欧亚国际

来自德国Fraunhofer的科学家利用2套CT断层扫描系统，发表了题为Semiautomated 3D Root Segmentation and evalsuation Based on X-Ray CT Imagery的文章，文章发表了知名期刊Plant Phenomics（植物表型组学）上面。

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

Stefan Gerth,1 Joelle Claußen,1 Anja Eggert,1 Norbert Wörlein,1 Michael Waininger,1 Thomas Wittenberg,1,2 and Norman Uhlmann1

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 evalsuate 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 evalsuated. 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 (Lroot ), root volume over depth, root growth angles (θmin ,θmean , and θmax ), root surrounding soil density Dsoil , 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.