In this talk, I address the problem of quantum tomography in open quantum systems. Instead of using single projective measurements on the same calibrated state, which provide mean values of some operators on this state, we use full measurement trajectories, either in discrete-time systems and in diffusive systems. I begin by presenting a discretization scheme of the stochastic master equation for diffusive systems. Then, we obtain a finite-time evolution similar to the Belavkin filter describing the evolution of discrete-time systems. In a second-time, I show how to build the log-likelihood functions of measurement trajectories, and how to maximize it with respect to initial state or parameters involved in the measurement operators. Thus, we perform quantum tomography based on MaxLike estimation. Finally, we show how to get an estimation of the uncertainty on the estimated values, and we apply this technique to experimental data coming from both types of systems: discrete-time and diffusive systems.