© 2015 IEEE.Studying the behaviour of cells using time-lapse microscopic imaging requires automated processing pipelines that enable quantitative analysis of a large number of cells. We propose a pipeline based on state-of-the-art methods for background motion compensation, cell detection, and tracking which are integrated into a novel semi-automated, learning based analysis tool. Motion compensation is performed by employing an efficient nonlinear registration method based on powerful discrete graph optimisation. Robust detection and tracking of cells is based on classifier learning which only requires a small number of manual annotations. Cell motion trajectories are generated using a recent global data association method and linear programming. Our approach is robust to the presence of significant motion and imaging artifacts. Promising results are presented on different sets of in-vivo fluorescent microscopic image sequences.