Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants
Pepper production is a critical component of the global agricultural economy, with exports reaching a remarkable $6.9B in 2023. This underscores the crop’s importance as a major economic driver of export revenue for producing nations. <i>Botrytis cinerea</i>, the causative agent of gray...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
|
| Series: | Agriculture |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2077-0472/15/2/164 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832589483446370304 |
|---|---|
| author | Dimitrios Kapetas Eleni Kalogeropoulou Panagiotis Christakakis Christos Klaridopoulos Eleftheria Maria Pechlivani |
| author_facet | Dimitrios Kapetas Eleni Kalogeropoulou Panagiotis Christakakis Christos Klaridopoulos Eleftheria Maria Pechlivani |
| author_sort | Dimitrios Kapetas |
| collection | DOAJ |
| description | Pepper production is a critical component of the global agricultural economy, with exports reaching a remarkable $6.9B in 2023. This underscores the crop’s importance as a major economic driver of export revenue for producing nations. <i>Botrytis cinerea</i>, the causative agent of gray mold, significantly impacts crops like fruits and vegetables, including peppers. Early detection of this pathogen is crucial for a reduction in fungicide reliance and economic loss prevention. Traditionally, visual inspection has been a primary method for detection. However, symptoms often appear after the pathogen has begun to spread. This study employs the Deep Learning algorithm YOLO for single-class segmentation on plant images to extract spatial details of pepper leaves. The dataset included hyperspectral images at discrete wavelengths (460 nm, 540 nm, 640 nm, 775 nm, and 875 nm) from derived vegetation indices (CVI, GNDVI, NDVI, NPCI, and PSRI) and from RGB. At an Intersection over Union with a 0.5 threshold, the Mean Average Precision (mAP50) achieved by the leaf-segmentation solution YOLOv11-Small was 86.4%. The extracted leaf segments were processed by multiple Transformer models, each yielding a descriptor. These descriptors were combined in ensemble and classified into three distinct classes using a K-nearest neighbor, a Long Short-Term Memory (LSTM), and a ResNet solution. The Transformer models that comprised the best ensemble classifier were as follows: the Swin-L (P:4 × 4–W:12 × 12), the ViT-L (P:16 × 16), the VOLO (D:5), and the XCIT-L (L:24–P:16 × 16), with the LSTM-based classification solution on the RGB, CVI, GNDVI, NDVI, and PSRI image sets. The classifier achieved an overall accuracy of 87.42% with an F1-Score of 81.13%. The per-class F1-Scores for the three classes were 85.25%, 66.67%, and 78.26%, respectively. Moreover, for <i>B. cinerea</i> detection during the initial as well as quiescent stages of infection prior to symptom development, qPCR-based methods (RT-qPCR) were used for quantification of <i>in planta</i> fungal biomass and integrated with the findings from the AI approach to offer a comprehensive strategy. The study demonstrates early and accurate detection of <i>B. cinerea</i> on pepper plants by combining segmentation techniques with Transformer model descriptors, ensembled for classification. This approach marks a significant step forward in the detection and management of crop diseases, highlighting the potential to integrate such methods into <i>in situ</i> systems like mobile apps or robots. |
| format | Article |
| id | doaj-art-8fd0824722a641b69ffb2594c374a10c |
| institution | Kabale University |
| issn | 2077-0472 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj-art-8fd0824722a641b69ffb2594c374a10c2025-01-24T13:15:57ZengMDPI AGAgriculture2077-04722025-01-0115216410.3390/agriculture15020164Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper PlantsDimitrios Kapetas0Eleni Kalogeropoulou1Panagiotis Christakakis2Christos Klaridopoulos3Eleftheria Maria Pechlivani4Information Technologies Institute, Centre for Research and Technology Hellas, 57001 Thessaloniki, GreeceLaboratory of Mycology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, 14561 Athens, GreeceInformation Technologies Institute, Centre for Research and Technology Hellas, 57001 Thessaloniki, GreeceiKnowHow S.A., 15451 Athens, GreeceInformation Technologies Institute, Centre for Research and Technology Hellas, 57001 Thessaloniki, GreecePepper production is a critical component of the global agricultural economy, with exports reaching a remarkable $6.9B in 2023. This underscores the crop’s importance as a major economic driver of export revenue for producing nations. <i>Botrytis cinerea</i>, the causative agent of gray mold, significantly impacts crops like fruits and vegetables, including peppers. Early detection of this pathogen is crucial for a reduction in fungicide reliance and economic loss prevention. Traditionally, visual inspection has been a primary method for detection. However, symptoms often appear after the pathogen has begun to spread. This study employs the Deep Learning algorithm YOLO for single-class segmentation on plant images to extract spatial details of pepper leaves. The dataset included hyperspectral images at discrete wavelengths (460 nm, 540 nm, 640 nm, 775 nm, and 875 nm) from derived vegetation indices (CVI, GNDVI, NDVI, NPCI, and PSRI) and from RGB. At an Intersection over Union with a 0.5 threshold, the Mean Average Precision (mAP50) achieved by the leaf-segmentation solution YOLOv11-Small was 86.4%. The extracted leaf segments were processed by multiple Transformer models, each yielding a descriptor. These descriptors were combined in ensemble and classified into three distinct classes using a K-nearest neighbor, a Long Short-Term Memory (LSTM), and a ResNet solution. The Transformer models that comprised the best ensemble classifier were as follows: the Swin-L (P:4 × 4–W:12 × 12), the ViT-L (P:16 × 16), the VOLO (D:5), and the XCIT-L (L:24–P:16 × 16), with the LSTM-based classification solution on the RGB, CVI, GNDVI, NDVI, and PSRI image sets. The classifier achieved an overall accuracy of 87.42% with an F1-Score of 81.13%. The per-class F1-Scores for the three classes were 85.25%, 66.67%, and 78.26%, respectively. Moreover, for <i>B. cinerea</i> detection during the initial as well as quiescent stages of infection prior to symptom development, qPCR-based methods (RT-qPCR) were used for quantification of <i>in planta</i> fungal biomass and integrated with the findings from the AI approach to offer a comprehensive strategy. The study demonstrates early and accurate detection of <i>B. cinerea</i> on pepper plants by combining segmentation techniques with Transformer model descriptors, ensembled for classification. This approach marks a significant step forward in the detection and management of crop diseases, highlighting the potential to integrate such methods into <i>in situ</i> systems like mobile apps or robots.https://www.mdpi.com/2077-0472/15/2/164deep learningsegmentationdescriptor classificationimage classificationvision transformers<i>Botrytis cinerea</i> |
| spellingShingle | Dimitrios Kapetas Eleni Kalogeropoulou Panagiotis Christakakis Christos Klaridopoulos Eleftheria Maria Pechlivani Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants Agriculture deep learning segmentation descriptor classification image classification vision transformers <i>Botrytis cinerea</i> |
| title | Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants |
| title_full | Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants |
| title_fullStr | Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants |
| title_full_unstemmed | Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants |
| title_short | Comparative Evaluation of AI-Based Multi-Spectral Imaging and PCR-Based Assays for Early Detection of <i>Botrytis cinerea</i> Infection on Pepper Plants |
| title_sort | comparative evaluation of ai based multi spectral imaging and pcr based assays for early detection of i botrytis cinerea i infection on pepper plants |
| topic | deep learning segmentation descriptor classification image classification vision transformers <i>Botrytis cinerea</i> |
| url | https://www.mdpi.com/2077-0472/15/2/164 |
| work_keys_str_mv | AT dimitrioskapetas comparativeevaluationofaibasedmultispectralimagingandpcrbasedassaysforearlydetectionofibotrytiscinereaiinfectiononpepperplants AT elenikalogeropoulou comparativeevaluationofaibasedmultispectralimagingandpcrbasedassaysforearlydetectionofibotrytiscinereaiinfectiononpepperplants AT panagiotischristakakis comparativeevaluationofaibasedmultispectralimagingandpcrbasedassaysforearlydetectionofibotrytiscinereaiinfectiononpepperplants AT christosklaridopoulos comparativeevaluationofaibasedmultispectralimagingandpcrbasedassaysforearlydetectionofibotrytiscinereaiinfectiononpepperplants AT eleftheriamariapechlivani comparativeevaluationofaibasedmultispectralimagingandpcrbasedassaysforearlydetectionofibotrytiscinereaiinfectiononpepperplants |