A method for aligning a pair of images includes providing a pair of images, identifying salient feature regions in both a first image and a second image, wherein each region is associated with a spatial scale, representing feature regions by a center point of each region, registering the feature points of one image with the feature points of the other image based on local intensities, ordering said feature pairs by a similarity measure, and optimizing a joint correspondence set of feature pairs by refining the center points to sub-pixel accuracy.