Current imaging techniques can capture temporal sequences of 3D images with very high time resolution over several hours. Com- paring sequences covering the same time period opens the way to the study of developmental variability. Stitching together sequences captured from different embryos may help producing a sequence covering the whole development of the animal of interest. For this, it is necessary to align two sequences in both time and space. We present here a method to align two 3D+t time series, based on the detection and pairing of 3D+t landmarks. These landmarks, which correspond to periods of fast morphogenetic change, are de- duced from the analysis of the non-linear transformations that allow to co-register pairs of consecutive 3D images in each sequence.