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In this paper, a new method for motion flow estimation that considers errors in all the derivative measurements is presented. Based on the total least squares (TLS) model, we accurately estimate the motion flow in the general noise case by combining noise model (in form of covariance matrix) with a parametric motion model. The proposed algorithm is tested on two different types of biological motion, a growing plant root and a gastrulating embryo, with sequences obtained microscopically. The local, instantaneous velocity field estimated by the algorithm reveals the behavior of the underlying cellular elements.