Identification and Measurement of Individual Roots in Minirhizotron Images of Dense Root Systems

Semantic segmentation networks are prone to over segmentation in areas where objects are tightly clustered. In minirhizotron images with densely packed plant root systems this can lead to a failure to separate individual roots, thereby skewing the root length and width measurements. We propose to deal with this problem by adding additional output heads to the segmentation model, one of which is used with a ridge detection algorithm as an intermediate step and a second one that directly estimates root width. With this method we are able to improve detection and width measurements in densely packed roots systems without negative effects on sparse root systems.