1. A method of using an addressable array of biopolymers on a substrate which array has been exposed to a sample, comprising: (a) detecting signals from the exposed array to obtain a signal image of the array; (b) establishing, based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image, and displaying the established shapes; (c) processing each region of each set according to a corresponding routine for that set; and (d) saving the displayed shapes in a first file and at least some of the processed results in a second file.