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

Yuki Kojima (), Takeru Toda, Shoichiro Hamamoto, Yutaka Ohtake and Kohji Kamiya
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Yuki Kojima: Department of Civil Engineering, Gifu University, 1-1 Yanagido, Gifu City 501-1193, Gifu, Japan
Takeru Toda: Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu City 501-1193, Gifu, Japan
Shoichiro Hamamoto: Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Hokkaido, Japan
Yutaka Ohtake: Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
Kohji Kamiya: Department of Civil Engineering, Gifu University, 1-1 Yanagido, Gifu City 501-1193, Gifu, Japan

Agriculture, 2025, vol. 15, issue 13, 1-12

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.

Keywords: plant root system; soil structure; X-ray CT; image analysis (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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