Table 1. Measures for cells segmented on surface projections (2.5D).
| Measure | Unit | Description |
|---|---|---|
| Geometry | ||
| Area | µm2 | Area of the cell (sum of its triangle area) |
| Aspect ratio | - | Ratio of length major axis and length minor axis (see below) |
| Average radius | µm | Average distance from the center of gravity of a cell to its border |
| Junction distance | µm | Max or min distance between neighboring junctions of a cell |
| Length major axis | µm | Length of the major axis of the 2D shape analysis (computes a PCA on the triangle positions weighted by their area) |
| Length minor axis | µm | Length of the minor axis of the 2D shape analysis (computes a PCA on the triangle positions weighted by their area) |
| Maximum radius | µm | Maximum distance from the cell center to its border |
| Minimum radius | µm | Minimum distance from the cell center to its border |
| Perimeter | µm | Sum of the length of the border segments of a cell |
| Lobeyness | ||
| Circularity | - | Perimeter^2/(4*PI*Area) |
| Lobeyness | - | Ratio of cell perimeter to convex hull perimeter (1 for convex shapes) |
| Rectangularity | - | Ratio of cell area to the area of the smallest rectangle that can contain the cell (1 for rectangular shapes, lower values for irregular shapes) |
| Solidarity | - | Ratio of the convex hull area to the cell area (1 for convex shapes, higher values for complicated shapes) |
| Visibility pavement | - | 1-(visibility stomata) (see below) |
| Visibility stomata | - | Estimate of visibility in the cell 1 for convex shapes, decreases with the complexity of the contour |
| Location | ||
| Bezier coord | µm | Associated Bezier coordinate of a cell Requires a Bezier grid |
| Bezier line coord | µm | Associated Bezier coordinate of a cell Requires a Bezier curve |
| Cell coordinate | µm | Cartesian coordinate of a cell |
| Cell distance | µm/cells | Distance to the nearest selected cell (finds the shortest path to a selected cell through the cell connectivity graph, edge weights: Euclidean, cell number or 1/wall area) |
| Distance to Bezier | µm | Euclidean distance to the Bezier curve or grid |
| Distance to mesh | µm | Euclidean distance to the nearest vertex in the other mesh |
| Major axis theta | ° | Angle between the long axis of the cell and a reference direction |
| Polar coord | °/µm | Polar coordinate around a specified Cartesian axis |
| Network | ||
| Neighbors | Count | Number of neighbors of a cell |
| Betweenness centrality | - | Computes the betweenness centrality of the cell connectivity graph Edges can be weighted by the length of the shared wall between neighboring cells |
| Betweenness current flow | - | Computes the betweenness current flow of the cell connectivity graph Edges can be weighted by the length of the shared wall between neighboring cells |
| Signal | ||
| Signal border | Average amount of border signal in a cell | |
| Signal interior | Average amount of interior signal in a cell | |
| Signal parameters | Advanced and general process that allows the setting of parameters to compute different kinds of signal quantifications | |
| Signal total | Average amount of total (=border + interior) signal in a cell | |
| Other measure processes | ||
| Mesh/lineage tracking/heat map proliferation | Cells | Proliferation |
| Mesh/cell axis/custom/custom direction angle | ° | Angle between a cell axis and a custom axis |
| Mesh/division analysis/compute division plane angles | ° | Angle between division planes and/or cell axes |
PCA: principal component analysis.