This paper describes a new method for estimating the 3D, non-rigid object motion in a time sequence of images. The method is a generalization of a standard optical flow algorithm that is incorporated into a successive quadratic approximation framework. The method was evaluated for gated cardiac emission tomography using images obtained from a mathematical, 4D phantom and a physical, dynamic phantom. The results showed that the proposed method offers improved motion estimation accuracy relative to the standard optical flow method. Convergence of the proposed algorithm was evidenced with a monotonically decreasing objective function value with iteration. Practical application of the motion estimation method in cardiac emission tomography includes quantitative myocardial motion estimation and 4D, motion-compensated image reconstruction.