1. A computer-implemented method of determining feature intensities from image data from a probe array, the method comprising: a. obtaining image data for a plurality of features of the probe array, wherein the image data comprises a set of pixels, wherein the set of pixels comprises groups of pixels associated with each feature, wherein the groups are aligned with each feature, wherein the groups of pixels indicate a center pixel for each feature; b. determining observed pixel intensities for one or more pixels in the set of pixels; c. determining initial feature intensities for the plurality of features, wherein the initial feature intensities are based upon the observed pixel intensities; d. determining a theoretical pixel intensity for one or more pixels in the set of pixels from feature intensities of one or more of the plurality of features; e. determining an error for each pixel in the set of pixels, wherein the error is based upon the observed pixel intensity and the theoretical pixel intensity; and f. determining a corrected feature intensity for the plurality of features, wherein the corrected feature intensity is based upon a previously determined feature intensity and the error, and g. repeating steps d-f comparing the corrected feature intensities against previously determined feature intensities until the corrected feature intensities converge; and h. after convergence, outputting the adjusted feature intensities.