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The emission of solar-induced chlorophyll fluorescence (F) is a pivotal process to infer vegetation health and functioning that can be monitored by remote sensing. However, most of the current remote sensing methods retrieve only F at top-of-canopy level, therefore making the link with physiological processes occurring at photosystem level not trivial. In this study, we develop a novel machine learning Fourier (phasor)-based algorithm to retrieve F both at canopy level and after considering the reabsorption (i.e. photosystem level), consistently with relevant biophysical variables, exploiting the canopy apparent reflectance spectra (Rapp). In particular, Rapp is divided in consecutive spectral windows, where the Discrete Fourier Transform (DFT) is computed. Then, the DFT results in each window are exploited to estimate the fluorescence spectra and biophysical parameters, together with their uncertainties, by means of a supervised machine learning algorithm coupled to a statistical-based retrieval pipeline. The algorithm has been trained through synthetic Rapp spectra, obtained from simulations based on a Radiative Transfer (RT) model. As a proof of concept, the theoretical approach is then applied to experimental data, acquired both from crops and forests, at close and high soil-sensor distance respectively, to evaluate the retrieval accuracy of biophysical and F parameters. In particular, for the first time Rapp is used to extract the temporal evolution of F at canopy and photosystem levels and its quantum efficiency together with different biophysical variables, during the growing season of two agricultural crops. Furthermore, tower-based solar-induced fluorescence measurements in a deciduous forest are exploited to evaluate the performance of our algorithm when the atmospheric reabsorption and scattering are not negligible. The reliability of the proposed method is evaluated through a comparison with F spectra extracted from the state of the art SpecFit retrieval

Vegetation responds at varying temporal scales to changing soil water availability. These process dynamics complicate assessments of plant-water relations but also offer various access points to advance understanding of vegetation responses to environmental change. Remote sensing (RS) provides large capacity to quantify sensitive and robust information of vegetation responses and underlying abiotic change driver across observational scales. Retrieved RS based vegetation parameters are often sensitive to various environmental and plant specific factors in addition to the targeted plant response. Further, individual plant responses to water limitation act at different temporal and spatial scales, while RS sampling schemes are often not optimized to assess these dynamics. The combination of these aspects complicates the interpretation of RS parameter when assessing plant-water relations. We consequently aim to advance insight on the sensitivity of physiological, biochemical and structural RS parameter for plant adaptation in response to emerging soil water limitation. We made a field experiment in maize in Tuscany (Central Italy), while irrigation was stopped in some areas of the drip-irrigated field. Within a period of two weeks, we measured the hydraulic and physiological state of maize plants in situ and complemented these detailed measurements with extensive airborne observations (e.g. sun-induced chlorophyll fluorescence (SIF), vegetation indices sensitive for photosynthesis, pigment and water content, land surface temperature). We observe a double response of far-red SIF with a short-term increase after manifestation of soil water limitation and a decrease afterwards. We identify different response times of RS parameter representing different plant adaptation mechanisms ranging from short term responses (e.g. stomatal conductance, photosynthesis) to medium term changes (e.g. pigment decomposition, changing leaf water content). Our study demonstrates complementari

Vegetation responds at varying temporal scales to changing soil water availability. These process dynamics complicate assessments of plant-water relations but also offer various access points to advance understanding of vegetation responses to environmental change. Remote sensing (RS) provides large capacity to quantify sensitive and robust information of vegetation responses and underlying abiotic change driver across observational scales. Retrieved RS based vegetation parameters are often sensitive to various environmental and plant specific factors in addition to the targeted plant response. Further, individual plant responses to water limitation act at different temporal and spatial scales, while RS sampling schemes are often not optimized to assess these dynamics. The combination of these aspects complicates the interpretation of RS parameter when assessing plant-water relations. We consequently aim to advance insight on the sensitivity of physiological, biochemical and structural RS parameter for plant adaptation in response to emerging soil water limitation. We made a field experiment in maize in Tuscany (Central Italy), while irrigation was stopped in some areas of the drip-irrigated field. Within a period of two weeks, we measured the hydraulic and physiological state of maize plants in situ and complemented these detailed measurements with extensive airborne observations (e.g. sun-induced chlorophyll fluorescence (SIF), vegetation indices sensitive for photosynthesis, pigment and water content, land surface temperature). We observe a double response of far-red SIF with a short-term increase after manifestation of soil water limitation and a decrease afterwards. We identify different response times of RS parameter representing different plant adaptation mechanisms ranging from short term responses (e.g. stomatal conductance, photosynthesis) to medium term changes (e.g. pigment decomposition, changing leaf water content). Our study demonstrates complementari

The contribution presents the development and testing of a fluorescence retrieval scheme based on the ESA's FLuorescence EXplorer mission concept. The algorithm employs on a coupled surface-atmosphere forward model at oxygen absorption bands: i) the atmospheric effect is computed by MODTRAN5; ii) the surface reflectance and fluorescence are modeled by means of the Spectral Fitting approach. The algorithm, previously tested on numerical simulations, was further implemented and optimized to process real observations collected by the FLEX airborne demonstrator HyPlant. The retrieval scheme has been tested on a number of flight lines collected in several locations, different ecosystems types, atmospheric conditions and instrument observation conditions. For the first time, this work shows the capability of retrieving canopy fluorescence from real airborne observations by means of a physically-based algorithm as envisaged for FLEX. The results achieved on the large core data sets of imageries show the consistency of the physical retrieval algorithm for a wide range of scenarios and fluorescence values are in line with ground observations.

The contribution presents the development and testing of a fluorescence retrieval scheme based on the ESA's FLuorescence EXplorer mission concept. The algorithm employs on a coupled surface-atmosphere forward model at oxygen absorption bands: i) the atmospheric effect is computed by MODTRAN5; ii) the surface reflectance and fluorescence are modeled by means of the Spectral Fitting approach. The algorithm, previously tested on numerical simulations, was further implemented and optimized to process real observations collected by the FLEX airborne demonstrator HyPlant. The retrieval scheme has been tested on a number of flight lines collected in several locations, different ecosystems types, atmospheric conditions and instrument observation conditions. For the first time, this work shows the capability of retrieving canopy fluorescence from real airborne observations by means of a physically-based algorithm as envisaged for FLEX. The results achieved on the large core data sets of imageries show the consistency of the physical retrieval algorithm for a wide range of scenarios and fluorescence values are in line with ground observations.

Retrieval of Sun-Induced Chlorophyll Fluorescence (F) spectrum is one of the challenging perspectives for further advancing F studies towards a better characterization of vegetation structure and functioning. In this study, a simplified Spectral Fitting retrieval algorithm suitable for retrieving the F spectrum with a limited number of parameters is proposed (two parameters for F). The novel algorithm is developed and tested on a set of radiative transfer simulations obtained by coupling SCOPE and MODTRAN5 codes, considering different chlorophyll content, leaf area index and noise levels to produce a large variability in fluorescence and reflectance spectra. The retrieval accuracy is quantified based on several metrics derived from the F spectrum (i.e., red and far-red peaks, O2 bands and spectrally-integrated values). Further, the algorithm is employed to process experimental field spectroscopy measurements collected over different crops during a long-lasting field campaign. The reliability of the retrieval algorithm on experimental measurements is evaluated by cross-comparison with F values computed by an independent retrieval method (i.e., SFM at O2 bands). For the first time, the evolution of the F spectrum along the entire growing season for a forage crop is analyzed and three diverse F spectra are identified at different growing stages. The results show that red F is larger for young canopy; while red and far-red F have similar intensity in an intermediate stage; finally, far-red F is significantly larger for the rest of the season.

Hyperspectral remote sensing (RS) provides unique possibilities to monitor peatland vegetation traits and their temporal dynamics at a fine spatial scale. Peatlands provide a vital contribution to ecosystem services by their massive carbon storage and wide heterogeneity. However, monitoring, understanding, and disentangling the diverse vegetation traits from a heterogeneous landscape using complex RS signal is challenging, due to its wide biodiversity and distinctive plant species composition. In this work, we aim to demonstrate, for the first time, the large heterogeneity of peatland vegetation traits using well-established vegetation indices (VIs) and Sun-Induced Fluorescence (SIF) for describing the spatial heterogeneity of the signals which may correspond to spatial diversity of biochemical and structural traits. SIF originates from the initial reactions in photosystems and is emitted at wavelengths between 650–780 nm, with the first peak at around 687 nm and the second peak around 760 nm. We used the first HyPlant airborne data set recorded over a heterogeneous peatland area and its surrounding ecosystems (i.e., forest, grassland) in Poland. We deployed a comparative analysis of SIF and VIs obtained from differently managed and natural vegetation ecosystems, as well as from diverse small-scale peatland plant communities. Furthermore, spatial relationships between SIF and VIs from large-scale vegetation ecosystems to small-scale peatland plant communities were examined. Apart from signal variations, we observed a positive correlation between SIF and greenness-sensitive VIs, whereas a negative correlation between SIF and a VI sensitive to photosynthesis was observed for large-scale vegetation ecosystems. In general, higher values of SIF were associated with higher biomass of vascular plants (associated with higher Leaf Area Index (LAI)). SIF signals, especially SIF760, were strongly associated with the functional diversity of the peatland vegetation. At the peatl

Retrieval of Sun-Induced Chlorophyll Fluorescence (F) spectrum is one of the challenging perspectives for further advancing F studies towards a better characterization of vegetation structure and functioning. In this study, a simplified Spectral Fitting retrieval algorithm suitable for retrieving the F spectrum with a limited number of parameters is proposed (two parameters for F). The novel algorithm is developed and tested on a set of radiative transfer simulations obtained by coupling SCOPE and MODTRAN5 codes, considering different chlorophyll content, leaf area index and noise levels to produce a large variability in fluorescence and reflectance spectra. The retrieval accuracy is quantified based on several metrics derived from the F spectrum (i.e., red and far-red peaks, O2 bands and spectrally-integrated values). Further, the algorithm is employed to process experimental field spectroscopy measurements collected over different crops during a long-lasting field campaign. The reliability of the retrieval algorithm on experimental measurements is evaluated by cross-comparison with F values computed by an independent retrieval method (i.e., SFM at O2 bands). For the first time, the evolution of the F spectrum along the entire growing season for a forage crop is analyzed and three diverse F spectra are identified at different growing stages. The results show that red F is larger for young canopy; while red and far-red F have similar intensity in an intermediate stage; finally, far-red F is significantly larger for the rest of the season.

Hyperspectral remote sensing (RS) provides unique possibilities to monitor peatland vegetation traits and their temporal dynamics at a fine spatial scale. Peatlands provide a vital contribution to ecosystem services by their massive carbon storage and wide heterogeneity. However, monitoring, understanding, and disentangling the diverse vegetation traits from a heterogeneous landscape using complex RS signal is challenging, due to its wide biodiversity and distinctive plant species composition. In this work, we aim to demonstrate, for the first time, the large heterogeneity of peatland vegetation traits using well-established vegetation indices (VIs) and Sun-Induced Fluorescence (SIF) for describing the spatial heterogeneity of the signals which may correspond to spatial diversity of biochemical and structural traits. SIF originates from the initial reactions in photosystems and is emitted at wavelengths between 650–780 nm, with the first peak at around 687 nm and the second peak around 760 nm. We used the first HyPlant airborne data set recorded over a heterogeneous peatland area and its surrounding ecosystems (i.e., forest, grassland) in Poland. We deployed a comparative analysis of SIF and VIs obtained from differently managed and natural vegetation ecosystems, as well as from diverse small-scale peatland plant communities. Furthermore, spatial relationships between SIF and VIs from large-scale vegetation ecosystems to small-scale peatland plant communities were examined. Apart from signal variations, we observed a positive correlation between SIF and greenness-sensitive VIs, whereas a negative correlation between SIF and a VI sensitive to photosynthesis was observed for large-scale vegetation ecosystems. In general, higher values of SIF were associated with higher biomass of vascular plants (associated with higher Leaf Area Index (LAI)). SIF signals, especially SIF760, were strongly associated with the functional diversity of the peatland vegetation. At the peatl

The first European Space Agency (ESA) and NASA collaboration in an airborne campaign to support ESA's FLuorescence EXplorer (FLEX) mission was conducted in North Carolina, USA during September-October 2013 (FLEX-US 2013) at the Parker Tract Loblolly Pine (LP) Plantation (Plymouth, NC, USA). This campaign combined two unique airborne instrument packages to obtain simultaneous observations of solar-induced fluorescence (SIF), LiDAR-based canopy structural information, visible through shortwave infrared (VSWIR) reflectance spectra, and surface temperature, to advance vegetation studies of carbon cycle dynamics and ecosystem health. We obtained statistically significant results for fluorescence, canopy temperature, and tower fluxes from data collected at four times of day over two consecutive autumn days across an age class chronosequence. Both the red fluorescence (F685) and far-red fluorescence (F740) radiances had highest values at mid-day, but their fluorescence yields exhibited different diurnal responses across LP age classes. The diurnal trends for F685 varied with forest canopy temperature difference (canopy minus air), having a stronger daily amplitude change for young vs. old canopies. The Photochemical Reflectance Index (PRI) was positively correlated with this temperature variable over the diurnal cycle. Tower measurements from mature loblolly stand showed the red/far-red fluorescence ratio was linearly related to canopy light use efficiency (LUE) over the diurnal cycle, but performed even better for the combined morning/afternoon (without midday) observations. This study demonstrates the importance of diurnal observations for interpretation of fluorescence dynamics, the need for red fluorescence to understand canopy physiological processes, and the benefits of combining fluorescence, reflectance, and structure information to clarify canopy function versus structure characteristics for a coniferous forest

The first European Space Agency (ESA) and NASA collaboration in an airborne campaign to support ESA's FLuorescence EXplorer (FLEX) mission was conducted in North Carolina, USA during September-October 2013 (FLEX-US 2013) at the Parker Tract Loblolly Pine (LP) Plantation (Plymouth, NC, USA). This campaign combined two unique airborne instrument packages to obtain simultaneous observations of solar-induced fluorescence (SIF), LiDAR-based canopy structural information, visible through shortwave infrared (VSWIR) reflectance spectra, and surface temperature, to advance vegetation studies of carbon cycle dynamics and ecosystem health. We obtained statistically significant results for fluorescence, canopy temperature, and tower fluxes from data collected at four times of day over two consecutive autumn days across an age class chronosequence. Both the red fluorescence (F685) and far-red fluorescence (F740) radiances had highest values at mid-day, but their fluorescence yields exhibited different diurnal responses across LP age classes. The diurnal trends for F685 varied with forest canopy temperature difference (canopy minus air), having a stronger daily amplitude change for young vs. old canopies. The Photochemical Reflectance Index (PRI) was positively correlated with this temperature variable over the diurnal cycle. Tower measurements from mature loblolly stand showed the red/far-red fluorescence ratio was linearly related to canopy light use efficiency (LUE) over the diurnal cycle, but performed even better for the combined morning/afternoon (without midday) observations. This study demonstrates the importance of diurnal observations for interpretation of fluorescence dynamics, the need for red fluorescence to understand canopy physiological processes, and the benefits of combining fluorescence, reflectance, and structure information to clarify canopy function versus structure characteristics for a coniferous forest