Supporting agricultural statistics through multispectral UAV-based crop cover mapping in complex smallholder farming systems in Mozambique

Abstract

Reliable agricultural statistics support food security monitoring and evidence-based decision making. In Mozambique, official agricultural statistics are primarily derived from the Integrated Agricultural Survey (IAI), an enumerator-based field survey that provides essential contextual information on agricultural production but remains labour-intensive, costly and spatially and temporally constrained, particularly in remote rural areas. While satellite remote sensing offers complementary, wall-to-wall coverage, its spatial resolution is often insufficient to directly capture the fragmented fields, mixed and intercropping patterns, shifting cultivation and strong sub-field variability typical of smallholder farming systems. Consequently, consistent estimation of crop area and crop type derived from enumerator-based crop cover assessments remains challenging in these landscapes.This study investigates the potential of high-resolution multispectral data acquired with Uncrewed Aerial Vehicles (UAVs) to complement field surveys by providing spatially explicit and internally consistent crop cover and crop fraction estimates at the field and sub-field scale. By resolving individual crops and dominant intercropping systems, UAV-based observations support the interpretation of farmer-reported crop cover proportions, improve consistency across enumerators, and enable post-survey correction of crop area estimates, while providing a basis for future integration with coarser-resolution satellite remote sensing. High-resolution RGB and multispectral imagery (green, red, red edge, and near-infrared; ≤5 cm ground sampling distance) was collected using a DJI Mavic 3M with RTK over 30 sampling areas of 500 × 500 m in Manica Province during the 2025 agricultural season. In parallel, a field survey recorded standardized observations of agricultural activity, including crop type (of most field and tree crops), intercropping combinations and enumerator-based estimates of fractional crop cover. UAV images were processed using a workflow tailored to heterogeneous smallholder landscapes to produce orthomosaics, digital surface models (DSMs), and vegetation indices. These products were linked to field observations through segments representing relatively homogeneous land units, enabling direct comparison between UAV-derived and survey-based crop cover estimates.For crop classification, training polygons were delineated on RGB orthomosaics for single-crop fields (e.g. maize, beans, sorghum and cassava) and common intercropping combinations (e.g. maize–beans). Annotated mosaics were tiled and augmented and used to train convolutional neural network models (e.g. UNet++), incorporating multispectral vegetation indices and DSM-derived height information as additional input channels. Model performance was evaluated using Intersection over Union, Dice coefficients, and regression metrics for fractional cover accuracy.A comparison framework was implemented to relate UAV-derived crop type, crop combinations and fractional cover to field survey observations while explicitly accounting for measurement uncertainty. Model II regression quantified systematic bias and proportional differences between the two methods. Initial results indicate that UAV-derived estimates provide spatially consistent crop cover information in fields with complex intercropping structures. Ongoing work focuses on refining segmentation accuracy, analysing residual discrepancies and assessing how UAV-derived crop cover information can be integrated to expand the spatial coverage and reliability of agricultural statistics in smallholder landscapes.