Abraham George Smith, Marta Malinowska, Anja Karine Ruud, Luc Janss, Lene Krusell, Jens Due Jensen, Torben Asp
{"title":"Automated Seminal Root Angle Measurement with Corrective Annotation","authors":"Abraham George Smith, Marta Malinowska, Anja Karine Ruud, Luc Janss, Lene Krusell, Jens Due Jensen, Torben Asp","doi":"10.1093/aobpla/plae046","DOIUrl":null,"url":null,"abstract":"Measuring seminal root angle is an important aspect of root phenotyping, yet au- tomated 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 auto- mated 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, indicat- ing 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","PeriodicalId":48955,"journal":{"name":"AoB Plants","volume":"17 1","pages":""},"PeriodicalIF":2.6000,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"AoB Plants","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/aobpla/plae046","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Measuring seminal root angle is an important aspect of root phenotyping, yet au- tomated 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 auto- mated 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, indicat- ing 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
期刊介绍:
AoB PLANTS is an open-access, online journal that has been publishing peer-reviewed articles since 2010, with an emphasis on all aspects of environmental and evolutionary plant biology. Published by Oxford University Press, this journal is dedicated to rapid publication of research articles, reviews, commentaries and short communications. The taxonomic scope of the journal spans the full gamut of vascular and non-vascular plants, as well as other taxa that impact these organisms. AoB PLANTS provides a fast-track pathway for publishing high-quality research in an open-access environment, where papers are available online to anyone, anywhere free of charge.