Fig. 3

Filling the hollow space inside the stem and thick roots. A A slice of \(I\) showing the cross-section of the stem with the outline of segmentations \(B_{mid} ,B_{low}\) (red and blue) at thresholds \(t_{mid} ,t_{low}\). The hollow space within the stem is connected to the outside in \(B_{mid}\) but is closed off by the stem’s shell in \(B_{low}\). B Eroding \(B_{low}\) onto \(B_{mid}\), while preserving its topology, results in the shape \(B_{mid} ^{\prime}\)(green), which adds a minimal set of voxels to \(B_{mid}\) to “close off” the hollow space. C The hollow space is filled by raising the intensity value of the voxels in the void of \(B_{mid} ^{\prime}\) and the voxels in \(B_{mid} ^{\prime}\backslash B_{mid}\) adjacent to the void to \(B_{mid}\). This creates a new image \(I^{\prime}\)