Implementation of a Sentinel-2 Based Exploratory Workflow for the Estimation of Above Ground Biomass

Molisse, G., Emin, D., & Costa, H. (2022). Implementation of a Sentinel-2 Based Exploratory Workflow for the Estimation of Above Ground Biomass. In 2022 IEEE Mediterranean and Middle-East Geoscience and Remote Sensing Symposium, M2GARSS 2022 - Proceedings (pp. 74-77). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/M2GARSS52314.2022.9839897 ----Funding Information: This study was carried out in the framework of the MAIL project, which was funded by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 823805.This work presents a Sentinel-2 based exploratory workflow for the estimation of Above Ground Biomass (AGB) in a Mediterranean forest. Up-to-date and reliable mapping of AGB has been increasingly required by international commitments under the climate convention, and in the last decades, remote sensing-based studies on the topic have been widely investigated. After the generation of several vegetation and topographic features, the proposed approach consists of 4 major steps: 1) Feature selection 2) AGB prediction with k-Nearest Neighbour (kNN), Random Forest (RF), Extreme Gradient Boosting (XGB), and Artificial Neural Networks (ANN); 3) hyper-parameters fine-tuning with Bayesian Optimization; and finally, 4) model explanation with the SHapley Additive exPlanations (SHAP) package. The following results were obtained: 1) before hyper-parameters optimization, the Deep Neural Network (DNN) yielded the best performance with a Root Mean Squared Error (RMSE) of 42.30 t/ha; 2) after hyper-parameters fine-tuning with Bayesian Optimization, the Extreme Gradient Boosting (XGB) model yielded the best performance with a RMSE of 37.79 t/ha; 3) model explanation with SHAP allowed for a deeper understanding of the features impact on the model predictions. Finally, the predicted AGB throughout the study area showed an average value of 83 t/ha, ranging from 0t/ha to 346.56 t/ha.authorsversionpublishe

Diurnal dynamics of non‐photochemical quenching in Arabidopsis npq mutants assessed by solar‐induced fluorescence and reflectance measurements in the field

Solar‐induced fluorescence (SIF) is highly relevant in mapping photosynthesis from remote‐sensing platforms. This requires linking SIF to photosynthesis and understanding the role of nonphotochemical quenching (NPQ) mechanisms under field conditions. Hence, active and passive fluorescence were measured in Arabidopsis with altered NPQ in outdoor conditions. Plants with mutations in either violaxanthin de‐epoxidase (npq1) or PsbS protein (npq4) exhibited reduced NPQ capacity. Parallel measurements of NPQ, photosystem II efficiency, SIF and spectral reflectance (ρ) were conducted diurnally on one sunny summer day and two consecutive days during a simulated cold spell. Results showed that both npq mutants exhibited higher levels of SIF compared to wild‐type plants. Changes in reflectance were related to changes in the violaxanthin–antheraxanthin–zeaxanthin cycle and not to PsbS‐mediated conformational changes. When plants were exposed to cold temperatures, rapid onset of photoinhibition strongly quenched SIF in all lines. Using well‐characterized Arabidopsis npq mutants, we showed for the first time the quantitative link between SIF, photosynthetic efficiency, NPQ components and leaf reflectance. We discuss the functional potential and limitations of SIF and reflectance measurements for estimating photosynthetic efficiency and NPQ in the field

Diurnal dynamics of nonphotochemical quenching in Arabidopsis npq

Solar‐induced fluorescence (SIF) is highly relevant in mapping photosynthesis from remote‐sensing platforms. This requires linking SIF to photosynthesis and understanding the role of nonphotochemical quenching (NPQ) mechanisms under field conditions. Hence, active and passive fluorescence were measured in Arabidopsis with altered NPQ in outdoor conditions. Plants with mutations in either violaxanthin de‐epoxidase (npq1) or PsbS protein (npq4) exhibited reduced NPQ capacity. Parallel measurements of NPQ, photosystem II efficiency, SIF and spectral reflectance (ρ) were conducted diurnally on one sunny summer day and two consecutive days during a simulated cold spell. Results showed that both npq mutants exhibited higher levels of SIF compared to wild‐type plants. Changes in reflectance were related to changes in the violaxanthin–antheraxanthin–zeaxanthin cycle and not to PsbS‐mediated conformational changes. When plants were exposed to cold temperatures, rapid onset of photoinhibition strongly quenched SIF in all lines. Using well‐characterized Arabidopsis npq mutants, we showed for the first time the quantitative link between SIF, photosynthetic efficiency, NPQ components and leaf reflectance. We discuss the functional potential and limitations of SIF and reflectance measurements for estimating photosynthetic efficiency and NPQ in the field

Quality assessment of Sun-Induced Fluorescence maps from the airborne imaging spectrometer HyPlant

The ability to investigate the Earth’s environment will be greatly improved by hyperspectral satellite data. The FLuorescence EXplorer (FLEX) will be the first hyperspectral mission designed to monitor the photosynthetic activity of the terrestrial vegetation layer by using a completely novel technique measuring the sun-induced chlorophyll fluorescence (SIF) signal that originates from the core of the photosynthetic machinery. In preparation of the upcoming FLEX satellite mission that will be launched in 2022 a large field campaign, namely FLEXSense, was conducted in summer 2018 including representative study sites at several locations in middle and south Europe as well as North America.During the different/various field activities, airborne data was acquired with the hyperspectral airborne imager HyPlant, whichthat consists of two sensor heads. The DUAL module is a line-imaging push-broom sensor, which providinges contiguous spectral information from 370 to 2500 nm. The vegetationchlorophyll fluorescence signal is measured with a separate push-broom sensor, the FLUO module, which produces data at high spectral resolution (0.25 nm) in the spectral region of the two oxygen absorption bands covering a range from 670 to 780 nm. Currently, two different algorithms are used routinely to retrieve red (SIF680) and far-red SIF (SIF760) from HyPlant data. Both methods are based on the oxygen absorption bands., but wWhile the improved Fraunhofer Line Depth (iFLD) method employs a semi-empirical atmospheric correction (i.e., bare-soils), the Spectral Fitting method (SFM) makes useis based onof a physically-based atmospheric modeling (MODTRAN5 code). A common method of testing the reliability of remotely-sensed SIF (in this study airborne maps) is the comparison with “ground truth” data. In many cases, however, ground measurements of SIF are not available or are too work-intensive to be measured at regional level. For that reason we developedwant to present an alternative approach how the quality of airborne SIF maps can be assessed. For this purpose we applyhave developed so-called ’quality criteria’, which should help to find errors and artefacts that have arisen during the SIF retrieval. This method was applied to determine the quality of individual SIF maps derived from HyPlant images acquired during the 2018 FLEXSense campaign. The application of the proposed quality features proved to be a valuable tool for assessing the quality of SIF maps derived from HyPlant airborne data. Therefore, we propose to apply the different criteria even in the case of a with sufficient number of ground reference measurements are available, as because they provide important additional information about the quality of spatial SIF products is provided, especially when comparing the outputs of different retrieval methods

Specim IQ: Evaluation of a New, Miniaturized Handheld Hyperspectral Camera and Its Application for Plant Phenotyping and Disease Detection

Hyperspectral imaging sensors are promising tools for monitoring crop plants or vegetation in different environments. Information on physiology, architecture or biochemistry of plants can be assessed non-invasively and on different scales. For instance, hyperspectral sensors are implemented for stress detection in plant phenotyping processes or in precision agriculture. Up to date, a variety of non-imaging and imaging hyperspectral sensors is available. The measuring process and the handling of most of these sensors is rather complex. Thus, during the last years the demand for sensors with easy user operability arose. The present study introduces the novel hyperspectral camera Specim IQ from Specim (Oulu, Finland). The Specim IQ is a handheld push broom system with integrated operating system and controls. Basic data handling and data analysis processes, such as pre-processing and classification routines are implemented within the camera software. This study provides an introduction into the measurement pipeline of the Specim IQ as well as a radiometric performance comparison with a well-established hyperspectral imager. Case studies for the detection of powdery mildew on barley at the canopy scale and the spectral characterization of Arabidopsis thaliana mutants grown under stressed and non-stressed conditions are presente

CloudRoots: an integrated field experiment and modelling approach to study soil-plant-atmosphere interactions

Due to their high-quality routine measurement programme, ICOS sites lend themselves as anchors for additional experiments. As an example, we describe the CloudRoots campaign near the agricultural site Selhausen (DE-RuS)in spring 2018. Little is known about the two-way feedback between stomatal control (controlling the partitioning of energy into sensible and latent heat) and cloud development (affecting potential evapotranspiration). Coupled models of the soil-vegetation-boundary layer continuum have the potential to explain this, but their calculations are only as robust as the data used to parameterize or validate the model. For observations and modelling, the challenge is ininterconnecting processes at leaf level to the physics of turbulence and clouds. We temporarily amend the existing radiation, flux and soil dynamics/respiration measurements of the ICOS site by scintillometry, sap-flow and leaf-level flux measurements, vertical profiles and isotope measurements. Scintillometers provide minute-scale turbulent fluxes enabling to connect stomatal responses to the energy, moisture and CO2 fluxes at this timescale [1]. Sap-flow [2], leaf-level chamber, canopy-resolving profile [3] and isotope measurements have the potential to distinguish stomatal CO2 and H2O fluxes from the eddy-covariance based net fluxes. Relating the leaf and canopy level measurements to cloud development and potential cross-scale feedbacks are integrated and explored with the CLASS model ([4], https://classmodel.github.io). The campaign is partnering with two complementary test campaigns for the FLEX mission(https://earth.esa.int/web/guest/missions/esa-future-missions/flex) and the MOSES project (https://moses.eskp.de/home/), taking place, among others, in the same region in spring and summer 2018. The poster will show first results and method intercomparisons from the CloudRoots field campaign.[1] van Kesteren et al. 2013, Agric. For. Meteorol. 178-179:75-105[2] Langensiepen et al. 2014, Agric. For. Meteorol. 186:34[3] Ney and Graf 2018, Bound.-Layer Meteorol. 166:449[4] Vilà-Guerau de Arellano et al. 2015, Atmospheric Boundary Layer: Integrating air chemistry and land interactions. Cambridge University Press

CloudRoots – an integrated measurement and modelling approach for soil-plant-atmosphere interactions applied to an ICOS site

Due to their high-quality routine measurement programme, ICOS sites lend themselves as anchors for additional experiments. As an example, we describe the CloudRoots campaign near the agricultural site Selhausen (DE-RuS) in spring 2018.Little is known about the two-way feedback between stomatal control (controlling the partitioning of energy into sensible and latent heat) and cloud development (affecting potential evapotranspiration). Coupled models of the soil-vegetation-boundary layer continuum have the potential to explain this, but their calculations are only as robust as the data used to parameterize or validate the model. For observations and modelling, the challenge is in interconnecting processes at leaf level to the physics of turbulence and clouds.We temporarily amend the existing radiation, flux and soil dynamics/respiration measurements of the ICOS site by scintillometry, sap-flow and leaf-level flux measurements, vertical profiles and isotope measurements. Scintillometers provide minute-scale turbulent fluxes enabling to connect stomatal responses to the energy, moisture and CO2 fluxes at this timescale [1]. Sap-flow [2], leaf-level chamber, canopy-resolving profile [3] and isotope measurements have the potential to distinguish stomatal CO2 and H2O fluxes from the eddy-covariance based net fluxes. Relating the leaf and canopy level measurements to cloud development and potential cross-scale feedbacks are integrated and explored with the CLASS model ([4], https://classmodel.github.io).The campaign is partnering with two complementary test campaigns for the FLEX mission (https://earth.esa.int/web/guest/missions/esa-future-missions/flex) and the MOSES project (https://moses.eskp.de/home/), taking place, among others, in the same region in spring and summer 2018. The poster will show first results and method intercomparisons from the CloudRoots field campaign.[1] van Kesteren et al. 2013, Agric. For. Meteorol. 178-179:75-105[2] Langensiepen et al. 2014, Agric. For. Meteorol. 186:34[3] Ney and Graf 2018, Bound.-Layer Meteorol. 166:449[4] Vilà-Guerau de Arellano et al. 2015, Atmospheric Boundary Layer: Integrating air chemistry and land interactions. Cambridge University Press

CloudRoots: Integration of advanced instrumental techniques and process modelling of sub-hourly and sub-kilometre land-Atmosphere interactions

The CloudRoots field experiment was designed to obtain a comprehensive observational dataset that includes soil, plant, and atmospheric variables to investigate the interaction between a heterogeneous land surface and its overlying atmospheric boundary layer at the sub-hourly and sub-kilometre scale. Our findings demonstrate the need to include measurements at leaf level to better understand the relations between stomatal aperture and evapotranspiration (ET) during the growing season at the diurnal scale. Based on these observations, we obtain accurate parameters for the mechanistic representation of photosynthesis and stomatal aperture. Once the new parameters are implemented, the model reproduces the stomatal leaf conductance and the leaf-level photosynthesis satisfactorily. At the canopy scale, we find a consistent diurnal pattern on the contributions of plant transpiration and soil evaporation using different measurement techniques. From highly resolved vertical profile measurements of carbon dioxide (<span classCombining double low line"inline-formula") and other state variables, we infer a profile of the <span classCombining double low line"inline-formula" assimilation in the canopy with non-linear variations with height. Observations taken with a laser scintillometer allow us to quantify the non-steadiness of the surface turbulent fluxes during the rapid changes driven by perturbation of photosynthetically active radiation by cloud flecks. More specifically, we find 2&thinsp;min delays between the cloud radiation perturbation and ET. To study the relevance of advection and surface heterogeneity for the land-Atmosphere interaction, we employ a coupled surface-Atmospheric conceptual model that integrates the surface and upper-Air observations made at different scales from leaf to the landscape. At the landscape scale, we calculate a composite sensible heat flux by weighting measured fluxes with two different land use categories, which is consistent with the diurnal evolution of the boundary layer depth. Using sun-induced fluorescence measurements, we also quantify the spatial variability of ET and find large variations at the sub-kilometre scale around the CloudRoots site. Our study shows that throughout the entire growing season, the wide variations in stomatal opening and photosynthesis lead to large diurnal variations of plant transpiration at the leaf, plant, canopy, and landscape scales. Integrating different advanced instrumental techniques with modelling also enables us to determine variations of ET<span idCombining double low line"page4376" that depend on the scale where the measurement were taken and on the plant growing stage

CloudRoots: integration of advanced instrumental techniques and process modelling of sub-hourly and sub-kilometre land–atmosphere interactions

The CloudRoots field experiment was designed to obtain a comprehensive observational dataset that includes soil, plant, and atmospheric variables to investigate the interaction between a heterogeneous land surface and its overlying atmospheric boundary layer at the sub-hourly and sub-kilometre scale. Our findings demonstrate the need to include measurements at leaf level to better understand the relations between stomatal aperture and evapotranspiration (ET) during the growing season at the diurnal scale. Based on these observations, we obtain accurate parameters for the mechanistic representation of photosynthesis and stomatal aperture. Once the new parameters are implemented, the model reproduces the stomatal leaf conductance and the leaf-level photosynthesis satisfactorily. At the canopy scale, we find a consistent diurnal pattern on the contributions of plant transpiration and soil evaporation using different measurement techniques. From highly resolved vertical profile measurements of carbon dioxide (CO2) and other state variables, we infer a profile of the CO2 assimilation in the canopy with non-linear variations with height. Observations taken with a laser scintillometer allow us to quantify the non-steadiness of the surface turbulent fluxes during the rapid changes driven by perturbation of photosynthetically active radiation by cloud flecks. More specifically, we find 2 min delays between the cloud radiation perturbation and ET. To study the relevance of advection and surface heterogeneity for the land–atmosphere interaction, we employ a coupled surface–atmospheric conceptual model that integrates the surface and upper-air observations made at different scales from leaf to the landscape. At the landscape scale, we calculate a composite sensible heat flux by weighting measured fluxes with two different land use categories, which is consistent with the diurnal evolution of the boundary layer depth. Using sun-induced fluorescence measurements, we also quantify the spatial variability of ET and find large variations at the sub-kilometre scale around the CloudRoots site. Our study shows that throughout the entire growing season, the wide variations in stomatal opening and photosynthesis lead to large diurnal variations of plant transpiration at the leaf, plant, canopy, and landscape scales. Integrating different advanced instrumental techniques with modelling also enables us to determine variations of ET that depend on the scale where the measurement were taken and on the plant growing stage