Database/Software Article | Open Access

Volume 2025 |Article ID 100103 | https://doi.org/10.1016/j.plaphe.2025.100103

LenRuler: a rice-centric method for automated radicle length measurement with multicrop validation

Jinfeng Zhao,^1,3 Zeyu Hou,^2,3 Hua Hua,^1,3 Qianlong Nie,² Yuqian Pang,² Yan Ma ,² and Xuehui Huang¹

¹Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
²College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai, 200234, China
³These authors contributed equally to this work

Abstract

Radicle length is a critical indicator of seed vigor, germination capacity, and seedling growth potential. However, existing measurement methods face challenges in automation, efficiency, and generalizability, often requiring manual intervention or re-annotation for different seed types. To address these limitations, this paper proposes an automated method, LenRuler, with a primary focus on rice seeds and validation in multiple crops. The method leverages the Segment Anything Model (SAM) as the foundational segmentation model and employs a coarse-to-fine segmentation strategy combined with Gaussian-based classification to automatically generate bounding boxes and centroids, which are then fed into SAM for precise segmentation of the seed coat and radicle. The radicle length is subsequently computed by converting the geodesic distance between the radicle skeleton's farthest endpoint and its nearest intersection with the seed coat skeleton into the true length. Experiments on the Riceseed1 dataset show that the proposed method achieves a Dice coefficient of 0.955 and a Pixel Accuracy of 0.944, demonstrating excellent segmentation performance. Radicle length measurement experiments on the Riceseed2 test set show that the Mean Absolute Error (MAE) was 0.273 mm and the coefficient of determination (R2) was 0.982, confirming the method's high precision for rice. On the Otherseed dataset, the predicted radicle lengths for maize (Zea mays), pearl millet (Pennisetum glaucum), and rye (Secale cereale) are consistent with the observed radicle length distributions, demonstrating strong cross-species performance. These results establish LenRuler as an accurate and automated solution for radicle length measurement in rice, with validated applicability to other crop species.