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This paper describes a new method for removing geometric distortion in images of submerged objects observed from outside shallow water. We focus on the problem of analyzing video sequences when the water surface is disturbed by waves. The water waves will affect the appearance of the individual video frames such that no single frame is completely free of geometric distortion. This suggests that, in principle, it is possible to perform a selection of a set of low distortion sub-regions from each video frame and combine them to form a single undistorted image of the observed object. The novel contribution in this paper is to use a multi-stage clustering algorithm combined with frequency domain measurements that allow us to select the best set of undistorted sub-regions of each frame in the video sequence. We evaluate the new algorithm on video sequences created both in our laboratory, as well as in natural environments. Results show that our algorithm is effective in removing distortion caused by water motion. [ABSTRACT FROM AUTHOR]