Automated seminal root angle measurement with corrective annotation

TY - JOUR

T1 - Automated seminal root angle measurement with corrective annotation

AU - Smith, Abraham George

AU - Malinowska, Marta

AU - Ruud, Anja Karine

AU - Janss, Luc

AU - Krusell, Lene

AU - Jensen, Jens Due

AU - Asp, Torben

PY - 2024/10/1

Y1 - 2024/10/1

N2 - 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 single nucleotide polymorphisms (SNPs) significantly associated with angle and length, shedding light on the genetic basis of root architecture.

AB - 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 single nucleotide polymorphisms (SNPs) significantly associated with angle and length, shedding light on the genetic basis of root architecture.

KW - AI

KW - QTL

KW - barley

KW - root image analysis

KW - seminal root angle

UR - http://www.scopus.com/inward/record.url?scp=85208107206&partnerID=8YFLogxK

U2 - 10.1093/aobpla/plae046

DO - 10.1093/aobpla/plae046

M3 - Journal article

C2 - 39465185

SN - 2041-2851

VL - 16

JO - AoB Plants

JF - AoB Plants

IS - 5

M1 - plae046

ER -