A scene-based non-uniformity correction method super-resolution for eliminating fixed pattern noise in a video having a plurality of input images is disclosed, comprising the steps of warping each of the plurality of images with respect to a reference image to obtain a warped set of images; performing one of averaging and deblurring on the warped set of images to obtain an initial estimate of a reference true scene frame; warping the initial estimate of the reference true scene frame with respect to each of the plurality of images to obtain a set of estimated true signal images; performing a least square fit algorithm to estimate a gain image and an offset image given the set of estimated true signal images; applying the estimated gain image and estimated offset image to the plurality of images to obtain a clean set of images; and applying a super-resolution algorithm to the clean set of images to obtain a higher resolution version of the reference true scene frame.