A method and system for improving image quality by compounding a plurality of images to mitigate the effects of image noise. The method utilizes the independency between noise components for multiple image compounding. An effective measurement is designed to regularize the independency between noise in a traditional generative model based filtering framework, thereby enabling a more robust algorithmic solution to inaccurate signal/noise modeling. The method generally comprises selecting a plurality of images, calculating the residual error on each image; calculating the noise likelihood of each image, calculating the signal likelihood of the image, performing an independence analysis to regularize an independence constraint between the residual errors of the images, and summing the signal likelihood, noise likelihood and pairwise independency to approximate the joint independency between the residual errors.