1. A method of aligning a pair of images comprising the steps of: providing a pair of images with a first image and a second image, wherein said images comprise a plurality of intensities corresponding to a domain of pixels in a 3-dimensional space, identifying salient feature regions in both the first image and the 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.