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Table 1 Summary of the parameters, their values, their effects and their sensitivity on the segmentation accuracy

From: An improved method for the segmentation of roots from X-ray computed tomography 3D images: Rootine v.2

Step Parameter Value Effect Sensitivity on the segmentation accuracy
Worse case Best case
Image filtering Contrast threshold (\({t}_{con}\)) 60 60 Controls the degree of smoothening (i.e., noise removal) of the input image Medium
Edge enhancement Blur radius 1 0.9 Both parameters control the degree of sharpening of the image, i.e., increase the contrast at the boundaries between roots and pores and soil matrix High
Mask weight 0.7 0.8
Background removal Root gray value factor (\({f}_{r}\)) 0.10 0.18 Sets the average gray value of the roots Very high
Root gray value range (\({R}_{r}\)) 65 70 Controls the root gray value window around the average root gray value. If set too high, overestimation of roots into their surroundings will occur. If set too low, loss of roots will occur Very high
Detect fine roots Minimum root diameter (\({d}_{r,min}\)) 4 4 Controls the root recovery of the fine roots. If set too high, the fine roots are not detected. If set too low, over-segmentation may occur depending on the noise level of the image High
Detect coarse roots Maximum root diameter (\({d}_{r,max}\)) 28 28 Controls the accuracy of the root diameter outline of the biggest root. If set too high, the diameter of the biggest root is overestimated and computational time is wasted. If set too low, the diameter of the biggest root is underestimated Medium
False positives removal Kernel size of median filter 3 2 Controls the degree of smoothening of the roots and trimming of over-segmented voxels. If set too high, root loss occurs whereas low values result in the presence of false positives High
False negatives recovery Size threshold (\({t}_{s}\)) 25 25 Both parameters control the quality of the false negatives added in the root system. If set too low, many false positives are considered negatives, If set too high, root loss occurs High
Vesselness threshold (\({t}_{v}\)) 0.85 0.9 High