Robust Skeletonization for Plant Root Structure Reconstruction from MRI

Structural reconstruction of plant roots from MRI is challenging, because of low resolution and low signal-to-noise ratio of the 3D measurements which may lead to disconnectivities and wrongly connected roots. We propose a two-stage approach for this task. The first stage is based on semantic root vs. soil segmentation and finds lowest-cost paths from any root voxel to the shoot. The second stage takes the largest fully connected component generated in the first stage and uses 3D skeletonization to extract a graph structure. We evaluate our method on 22 MRI scans and compare to human expert reconstructions.

3D U-Net for Segmentation of Plant Root MRI Images in Super-Resolution

Magnetic resonance imaging (MRI) enables plant scientists to non-invasively study root system development and root-soil interaction. Challenging recording conditions, such as low resolution and a high level of noise hamper the performance of traditional root extraction algorithms, though. We propose to increase signal-to-noise ratio and resolution by segmenting the scanned volumes into root and soil in super-resolution using a 3D U-Net. Tests on real data show that the trained network is capable to detect most roots successfully and even finds roots that were missed by human annotators. Our experiments show that the segmentation performance can be further improved with modifications of the loss function.