Figure 7. Time-lapse analysis and visualization of 3D meshes.

(A) Cross section of the confocal stack of the first time point of a live imaged A. thaliana root. (B, C) The 3D segmentations of two time points imaged 6 hr apart. Shown are the cell lineages that were generated using the semi-automatic procedure following a manual correction. (D) Exploded view of the second time point with cells separated by cell types (see also Figure 4D). Cells are heat colored by their volume increase between the two time points. (E–H) Quantification of cellular growth along different directions within the organ. (E) Plot of the heat map data of (D). The cellular data was binned based on the distance of cells from the quiescent center (QC). Shown are mean values and standard deviations per bin. (F–H) Similarly binned data plots of the change in cell length (F), width (G), and depth (H). It can be seen that the majority of growth results from an increase in cell length. See Figure 7—figure supplement 1 for a detailed analysis of the cells in the endodermis. (I) Different ways to visualize 3D growth demonstrated using a single cortex cell: principal directions of growth (PDGs) averaged over the entire cell volume (left), PDGs averaged over the cell walls projected onto the walls (top right), and subcellular vertex-level PDGs projected onto the cell walls (bottom right). Scale bars: (A–D) 20 μm; (I) 5 μm. See also user guide Chapter 21 ‘Mesh 3D analysis and quantification’ and tutorial videos S6 and S7 available at https://doi.org/10.5061/dryad.m905qfv1r.

Figure 7—figure supplement 1. Time-lapse analysis of cellular geometry in the A. thaliana root endodermis.

(A) Cross section of the confocal image of time point 1. (B) Segmentation with extended cell-type labeling in the endodermis. The root cell-type labeling of Figure 4D was extended by identifying the xylem cells (light purple) in the stele (cyan), their adjacent pericycle cells (blue), and assigned the endodermis cells neighboring those pericycle cells as xylem file cells (X, red). Then the endodermis cells at right angles to the xylem files were assigned phloem file (P, purple) and the remaining other endodermis cells (E, yellow). (C) Side view of one cell file of each cell type. As the cell types do not change along the cell file, it was possible to automatically assign the cell files based on their circumferential coordinate. (D) Cell files of (C) with a heat map of cell length indicating smaller cells in the xylem pole. (E–J) Quantifications of cell geometry and development in the endodermis cell types. Cellular data was binned according to their distance from the quiescent center (QC) (E–H). Shown are mean values and standard deviations per bin (E–H) or cell type (I, J). Phloem file cells showed a larger volume (E), which was caused by a greater cell length (F), an observation that has been made before by Andersen et al., 2018. In contrast, xylem file and other endodermis cells were smaller in volume due to different reasons: while xylem file cells were the shortest (E), rest endodermis cells showed a lower cell width with increasing distance from the QC (G). The time-lapse analysis confirmed above observations: while volume change was similar across the cell types (H), phloem file cells showed a lower proliferation rate (I), whereas rest endodermis cells showed the smallest extension of cell width (J). Scale bars: (A, B) 20 μm; (C, D) 50 μm.