Automatic tracking of cell deformation during development using time-lapse confocal microscopy is a challenging task. In plant cell tissues, large deformations and several division cycles can occur between two consecutive time-points making the image registration and tracking procedure particularly difficult. Here, we propose an iterative approach where an initial registration transformation and cell-to-cell mapping are alternatively refined using high-confidence associations selected on the basis of a geometric context preservation score. The method, evaluated on a long time-lapse series of floral meristem, clearly demonstrates its superiority over a non-iterative approach. In addition, we show that the geometric context preservation score can be used to define a lineage quality assessment metric that makes it possible for an expert to provide locally nudges to finalize the lineage detection if necessary in a semi-automatic way.