Robust Skeletonization for Plant Root Structure Reconstruction from MRI

• URL: http://arxiv.org/abs/2010.14440v1
• Date: Tue, 27 Oct 2020 16:54:40 GMT
• Title: Robust Skeletonization for Plant Root Structure Reconstruction from MRI
• Authors: Jannis Horn, Yi Zhao, Nils Wandel, Magdalena Landl, Andrea Schnepf, and Sven Behnke
• Abstract summary: We propose a two-stage approach for structural reconstruction of plant roots from MRI scans. 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.
• Score: 20.758304602972764
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: 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.

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