Figure 2. Methods to define positional information and their application to data analysis in plant organs.

(A) Y-axis aligned A. thaliana root. The cells are colored according to the y-coordinate of their centroid position. (B) Plot of cell volumes of epidermis cells of the root in (A) along the y-axis with a fitted trend line. (C) Seedling of A. thaliana with a surface segmentation of the epidermis. A manually defined Bezier curve (white) allows the assignment of accurate cell coordinates along a curved organ axis. (D) Side and top views of an A. thaliana sepal with a proximal-distal (PD) axis heat coloring. The cell coordinates were assigned by computing the distance to manually selected cells (outlined in red) at the organ base. This method allows organ coordinates to be assigned in highly curved tissues. (E) Side and top views of (D) with a heat map coloring based on cellular growth to the next time point. (F) Plot summarizing the growth data of (E) using the PD-axis coordinates from (D). See Figure 2—figure supplement 1 for the analysis of the complete time-lapse series. Scale bars: (A) 20 μm; (C) 100 μm; (D, E) 50 μm. See also user guide Chapter 23 ‘Organ-centric coordinate systems’ and tutorial video S3video S3 available at https://doi.org/10.5061/dryad.m905qfv1r.

Figure 2—figure supplement 1. From cellular resolution heat maps to a global analysis of A. thaliana sepal development using organ-centric coordinates.

(A, B) Heat maps of cell area extension (A) and cell proliferation (B) for each time point (visualized on the earlier point). (C) Plot of the heat map data from (A) vs. the distance of cells to the base of the organ (see also Figure 2D). The distance of the maximum of the growth zone from the base or the organ is relatively constant. However, organ length increases about 10× between the first and last time points, making a comparison of the different curves difficult. (D–F) When plotting the same data with normalized cell distance values averaged using 20 bins along the proximal-distal axis, it becomes more apparent that the growth zone moves from the proximal to the distal regions over the course of development (D). The trend of lower and more proximal maxima (highlighted with arrows) is even clearer when proliferation is plotted in the same way (E). (F) Cell area data plotted as in (D) and (E). Average cell areas increase mainly at the distal end during later time points. Scale bars: (A, B) 100 μm.