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Plant traits play a pivotal role in steering ecosystem dynamics. As plant canopies have evolved to interact with light, spectral data convey information on a variety of plant traits. Machine learning techniques have been used successfully to retrieve diverse traits from hyperspectral data. Nonetheless, the efficacy of machine learning is restricted by limited access to high-quality reference data for training. Previous studies showed that aggregating data across domains, sensors, or growth forms provided by collaborative efforts of the scientific community enables the creation of transferable models. However, even such curated databases are still sparse for several traits. To address these challenges, we investigated the potential of filling such data gaps with simulated hyperspectral data generated through the most widely-used radiative transfer model (RTM) PROSAIL. We coupled trait information from the TRY plant trait database with information on plant communities from the sPlot database, to build a realistic input trait dataset for the RTM-based simulation of canopy spectra. Our findings indicate that simulated data can alleviate the effects of data scarcity for highly underrepresented traits. In most other cases, however, the effects of including simulated data from RTMs are negligible or even negative. While more complex RTM models promise further improvements, their parameterization remains challenging. This highlights two key observations: firstly, RTM models, such as PROSAIL, exhibit limitations in producing realistic spectra across diverse ecosystems; secondly, real-world data repurposed from various sources exhibit superior retrieval success compared to simulated data. As a result, we advocate to emphasize the importance of active data sharing over secrecy and overreliance on modeling to address data limitations.

Nitrogen is one of the most important macronutrients for plant growth and timely estimation of canopy nitrogen content (CNC) is crucial for agricultural applications. Remote sensing has emerged as an important tool to quantify CNC using either empirically or physically based methods. Most empirical methods use chlorophyll related spectral indices and are dependent on the relationship between nitrogen and chlorophyll, which varies with vegetation types and growth stages. In contrast, physically based methods use the full-range reflectance data and retrieve CNC from coupled leaf and canopy radiative transfer models (such as PROSPECT-PRO + 4SAIL, PROSAIL-PRO). However, the subtle absorption features of nitrogen and protein in fresh leaves hinder the accurate estimation of CNC. Therefore, this study proposed an efficient and mechanistic framework to estimate CNC (PROSAIL-NAM) by coupling PROSAIL-PRO with a nitrogen allocation model, which divided the total nitrogen into non-photosynthetic nitrogen (NPN) and photosynthetic nitrogen (PN). At the canopy level, PN and NPN are assumed to be proportional to canopy chlorophyll content (CCC) and canopy dry matter content (CDM), respectively. The PROSAIL-PRO model was first used to estimate CCC and CDM, and then the resulting CCC and CDM were fed to the nitrogen allocation model to estimate CNC. The estimation accuracy of CNC was assessed with six diverse datasets: four from field crop experiments across geographic sites, one from multiple ecosystems, and one from a satellite-ground joint experiment. Our results showed that satisfactory estimations of CNC were obtained when CCC and CDM were estimated using a model inversion method (RMSE = 0.54–1.56 g/m2) and a hybrid retrieval method (RMSE = 0.49–2.25 g/m2). The model inversion method was comparable with the hybrid retrieval method for ground platforms, but performed better for airborne and satellite platforms. In addition, the traditional protein-nitrogen conversion model obtained CNC from the canopy protein content and led to clear overestimations of CNC with RMSE > 1.95 g/m2. This study represents a first attempt to develop a robust approach by coupling PROSAIL-PRO with a nitrogen allocation model for accurate estimation of CNC across geographic sites, ecosystems, and platforms. These finding will advance the monitoring of CNC from regional to global scales.

Hyperspectral imaging is widespread in crop nitrogen (N) monitoring for precision agriculture, although approaches that address the agronomical recommendation of the optimal N rate are still lacking. Here, two approaches are explored in defining the optimal N rate to be supplied in fertigated processing tomatoes through hyperspectral imaging. The first one, called the N uptake approach, focuses on the virtual reproduction of the critical N uptake curve through the estimation of both aboveground biomass and crop N uptake. The estimated biomass is used to derive the critical N uptake, and the optimal N rate is computed as the difference between the critical N uptake and the estimated actual N uptake. The second approach focuses on the monitoring of the Nitrogen Nutrition Index (NNI) and biomass. Again, the biomass is used to calculate the critical N uptake, which, when combined with the estimated NNI, resolves the equation to retrieve the actual crop N uptake. A modeling stage was included to estimate the N-related variables from crop canopy reflectance across the full spectrum (400–1000 nm). Canopy reflectance was measured by using an unmanned aerial vehicle at five growth stages of processing tomatoes grown under experimental plot conditions with different N rates. Three nonparametric algorithms were trained, i.e., Gaussian Process Regression (GPR), Support Vector Regression (SVR), and Partial Least Square Regression (PLSR). Multicollinearity of spectral bands was prevented with a principal component analysis, and models were 5-fold cross-validated. Considering the pivotal role of biomass in the selected N rate estimation approaches, two distinct biomass estimation methods were explored. The direct biomass retrieval from spectral data was compared with the indirect biomass retrieval from the remotely sensed LAI applying empirical regressions. PLSR outperformed the other algorithms in estimating N uptake (Relative Root Mean Square Error, RRMSE=21.8 %), while SVR better estimated NNI (RRMSE=10.2 %) and direct biomass (RRMSE=19.4 %). The indirect estimation of biomass outperformed the direct approach when GPR is used (RRMSE 18.2 % vs. 21.4 %), although the influence of soil background at early growth stages determines an unreliable biomass estimation for both methods. The NNI approach outperformed the N uptake approach in estimating the optimal N rate, especially when the biomass is directly retrieved from GPR. The promising estimation performances in N rate estimation (R2=0.88 and RRMSE=36 %) revealed the effectiveness of hyperspectral imaging in entering the agronomical scheduling of precision N management.

Operational Earth observation missions, like the Sentinel-3 (S3) satellites, aim to provide imagery for long-term environmental assessment to monitor and analyze vegetation changes and dynamics. However, the S3 archive is limited in temporal availability to the year 2016. Although S3 provides continuity of previous missions, key vegetation products (VPs) including leaf area index (LAI), fraction of photosynthetically active radiation (FAPAR), fractional vegetation cover (FVC), and leaf chlorophyll content (LCC), can be reliably produced from Ocean and Land Colour Instrument (OLCI) data only since the sensors' launch. To overcome this limitation, our study proposes a reconstruction workflow that extends the data record beyond its data acquisition. By using multi-output Gaussian process regression (MOGPR) fusion, we explored guiding predictor VPs from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor for the reconstruction of multi-decadal (spanning two decades, 2002–2022) temporal profiles of four OLCI-derived VPs (S3-MOGPR), moving past S3's launch. We first evaluated three MODIS-derived inputs as predictor variables: LAI, FAPAR, and the Normalised Difference Vegetation Index (NDVI) over nine sites with distinct land covers from the Ground-Based Observations for Validation (GBOV) service. Each predictor produced a distinct time series for the four reconstructed S3 VPs. To determine which predictor variable most accurately reconstructs data streams of the targeted variable, all S3-MOGPR VPs were compared to satellite-based products from the Copernicus Global Land Service (CGLS). MOGPR models were trained for 2019 and compared to reference data. Since MODIS LAI demonstrated the best reconstruction performance of all predictors, S3-MOGPR VPs were fully reconstructed from 2022 back to 2002 using guiding MODIS LAI and evaluated with in-situ data. The most consistent reconstructed product was FVC (R=0.96, NRMSE = 0.17) over mixed forests compared to CGLS estimates. FVC also yielded the highest validation statistics (R=0.93, ρ=0.92, NRMSE = 0.14) over croplands. The highest correlation coefficients were achieved by the predictor variable LAI reconstructing FVC with mean R, ρ and NRMSE = 0.11 among all sites of 0.91 and 0.88, respectively. In the absence of both satellite and ground-based LCC reference measurements, the reconstructed LCC profiles were compared to the OLCI and MERIS Terrestrial Chlorophyll Index (OTCI, MTCI). The correlation metrics provided strong evidence of the reconstructed LCC product's integrity, with the highest correlation over deciduous broadleaf, mixed forests and croplands (R>0.9). The lowest correlations for all reconstructed variables appeared over evergreen broadleaf forests, driven by the absence of seasonal patterns. Altogether, by leveraging the flexibility of the MOGPR algorithm with guiding historical data, contemporary EO data can be extrapolated into the past.

Crop phenology data offer crucial information for crop yield estimation, agricultural management, and assessment of agroecosystems. Such information becomes more important in the context of increasing year-to-year climatic variability. The dataset provides in-situ crop phenology data (first leaves emergence and harvest date) of major European crops (wheat, corn, sunflower, rapeseed) from seventeen field study sites in Bulgaria and two in France. Additional information such as the sowing date, area of each site, coordinates, method and equipment used for phenophase data estimation, and photos of the France sites are also provided. The georeferenced ground-truth dataset provides a solid base for a better understanding of crop growth and can be used to validate the retrieval of phenological stages from remote sensing data.

Non-photosynthetic vegetation (NPV) is considered a key quantifiable variable in the context of new spaceborne imaging spectroscopy missions. Knowledge of NPV is essential for all terrestrial ecosystems, and its mapping is beneficial for agriculture and forestry. In agriculture, crop residues (CR) play an important role in tillage, erosion control and soil health management. In forest management, NPV mapping supports understanding the dynamics of important ecological processes such as fire, erosion, and land use changes. Whereas the fractional cover of NPV has been extensively studied across managed and natural ecosystems, so far little attention has been paid to the quantification of biomass of senescent material. In this comprehensive survey, we summarize past attempts to quantify landscape-scale NPV or CR cover (in %) and biomass (in g/m2) from optical Earth observation data, with a particular focus on hyperspectral data exploitation. Given three decades of spectroscopy studies on NPV or CR cover detection, we identify the following methodological trends: (1) a shift from unmixing approaches towards regression-based models; (2) a shift from two-band indices towards multi-band equations; and (3) a shift from linear regression towards data-driven machine learning models. (4) In addition, gradual progress in radiative transfer modelling (RTM) in describing the interaction of radiation with non-photosynthetic plant material has been achieved. These trends have enabled progress from merely identifying the presence of NPV and CR to the explicit quantification of NPV biomass over croplands and grasslands. We highlight the potential of recent and upcoming next-generation spaceborne missions and their unprecedented hyperspectral and enhanced multispectral data streams and propose to implement efficient workflows for the operational delivery of global NPV products along with associated uncertainties. In summary, this survey emphasizes the significance of imaging spectroscopy as an efficient way to quantify NPV and support the management of croplands, grasslands, forests, and natural vegetation.

The continuous monitoring of the terrestrial Earth system by a growing number of optical satellite missions provides valuable insights into vegetation and cropland characteristics. Satellite missions typically provide different levels of data, such as level 1 top-of-atmosphere (TOA) radiance and level 2 bottom-of-atmosphere (BOA) reflectance products. Exploiting TOA radiance data directly offers the advantage of bypassing the complex atmospheric correction step, where errors can propagate and compromise the subsequent retrieval process. Therefore, the objective of our study was to develop models capable of retrieving vegetation traits directly from TOA radiance data from imaging spectroscopy satellite missions. To achieve this, we constructed hybrid models based on radiative transfer model (RTM) simulated data, thereby employing the vegetation SCOPE RTM coupled with the atmosphere LibRadtran RTM in conjunction with Gaussian process regression (GPR). The retrieval evaluation focused on vegetation canopy traits, including the leaf area index (LAI), canopy chlorophyll content (CCC), canopy water content (CWC), the fraction of absorbed photosynthetically active radiation (FAPAR), and the fraction of vegetation cover (FVC). Employing band settings from the upcoming Copernicus Hyperspectral Imaging Mission (CHIME), two types of hybrid GPR models were assessed: (1) one trained at level 1 (L1) using TOA radiance data and (2) one trained at level 2 (L2) using BOA reflectance data. Both the TOA- and BOA-based GPR models were validated against in situ data with corresponding hyperspectral data obtained from field campaigns. The TOA-based hybrid GPR models revealed a range of performance from moderate to optimal results, thus reaching R2 = 0.92 (LAI), R2 = 0.72 (CCC) and 0.68 (CWC), R2 = 0.94 (FAPAR), and R2 = 0.95 (FVC). To demonstrate the models’ applicability, the TOA- and BOA-based GPR models were subsequently applied to imagery from the scientific precursor missions PRISMA and EnMAP. The resulting trait maps showed sufficient consistency between the TOA- and BOA-based models, with relative errors between 4% and 16% (R2 between 0.68 and 0.97). Altogether, these findings illuminate the path for the development and enhancement of machine learning hybrid models for the estimation of vegetation traits directly tailored at the TOA level.

The Granger Causality (GC) statistical test explores the causal relationships between different time series variables. By employing the GC method, the underlying causal links between environmental drivers and global vegetation properties can be untangled, which opens possibilities to forecast the increasing strain on ecosystems by droughts, global warming, and climate change. This study aimed to quantify the spatial distribution of four distinct satellite vegetation products’ (VPs) sensitivities to four environmental land variables (ELVs) at the global scale given the GC method. The GC analysis assessed the spatially explicit response of the VPs: (i) the fraction of absorbed photosynthetically active radiation (FAPAR), (ii) the leaf area index (LAI), (iii) solar-induced fluorescence (SIF), and, finally, (iv) the normalized difference vegetation index (NDVI) to the ELVs. These ELVs can be categorized as water availability assessing root zone soil moisture (SM) and accumulated precipitation (P), as well as, energy availability considering the effect of air temperature (T) and solar shortwave (R) radiation. The results indicate SM and P are key drivers, particularly causing changes in the LAI. SM alone accounts for 43%, while P accounts for 41%, of the explicitly caused areas over arid biomes. SM further significantly influences the LAI at northern latitudes, covering 44% of cold and 50% of polar biome areas. These areas exhibit a predominant response to R, which is a possible trigger for snowmelt, showing more than 40% caused by both cold and polar biomes for all VPs. Finally, T’s causality is evenly distributed amongst all biomes with fractional covers between ∼10 and 20%. By using the GC method, the analysis presents a novel way to monitor the planet’s ecosystem, based on solely two years as input data, with four VPs acquired by the synergy of Sentinel-3 (S3) and 5P (S5P) satellite data streams. The findings indicated unique, biome-specific responses of vegetation to distinct environmental drivers.

Global mapping of essential vegetation traits (EVTs) through data acquired by Earth-observing satellites provides a spatially explicit way to analyze the current vegetation states and dynamics of our planet. Although significant efforts have been made, there is still a lack of global and consistently derived multi-temporal trait maps that are cloud-free. Here we present the processing chain for the spatiotemporally continuous production of four EVTs at a global scale: (1) fraction of absorbed photosynthetically active radiation (FAPAR), (2) leaf area index (LAI), (3) fractional vegetation cover (FVC), and (4) leaf chlorophyll content (LCC). The proposed workflow presents a scalable processing approach to the global cloud-free mapping of the EVTs. Hybrid retrieval models, named S3-TOA-GPR-1.0-WS, were implemented into Google Earth Engine (GEE) using Sentinel-3 Ocean and Land Color Instrument (OLCI) Level-1B for the mapping of the four EVTs along with associated uncertainty estimates. We used the Whittaker smoother (WS) for the temporal reconstruction of the four EVTs, which led to continuous data streams, here applied to the year 2019. Cloud-free maps were produced at 5 km spatial resolution at 10-day time intervals. The consistency and plausibility of the EVT estimates for the resulting annual profiles were evaluated by per-pixel intra-annually correlating against corresponding vegetation products of both MODIS and Copernicus Global Land Service (CGLS). The most consistent results were obtained for LAI, which showed intra-annual correlations with an average Pearson correlation coefficient (R) of 0.57 against the CGLS LAI product. Globally, the EVT products showed consistent results, specifically obtaining higher correlation than R> 0.5 with reference products between 30 and 60° latitude in the Northern Hemisphere. Additionally, intra-annual goodness-of-fit statistics were also calculated locally against reference products over four distinct vegetated land covers. As a general trend, vegetated land covers with pronounced phenological dynamics led to high correlations between the different products. However, sparsely vegetated fields as well as areas near the equator linked to smaller seasonality led to lower correlations. We conclude that the global gap-free mapping of the four EVTs was overall consistent. Thanks to GEE, the entire OLCI L1B catalogue can be processed efficiently into the EVT products on a global scale and made cloud-free with the WS temporal reconstruction method. Additionally, GEE facilitates the workflow to be operationally applicable and easily accessible to the broader community.

The monitoring of soil moisture content (SMC) at very high spatial resolution (

Optical Earth Observation is often limited by weather conditions such as cloudiness. Radar sensors have the potential to overcome these limitations, however, due to the complex radar-surface interaction, the retrieving of crop biophysical variables using this technology remains an open challenge. Aiming to simultaneously benefit from the optical domain background and the all-weather imagery provided by radar systems, we propose a data fusion approach focused on the cross-correlation between radar and optical data streams. To do so, we analyzed several multiple-output Gaussian processes (MOGP) models and their ability to fuse efficiently Sentinel-1 (S1) Radar Vegetation Index (RVI) and Sentinel-2 (S2) vegetation water content (VWC) time series over a dry agri-environment in southern Argentina. MOGP models not only exploit the auto-correlations of S1 and S2 data streams independently but also the inter-channel cross-correlations. The S1 RVI and S2 VWC time series at the selected study sites being the inputs of the MOGP models proved to be closely correlated. Regarding the set of assessed models, the Convolutional Gaussian model (CONV) delivered noteworthy accurate data fusion results over winter wheat croplands belonging to the 2020 and 2021 campaigns (NRMSEwheat2020 = 16.1%; NRMSEwheat2021 = 10.1%). Posteriorly, we removed S2 observations from the S1 & S2 dataset corresponding to the complete phenological cycles of winter wheat from September to the end of December to simulate the presence of clouds in the scenes and applied the CONV model at the pixel level to reconstruct spatiotemporally-latent VWC maps. After applying the fusion strategy, the phenology of winter wheat was successfully recovered in the absence of optical data. Strong correlations were obtained between S2 VWC and S1 & S2 MOGP VWC reconstructed maps for the assessment dates (R2¯wheat−2020 = 0.95, R2¯wheat−2021 = 0.96). Altogether, the fusion of S1 SAR and S2 optical EO data streams with MOGP offers a powerful innovative approach for cropland trait monitoring over cloudy high-latitude regions.

Synthetic aperture radar (SAR) data provides an appealing opportunity for all-weather day or night Earth surface monitoring. The European constellation Sentinel-1 (S1) consisting of S1-A and S1-B satellites offers a suitable revisit time and spatial resolution for the observation of croplands from space. The C-band radar backscatter is sensitive to vegetation structure changes and phenology as well as soil moisture and roughness. It also varies depending on the local incidence angle (LIA) of the SAR acquisition’s geometry. The LIA backscatter dependency could therefore be exploited to improve the retrieval of the crop biophysical variables. The availability of S1 radar time-series data at distinct observation angles holds the feasibility to retrieve leaf area index (LAI) evolution considering spatiotemporal coverage of intensively cultivated areas. Accordingly, this research presents a workflow merging multi-date S1 smoothed data acquired at distinct LIA with a Gaussian processes regression (GPR) and a cross-validation (CV) strategy to estimate cropland LAI of irrigated winter wheat. The GPR-S1-LAI model was tested against in situ data of the 2020 winter wheat campaign in the irrigated valley of Colorador river, South of Buenos Aires Province, Argentina. We achieved adequate validation results for LAI with RCV2 = 0.67 and RMSECV = 0.88 m2 m−2. The trained model was further applied to a series of S1 stacked images, generating temporal LAI maps that well reflect the crop growth cycle. The robustness of the retrieval workflow is supported by the associated uncertainties along with the obtained maps. We found that processing S1 smoothed imagery with distinct acquisition geometries permits accurate radar-based LAI modeling throughout large irrigated areas and in consequence can support agricultural management practices in cloud-prone agri-environments.

Earth observation offers an unprecedented opportunity to monitor intensively cultivated areas providing key support to assess fertilizer needs and crop water uptake. Routinely, vegetation traits mapping can help farmers to monitor plant development along the crop’s phenological cycle, which is particularly relevant for irrigated agricultural areas. The high spatial and temporal resolution of the Sentinel-2 (S2) multispectral instrument leverages the possibility to estimate leaf area index (LAI), canopy chlorophyll content (CCC), and vegetation water content (VWC) from space. Therefore, our study presents a hybrid retrieval workflow combining a physically-based strategy with a machine learning regression algorithm, i.e., Gaussian processes regression, and an active learning technique to estimate LAI, CCC and VWC of irrigated winter wheat. The established hybrid models of the three traits were validated against in-situ data of a wheat campaign in the Bonaerense valley, South of the Buenos Aires Province, Argentina, in the year 2020. We obtained good to highly accurate validation results with LAI: R2 = 0.92, RMSE = 0.43 m2 m−2, CCC: R2 = 0.80, RMSE = 0.27 g m−2 and VWC: R2 = 0.75, RMSE = 416 g m−2. The retrieval models were also applied to a series of S2 images, producing time series along the seasonal cycle, which reflected the effects of fertilizer and irrigation on crop growth. The associated uncertainties along with the obtained maps underlined the robustness of the hybrid retrieval workflow. We conclude that processing S2 imagery with optimised hybrid models allows accurate space-based crop traits mapping over large irrigated areas and thus can support agricultural management decisions.

Information about pigment and water contents provides comprehensive insights for evaluating photosynthetic potential and activity of agricultural crops. In this study, we present the concept of using spectral integral ratios (SIR) to retrieve three biochemical traits, namely chlorophyll a and b (Cab), carotenoids (Ccx), and water (Cw) content, simultaneously from hyperspectral measurements in the wavelength range 460−1100 nm. The SIR concept is based on automatic separation of respective absorption features through local peak and intercept analysis between log-transformed reflectance and convex hulls. The algorithm was tested on two synthetically established databases using a physiologically constrained look-up-table (LUT) generated by (i) the leaf optical properties model PROSPECT and (ii) the canopy radiative transfer model (RTM) PROSAIL. LUT constraints were realized based on natural Ccx-Cab relations and green peak locations identified in the leaf optical database ANGERS. Linear regression between obtained SIRs and model parameters resulted in coefficients of determination (R²) of 0.66 (i and ii) for Ccx, R2 = 0.85 (i) and 0.53 (ii) for Cab, and R2 = 0.97 (i) and 0.67 (ii) for Cw, respectively. Using the model established from the PROSPECT LUT, leaf level validation was carried out based on ANGERS data with reasonable results both in terms of goodness of fit and root mean square error (RMSE) (Ccx: R2 = 0.86, RMSE = 2.1 μg cm−2; Cab: R2 = 0.67, RMSE = 12.5 μg cm-2; Cw: R2 = 0.89, RMSE = 0.007 cm). The algorithm was applied to airborne spectrometric HyMap data acquired on 12th July 2003 in Barrax, Spain and to AVIRIS-NG data recorded on 2nd July 2018 southwest of Munich, Germany. Mapping of the SIR results as multiband images (3-segment SIR) allows for intuitive visualization of dominant absorptions with respect to the three considered biochemical variables. Barrax in situ validation using linear regression models derived from PROSAIL LUT showed satisfactory results regarding Cab (R2 = 0.84; RMSE = 9.06 μg cm-2) and canopy water content (CWC, R2 = 0.70; RMSE = 0.05 cm). Retrieved Ccx values were reasonable according to Cab-Ccx-dependence plausibility analysis. Hence, the presented SIR algorithm allows for computationally efficient and RTM supported robust retrievals of the two most important vegetation pigments as well as of water content and is ready to be applied on satellite imaging spectroscopy data available in the near future. The algorithm is publicly available as an interface supported tool within the 'Agricultural Applications' of the EnMAP-Box 3 hyperspectral remote sensing software suite.

Hyperspectral acquisitions have proven to be the most informative Earth observation data source for the estimation of nitrogen (N) content, which is the main limiting nutrient for plant growth and thus agricultural production. In the past, empirical algorithms have been widely employed to retrieve information on this biochemical plant component from canopy reflectance. However, these approaches do not seek for a cause-effect relationship based on physical laws. Moreover, most studies solely relied on the correlation of chlorophyll content with nitrogen, and thus neglected the fact that most N is bound in proteins. Our study presents a hybrid retrieval method using a physically-based approach combined with machine learning regression to estimate crop N content. Within the workflow, the leaf optical properties model PROSPECT-PRO including the newly calibrated specific absorption coefficients (SAC) of proteins, was coupled with the canopy reflectance model 4SAIL to PROSAIL-PRO. The latter was then employed to generate a training database to be used for advanced probabilistic machine learning methods: a standard homoscedastic Gaussian process (GP) and a heteroscedastic GP regression that accounts for signal-to-noise relations. Both GP models have the property of providing confidence intervals for the estimates, which sets them apart from other machine learners. Moreover, a GP-based sequential backward band removal algorithm was employed to analyze the band-specific information content of PROSAIL-PRO simulated spectra for the estimation of aboveground N. Data from multiple hyperspectral field campaigns, carried out in the framework of the future satellite mission Environmental Mapping and Analysis Program (EnMAP), were exploited for validation. In these campaigns, corn and winter wheat spectra were acquired to simulate spectral EnMAP data. Moreover, destructive N measurements from leaves, stalks and fruits were collected separately to enable plant-organ-specific validation. The results showed that both GP models can provide accurate aboveground N simulations, with slightly better results of the heteroscedastic GP in terms of model testing and against in situ N measurements from leaves plus stalks, with root mean square error (RMSE) of 2.1 g/m². However, the inclusion of fruit N content for validation deteriorated the results, which can be explained by the inability of the radiation to penetrate the thick tissues of stalks, corn cobs and wheat ears. GP-based band analysis identified optimal spectral settings with ten bands mainly situated in the shortwave infrared (SWIR) spectral region. Use of well-known protein absorption bands from the literature showed comparative results. Finally, the heteroscedastic GP model was successfully applied on airborne hyperspectral data for N mapping. We conclude that GP algorithms, and in particular the heteroscedastic GP, should be implemented for global agricultural monitoring of aboveground N from future imaging spectroscopy data.

In preparation for new-generation imaging spectrometer missions and the accompanying unprecedented inflow of hyperspectral data, optimized models are needed to generate vegetation traits routinely. Hybrid models, combining radiative transfer models with machine learning algorithms, are preferred, however, dealing with spectral collinearity imposes an additional challenge. In this study, we analyzed two spectral dimensionality reduction methods: principal component analysis (PCA) and band ranking (BR), embedded in a hybrid workflow for the retrieval of specific leaf area (SLA), leaf area index (LAI), canopy water content (CWC), canopy chlorophyll content (CCC), the fraction of absorbed photosynthetic active radiation (FAPAR), and fractional vegetation cover (FVC). The SCOPE model was used to simulate training data sets, which were optimized with active learning. Gaussian process regression (GPR) algorithms were trained over the simulations to obtain trait-specific models. The inclusion of PCA and BR with 20 features led to the so-called GPR-20PCA and GPR-20BR models. The 20PCA models encompassed over 99.95% cumulative variance of the full spectral data, while the GPR-20BR models were based on the 20 most sensitive bands. Validation against in situ data obtained moderate to optimal results with normalized root mean squared error (NRMSE) from 13.9% (CWC) to 22.3% (CCC) for GPR-20PCA models, and NRMSE from 19.6% (CWC) to 29.1% (SLA) for GPR-20BR models. Overall, the GPR-20PCA slightly outperformed the GPR-20BR models for all six variables. To demonstrate mapping capabilities, both models were tested on a PRecursore IperSpettrale della Missione Applicativa (PRISMA) scene, spectrally resampled to Copernicus Hyperspectral Imaging Mission for the Environment (CHIME), over an agricultural test site (Jolanda di Savoia, Italy). The two strategies obtained plausible spatial patterns, and consistency between the two models was highest for FVC and LAI (R2=0.91, R2=0.86) and lowest for SLA mapping (R2=0.53). From these findings, we recommend implementing GPR-20PCA models as the most efficient strategy for the retrieval of multiple crop traits from hyperspectral data streams. Hence, this workflow will support and facilitate the preparations of traits retrieval models from the next-generation operational CHIME.

Thanks to the emergence of cloud-computing platforms and the ability of machine learning methods to solve prediction problems efficiently, this work presents a workflow to automate spatiotemporal mapping of essential vegetation traits from Sentinel-3 (S3) imagery. The traits included leaf chlorophyll content (LCC), leaf area index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR), and fractional vegetation cover (FVC), being fundamental for assessing photosynthetic activity on Earth. The workflow involved Gaussian process regression (GPR) algorithms trained on top-of-atmosphere (TOA) radiance simulations generated by the coupled canopy radiative transfer model (RTM) SCOPE and the atmospheric RTM 6SV. The retrieval models, named to S3-TOA-GPR-1.0, were directly implemented in Google Earth Engine (GEE) to enable the quantification of the traits from TOA data as acquired from the S3 Ocean and Land Colour Instrument (OLCI) sensor. Following good to high theoretical validation results with normalized root mean square error (NRMSE) ranging from 5% (FAPAR) to 19% (LAI), a three fold evaluation approach over diverse sites and land cover types was pursued: (1) temporal comparison against LAI and FAPAR products obtained from Moderate Resolution Imaging Spectroradiometer (MODIS) for the time window 2016–2020, (2) spatial difference mapping with Copernicus Global Land Service (CGLS) estimates, and (3) direct validation using interpolated in situ data from the VALERI network. For all three approaches, promising results were achieved. Selected sites demonstrated coherent seasonal patterns compared to LAI and FAPAR MODIS products, with differences between spatially averaged temporal patterns of only 6.59%. In respect of the spatial mapping comparison, estimates provided by the S3-TOA-GPR-1.0 models indicated highest consistency with FVC and FAPAR CGLS products. Moreover, the direct validation of our S3-TOA-GPR-1.0 models against VALERI estimates indicated good retrieval performance for LAI, FAPAR and FVC. We conclude that our retrieval workflow of spatiotemporal S3 TOA data processing into GEE opens the path towards global monitoring of fundamental vegetation traits, accessible to the whole research community.

Monitoring cropland phenology from optical satellite data remains a challenging task due to the influence of clouds and atmospheric artifacts. Therefore, measures need to be taken to overcome these challenges and gain better knowledge of crop dynamics. The arrival of cloud computing platforms such as Google Earth Engine (GEE) has enabled us to propose a Sentinel-2 (S2) phenology end-to-end processing chain. To achieve this, the following pipeline was implemented: (1) the building of hybrid Gaussian Process Regression (GPR) retrieval models of crop traits optimized with active learning, (2) implementation of these models on GEE (3) generation of spatiotemporally continuous maps and time series of these crop traits with the use of gap-filling through GPR fitting, and finally, (4) calculation of land surface phenology (LSP) metrics such as the start of season (SOS) or end of season (EOS). Overall, from good to high performance was achieved, in particular for the estimation of canopy-level traits such as leaf area index (LAI) and canopy chlorophyll content, with normalized root mean square errors (NRMSE) of 9% and 10%, respectively. By means of the GPR gap-filling time series of S2, entire tiles were reconstructed, and resulting maps were demonstrated over an agricultural area in Castile and Leon, Spain, where crop calendar data were available to assess the validity of LSP metrics derived from crop traits. In addition, phenology derived from the normalized difference vegetation index (NDVI) was used as reference. NDVI not only proved to be a robust indicator for the calculation of LSP metrics, but also served to demonstrate the good phenology quality of the quantitative trait products. Thanks to the GEE framework, the proposed workflow can be realized anywhere in the world and for any time window, thus representing a shift in the satellite data processing paradigm. We anticipate that the produced LSP metrics can provide meaningful insights into crop seasonal patterns in a changing environment that demands adaptive agricultural production.

Non-photosynthetic vegetation (NPV) biomass has been identified as a priority variable for upcoming spaceborne imaging spectroscopy missions, calling for a quantitative estimation of lignocellulosic plant material as opposed to the sole indication of surface coverage. Therefore, we propose a hybrid model for the retrieval of non-photosynthetic cropland biomass. The workflow included coupling the leaf optical model PROSPECT-PRO with the canopy reflectance model 4SAIL, which allowed us to simulate NPV biomass from carbon-based constituents (CBC) and leaf area index (LAI). PROSAIL-PRO provided a training database for a Gaussian process regression (GPR) algorithm, simulating a wide range of non-photosynthetic vegetation states. Active learning was employed to reduce and optimize the training data set. In addition, we applied spectral dimensionality reduction to condense essential information of non-photosynthetic signals. The resulting NPV-GPR model was successfully validated against soybean field data with normalized root mean square error (nRMSE) of 13.4% and a coefficient of determination (R2) of 0.85. To demonstrate mapping capability, the NPV-GPR model was tested on a PRISMA hyperspectral image acquired over agricultural areas in the North of Munich, Germany. Reliable estimates were mainly achieved over senescent vegetation areas as suggested by model uncertainties. The proposed workflow is the first step towards the quantification of non-photosynthetic cropland biomass as a next-generation product from near-term operational missions, such as CHIME.

The inference of functional vegetation traits from remotely sensed signals is key to providing efficient information for multiple plant-based applications and to solve related problems [...]

In support of cropland monitoring, operational Copernicus Sentinel-2 (S2) data became available globally and can be explored for the retrieval of important crop traits. Based on a hybrid workflow, retrieval models for six essential biochemical and biophysical crop traits were developed for both S2 bottom-of-atmosphere (BOA) L2A and S2 top-of-atmosphere (TOA) L1C data. A variational heteroscedastic Gaussian process regression (VHGPR) algorithm was trained with simulations generated by the combined leaf-canopy reflectance model PROSAILat the BOA scale and further combined with the Second Simulation of a Satellite Signal in the Solar Spectrum (6SV) atmosphere model at the TOA scale. Established VHGPR models were then applied to S2 L1C and L2A reflectance data for mapping: leaf chlorophyll content (Cab), leaf water content (Cw), fractional vegetation coverage (FVC), leaf area index (LAI), and upscaled leaf biochemical compounds, i.e., LAI ∗ Cab (laiCab) and LAI ∗ Cw (laiCw). Estimated variables were validated using in situ reference data collected during the Munich-North-Isar field campaigns within growing seasons of maize and winter wheat in the years 2017 and 2018. For leaf biochemicals, retrieval from BOA reflectance slightly outperformed results from TOA reflectance, e.g., obtaining a root mean squared error (RMSE) of 6.5 μμg/cm2 (BOA) vs. 8 μμg/cm2 (TOA) in the case of Cab. For the majority of canopy-level variables, instead, estimation accuracy was higher when using TOA reflectance data, e.g., with an RMSE of 139 g/m2 (BOA) vs. 113 g/m2 (TOA) for laiCw. Derived maps were further compared against reference products obtained from the ESA Sentinel Application Platform (SNAP) Biophysical Processor. Altogether, the consistency between L1C and L2A retrievals confirmed that crop traits can potentially be estimated directly from TOA reflectance data. Successful mapping of canopy-level crop traits including information about prediction confidence suggests that the models can be transferred over spatial and temporal scales and, therefore, can contribute to decision-making processes for cropland management.

Conventional methods of plant nutrient estimation for nutrient management need a huge number of leaf or tissue samples and extensive chemical analysis, which is time-consuming and expensive. Remote sensing is a viable tool to estimate the plant’s nutritional status to determine the appropriate amounts of fertilizer inputs. The aim of the study was to use remote sensing to characterize the foliar nutrient status of mango through the development of spectral indices, multivariate analysis, chemometrics, and machine learning modeling of the spectral data. A spectral database within the 350–1050 nm wavelength range of the leaf samples and leaf nutrients were analyzed for the development of spectral indices and multivariate model development. The normalized difference and ratio spectral indices and multivariate models–partial least square regression (PLSR), principal component regression, and support vector regression (SVR) were ineffective in predicting any of the leaf nutrients. An approach of using PLSR-combined machine learning models was found to be the best to predict most of the nutrients. Based on the independent validation performance and summed ranks, the best performing models were cubist (R2 ≥ 0.91, the ratio of performance to deviation (RPD) ≥ 3.3, and the ratio of performance to interquartile distance (RPIQ) ≥ 3.71) for nitrogen, phosphorus, potassium, and zinc, SVR (R2 ≥ 0.88, RPD ≥ 2.73, RPIQ ≥ 3.31) for calcium, iron, copper, boron, and elastic net (R2 ≥ 0.95, RPD ≥ 4.47, RPIQ ≥ 6.11) for magnesium and sulfur. The results of the study revealed the potential of using hyperspectral remote sensing data for non-destructive estimation of mango leaf macro- and micro-nutrients. The developed approach is suggested to be employed within operational retrieval workflows for precision management of mango orchard nutrients.

The current exponential increase of spatiotemporally explicit data streams from satellite-based Earth observation missions offers promising opportunities for global vegetation monitoring. Intelligent sampling through active learning (AL) heuristics provides a pathway for fast inference of essential vegetation variables by means of hybrid retrieval approaches, i.e., machine learning regression algorithms trained by radiative transfer model (RTM) simulations. In this study we summarize AL theory and perform a brief systematic literature survey about AL heuristics used in the context of Earth observation regression problems over terrestrial targets. Across all relevant studies it appeared that: (i) retrieval accuracy of AL-optimized training data sets outperformed models trained over large randomly sampled data sets, and (ii) Euclidean distance-based (EBD) diversity method tends to be the most efficient AL technique in terms of accuracy and computational demand. Additionally, a case study is presented based on experimental data employing both uncertainty and diversity AL criteria. Hereby, a a simulated training data base by the PROSAIL-PRO canopy RTM is used to demonstrate the benefit of AL techniques for the estimation of total leaf carotenoid content (Cxc) and leaf water content (Cw). Gaussian process regression (GPR) was incorporated to minimize and optimize the training data set with AL. Training the GPR algorithm on optimally AL-based sampled data sets led to improved variable retrievals compared to training on full data pools, which is further demonstrated on a mapping example. From these findings we can recommend the use of AL-based sub-sampling procedures to select the most informative samples out of large training data pools. This will not only optimize regression accuracy due to exclusion of redundant information, but also speed up processing time and reduce final model size of kernel-based machine learning regression algorithms, such as GPR. With this study we want to encourage further testing and implementation of AL sampling methods for hybrid retrieval workflows. AL can contribute to the solution of regression problems within the framework of operational vegetation monitoring using satellite imaging spectroscopy data, and may strongly facilitate data processing for cloud-computing platforms.

Decades after release of the first PROSPECT + SAIL (commonly called PROSAIL) versions, the model is still the most famous representative in the field of canopy reflectance modelling and has been widely used to obtain plant biochemical and structural variables, particularly in the agricultural context. The performance of the retrieval is usually assessed by quantifying the distance between the estimated and the in situ measured variables. While this has worked for hundreds of studies that obtained canopy density as a one-sided Leaf Area Index (LAI) or pigment content, little is known about the role of the canopy geometrical properties specified as the Average Leaf Inclination Angle (ALIA). In this study, we exploit an extensive field dataset, including narrow-band field spectra, leaf variables and canopy properties recorded in seven individual campaigns for winter wheat (4x) and silage maize (3x). PROSAIL outputs generally did not represent field spectra well, when in situ variables served as input for the model. A manual fitting of ALIA and leaf water (EWT) revealed significant deviations for both variables (RMSE = 14.5°, 0.020 cm) and an additional fitting of the brown leaf pigments (Cbrown) was necessary to obtain matching spectra at the near infrared (NIR) shoulder. Wheat spectra tend to be underestimated by the model until the emergence of inflorescence when PROSAIL begins to overestimate crop reflectance. This seasonal pattern could be attributed to an attenuated development of ALIAopt compared to in situ measured ALIA. Segmentation of nadir images of wheat was further used to separate spectral contributors into dark background, ears and leaves + stalks. It could be shown that the share of visible fruit ears from nadir view correlates positively with the deviations between field spectral measurement and PROSAIL spectral outputs (R² = 0.78 for aggregation by phenological stages), indicating that retrieval errors increase for ripening stages. An appropriate model parameterization is recommended to assure accurate retrievals of biophysical and biochemical products of interest. The interpretation of inverted ALIA as physical leaf inclinations is considered unfeasible and we argue in favour of treating it as a free calibration parameter.

Satellite hyperspectral Earth observation missions have strong potential to support sustainable agriculture by providing accurate spatial and temporal information of important vegetation biophysical and biochemical variables. To meet this goal, possible error sources in the modelling approaches should be minimized. Thus, first of all, the capability of a model to reproduce the measured spectral signals has to be tested before applying any retrieval algorithm. For an exemplary demonstration, the coupled PROSPECT-D and SAIL radiative transfer models (PROSAIL) were employed to emulate the setup of future hyperspectral sensors in the visible and near-infrared (VNIR) spectral regions with a 6.5 nm spectral sampling distance. Model uncertainties were determined to subsequently exclude those wavelengths with the highest mean absolute error (MAE) between model simulation and spectral measurement. The largest mismatch could be found in the green visible and red edge regions, which can be explained by complex interactions of several biochemical and structural variables in these spectral domains. For leaf area index (LAI, m2·m−2) retrieval, results indicated only a small improvement when using optimized spectral samplings. However, a significant increase in accuracy for leaf chlorophyll content (LCC, µg·cm−2) estimations could be obtained, with the relative root mean square error (RMSE) decreasing from 26% (full VNIR range) to 15% (optimized VNIR) for maize and from 77% to 29% for soybean, respectively. We therefore recommend applying a specific model-error threshold (MAE of ~0.01) to stabilize the retrieval of crop biochemical variables.

Quantitative equivalent water thickness on canopy level (EWTcanopy) is an important land surface variable and retrieving EWTcanopy from remote sensing has been targeted by many studies. However, the effect of radiative penetration into the canopy has not been fully understood. Therefore, in this study the Beer-Lambert law is applied to inversely determine water content information in the 930 to 1060 nm range of canopy reflectance from measured winter wheat and corn spectra collected in 2015, 2017, and 2018. The spectral model was calibrated using a look-up-table (LUT) of 50,000 PROSPECT spectra. Internal model validation was performed using two leaf optical properties datasets (LOPEX93 and ANGERS). Destructive in-situ measurements of water content were collected separately for leaves, stalks, and fruits. Correlation between measured and modelled water content was most promising for leaves and ears in case of wheat, reaching coefficients of determination (R2) up to 0.72 and relative RMSE (rRMSE) of 26% and in case of corn for the leaf fraction only (R2 = 0.86, rRMSE = 23%). These findings indicate that, depending on the crop type and its structure, different parts of the canopy are observed by optical sensors. The results from the Munich-North-Isar test sites indicated that plant compartment specific EWTcanopy allows us to deduce more information about the physical meaning of model results than from equivalent water thickness on leaf level (EWT) which is upscaled to canopy water content (CWC) by multiplication of the leaf area index (LAI). Therefore, it is suggested to collect EWTcanopy data and corresponding reflectance for different crop types over the entire growing cycle. Nevertheless, the calibrated model proved to be transferable in time and space and thus can be applied for fast and effective retrieval of EWTcanopy in the scope of future hyperspectral satellite missions.

The future German Environmental Mapping and Analysis Program (EnMAP) mission, due to launch in late 2019, will deliver high resolution hyperspectral data from space and will thus contribute to a better monitoring of the dynamic surface of the earth. Exploiting the satellite’s ±30° across-track pointing capabilities will allow for the collection of hyperspectral time-series of homogeneous quality. Various studies have shown the possibility to retrieve geo-biophysical plant variables, like leaf area index (LAI) or leaf chlorophyll content (LCC), from narrowband observations with fixed viewing geometry by inversion of radiative transfer models (RTM). In this study we assess the capability of the well-known PROSPECT 5B + 4SAIL (Scattering by Arbitrarily Inclined Leaves) RTM to estimate these variables from off-nadir observations obtained during a field campaign with respect to EnMAP-like sun–target–sensor-geometries. A novel approach for multiple inquiries of a large look-up-table (LUT) in hierarchical steps is introduced that accounts for the varying instances of all variables of interest. Results show that anisotropic effects are strongest for early growth stages of the winter wheat canopy which influences also the retrieval of the variables. RTM inversions from off-nadir spectra lead to a decreased accuracy for the retrieval of LAI with a relative root mean squared error (rRMSE) of 18% at nadir vs. 25% (backscatter) and 24% (forward scatter) at off-nadir. For LCC estimations, however, off-nadir observations yield improvements, i.e., rRMSE (nadir) = 24% vs. rRMSE (forward scatter) = 20%. It follows that for a variable retrieval through RTM inversion, the final user will benefit from EnMAP time-series for biophysical studies regardless of the acquisition angle and will thus be able to exploit the maximum revisit capability of the mission.