A method of aligning a pair of images includes providing a pair of images with a first image and a second image, wherein the images comprise a plurality of intensities corresponding to a domain of points in a D-dimensional space. Salient feature regions are identified in both the first image and the second image, a correspondence between each pair of salient feature regions is hypothesized, wherein a first region of each pair is on the first image and a second region of each pair is on the second image, the likelihood of the hypothesized correspondence of each pair of feature regions is measured, and a joint correspondence is determined from a set of pairs of feature regions with the greatest likelihood of correspondence.