A method for aligning two different magnified images of the same subject includes a first step of precomputing rigid transformations for the two different images globally (i.e., for all or approximately all regions of the images). Pairs of corresponding features in the two different magnified images are identified and transformation values are assigned to each of the pairs of corresponding features, in a second step, while images are being generated for display to a user, a locally optimal rigid transformation for the current field of view is computed, in a third step the images are aligned as per the locally optimal rigid transformation. Non-zero weight is given to transformation values for pairs of features that are outside the current field of view. Typically, the second and third steps are repeated many times as the images are generated for display and user either changes magnification or pans/navigates to a different location in the images.
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