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, said method comprising the steps of: (a) 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; (b) selecting a primary image from the subset of images; and (c) 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; (d) 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 (e) registering remaining images in said set of images with said template.