Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery

Stefan Gerth; Joelle Claußen; Anja Eggert; Norbert Wörlein; Michael Waininger; Thomas Wittenberg; Norman Uhlmann

doi:10.34133/2021/8747930

Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery

Plant Phenomics. 2021 Feb 15:2021:8747930. doi: 10.34133/2021/8747930. eCollection 2021.

Authors

Stefan Gerth¹, Joelle Claußen¹, Anja Eggert¹, Norbert Wörlein¹, Michael Waininger¹, Thomas Wittenberg^{1

2}, Norman Uhlmann¹

Affiliations

¹ Development Center X-Ray Technology (EZRT), Fraunhofer Institute for Integrated Systems (IIS), Flugplatzstraße 75, 90768 Fürth, Germany.
² Biomedical Engineering Department, Fraunhofer Institute for Integrated Systems (IIS), Am Wolfsmantel 33 11, 91058 Erlangen, Germany.

Abstract

Background: Computed X-ray tomography (CTX) is a high-end nondestructive approach for the visual assessment of root architecture in soil. Nevertheless, in order to evaluate high-resolution CTX data of root architectures, manual segmentation of the depicted root systems from large-scale volume data is currently necessary, which is both time consuming and error prone. The duration of such a segmentation is of importance, especially for time-resolved growth analysis, where several instances of a plant need to be segmented and evaluated. Specifically, in our application, the contrast between soil and root data varies due to different growth stages and watering situations at the time of scanning. Additionally, the root system itself is expanding in length and in the diameter of individual roots.

Objective: For semiautomated and robust root system segmentation from CTX data, we propose the RootForce approach, which is an extension of Frangi's "multi-scale vesselness" method and integrates a 3D local variance. It allows a precise delineation of roots with diameters down to several μm in pots with varying diameters. Additionally, RootForce is not limited to the segmentation of small below-ground organs, but is also able to handle storage roots with a diameter larger than 40 voxels.

Results: Using CTX volume data of full-grown bean plants as well as time-resolved (3D + time) growth studies of cassava plants, RootForce produces similar (and much faster) results compared to manual segmentation of the regarded root architectures. Furthermore, RootForce enables the user to obtain traits not possible to be calculated before, such as total root volume (V _root), total root length (L _root), root volume over depth, root growth angles (θ _min, θ _mean, and θ _max), root surrounding soil density D _soil, or form fraction F. Discussion. The proposed RootForce tool can provide a higher efficiency for the semiautomatic high-throughput assessment of the root architectures of different types of plants from large-scale CTX. Furthermore, for all datasets within a growth experiment, only a single set of parameters is needed. Thus, the proposed tool can be used for a wide range of growth experiments in the field of plant phenotyping.