One major limitation of the motion estimation methods that are available in the literature concerns the availability of the uncertainty on the result. This is however assessed by a number of filtering methods, such as the ensemble Kalman filter (EnKF). The paper consequently discusses the use of a description of the displayed structures in an ensemble Kalman filter, which is applied for estimating motion on image acquisitions. An example of such structure is a cloud on meteorological satellite acquisitions. Compared to the Kalman filter, EnKF does not require propagating in time the error covariance matrix associated to the estimation, resulting in reduced computational requirements. However, EnKF is also known for exhibiting a shrinking effect when taking into account the observations on the studied system at the analysis step. Methods are available in the literature for correcting this shrinking effect, but they do not involve the spatial content of images and more specifically the structures that are displayed on the images. Two solutions are described and compared in the paper, which are first a dedicated localization function and second an adaptive domain decomposition. Both methods proved being well suited for fluid flows images, but only the domain decomposition is suitable for an operational setting. In the paper, the two methods are applied on synthetic data and on satellite images of the atmosphere, and the results are displayed and evaluated.