Marine stratocumulus (MSC) are shallow marine boundary layer clouds that have a significant cooling contribution to the Earth’s radiative balance. The amplitude of this cooling effect strongly depends on the properties of closed and open cells comprising MSC cloud fields. Systematic study of the underlying processes associated with cloud cell properties requires accurate and reliable cell characterization. Here we propose a method for cell segmentation of MSC clouds as observed from geostationary satellite images. The method, which is based on watershed transformation, is found to be highly efficient in segmentation of both open and closed MSC scenes. Application of the suggested methodology over a Lagrangian framework that track the clouds as they are advected by the wind and comparison of the results between pairs of consecutive images indicate that the resulted segmentation is robust and consistent. The methodology developed in this work opens the way to systematic investigation of spatiotemporal changes in MSC cloud field properties, which will improve our understanding of MSC clouds and their role in regulating Earth’s radiative budget.