Reading chemical arrays

Methods of using an addressable array of biopolymers which has been exposed to a sample, and apparatus and computer program products for use of the arrays. In one embodiment the method includes detecting signals from the exposed array to obtain a signal image of the array. The array signal image is saved in a memory. Based on the detected signals, a shape of each region in one or more sets of multiple regions on the array signal image is established. A definition of the shapes of the established regions of each set is saved in a memory. Each region of each set is processed according to a corresponding routine for that set.