Robust Skeletonization for Plant Root Structure Reconstruction from MRI

Robust Skeletonization for Plant Root Structure Reconstruction from MRI

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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Acknowledgment

This research was supported by grants BE 2556/15 and SCHN 1361/3-1 of German Research Foundation (DFG).

References

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