Skip to main content
Fig. 7 | Plant Methods

Fig. 7

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

Fig. 7

Illustration of the postprocessing steps implemented in Rootine v.2. First, a 3D Median filter is applied on the results of the root segmentation step. Then, all connected objects are kept by applying the “Keep Largest” function. In order to ensure full connectivity of the roots at the top of the stack, a slice is added at the top (left-hand side of the figure). The remaining unconnected objects are subjected to a test evaluating their shape, i.e., their “vesselness” and size. This is illustrated here by showing a Z-Projection of a 400 × 400 × 400 image from the best case scenario dataset (right-hand side of the figure). The green scale bar indicates the vesselness score whereas the red scale bar indicates the size score. The intensity of the yellow color depicts the combination of these two scores. If an object meets both the vesselness and size threshold, it is considered as a false negative and will subsequently be added to the connected root system. If not, it will be considered as a false positive and will be discarded

Back to article page