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This paper addresses the problem of registering regions of interest in two video sequences. Potential applications include blob fusion and target tracking in blurry sequences. It is assumed that the moving target is tracked successfully in one of the two sequences and isrepresented by a bounding box in each frame of the first sequence. The goal is to find the corresponding bounding box for each frame of the second video sequence. The registration algorithm developed in this paper is based on mutual information. To facilitate the registration process, the two cameras are assumed to be calibrated such that the geometrical transformation required to register the corresponding bounding boxes is a 2D rigid body transformation without rotation. Visual and IR video sequences are used to test the proposed approach.