(
A–C) Methods supported by the 3D Cell Atlas add-on demonstrated on a
A. thaliana root (
Montenegro-Johnson et al., 2015). (
A) Longitudinal cross section with a heat map of circumferential cell size. The white dashed line is the manually defined central axis. (
B) The 2D heat plot of radial distance (heat map: in
Figure 4B) and circumferential cell size (heat map in
A) reveals a distinct clustering and can be used directly to assign the different cell types (dashed ellipses). (
C) Final result of the cell-type assignment. (
D) The 3D Cell Atlas meristem (
Montenegro-Johnson et al., 2019) allows the assignment of cell layers (as also seen in
Figure 4C) and types in the meristem. (
E–G) Cell-type-specific data analysis on the example of the
A. thaliana gynoecium (
Figure 4E–H). (
E) Violin plot of the rectangularity of different cell types. Valve tissue cells are less rectangular and have higher variance compared to replum cells and stomata. (
F, G) 2D scatter plots with fitting ellipses. Choosing different measures as x- or y-axis allows the separation of different cell types as demonstrated in
Figure 4G. Scale bars: (
A, C, D) 20 μm.