Recent microscopy techniques allow imaging temporal 3D stacks of developing organs or embryos with a cellular level of resolution and with a sufficient acquisition frequency to accurately track cell lineages. Imaging multiple organs or embryos in different experimental conditions may help decipher the impact of genetic backgrounds and environmental inputs on the developmental pro-gram. For this, we need to precisely compare distinct individuals and to compute population statistics. The first step of this procedure is to develop methods to register individuals. From a previous work of cell segmentation from microscopy im-ages, we here demonstrate how to extract the symmetry plane of em-bryos at early stages, and how to use this information as a geometri-cal constraint to both register these embryos and obtain a cell-to-cell mapping.