured at different reference points; (d) selecting a primary image comprising either a single image or a compilation of multiple merged images from the subset of images, said selecting comprising: (d1) selecting the four different color images from a single cycle within the subset of images, (d2) merging signals from at least two different color images of each cycle into a candidate primary image for said cycle, (d3) repeating steps (d1) and (d2), thereby forming a plurality of candidate primary images, and (d4) selecting the candidate primary image from among the candidate primary images that includes the most signals, thereby obtaining a primary image; (e) registering the signals depicted in the images of the subset of images with the signals depicted in the primary image, so as to determine the location of the signals depicted in the images with respect to each other, thereby producing signal clumps; (f) selecting a signal from each of said signal clumps, thereby forming a template that permits the identification of the locations of features of said specimen; and (g) registering remaining images in said set of images with said template.