We present methods for segmenting the sepal and shoot apical meristem of the Arabidopsis thaliana plant. We propose a mathematical morphology pipeline and a modified numerical scheme for the active contours without edges algorithm to extract the geometry and topology of plant cells imaged using confocal laser scanning microscopy. We demonstrate our methods in typical images used in the studies of cell endoreduplication and hormone transport and show that in practice they produce highly accurate results requiring little human intervention to cope with image aberrations.