Methods and systems for correcting non-uniformity in focal plane arrays include averaging pixel intensity values from a plurality of data captures to generate an image, spatially median filtering the image to generate a median filtered image, temporally stacking the median filtered image with at least one previously median filtered images to generate a median filtered image stack, and temporally median filtering a pixel offset value stack corresponding to each of a plurality of filtered pixel locations within the median filtered image stack to generate a process dataset.