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• Soil reflectance composites were generated with Sentinel-2 L2A data. • A multi-channel CNN learning framework for soil organic carbon prediction is proposed. • A dual input deep learning architecture improves the predictions. • The framework produced results that can be interpreted. The Copernicus Sentinel-2 multispectral imagery data may be aggregated to extract large-scale, bare soil, reflectance composites, which enable soil mapping applications. In this paper, this approach was tested in the German federal state of Bavaria, to provide estimations for soil organic carbon (SOC). Different temporal ranges were considered for the generation of the composites, including multi-annual and seasonal ranges. A novel multi-channel convolutional neural network (CNN) is proposed. By leveraging the advantages of deep learning techniques, it utilizes complementary information from different spectral pre-treatment techniques. The SOC predictions indicated little dissimilarity amongst the different composites, with the best performance attained for the six-year composite containing only spring months (RMSE = 12.03 g C · kg−1, R2 = 0.64, RPIQ = 0.89). It has been demonstrated that these outcomes outperform other well-known machine learning techniques. An ablation analysis was accordingly performed to evaluate the interplay of the CNN's different components to disentangle the advantages of each aspect of the proposed framework. Finally, a DUal inPut deep LearnIng architecture, named DUPLICITE, is proposed, which concatenates deep spectral features derived from the CNN mentioned earlier, as well as topographical and environmental covariates through an artificial neural network (ANN) to exploit their complementarity. The proposed approach was demonstrated to provide an improvement in the overall prediction performance (RMSE = 11.60 gC · kg−1, R2 = 0.67, RPIQ = 0.92). [ABSTRACT FROM AUTHOR]

• We provide a UAV-based multispectral imagery approach objectifying FHM strategies. • A CNN was trained using 17,643 images of trees with health status and species labels. • Analysis was done at 235 plots distributed across Bavaria over three years. • The highly heterogenous dataset benefits model generalization and transferability. • We provide a pipeline to generate reference data and for DL image classification. Uncrewed Aerial Vehicles (UAVs) have emerged as a promising tool for complementing terrestrial surveys, offering unique advantages for forest health monitoring (FHM). UAVs have the potential to improve or even replace core tasks such as crown condition assessment, bridging the gap between ground-based surveys and traditional remote sensing platforms. However, present approaches have not yet fully exploited the very high temporal resolution and flexible and convenient utilization that UAVs offer even under cloudy skies. In this paper, we provide a standardized data pipeline to semi-automatically generate reference data and for monitoring forest health by merging ground-based and UAV-based data related to species-specific forest health. Furthermore, we investigated the potential of Convolutional Neural Networks (CNNs) to classify the main tree species and their crown conditions based on the reference data. Therefore, we acquired high resolution multispectral drone imagery of 235 different ICP large scale forest monitoring plots (Level-I plots) distributed across Bavaria for three consecutive years (2020–2022). Using this highly heterogeneous time-series dataset, encompassing diverse weather and lighting conditions, forest stand characteristics, and spatial distribution of study areas, we successfully classified five tree species, three genus level classes and dead trees, including the health status of the main tree species occurring in Germany. This way we managed to classify 14 distinct classes with an average macro F1-score of 0.61 using the EfficientNet CNN architecture. The highest class-specific F1-score apart from the class of dead trees (0.97) was achieved by the class of Picea abies healthy (0.80). If participating countries of the ICP Forests program adopt our approach to harmonize terrestrial and UAV-based monitoring, many ground-based tasks could be reduced or replaced, leading to significant time and cost savings. We provide standardized and open-source monitoring and analysis strategies that can be potentially extended throughout Europe. Our findings demonstrate that UAV monitoring and deep learning can modernize forest management for efficiency and sustainability. We recommend integrating drones with ground surveys in forest monitoring systems to take advantage of their benefits. [ABSTRACT FROM AUTHOR]