The complexity of dynamical laws governing 3D atmospheric flows associated with incomplete and noisy observations makes the recovery of atmospheric dynamics from satellite images sequences very difficult. In this report, we face the challenging problem of estimating physical sound and time consistent horizontal motion fields at various atmospheric depths for a whole image sequence. Based on a vertical decomposition of the atmosphere, we propose two dynamically consistent atmospheric motion estimators relying on different multi-layer dynamical models. Both estimators use a framework derived from data assimilation and are applied on noisy and incomplete pressure difference observations derived from satellite images. In the first model, dense ...