1. A computer-implemented method of modifying image data comprising: accessing image data of a feature of a biological probe array hybridized with nucleic acids, wherein said image data of the feature comprises a set of observed pixel values; determining a theoretical pixel intensity with a transfer function representing the proportion of the intensity in a set of pixels due to a feature, a feature intensity of said feature, and a background value of said feature; determining an optimized multiplicative error function using a multiplicative error function and a standard deviation function, wherein said multiplicative error function comprises said theoretical pixel intensity and said set of observed pixel values; and determining said feature intensity with an update rule for said feature intensity using a weight function representing the weight of said pixel and the optimized multiplicative error function where said update rule for said feature intensity iteratively generates a unique value to which said feature intensity converges obtaining an observed pixel intensity chart comprised of cells including a plurality a pixels for each cell wherein each pixel has an observed pixel intensity and wherein each cell has a center pixel, producing a feature intensity chart by averaging the pixel intensities of the plurality of pixels within each cell, producing a transfer function intensity chart having pixel intensities calculated using a transfer function that relates the distance of each pixel from the center pixel with an intensity value that is proportional to the observed feature intensity, multiplying the transfer function intensity chart by the feature intensity chart to form product image files, and summing the product image files together to produce a summed image file.