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Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections.
Sci Rep. 2021 11 30; 11(1):23109.SR

Abstract

Tomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000-1700 nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390-1420 nm contributes most to the model's final decision.

Authors+Show Affiliations

BioSense Institute, University of Novi Sad, 21000, Novi Sad, Serbia. sanja.brdar@biosense.rs.BioSense Institute, University of Novi Sad, 21000, Novi Sad, Serbia.Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.BioSense Institute, University of Novi Sad, 21000, Novi Sad, Serbia.Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.Wageningen University and Research, 6708 PB, Wageningen, The Netherlands. aneesh.chauhan@wur.nl.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34848748

Citation

Brdar, Sanja, et al. "Predicting Sensitivity of Recently Harvested Tomatoes and Tomato Sepals to Future Fungal Infections." Scientific Reports, vol. 11, no. 1, 2021, p. 23109.
Brdar S, Panić M, Hogeveen-van Echtelt E, et al. Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections. Sci Rep. 2021;11(1):23109.
Brdar, S., Panić, M., Hogeveen-van Echtelt, E., Mensink, M., Grbović, Ž., Woltering, E., & Chauhan, A. (2021). Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections. Scientific Reports, 11(1), 23109. https://doi.org/10.1038/s41598-021-02302-2
Brdar S, et al. Predicting Sensitivity of Recently Harvested Tomatoes and Tomato Sepals to Future Fungal Infections. Sci Rep. 2021 11 30;11(1):23109. PubMed PMID: 34848748.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections. AU - Brdar,Sanja, AU - Panić,Marko, AU - Hogeveen-van Echtelt,Esther, AU - Mensink,Manon, AU - Grbović,Željana, AU - Woltering,Ernst, AU - Chauhan,Aneesh, Y1 - 2021/11/30/ PY - 2021/07/04/received PY - 2021/11/10/accepted PY - 2021/12/1/entrez PY - 2021/12/2/pubmed PY - 2022/2/15/medline SP - 23109 EP - 23109 JF - Scientific reports JO - Sci Rep VL - 11 IS - 1 N2 - Tomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000-1700 nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390-1420 nm contributes most to the model's final decision. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/34848748/Predicting_sensitivity_of_recently_harvested_tomatoes_and_tomato_sepals_to_future_fungal_infections_ L2 - https://doi.org/10.1038/s41598-021-02302-2 DB - PRIME DP - Unbound Medicine ER -