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

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: 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: 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.

Plant phenotyping relevance

根系CT画像からの3Dセグメンテーションを半自動化するツール開発であり、植物表現型取得の中心的手法である。

Code and data availability

The article describes the RootForce semiautomatic root segmentation tool applied to bean and cassava X-ray CT data, but contains no data availability statement, public dataset deposit, or author code release. The only URLs present are a potting soil vendor link (Einheitserde), a cited RooTrak PubMed reference, and two

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