Quantifying Leaf Symptoms of Sorghum Charcoal Rot in Images of Field-Grown Plants 9 Using Deep Neural Networks

Gonzalez, E. M.; Zarei, A.; Calleja, S.; Christenson, C.; Rozzi, B.; Demieville, J.; Hu, J.; Eveland, A. L.; Dilkes, B. L.; Barnard, K.; Lyons, E.; Pauli, D.

doi:10.1101/2024.04.17.589978

bioRxiv · 10.1101/2024.04.17.589978

Quantifying Leaf Symptoms of Sorghum Charcoal Rot in Images of Field-Grown Plants 9 Using Deep Neural Networks

Gonzalez, E. M.·Zarei, A.·Calleja, S.·Christenson, C.·Rozzi, B.·Demieville, J.·Hu, J.·Eveland, A. L.·Dilkes, B. L.·Barnard, K.·Lyons, E.·Pauli, D.

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Abstract

Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red-green-blue (RGB) images of sorghum plants exhibiting symptoms of infection. EfficientNet-B3 and a fully convolutional network (FCN) emerged as the top-performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet-B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models validation scores increased linearly, and their processing time decreased exponentially. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a base for drone-based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web-based application where users can easily analyze their own images. Core ideasO_LIAutomated phenotyping tools are required for the efficient detection and quantification of charcoal rot of sorghum. C_LIO_LIClassification and segmentation models can distinguish between concurrent plant stresses with similar symptoms. C_LIO_LILarger image patch sizes generally improve model performance and reduce processing time. C_LI

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Gonzalez, E. M., Zarei, A., Calleja, S., Christenson, C., Rozzi, B., Demieville, J., Hu, J., Eveland, A. L., Dilkes, B. L., Barnard, K., Lyons, E., Pauli, D.. 2024-04-19. Quantifying Leaf Symptoms of Sorghum Charcoal Rot in Images of Field-Grown Plants 9 Using Deep Neural Networks. https://doi.org/10.1101/2024.04.17.589978

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