Table 1 Proxy traits proposed here

Centroid

The weighted centre of mass of the root system

Centre of mass of all root pixels

Mass

A normalised sum of all likelihoods generated by L in a given image or well

Sum of all root pixels

Width/depth (M)

Bounding box width and depth of the root system. Calculated as maximum point of mass on the extremities of the root system. We define this as: \(\arg \max_{x} (L(x,y) \cdot x )\) and similarly for y and the other sides of the bounding box

Maximum width and depth reached by all root pixels

Width/depth (p95)

Alternative bounding box width and depth of the root system. Calculated to enclose 95% of the calculated root likelihood

Maximum width and depth reached by all root pixels, discounting a small number of root outliers

Depth (p99)

Alternative depth measurement, calculated as 99% of the root likelihood

Maximum depth reached by all root pixels, discounting less outliers than p95

Quadrant mass

The mass trait split horizontally into four regions for each well, giving a measure of root material within each quadrant (see Fig. 2a)

Root pixel count in four regions (at varying depths)

Orientation

Ten brackets of orientation representing the direction of the root system at each pixel. These range from 0°, horizontal, to 90°, vertical. (see Additional file 1: Figure S1)

Histogram of all root angles

Quadrant orientation

The orientation trait split horizontally into four regions for each well (as previously). Orientations are now grouped into four brackets per quadrant, rather than 10, giving 16 values for each well in total

Histogram of root angles at different depths

Leaf hue

The average hue for each leaf pixel in the top image, for each well

Average pixel hue i.e. leaf colour

Leaf area

Total pixel count for all non-white pixels in the top image, per well. Non-white is defined as having a saturation value above a low threshold of 20%

Pixel count of leaf area