New-generation rice seed germination assessment: high efficiency and flexibility via SeedRuler web-based platform.

Abstract

Introduction The germination rate of rice seed is a critical indicator in agricultural research and production, directly influencing crop yield and quality. Traditional assessment methods based on manual visual inspection are often time-consuming, labor-intensive, and prone to subjectivity. Existing automated approaches, while helpful, typically suffer from limitations such as rigid germination standards, strict imaging requirements, and difficulties in handling the small size, dense arrangement, and variable radicle lengths of rice seeds. Methods To address these challenges, we present SeedRuler, a versatile, web-based application designed to improve the accuracy, efficiency, and usability of rice seed germination analysis. SeedRuler integrates three core components: SeedRuler-IP, a traditional image processing-based module; SeedRuler-YOLO, a deep learning model built on YOLOv5 for high-precision object detection; and SeedRuler-SAM, which leverages the Segment Anything Model (SAM) for fine-grained seed segmentation. A dataset of 1,200 rice seed images was collected and manually annotated to train and evaluate the system. An interactive module enables users to flexibly define germination standards based on specific experimental needs. Results SeedRuler-YOLO achieved a mean average precision (mAP) of 0.955 and a mean absolute error (MAE) of 0.110, demonstrating strong detection accuracy. Both SeedRuler-IP and SeedRuler-SAM support interactive germination standard customization, enhancing adaptability across diverse use cases. In addition, SeedRuler incorporates an automated seed size measurement function developed in our prior work, enabling efficient extraction of seed length and width from each image. The entire analysis pipeline is optimized for speed, delivering germination results in under 30 seconds per image. Conclusions SeedRuler overcomes key limitations of existing methods by combining classical image processing with advanced deep learning models, offering accurate, scalable, and user-friendly germination analysis. Its flexible standard-setting and automated measurement features further enhance usability for both researchers and agricultural practitioners. SeedRuler represents a significant advancement in rice seed phenotyping, supporting more informed decision-making in seed selection, breeding, and crop management.

Plant phenotyping relevance

イネ種子の発芽状態と種子サイズを画像から抽出するウェブ型フェノタイピング手法を開発し、データセットで性能評価しているため、方法が研究の中心である。

Code and data availability

The paper's rice seed germination image dataset (1,200 annotated images) is publicly deposited on Kaggle, and the SeedRuler platform (web tool plus offline software package with user manual) is freely available at the authors' lab site.