The understanding of morphogenesis in plants requires the observation of living meristems during time. To that end, we have designed an imaging protocol coupled with dedicated software that allows a high-resolution 3D reconstruction of the still meristem. Comparing successive reconstructions enables us to automatically track cell lineages during meristem development and yield access to a high-resolution 3D+time reconstruction of the meristem. Experiments are conducted at early stages of floral morphogenesis of Arabidopsis flower.