The shoot apical meristem (SAM) is at the origin of all the plant above-ground organs (including stems, leaves and flowers) and is a biological object of interest for the understanding of plant morphogenesis. The quantification of tissue growth at a cellular level requires the analysis of 3D microscopic image sequences of developing meristems. To address inter-individual variability, it is also required to compare individuals. This obviously implies the ability to process inter-individual registration, i.e. to compute spatial and temporal correspondences between sequences from different meristems. In the present work, we propose a spatial registration method dedicated to microscopy floral meristem (FM) images, and the identification, for a given still image of a meristem, of its best corresponding time-point in a sequence of an other individual (temporal registration).