Organ morphogenesis is a complex process and numerous factors must be considered while choosing a method for its quantitative investigation. Few methods facilitate imaging. These are sequential replica methods combined with scanning electron microscopy and sequential confocal microscopy imaging. The latter is now the most used method to study spatiotemporal changes of organ geometry, growth and involvement of molecular factors in regulating organ development. The time-lapse confocal imaging combined with quantitative analysis of the spatiotemporal pattern of auxin efflux proteins (PIN-FORMED) was used to investigate growth and morphogenesis of gynoecium and enabled detailed insight into gynoecium development. Yet time-lapse imaging of the gynoecium, concealed within a flower bud, presents challenges in ensuring high-quality data during all the stages of such investigations (sample preparation, maintenance of growing organ during the relatively long time of its development, laser exposure time, etc.). Analysis of vast quantitative data was facilitated by MorphoGraphX.