Small unmanned aerial systems (UAS) have allowed the mapping of vegetation at very high spatial resolution, but a lack of standardisation has led to uncertainties regarding data quality. For reflectance measurements and vegetation indices (Vis) to be comparable between sites and over time, careful flight planning and robust radiometric calibration procedures are required. Two sources of uncertainty that have received little attention until recently are illumination geometry and the effect of flying height. This study developed methods to quantify and visualise these effects in imagery from the Parrot Sequoia, a UAV-mounted multispectral sensor. Change in illumination geometry over one day (14 May 2018) had visible effects on both individual images and orthomosaics. Average near-infrared (NIR) reflectance and NDVI in regions of interest were slightly lower around solar noon, and the contrast between shadowed and well-illuminated areas increased over the day in all multispectral bands. Per-pixel differences in NDVI maps were spatially variable, and much larger than average differences in some areas. Results relating to flying height were inconclusive, though small increases in NIR reflectance with height were observed over a black sailcloth tarp. These results underline the need to consider illumination geometry when carrying out UAS vegetation surveys.

Historic Environment Scotland (HES) is the lead public body which investigates, promotes and cares for the historic environment in Scotland. It undertakes a range of archaeological airborne work from detailed documentation of individual sites to extensive national programmes of prospection. In undertaking this work HES draws on a variety of aerial platforms to collect imagery, including light aircraft and unmanned aerial vehicles (UAV—used throughout this paper as an umbrella term). In all cases, the archaeological questions at hand are the key driver for choice of methodology and platforms, recognising that different types of survey and documentation demand different responses. Differing strands of aerial work will be briefly described, followed by short case studies that illustrate the range of our activities, concluding with thoughts on the context of UAV work for archaeological applications.

Solar induced chlorophyll fluorescence has been shown to be increasingly an useful proxy for the estimation of gross primary productivity (GPP), at a range of spatial scales. Here, we explore the seasonality in a continuous time series of canopy solar induced fluorescence (hereafter SiF) and its relation to canopy gross primary production (GPP), canopy light use efficiency (LUE), and direct estimates of leaf level photochemical efficiency in an evergreen canopy. SiF was calculated using infilling in two bands from the incoming and reflected radiance using a pair of Ocean Optics USB2000+ spectrometers operated in a dual field of view mode, sampling at a 30 min time step using custom written automated software, from early spring through until autumn in 2011. The optical system was mounted on a tower of 18 m height adjacent to an eddy covariance system, to observe a boreal forest ecosystem dominated by Scots pine. (Pinus sylvestris) A Walz MONITORING-PAM, multi fluorimeter system, was simultaneously mounted within the canopy adjacent to the footprint sampled by the optical system. Following correction of the SiF data for O₂ and structural effects, SiF, SiF yield, LUE, the photochemicsl reflectance index (PRI), and the normalized difference vegetation index (NDVI) exhibited a seasonal pattern that followed GPP sampled by the eddy covariance system. Due to the complexities of solar azimuth and zenith angle (SZA) over the season on the SiF signal, correlations between SiF, SiF yield, GPP, and LUE were assessed on SZA <50° and under strictly clear sky conditions. Correlations found, even under these screened scenarios, resulted around ~r² = 0.3. The diurnal responses of SiF, SiF yield, PAM estimates of effective quantum yield (ΔF/F_m′), and meteorological parameters demonstrated some agreement over the diurnal cycle. The challenges inherent in SiF retrievals in boreal evergreen ecosystems are discussed.

In intensively cultivated landscapes, many archaeological remains are buried under the ploughed soil, and detection depends on crop proxies that express subsurface features. Traditionally these proxies have been documented in visible light as contrasting areas of crop development commonly known as cropmarks. However, it is recognised that reliance on the visible electromagnetic spectrum has inherent limitations on what can be documented, and multispectral and thermal sensors offer the potential to greatly improve our ability to detect buried archaeological features in agricultural fields. The need for this is pressing, as ongoing agricultural practices place many subsurface archaeological features increasingly under threat of destruction. The effective deployment of multispectral and thermal sensors, however, requires a better understanding of when they may be most effective in documenting archaeologically induced responses. This paper presents the first known use of the FLIR Vue Pro-R thermal imager and Red Edge-M for exploring crop response to archaeological features from two UAV surveys flown in May and June 2019 over a known archaeological site. These surveys provided multispectral imagery, which was used to create vegetation index (VI) maps, and thermal maps to assess their effectiveness in detecting crop responses in the temperate Scottish climate. These were visually and statistically analysed using a Mann Whitney test to compare temperature and reflectance values. While the study was compromised by unusually damp conditions which reduced the potential for cropmarking, the VIs (e.g., Normalised Difference Vegetation Index, NDVI) did show potential to detect general crop stress across the study site when they were statistically analysed. This demonstrates the need for further research using multitemporal data collection across case study sites to better understand the interactions of crop responses and sensors, and so define appropriate conditions for large-area data collection. Such a case study-led multitemporal survey approach is an ideal application for UAV-based documentation, especially when “perfect” conditions cannot be guaranteed.

Peatland restoration projects are being employed worldwide as a form of climate change mitigation due to their potential for long-term carbon sequestration. Monitoring these environments (e.g., cover of keystone species) is therefore essential to evaluate success. However, existing studies have rarely examined peatland vegetation at fine scales due to its strong spatial heterogeneity and seasonal canopy development. The present study collected centimetre-scale multispectral Uncrewed Aerial Vehicle (UAV) imagery with a Parrot Sequoia camera (2.8 cm resolution; Parrot Drones SAS, Paris, France) in a temperate peatland over a complete growing season. Supervised classification algorithms were used to map the vegetation at the single-species level, and the Maximum Likelihood classifier was found to perform best at the site level (69% overall accuracy). The classification accuracy increased with the spatial resolution of the input data, and a large reduction in accuracy was observed when employing imagery of >11 cm resolution. Finally, the most accurate classifications were produced using imagery collected during the peak (July–August) or early growing season (start of May). These findings suggest that despite the strong heterogeneity of peatlands, these environments can be mapped at the species level using UAVs. Such an approach would benefit studies estimating peatland carbon emissions or using the cover of keystone species to evaluate restoration projects.

Drones are an increasingly popular choice for wildlife surveys due to their versatility, quick response capabilities, and ability to access remote areas while covering large regions. A novel application presented here is to combine drone imagery with neural networks to assess mortality within a bird colony. Since 2021, Highly Pathogenic Avian Influenza (HPAI) has caused significant bird mortality in the UK, mainly affecting aquatic bird species. The world’s largest northern gannet colony on Scotland’s Bass Rock experienced substantial losses in 2022 due to the outbreak. To assess the impact, RGB imagery of Bass Rock was acquired in both 2022 and 2023 by deploying a drone over the island for the first time. A deep learning neural network was subsequently applied to the data to automatically detect and count live and dead gannets, providing population estimates for both years. The model was trained on the 2022 dataset and achieved a mean average precision (mAP) of 37%. Application of the model predicted 18,220 live and 3761 dead gannets for 2022, consistent with NatureScot’s manual count of 21,277 live and 5035 dead gannets. For 2023, the model predicted 48,455 live and 43 dead gannets, and the manual count carried out by the Scottish Seabird Centre and UK Centre for Ecology and Hydrology (UKCEH) of the same area gave 51,428 live and 23 dead gannets. This marks a promising start to the colony’s recovery with a population increase of 166% determined by the model. The results presented here are the first known application of deep learning to detect dead birds from drone imagery, showcasing the methodology’s swift and adaptable nature to not only provide ongoing monitoring of seabird colonies and other wildlife species but also to conduct mortality assessments. As such, it could prove to be a valuable tool for conservation purposes.