Assessing plant area index and 3D plant area distribution in wheat canopies from a terrestrial LiDAR system for high-throughput plant phenotyping

This study investigates a new methodology to estimate plant area index ( PAI ) and its spatial distribution from 3D point clouds acquired by a system of 3 LiDARs (2 nadir-viewing and one at 45°) mounted on the Phenomobile Unmanned Ground Vehicle designed for high-throughput phenotyping of herbaceous crops. It relies on the computation of the gap fraction at the voxel level using the trajectories of the laser beams to numerically invert the Beer-Lambert law (BL), enabling the simultaneous estimation of PAI and AIA (Average Inclination Angle, in°). The method is evaluated on wheat crops both in silico (i.e. simulations based on the AdelWheat functional structural crop model coupled with a point cloud simulator) and in actual phenotyping trials of a panel of 10 bread wheat genotypes grown in two study sites under different treatments of plant density, water stress and sowing dates. The in silico validation indicates that the numeric inversion of BL with the LiDAR system of the Phenomobile leads to a relative error of 9.8% (RMSE = 0.32, R 2 = 0.99) and 8.4% (RMSE =5.4°, R 2 = 0.95) in the estimation of PAI and AIA , respectively. The validation in actual phenotyping experiments against destructive measurements produced satisfactory results for canopy PAI (RMSE = 1.44, R 2 = 0.82), while requiring prior knowledge on AIA , e.g. either by (i) introducing a regularization term in the cost function used to invert BL, to avoid unexpected high AIA estimations, (ii) using a fixed, reference value of 60°. The analysis of the results indicates that the inclusion of a regularization term mitigates the impact of actual differences in leaf inclination among cultivars on PAI accuracy, while providing a relative description of the actual variability in the vertical profile of leaf inclination across the different cultivars.