A method to allow an analyst or other user of molecular-array data to directly tailor pixel-intensity integration of scanned pixel-based representations of features of a molecular array to produce feature signals. The method is embodied in a graphical user interface that allows an analyst or other molecular-array user to input pixel-intensity-weighting functions into a computational system that applies the weighting functions prior to producing integrated feature signals. The GUI provides a user with the ability to select the origin of a feature-centric rectilinear coordinate system, to input a function that specifies the function that is applied to the raw pixel intensities within the region of interest prior to integration of the pixel intensities within the region of interest to produce a feature signal.