RootHairFinder: An image processing method for quantifying cereal root growth and root hairs simultaneously in a flat rhizotron system

Abstract

Abstract Root system architecture and root hairs highly influence plant resource uptake, yet their simultaneous quantification at the whole-plant scale remains challenging due to the conflicting requirements of high-resolution imaging and non-destructive, repeated measurements. Here, we present a plant growth and imaging system based on A3 sized flatbed rhizotrons, combined with a non–machine-learning image analysis workflow implemented in R, that enables repeated, in situ quantification of cereal root system architecture and root hair area over three weeks of growth. The system produces integrated outputs highlighting both whole-root architecture and the spatial distribution of surrounding root hair area from single images. Validation of the image analysis algorithm showed good segmentation performance, with average Matthews Correlation Coefficient values of 0.68 for root area and 0.65 for root hair area. To demonstrate its experimental applicability, the system was used to assess root growth and root hair responses under controlled environmental conditions, combining three irrigation regimes (2, 4, and 6 irrigation events per day) with three dry bulk density levels (1.4, 1.5, and 1.6 g cm⁻³). In addition to whole-system metrics, the approach enables analysis of root hair expansion at individual root tips. This methodology provides a rapid, scalable, and training-free method for integrated analysis of root architecture and root hairs under controlled physical conditions similar to soil, facilitating studies of root–soil interactions that require both spatial resolution and temporal continuity.

Plant phenotyping relevance

根系画像解析システムとRベースの画像分析ワークフローを開発し、根系構造と根毛面積の定量化およびアルゴリズム性能検証を中心に扱っているため、植物フェノタイピング手法として適格です。

Code and data availability

The paper's authors state that the RootHairFinder C++ file, R script, and example rhizotron data will be available via a GitHub repository and Zenodo upload, and the preprint's supplementary files already include RootHairFinder.cpp and example rhizotron images (Supplimentaryfile4.tif, Supplimentaryfile5.tif). This is a