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Vegetation indices, such as the Normalised Difference Vegetation Index (NDVI), are 13 common metrics used for measuring traits of interest in crop phenotyping. However traditional 14 measurements of these indices are often influenced by multiple confounding factors such as canopy 15 cover and reflectance of underlying soil, visible in canopy gaps. Digital cameras mounted to 16 Unmanned Aerial Vehicles offer the spatial resolution to investigate these confounding factors, 17 however incomplete methods for radiometric calibration into reflectance units limits how the data 18 can be applied to phenotyping. In this study, we assess the applicability of very high spatial 19 resolution (1cm) UAV-based imagery taken with commercial off the shelf (COTS) digital cameras 20 for both deriving calibrated reflectance imagery, and isolating vegetation canopy reflectance from 21 that of the underlying soil. We present new methods for successfully normalising the imagery for 22 exposure and solar irradiance effects, generating multispectral (RGB-NIR) orthomosaics of our 23 target field based wheat crop trial. Validation against measurements from a ground spectrometer 24 showed good results for reflectance (R2 ≥ 0.6) and NDVI (R2 ≥ 0.88). Application of imagery collected 25 through the growing season and masked using the Excess Green Red index was used to assess the 26 impact of canopy cover on NDVI measurements. Results showed the impact of canopy cover 27 artificially reducing plot NDVI values in the early season, where canopy development is low.

There is a growing need to increase global crop yields, whilst minimising use of resources such as land, fertilisers and water. Agricultural researchers use ground-based observations to identify, select and develop crops with favourable genotypes and phenotypes; however, the ability to collect rapid, high quality and high volume phenotypic data in open fields is restricting this. This study develops and assesses a method for deriving crop height and growth rate rapidly from multi-temporal, very high spatial resolution (1 cm/pixel), 3D digital surface models of crop field trials produced via Structure from Motion (SfM) photogrammetry using aerial imagery collected through repeated campaigns flying an Unmanned Aerial Vehicle (UAV) with a mounted Red Green Blue (RGB) camera. We compare UAV SfM modelled crop heights to those derived from terrestrial laser scanner (TLS) and to the standard field measurement of crop height conducted using a 2 m rule. The most accurate UAV-derived surface model and the TLS both achieve a Root Mean Squared Error (RMSE) of 0.03 m compared to the existing manual 2 m rule method. The optimised UAV method was then applied to the growing season of a winter wheat field phenotyping experiment containing 25 different varieties grown in 27 m2 plots and subject to four different nitrogen fertiliser treatments. Accuracy assessments at different stages of crop growth produced consistently low RMSE values (0.07, 0.02 and 0.03 m for May, June and July, respectively), enabling crop growth rate to be derived from differencing of the multi-temporal surface models. We find growth rates range from −13 mm/day to 17 mm/day. Our results clearly display the impact of variable nitrogen fertiliser rates on crop growth. Digital surface models produced provide a novel spatial mapping of crop height variation both at the field scale and also within individual plots. This study proves UAV based SfM has the potential to become a new standard for high-throughput phenotyping of in-field crop heights.