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Research article - Peer-reviewed, 2021

Automatic late blight lesion recognition and severity quantification based on field imagery of diverse potato genotypes by deep learning

Gao, Junfeng; Westergaard, Jesper Cairo; Sundmark, Ea Hoegh Riis; Bagge, Merethe; Liljeroth, Erland; Alexandersson, Erik


The plant pathogen Phytophthora infestans causes the severe disease late blight in potato, which can result in huge yield loss for potato production. Automatic and accurate disease lesion segmentation enables fast evaluation of disease severity and assessment of disease progress. In tasks requiring computer vision, deep learning has recently gained tremendous success for image classification, object detection and semantic segmentation. To test whether we could extract late blight lesions from unstructured field environments based on high-resolution visual field images and deep learning algorithms, we collected similar to 500 field RGB images in a set of diverse potato genotypes with different disease severity (0%-70%), resulting in 2100 cropped images. 1600 of these cropped images were used as the dataset for training deep neural networks and 250 cropped images were randomly selected as the validation dataset. Finally, the developed model was tested on the remaining 250 cropped images. The results show that the values for intersection over union (IoU) of the classes background (leaf and soil) and disease lesion in the test dataset were 0.996 and 0.386, respectively. Furthermore, we established a linear relationship (R-2 = 0.655) between manual visual scores of late blight and the number of lesions detected by deep learning at the canopy level. We also showed that imbalance weights of lesion and background classes improved segmentation performance, and that fused masks based on the majority voting of the multiple masks enhanced the correlation with the visual disease scores. This study demonstrates the feasibility of using deep learning algorithms for disease lesion segmentation and severity evaluation based on proximal imagery, which could aid breeding for crop resistance in field environments, and also benefit precision farming. (C) 2021 Elsevier B.V. All rights reserved.


Plant disease; Resistance breeding; Convolutional neural networks; Semantic segmentation; Multi-scale prediction; Mask fusion; Image-based crop phenotyping

Published in

Knowledge-Based Systems
2021, Volume: 214, article number: 106723
Publisher: ELSEVIER