Figure 10. Creation of cellular segmentations of leaf surfaces and downstream quantitative analyses.
(A–C) Generation of a surface segmentation of a C. hirsuta leaf in MorphoGraphX assisted by PlantSeg. (A) Confocal image of a 5-day-old C. hirsuta leaf (leaf number 5) with an enlarged region. (B) Top: Segmentation pipeline of MorphoGraphX: a surface mesh is extracted from the raw confocal data and used as a canvas to project the epidermis signal. A seed is placed in each cell on the surface for watershed segmentation. Bottom: PlantSeg facilitates the segmentation process in two different ways (red arrows): By creating clean wall signals which can be projected onto the mesh instead of the noisy raw data and by projecting the labels of the 3D segmentation onto the surface to obtain accurate seeds for the cells. Both methods reduce segmentation errors with the first method to do so more efficiently. (C) Fully segmented mesh in MorphoGraphX. (D–F) Quantification of cell parameters from segmented meshes. (D) Heatmap of cell growth in an A. thaliana 8th-leaf 4 to 5 days after emergence. (E) Comparison of cell lobeyness between A. thaliana and C. hirsuta 600 µm-long leaves. (F) Average cell lobeyness and area in A. thaliana and C. hirsuta binned by cell position along the leaf proximal-distal axis. Scale bars: 50 µm (A, C), 100 µm (D, E), 5 µm (inset in A, (B). Source files used for generating quantitative results (D–F) are available in Figure 10—source data 1.