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6 January 2026

Direct UAV-Based Detection of Botrytis cinerea in Vineyards Using Chlorophyll-Absorption Indices and YOLO Deep Learning

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Computer Science Department, ETSE—Universitat de València, 46100 Valencia, Spain
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Knowledge Genesis Group, Smart Enterprise, Samara State Technical University, 443100 Samara, Russia
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Authors to whom correspondence should be addressed.
This article belongs to the Special Issue AI-IoT for New Challenges in Smart Cities

Abstract

The transition toward Agriculture 5.0 requires intelligent and autonomous monitoring systems capable of providing early, accurate, and scalable crop health assessment. This study presents the design and field evaluation of an artificial intelligence (AI)–based unmanned aerial vehicle (UAV) system for the detection of Botrytis cinerea in vineyards using multispectral imagery and deep learning. The proposed system integrates calibrated multispectral data with vegetation indices and a YOLOv8 object detection model to enable automated, geolocated disease detection. Experimental results obtained under real vineyard conditions show that training the model using the Chlorophyll Absorption Ratio Index (CARI) significantly improves detection performance compared to RGB imagery, achieving a precision of 92.6%, a recall of 89.6%, an F1-score of 91.1%, and a mean Average Precision (mAP@50) of 93.9%. In contrast, the RGB-based configuration yielded an F1-score of 68.1% and an mAP@50 of 68.5%. The system achieved an average inference time below 50 ms per image, supporting near real-time UAV operation. These results demonstrate that physiologically informed spectral feature selection substantially enhances early Botrytis cinerea detection and confirm the suitability of the proposed UAV–AI framework for precision viticulture within the Agriculture 5.0 paradigm.

2. Materials and Methods

2.1. Study Overview

In this study an AI-UAV based detection system has been developed to detect Botrytis cinerea micoinfection in vineyards. The software of this system integrates multispectral imaging (taken with UAVs), computation of vegetation indices, and deep learning to detect Botrytis micoinfections in vines. The methodology used here agrees with the Agriculture 5.0 paradigm in which we have a combination of automated aerial sensing with artificial intelligence to enable data-driven decision-making and early detection of crop stress.

2.2. Study Area and Data Acquisition

The dataset used in this work originates from the experimental vineyard in Villena (Spain) located at the coordinates (lat, long) = (38.624217, −0.955320). Multispectral images were collected using the multispectral camera of a DJI Mavic 3M (DJI, Nanshan District, Shenzhen, China). While limited geographically, the physiological basis of CARI makes the approach transferable across grape varieties and canopy architectures. The UAV flights were conducted under stable illumination and low-wind conditions at an altitude of 40 m above ground level, ensuring a ground sampling distance (GSD) of approximately 1.1 cm/pixel for 20MP RGB camera (for 5MP multispectral camera is around 4.2 cm/pixel). Each flight captured five spectral bands—Green (560 nm), Red (650 nm), Red Edge (730 nm), and Near-Infrared (860 nm)—enabling the computation of chlorophyll sensitive vegetation indices. Radiometric calibration was performed using MicaSense calibration panels to correct for irradiance variations following the procedures described by Fawcett et al. [3].

2.3. Image Pre-Processing and Vegetation Indices

RAW images were processed in Python 3.11 using the MicaSense SDK (https://github.com/micasense/imageprocessing accessed on 4 January 2026) and standard libraries such as OpenCV (v4.10.0.84) [14], Rasterio (v1.3.10) [15], NumPy (v2.0) [16], and Matplotlib (v3.8.4) [17]. Band alignment was performed using the Scale-Invariant Feature Transform (SIFT) algorithm to ensure accurate pixel correspondence between spectral channels [18]. The reflectance values were normalized and a series of vegetation indices were computed, including CIG, CIRE, CVI, NDRE, NDVI, GNDVI, NGRDI, CARI, and MCARI. These indices were selected for their sensitivity to chlorophyll content, foliar pigmentation, and physiological stress, as supported by Haboudane et al. (2004) [1] and Main et al. (2011) [2].
In our case, the drone (DJI Mavic 3M) captures high-resolution images across multiple spectral bands: Green (560 nm ± 16 nm), Red (650 nm ± 16 nm), Red Edge (730 nm ± 16 nm), Near-Infrared (860 nm ± 26 nm) at 5MP, and standard RGB at 20MP. Each capture results in four images (one per band), which are transmitted to a cloud in TIFF format to preserve image quality and spectral information and another one in JPEG format containing RGB information.
The following tasks are needed for each capture:
  • Metadata Extraction: Extracts geolocation, camera settings, and other relevant metadata from the images.
  • Vignetting Correction: Applies correction algorithms to mitigate vignetting effects present in the images.
  • Image Alignment: Uses a transformation matrix to align images from different spectral bands, correcting distortions due to multiple cameras.
  • Spectral Indices Calculation: Computes nine spectral indices based on the different spectral bands to analyse vegetation health and characteristics computed from the captured spectral bands Near-Infrared (NIR), Red (R), Red Edge (RE), and Green (G). Each index provides insights based on specific combinations of these bands. Table 2 lists the indices, their corresponding formulas, and full names.
Table 2. List of Computed Spectral Indices [19].
Figure 3 shows in two parts the flux diagram of the image processing and the detection process with YOLO.
Figure 3. Flux diagram of the detection process.
Table 2 describes the different multispectral indexes that have been considered to be computed in the disease detection monitoring system. In this table, R stands for ‘Red reflectance’, G for ‘Green reflectance’. RE for ‘Red Edge reflectance’, and NIR for ‘Near Infrared reflectance’.

2.4. Dataset Preparation and Annotation

The image corpus used in this study was acquired using a DJI Mavic 3 Multispectral UAV over an experimental vineyard located in Villena (Spain). Data collection was conducted during the growing season under stable illumination and low-wind conditions. The multispectral payload of the UAV captures five spectral bands—Green (560 nm), Red (650 nm), Red Edge (730 nm), and Near-Infrared (860 nm) at 5 MP resolution, as well as RGB imagery at 20 MP resolution.
A total of 1575 RGB images were collected, and the corresponding multispectral image sets each consisted of four aligned spectral band images. The resulting ground sampling distance was approximately 1 cm/pixel for RGB images and 4 cm/pixel for multispectral images, allowing individual grape clusters and leaf regions to be resolved. Images were radiometrically calibrated using MicaSense calibration panels and geometrically aligned prior to analysis.
The dataset includes images of both healthy vegetation and vines affected by Botrytis cinerea, with infection symptoms verified through field inspection. Manual annotation was performed using the Roboflow platform [20] by domain-trained operators. Bounding boxes were assigned to image regions exhibiting visible or spectral indicators of Botrytis cinerea infection, while healthy vegetation areas were left unlabelled, consistent with single-class object detection protocols.
In total, a number of approximately 200 annotated instances of Botrytis cinerea were identified across the dataset. The annotated corpus was divided into training (70%), validation (20%), and testing (10%) subsets at the image level to avoid data leakage. Data augmentation techniques, including rotation, scaling, brightness adjustment, and cropping, were applied exclusively to the training set to improve generalization, consistent with methods in plant-disease detection literature [4].
This dataset provides a representative sample of vineyard conditions, canopy densities, and illumination variability, supporting the evaluation of the proposed UAV–AI detection framework under realistic operational scenarios.

2.5. Deep Learning Architecture

For automatic detection, the You Only Look Once (YOLOv8) architecture was used, a state-of-the-art object detection network known for real-time performance [8]. The model was trained for 300 epochs using a learning rate of 0.001, stochastic gradient descent (SGD) optimization, and batch normalization. Transfer learning was applied using pre-trained weights from the COCO dataset to accelerate convergence. All experiments were executed on a workstation equipped with an AMD Ryzen 5 3600 CPU, 16 GB RAM, and an NVIDIA RTX 3060 GPU (12 GB VRAM). The evaluation of the model was based on the precision, recall, and F1-score metrics.

2.6. Web-Based Visualization

A lightweight web application was developed using the Flask framework [21] and Flask-SQLAlchemy for database management. The platform allows users to visualize both raw RGB images and processed vegetation index layers, along with YOLO-based detection overlays. Public users can access limited visualizations, while registered users can query complete datasets for advanced analysis.

2.7. Performance Evaluation

In order to evaluate the model performance, and considering confusion matrix with true positive (TP), true negative (TN), false positive (FP) and false negative, we have used Precision, Recall, and F1-score metrics, as defined in Equations (1)–(4). Confusion matrices and precision–recall curves were computed to assess classification robustness.
Accuracy = T P + T N T P + T N + F P + F N
Precision = T P T P + F P
Recall = T P T P + F N
F 1 s c o r e = 2 · Precision · Recall Precision + Recall
To this end, we have evaluated and compared two training configurations: one using RGB images and another using the CARI index (Chlorophyll Absorption Ratio Index). The process for calculating Average Precision consists of several steps. First, the model is used to generate the prediction scores. The model outputs bounding box predictions associated with confidence scores. These predictions are ranked by confidence, and a precision–recall curve is computed by varying the detection threshold. The Average Precision (AP) is then calculated as the area under the precision–recall curve. The mean Average Precision (mAP) is obtained by averaging AP values across all classes, following standard object detection evaluation protocols.
The mean Average Precision (mAP) is computed by calculating the AP for each class and then taking the average across all classes, as shown in Equation (5). Because mAP captures the balance between precision and recall and accounts for both false positives and false negatives, it is considered an appropriate metric for most detection applications.
m A P = 1 N i = 1 N A P i

3. Results and Discussion

3.1. Model Performance

This study developed a UAV-AI–based detection system designed to identify Botrytis cinerea infections in vineyard crops, integrating multispectral imaging, vegetation indices, and deep learning.
The developed UAV-AI detection system has demonstrated strong performance in identifying Botrytis cinerea symptoms under real vineyard conditions. Table 3 shows a summary of the performance evaluation for each dataset. The quantitative performance metrics reported in Table 3 were calculated throughout the test subset, comprising approximately 200 annotated Botrytis cinerea instances across 1575 multispectral images. Each detected bounding box was evaluated against ground-truth annotations generated on the Roboflow platform. Figure 4 and Figure 5 present representative examples selected from this evaluation to illustrate typical spectral responses and detection outputs.
Table 3. Performance evaluation of the action of the YOLO training with different datasets.
Figure 4. Multispectral indexes combinations: (a) CARI, (b) MCARI, (c) CIG, and (d) CIRE.
Figure 5. Detection results of Botrytis with YOLO-CARI model.
The superior performance of the CARI-based configuration can be explained by the different spectral sensitivities of the vegetation indices and their relationship with chlorophyll absorption mechanisms. NDVI, defined as the normalized difference between near-infrared (NIR) and red reflectance, combines chlorophyll absorption effects in the red band with structural scattering effects in the NIR band. While NDVI is effective for assessing vegetation vigor and biomass, it tends to saturate in dense canopies and is strongly influenced by canopy geometry, row structure, soil background, and illumination variability, which limits its sensitivity to early physiological stress and pathogen-induced pigment degradation [1,2].
The Chlorophyll Index Green (CIG) improves sensitivity to chlorophyll concentration by incorporating green reflectance, which is inversely related to pigment content. However, green-band reflectance is only indirectly linked to chlorophyll absorption and remains sensitive to changes in illumination, leaf angle distribution, and specular reflection, particularly under heterogeneous vineyard conditions. Moreover, the continued reliance on NIR reflectance introduces structural effects that are not directly related to disease progression.
In contrast, the Chlorophyll Absorption Ratio Index (CARI) is specifically designed to isolate chlorophyll absorption features by exploiting the spectral contrast between the red and red-edge bands while applying a baseline correction using green reflectance. This formulation reduces the influence of non-physiological brightness variations, soil background effects, and canopy structural heterogeneity, allowing CARI to more effectively capture subtle biochemical changes associated with chlorophyll degradation [1]. Red-edge-based indices have been shown to be particularly sensitive to early stress conditions, as shifts in the red-edge slope occur prior to visible symptoms and before significant changes in NIR reflectance are observed [2,22]. Figure 4 shows the multispectral combinations of images for these indexes.
This property is especially relevant for the detection of Botrytis cinerea, as early infection stages primarily affect chlorophyll content and cellular integrity rather than canopy structure. Consequently, indices that emphasize chlorophyll absorption dynamics rather than structural contrast are better suited for early disease detection. The enhanced physiological specificity of CARI results in higher local contrast and reduced background variability in multispectral representations, which in turn facilitates more discriminative feature extraction by the YOLO-based object detection model.
The YOLOv8 model trained on multispectral data derived from the CARI (Chlorophyll Absorption Ratio Index) achieved a precision of 0.93, recall of 0.90, and F1-score of 0.91. In contrast, the RGB-based model yielded precision and recall values of 0.72 and 0.65, respectively, corresponding to an F1-score of 0.68. The 34% relative increase in F1 confirms the added value of spectral indices in enhancing feature separability and robustness to illumination changes. Similar results were reported by Kerkech et al. (2020) [4] and Vélez et al. (2023) [7], who observed improved classification accuracy using multispectral UAV data for vine disease detection.

3.2. Model Robustness and Environmental Conditions

The system maintained reliable detection across varying sunlight and canopy densities, with an average inference time below 50 ms per image—suitable for near real-time UAV operation. However, accuracy slightly declined under overcast conditions, consistent with the limitations reported by Fawcett et al. (2020) [3]. The trained YOLO-CARI model’s resilience suggests that integrating reflectance calibration and adaptive exposure correction can further enhance operational stability. Figure 5 shows an inference for the detection of Botrytis in a field in Villena with the YOLO-CARI model.

3.3. Comparison with Related Studies

Compared with existing approaches, such as pixel-based classification [23] or CNN models trained solely on RGB imagery [24], the proposed method achieves a higher detection precision with lower computational overhead. Furthermore, the web-based interface enables end-users to visualize detections and spectral indices, bridging the gap between AI outputs and actionable agricultural decisions—an essential component of precision agriculture systems [25,26].

3.4. Implications for Agriculture 5.0

The presented UAV-AI configuration illustrates how autonomous sensing and intelligent data analytics can contribute to the transition from Agriculture 4.0 to Agriculture 5.0. By coupling machine vision with automated aerial platforms, the system supports continuous monitoring, early disease mitigation, and resource-efficient interventions. This integration exemplifies the principles of smart, sustainable, and self-adaptive agricultural ecosystems envisioned for the next generation of precision farming [9,27].

4. Conclusions

This study presents an integrated UAV–AI system for early detection of Botrytis cinerea in vineyard crops, demonstrating how multispectral imaging and deep learning can be effectively combined to advance Agriculture 5.0 principles. The proposed system, based on the YOLOv8 architecture and CARI vegetation index, achieved an F1-score of 0.91, outperforming the RGB-based configuration by approximately 34%. This improvement confirms that chlorophyll-sensitive spectral indices and red-edge reflectance provide superior discrimination of stress-related patterns, enabling early identification of fungal infections.
The developed framework also highlights the potential to combine real-time UAV sensing with autonomous AI analytics for operational decision support. The inference speed achieved (<50 ms per image) and the consistent accuracy under field conditions position the system as a practical tool for precision viticulture, capable of reducing manual inspection time and improving sustainability through targeted interventions.
Beyond viticulture, this UAV–AI configuration can be adapted to a wide range of crops and stress factors, contributing to the transition from reactive to predictive agricultural management. Future work will focus on integrating temporal monitoring, adaptive learning, and edge-computing capabilities to enhance autonomy and scalability, further aligning with the Agriculture 5.0 paradigm of intelligent, data-driven, and environmentally responsible farming systems.

Author Contributions

Conceptualization, G.M.-F., J.S.-G. and M.G.-P.; methodology, J.S.-G., M.G.-P., G.M.-F. and E.P.-M.; software, G.M.-F. and E.P.-M.; validation, R.F.-J., P.B.-C. and A.L.; formal analysis, E.P.-M. and G.M.-F.; investigation, E.P.-M. and G.M.-F.; resources, J.S.-G. and M.G.-P.; data curation, E.P.-M.; writing—original draft preparation, G.M.-F. and J.S.-G.; writing—review and editing, M.G.-P., R.F.-J. and P.B.-C.; project administration, J.S.-G.; funding acquisition, J.S.-G. and M.G.-P. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Agencia Estatal de Investigación (AEI) and the European Regional Development Fund (ERDF) for funding this research within the projects with grant references TED2021-131040B-C33 (Agriculture 6.0) funded in the programme “Proyectos Estratégicos para la Transición Ecológica y Digital 2021” by MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR. The authors also acknowledge the Generalitat Valenciana, for the funding of the DRONIA project, with reference INREIA/2024/164 and the European Union NextGenerationEU/PRTR. Also for the funding of the research stay in companies (grant nr. CIAEST/2024/110).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The raw data supporting the conclusions of this article will be made available by the authors on request.

Acknowledgments

The authors would also like to thank the company IDS Topografía for the support and help provided in the context of the “Agricultura 6.0” project. During the preparation of this manuscript/study, the authors used ChatGPT4 for the purposes of translation, language improvement and text adaptation. The authors have reviewed and edited the output and take full responsibility for the content of this publication.

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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