Automated Seminal Root Angle Measurement with Corrective Annotation

Abstract

Measuring seminal root angle is an important aspect of root phenotyping, yet automated methods are lacking. We introduce SeminalRootAngle, a novel open-source automated method that measures seminal root angles from images. To ensure our method is flexible and user-friendly we build on an established corrective annotation training method for image segmentation. We tested SeminalRootAngle on a heterogeneous dataset of 662 spring barley rhizobox images, which presented challenges in terms of image clarity and root obstruction. Validation of our new automated pipeline against manual measurements yielded a Pearson correlation coefficient of 0.71. We also measure inter-annotator agreement, obtaining a Pearson correlation coefficient of 0.68, indicating that our new pipeline provides similar root angle measurement accuracy to manual approaches. We use our new SeminalRootAngle tool to identify SNPs significantly associated with angle and length, shedding light on the genetic basis of root architecture.

Plant phenotyping relevance

根の表現型である根角度を画像から自動抽出する手法・オープンソースツールを開発し、手動測定との妥当性検証も行っているため、方法が研究の中心である。

Code and data availability

The paper states that its 662-image barley rhizobox dataset is 'freely available under a Creative Commons license at this URL' and that code/installer are open-sourced 'at this URL', but the actual URLs are placeholder text in the PDF and do not match any allowed URL, so no paper-specific asset is actionable. The BayzR

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