(A) Light microscopy of cross sections obtained from Arabidopsis hypocotyls (organ position illustrated for a 9-day-old seedling, lower left) at 9 dag (upper left) and 35 dag (right). Size bars are 100 μm. Blue GUS staining due to the presence of an APL::GUS reporter gene in this Col-0 background line marks phloem bundles. (B) Overview of the developmental series (time points and distinct samples per genotype) analyzed in this study. (C) Example of a high-resolution hypocotyl section image assembled from 11 × 11 tiles. (D) The same image after pre-processing and binarization, and (E) subsequent segmentation using a watershed algorithm. (F) Number of mis-segmented cells as determined by careful visual inspection in 12 sections, plotted against the total number of cells per section (log scale).