1. A method of aligning a pair of images comprising at least one computer implementing 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 wherein representing salient feature region center points for one image in a KD-tree, querying said KD-tree for each feature to find a set of nearest neighbor features, and removing from said tree those nearest neighbor features with a lower saliency value and that have a center point within the scale of said each feature, wherein a substantially uniform distribution of salient feature regions in said image is achieved.