3D RECONSTRUCTION OF PLANT ROOTS FROM MRI IMAGES

Hannes Schulz, Johannes A. Postma, Dagmar van Dusschoten, Hanno Scharr, Sven Behnke

2012

Abstract

We present a novel method for deriving a structural model of a plant root system from 3D Magnetic Resonance Imaging (MRI) data of soil grown plants. The structural model allows calculation of physiologically relevant parameters. Roughly speaking, MRI images show local water content of the investigated sample. The small, local amounts of water in roots require a relatively high resolution, which results in low SNR images. However, the spatial resolution of the MRI images remains coarse relative to the diameter of typical fine roots, causing many gaps in the visible root system. To reconstruct the root structure, we propose a three step approach: 1) detect tubular structures, 2) connect all pixels to the base of the root using Dijkstra’s algorithm, and 3) prune the tree using two signal strength related thresholds. Dijkstra’s algorithm determines the shortest path of each voxel to the base of the plant root, weighing the Euclidean distance measure by a multi-scale vesselness measure. As a result, paths running within good root candidates are preferred over paths in bare soil. We test this method using both virtually generated MRI images of Maize and real MRI images of Barley roots. In experiments on synthetic data, we show limitations of our algorithm with regard to resolution and noise levels. In addition we show how to use our reconstruction for root phenotyping on real MRI data of Barley roots in soil.

Paper Citation

in Harvard Style

Schulz H., A. Postma J., van Dusschoten D., Scharr H. and Behnke S. (2012). 3D RECONSTRUCTION OF PLANT ROOTS FROM MRI IMAGES . In Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 2: VISAPP, (VISIGRAPP 2012) ISBN 978-989-8565-04-4, pages 24-33. DOI: 10.5220/0003869800240033

in Bibtex Style

@conference{visapp12,
author={Hannes Schulz and Johannes A. Postma and Dagmar van Dusschoten and Hanno Scharr and Sven Behnke},
title={3D RECONSTRUCTION OF PLANT ROOTS FROM MRI IMAGES},
booktitle={Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 2: VISAPP, (VISIGRAPP 2012)},
year={2012},
pages={24-33},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003869800240033},
isbn={978-989-8565-04-4},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Computer Vision Theory and Applications - Volume 2: VISAPP, (VISIGRAPP 2012)
TI - 3D RECONSTRUCTION OF PLANT ROOTS FROM MRI IMAGES
SN - 978-989-8565-04-4
AU - Schulz H.
AU - A. Postma J.
AU - van Dusschoten D.
AU - Scharr H.
AU - Behnke S.
PY - 2012
SP - 24
EP - 33
DO - 10.5220/0003869800240033