Table 3. MorphoGraphX workflows.

Workflow	Description	Used in figure	User guide chapter
MorphoGraphX legacy workflows	Processes and pipelines introduced in MorphoGraphX 1.0 (Barbier de Reuille et al., 2015)
Surface segmentation	Creating a surface mesh, projecting epidermal signal and segmentation	Figure 1A–C	The chapters at the beginning of the user guide deal with these basic topics: from chapter 1 ‘Introduction’ to 12 ‘Attribute maps & data export’
3D segmentation	Creating volumetric segmentation using ITK watershed	Figure 1—figure supplement 1A and B	20 ‘3D segmentation’
Parent labeling	Cell lineage tracing between two subsequent segmented time points of the same sample	Figure 1D and E	13 ‘Lineage tracking’
Cell geometry heat maps	Creating heat map of cellular data	Figure 1D, Figure 1—figure supplement 1C	10 ‘Cell geometry quantification’
Time-lapse heat maps	Creating heat maps using two parent labeled time points	Figure 1E	14 ‘Comparing data from two time points’
Growth directions	Computing growth directions using time-lapse data	Figure 1E	15 ‘Principal directions of growth (PDGs)’
MorphoGraphX 2 workflows	New processes and pipelines introduced in this article
Different methods of creating organ coordinates	Using world coordinates (X, Y, Z)	Figure 2A	23.3 ‘Further types of organ coordinates’
	Using polar coordinates	Figure 3G–I	23.3 ‘Further types of organ coordinates’
	Using Bezier line or grid	Figure 2C	23.2 ‘Bezier line and grid’
	Using cell distance heat maps	Figure 2D	23.1 ‘The cell distance measure’
	Using a separate organ surface mesh	Figure 4A	23.3 'Further types of organ coordinates'
Different methods of creating cell-type labelings	Using heat maps or organ coordinates	Figure 4E and F	24.4 ‘Cell type classification using a single heat map’
	Using 2D clustering	Figure 4G	24.5 ‘Cell type classification using two measures’
	Using support vector machines (SVMs)	Figure 4H	24.6 ‘Cell type classification using SVMs’
Organ directions	Deriving directions from coordinates or Bezier curves	Figure 3B and H	16 ‘Custom axis directions’ and 21.6 ‘Custom directions for 3D meshes’
Combining directions	Combining different kind of organ coordinates or directions	Figure 4B, Figure 5D–F	24.1 ‘Cell Atlas root” and 21.6 ‘Custom directions for 3D meshes’
Semi-automatic parent labeling	For lineage tracing	Figure 6A–C	17.2 ‘Semi-automatic parent labeling’
Morphing animations		Figure 6—figure supplement 1A and B	17.4 ‘Morphing animations’
3D growth analysis		Figure 7D–I	21.3 ‘Change maps 3D’ and 21.4 ‘PDGs 3D’
Division analysis	Analyzing cell divisions	Figure 8A–I, Figure 8—figure supplement 1A and E	25 ‘Division analysis’
Cell connectivity analysis	Analyzing cellular connectivity networks	Figure 8J and K	-
3D visualization	Exploded views	Figure 8—figure supplement 1C	21.5 ‘3D visualization options’
Signal quantification	Quantifying signal amount and direction	Figure 8L–N, Figure 8—figure supplement 2A–F	18 ‘Quantifying signal orientation’ and 21.7 ‘Signal orientation for 3D meshes’