In this study, we explore spectral heterogeneity within plant canopies, a characteristic often observed in stressed plants where certain leaves or intra-leaf regions exhibit stress symptoms while others remain unaffected. Considering this variability in spectral signatures holds promise for enhancing remote sensing methodologies aimed at plant stress detection. Typically, remote sensing techniques analyze the plant as a whole, potentially overlooking stress-related spectral signatures due to the inclusion of unaffected pixels. We used a clustering-based technique, which incorporates semi-supervised learning elements for tuning hyper-parameters, to differentiate spectral patterns associated with and unique to pixels from broomrape-infected (Orobanche spp. and Phelipanche spp.) carrots from unrelated patterns. Ground-based hyperspectral (400–1000 nm) images of broomrape-infected and non-infected carrot canopies were used in an agglomerative clustering procedure followed by spectral angle mapper (SAM) analysis to identify a spectral endmember indicative of broomrape infection symptoms. Pixels from this cluster constituted an average of 8.5–11.5 % from the canopies of infected plants. Subsequently, we: (a) examined the relationship between carrot leaf mineral content and the percentage of symptomatic pixels to explore stress-induced alterations creating the unique spectral signatures of infected plants; and (b) utilized the inverse mode of PROSPECT, a radiative transfer model (RTM), to derive primary plant traits from the distinct spectral data of each cluster. We found that deficits in two macro elements, phosphorous and potassium, along with two pigments, chlorophyll and carotenoid, were correlated with the symptomatic cluster in infected plants. The methodology presented in this study paves the way for further research into broomrape detection in various crop species, as well as other plant stressors.

Canopy-intercepted light, or photosynthetically active radiation, is fundamentally crucial for quantifying crop biomass development and yield potential. Fractional photosynthetically active radiation (PAR) (fPAR) is conventionally obtained by measuring the PAR both below and above the canopy using a mobile lightbar platform to predict the potential yield of nut crops. This study proposed a feasible and low-cost method for accurately estimating the canopy fPAR using aerial photogrammetry-based canopy three-dimensional models. We tested up to eight different varieties in three experimental almond orchards, including California's leading variety of 'Nonpareil'. To extract various canopy profile features, such as canopy cover and canopy volume index, we developed a complete data collection and processing pipeline called Virtual Orchard (VO) in Python environment. Canopy fPAR estimated by VO throughout the season was compared against midday canopy fPAR measured by a mobile lightbar platform in midseason, achieving a strong correlation (R ²) of 0.96. A low root mean square error (RMSE) of 2% for 'Nonpareil'. Furthermore, we developed regression models for predicting actual almond yield using both measures, where VO estimation of canopy fPAR, as a stronger indicator, achieved a much better prediction (R ² = 0.84 and RMSE = 195 lb acre^-1) than the lightbar (R ² = 0.70 and RMSE = 266 lb acre^-1) for 'Nonpareil'. Eight different new models for estimating potential yield were also developed using temporal analysis from May to August in 2019 by adjusting the ratio between fPAR and dry kernel yield previously found using a lightbar. Finally, we compared the two measures at two different spatial precision levels: per-row and per-block. fPAR estimated by VO at the per-tree level was also assessed. Results showed that VO estimated canopy fPAR performed better at each precision level than lightbar with up to 0.13 higher R ². The findings in this study serve as a fundamental link between aerial-based canopy fPAR and the actual yield of almonds.