Physical model inversion of the green spectral region to track assimilation rate in almond trees with an airborne nano-hyperspectral imager

Abstract Significant advances toward the remote sensing of photosynthetic activity have been achieved in the last decades, including sensor design and radiative transfer model (RTM) development. Nevertheless, finding methods to accurately quantify carbon assimilation across species and spatial scales remains a challenge. Most methods are either empirical and not transferable across scales or can only be applied if highly complex input data are available. Under stress, the photosynthetic rate is limited by the maximum carboxylation rate (Vcmax), which is determined by the leaf biochemistry and the environmental conditions. Vcmax has been connected to plant photoprotective mechanisms, photosynthetic activity and chlorophyll fluorescence emission. Recent RTM developments such as the Soil-Canopy Observation of Photosynthesis and Energy fluxes (SCOPE) model allow the simulation of the sun-induced chlorophyll fluorescence (SIF) and Vcmax effects on the canopy spectrum. This development provides an approach to retrieve Vcmax through RTM model inversion and track assimilation rate. In this study we explore SIF, narrow-band indices and RTM inversion to track changes in photosynthetic efficiency as a function of vegetation stress. We use hyperspectral imagery acquired over an almond orchard under different management strategies which affected the assimilation rates measured in the field. Vcmax used as an indicator of assimilation was retrieved through SCOPE model inversion from pure-tree crown hyperspectral data. The relationships between field-measured assimilation rates and Vcmax retrieved from model inversion were higher (r2 = 0.7–0.8) than when SIF was used alone (r2 = 0.5–0.6) or when traditional vegetation indices were used (r2 = 0.3–0.5). The method was proved successful when applied to two independent datasets acquired at two different dates throughout the season, ensuring its robustness and transferability. When applied to both dates simultaneously, the results showed a unique significant trend between the assimilation measured in the field and Vcmax derived using SCOPE (r2 = 0.56, p