Methods for registering first and second images which are offset by an x and/or y displacement in sub-pixel locations are provided. A preferred implementation of the methods includes the steps of: multiplying the first image by a window function to create a first windowed image; transforming the first windowed image with a Fourier transform to create a first image Fourier transform; multiplying the second image by the window function to create a second windowed image; transforming the second windowed image with a Fourier transform to create a second image Fourier transform; computing a collection of coordinate pairs from the first and second image Fourier transforms such that at each coordinate pair the values of the first and second image Fourier transforms are likely to have very little aliasing noise; computing an estimate of a linear Fourier phase relation between the-first and second image Fourier transforms using the Fourier phases of the first and second image Fourier transforms at the coordinate pairs in a minimum-least squares sense; and computing the displacements in the x and/or y directions from the linear Fourier phase relationship. Also provided are a computer program having computer readable program code and program storage device having a program of instructions for executing and performing the methods of the present invention, respectively.