Automating Leaf Area Measurement in Citrus: The Development and Validation of a Python-Based Tool

Abstract

Leaf area is a critical trait in plant physiology and agronomy, yet conventional measurement approaches such as those using ImageJ remain labor-intensive, user-dependent, and difficult to scale for high-throughput phenotyping. To address these limitations, we developed a fully automated, open-source Python tool for quantifying citrus leaf area from scanned images using multi-mask HSV segmentation, contour-hierarchy filtering, and batch calibration. The tool was validated against ImageJ across 11 citrus cultivars (n = 412 leaves), representing a broad range of leaf sizes and morphologies. Agreement between methods was near perfect, with correlation coefficients exceeding 0.997, mean bias within ±0.14 cm2, and error rates below 2.5%. Bland–Altman analysis confirmed narrow limits of agreement (±0.3 cm2) while scatter plots showed robust performance across both small and large leaves. Importantly, the Python tool successfully handled challenging imaging conditions, including low-contrast leaves and edge-aligned specimens, where ImageJ required manual intervention. Processing efficiency was markedly improved, with the full dataset analyzed in 7 s compared with over 3 h using ImageJ, representing a >1600-fold speed increase. By eliminating manual thresholding and reducing user variability, this tool provides a reliable, efficient, and accessible framework for high-throughput leaf area quantification, advancing reproducibility and scalability in digital phenotyping.

Plant phenotyping relevance

柑橘葉面積の画像ベース測定ツールを開発し、ImageJとの比較検証と高スループット性能評価を行っており、植物フェノタイピング手法が研究の中心である。

Code and data availability

The paper's authors publicly released the Python leaf-area analysis tool (source code and documentation) on GitHub with an archived citable version on Zenodo, as stated in the Data Availability Statement.