Segmentation of Plant Roots and Soil Constituents Through X-Ray Computed Tomography and Image Analysis to Reveal Plant Root Impacts on Soil Structure

Abstract

Plant roots influence various soil physical properties by altering the soil structure and pore configuration; however, a detailed understanding of these effects remains limited. In this study, we applied a relatively simple approach for segmenting plant roots and soil constituents using X-ray computed tomography (CT) images to evaluate root-induced changes in soil structure. The method combines manual initialization with a layer-wise automated region-growing approach, enabling the extraction of the root systems of soybean, Italian ryegrass, and Guinea grass. The method utilizes freely available software with a simple interface and does not require advanced image analysis skills, making it accessible to a wide range of researchers. The soil particles, pore water, and pore air were segmented using a Kriging-based thresholding technique. The segmented four-phase images allowed for the quantification of the volume fractions of soil constituents, pore size distributions, and coordination numbers. Furthermore, by separating the rhizosphere and bulk soil, we found that the root presence significantly reduced solid fractions and increased water content, particularly in the upper soil layers. Macropores and fine pores were observed near the roots, highlighting the complex structural impacts of root growth. While further validation is needed to assess the method’s applicability across different soil types and imaging conditions, it provides a practical basis for visualizing and quantifying root–soil interactions, and could contribute to advancing our understanding of how plant roots influence key soil hydraulic and thermal properties.

Plant phenotyping relevance

X線CT画像から植物根系を抽出・定量するセグメンテーション手法の開発が中心であり、根系という植物形態形質の取得に直接関係するため。

Code and data availability

The paper's CT-derived phenotype datasets (segmented root/soil images) and Python analysis scripts are not publicly deposited; the Data Availability Statement says they are available from the corresponding author upon request, so the paper-specific assets qualify only via author contact.

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