The paper describes an innovative approach to estimate velocity on an image sequence and simultaneously segment and track a given structure. It relies on the underlying dynamics' equations of the studied physical system. A data assimilation method is applied to solve evolution equations of image brightness, those of motion's dynamics, and those of distance map modelling the tracked structures. Results are first quantified on synthetic data with comparison to ground-truth. Then, the method is applied on meteorological satellite acquisitions of a tropical cloud, in order to track this structure on the sequence. The outputs of the approach are the continuous estimation of both motion and structure's boundary. The main advantage is that the method only relies on image data and on a rough segmentation of the structure at initial date.