Prototyping Sentinel-2 green LAI and brown LAI products for cropland monitoring.

For agricultural applications, identification of non-photosynthetic above-ground vegetation is of great interest as it contributes to assess harvest practices, detecting crop residues or drought events, as well as to better predict the carbon, water and nutrients uptake. While the mapping of green Leaf Area Index (LAI) is well established, current operational retrieval models are not calibrated for LAI estimation over senescent, brown vegetation. This not only leads to an underestimation of LAI when crops are ripening, but is also a missed monitoring opportunity. The high spatial and temporal resolution of Sentinel-2 (S2) satellites constellation offers the possibility to estimate brown LAI (LAI G ) next to green LAI (LAI G ). By using LAI ground measurements from multiple campaigns associated with airborne or satellite spectra, Gaussian processes regression (GPR) models were developed for both LAI G and LAI B , providing alongside associated uncertainty estimates, which allows to mask out unreliable LAI retrievals with higher uncertainties. A processing chain was implemented to apply both models to S2 images, generating a multiband LAI product at 20 m spatial resolution. The models were adequately validated with in-situ data from various European study sites (LAI G : R2 = 0.7, RMSE = 0.67 m2/m2; LAI B : R2 = 0.62, RMSE = 0.43 m2/m2). Thanks to the S2 bands in the red edge (B5: 705 nm and B6: 740 nm) and in the shortwave infrared (B12: 2190 nm) a distinction between LAI G and LAI B can be achieved. To demonstrate the capability of LAI B to identify when crops start senescing, S2 time series were processed over multiple European study sites and seasonal maps were produced, which show the onset of crop senescence after the green vegetation peak. Particularly, the LAI B product permits the detection of harvest (i.e., sudden drop in LAI B ) and the determination of crop residues (i.e., remaining LAI B ), although a better spectral sampling in the shortwave infrared would have been desirable to disentangle brown LAI from soil variability and its perturbing effects. Finally, a single total LAI product was created by merging LAI G and LAI B estimates, and then compared to the LAI derived from S2 L2B biophysical processor integrated in SNAP. The spatiotemporal analysis results confirmed the improvement of the proposed descriptors with respect to the standard SNAP LAI product accounting only for photosynthetically active green vegetation.

Mapping landscape canopy nitrogen content from space using PRISMA data.

Satellite imaging spectroscopy for terrestrial applications is reaching maturity with recently launched and upcoming science-driven missions, e.g. PRecursore IperSpettrale della Missione Applicativa (PRISMA) and Environmental Mapping and Analysis Program (EnMAP), respectively. Moreover, the high-priority mission candidate Copernicus Hyperspectral Imaging Mission for the Environment (CHIME) is expected to globally provide routine hyperspectral observations to support new and enhanced services for, among others, sustainable agricultural and biodiversity management. Thanks to the provision of contiguous visible-to-shortwave infrared spectral data, hyperspectral missions open enhanced opportunities for the development of new-generation retrieval models of multiple vegetation traits. Among these, canopy nitrogen content (CNC) is one of the most promising variables given its importance for agricultural monitoring applications. This work presents the first hybrid CNC retrieval model for the operational delivery from spaceborne imaging spectroscopy data. To achieve this, physically-based models were combined with machine learning regression algorithms and active learning (AL). The key concepts involve: (1) coupling the radiative transfer models PROSPECT-PRO and SAIL for the generation of a wide range of vegetation states as training data, (2) using dimensionality reduction to deal with collinearity, (3) applying an AL technique in combination with Gaussian process regression (GPR) for fine-tuning the training dataset on in field collected data, and (4) adding non-vegetated spectra to enable the model to deal with spectral heterogeneity in the image. The final CNC model was successfully validated against field data achieving a low root mean square error (RMSE) of 3.4 g/m2 and coefficient of determination (R 2) of 0.7. The model was applied to a PRISMA image acquired over agricultural areas in the North of Munich, Germany. Mapping aboveground CNC yielded reliable estimates over the whole landscape and meaningful associated uncertainties. These promising results demonstrate the feasibility of routinely quantifying CNC from space, such as in an operational context as part of the future CHIME mission.

Quantifying vegetation biophysical variables from the Sentinel-3/FLEX tandem mission: Evaluation of the synergy of OLCI and FLORIS data sources.

The ESA's forthcoming FLuorescence EXplorer (FLEX) mission is dedicated to the global monitoring of the vegetation's chlorophyll fluorescence by means of an imaging spectrometer, FLORIS. In order to properly interpret the fluorescence signal in relation to photosynthetic activity, essential vegetation variables need to be retrieved concomitantly. FLEX will fly in tandem with Sentinel-3 (S3), which conveys the Ocean and Land Colour Instrument (OLCI) that is designed to characterize the atmosphere and the terrestrial vegetation at a spatial resolution of 300 m. In this work we present the retrieval models of four essential biophysical variables: (1) Leaf Area Index (LAI), (2) leaf chlorophyll content (Cab), (3) fraction of absorbed photosynthetically active radiation (fAPAR), and (4) fractional vegetation cover (FCover). These variables can be operationally inferred by hybrid retrieval approaches, which combine the generalization capabilities offered by radiative transfer models (RTMs) with the flexibility and computational efficiency of machine learning methods. The RTM SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes) was used to generate a database of reflectance spectra corresponding to a large variety of canopy realizations, which served subsequently as input to train a Gaussian Process Regression (GPR) algorithm for each targeted variable. Three sets of GPR models were developed, based on different spectral band settings: (1) OLCI (21 bands between 400 and 1040 nm), (2) FLORIS (281 bands between 500 and 780 nm), and (3) their synergy. Their respective performances were assessed based on simulated reflectance scenes. Regarding the retrieval of Cab, the OLCI model gave good model performances (R2: 0.91; RMSE: 7.6 µg. cm -2), yet superior accuracies were achieved as a result of FLORIS' higher spectral resolution (R2: 0.96; RMSE: 4.8 µg. cm -2). The synergy of both datasets did not further enhance the variable retrieval. Regarding LAI, the improvement of the model performances by using only FLORIS spectra (R2: 0.87; RMSE: 1.05 m2.m-2) rather than only OLCI spectra (R2: 0.86; RMSE: 1.12 m2.m-2) was less evident but merging both data sets was more beneficial (R2: 0.88; RMSE: 1.01 m2.m-2). Finally, the three data sources gave good model performances for the retrieval of fAPAR and Fcover, with the best performing model being the Synergy model (fAPAR: R2: 0.99; RMSE: 0.02 and FCover: R2: 0.98; RMSE: 0.04). The ability of the models to process real data was subsequently demonstrated by applying the OLCI models to S3 surface reflectance products acquired over Western Europe and Argentina. Obtained maps showed consistent patterns and variable ranges, and comparison against corresponding Sentinel-2 products (coarsened to a 300 m spatial resolution) led to reasonable matches (R2: 0.5-0.7). Altogether, given the availability of the multiple data sources, the FLEX tandem mission will foster unique opportunities to quantify essential vegetation properties, and hence facilitate the interpretation of the measured fluorescence levels.

DATimeS: A machine learning time series GUI toolbox for gap-filling and vegetation phenology trends detection.

Optical remotely sensed data are typically discontinuous, with missing values due to cloud cover. Consequently, gap-filling solutions are needed for accurate crop phenology characterization. The here presented Decomposition and Analysis of Time Series software (DATimeS) expands established time series interpolation methods with a diversity of advanced machine learning fitting algorithms (e.g., Gaussian Process Regression: GPR) particularly effective for the reconstruction of multiple-seasons vegetation temporal patterns. DATimeS is freely available as a powerful image time series software that generates cloud-free composite maps and captures seasonal vegetation dynamics from regular or irregular satellite time series. This work describes the main features of DATimeS, and provides a demonstration case using Sentinel-2 Leaf Area Index time series data over a Spanish site. GPR resulted as an optimum fitting algorithm with most accurate gap-filling performance and associated uncertainties. DATimeS further quantified LAI fluctuations among multiple crop seasons and provided phenological indicators for specific crop types.

Fusing optical and SAR time series for LAI gap fillingwith multioutput Gaussian processes.

The availability of satellite optical information is often hampered by the natural presence of clouds, which can be problematic for many applications. Persistent clouds over agricultural fields can mask key stages of crop growth, leading to unreliable yield predictions. Synthetic Aperture Radar (SAR) provides all-weather imagery which can potentially overcome this limitation, but given its high and distinct sensitivity to different surface properties, the fusion of SAR and optical data still remains an open challenge. In this work, we propose the use of Multi-Output Gaussian Process (MOGP) regression, a machine learning technique that learns automatically the statistical relationships among multisensor time series, to detect vegetated areas over which the synergy between SAR-optical imageries is profitable. For this purpose, we use the Sentinel-1 Radar Vegetation Index (RVI) and Sentinel-2 Leaf Area Index (LAI) time series over a study area in north west of the Iberian peninsula. Through a physical interpretation of MOGP trained models, we show its ability to provide estimations of LAI even over cloudy periods using the information shared with RVI, which guarantees the solution keeps always tied to real measurements. Results demonstrate the advantage of MOGP especially for long data gaps, where optical-based methods notoriously fail. The leave-one-image-out assessment technique applied to the whole vegetation cover shows MOGP predictions improve standard GP estimations over short-time gaps (R2 of 74% vs 68%, RMSE of 0.4 vs 0.44 [m 2 m -2]) and especially over long-time gaps (R2 of 33% vs 12%, RMSE of 0.5 vs 1.09 [m 2 m -2]). A second assessment is focused on crop-specific regions, clustering pixels fulfilling specific model conditions where the synergy is profitable. Results reveal the MOGP performance is crop type and crop stage dependent. For long time gaps, best R2 are obtained over maize, ranging from 0.1 (tillering) to 0.36 (development) up to 0.81 (maturity); for moderate time gap, R2 = 0.93 (maturity) is obtained. Crops such as wheat, oats, rye and barley, can profit from the LAI-RVI synergy, with R2 varying between 0.4 and 0.6. For beet or potatoes, MOGP provides poorer results, but alternative descriptors to RVI should be tested for these specific crops in the future before discarding synergy real benefits. In conclusion, active-passive sensor fusion with MOGP represents a novel and promising approach to cope with crop monitoring over cloud-dominated areas.

Multi-Season Phenology Mapping of Nile Delta Croplands Using Time Series of Sentinel-2 and Landsat 8 Green LAI.

Space-based cropland phenology monitoring substantially assists agricultural managing practices and plays an important role in crop yield predictions. Multitemporal satellite observations allow analyzing vegetation seasonal dynamics over large areas by using vegetation indices or by deriving biophysical variables. The Nile Delta represents about half of all agricultural lands of Egypt. In this region, intensifying farming systems are predominant and multi-cropping rotations schemes are increasing, requiring a high temporal and spatial resolution monitoring for capturing successive crop growth cycles. This study presents a workflow for cropland phenology characterization and mapping based on time series of green Leaf Area Index (LAI) generated from NASA's Harmonized Landsat 8 (L8) and Sentinel-2 (S2) surface reflectance dataset from 2016 to 2019. LAI time series were processed for each satellite dataset, which were used separately and combined to identify seasonal dynamics for a selection of crop types (wheat, clover, maize and rice). For the combination of L8 with S2 LAI products, we proposed two time series smoothing and fitting methods: (1) the Savitzky-Golay (SG) filter and (2) the Gaussian Processes Regression (GPR) fitting function. Single-sensor and L8-S2 combined LAI time series were used for the calculation of key crop Land Surface Phenology (LSP) metrics (start of season, end of season, length of season), whereby the detection of cropland growing seasons was based on two established threshold methods, i.e., a seasonal or a relative amplitude value. Overall, the developed phenology extraction scheme enabled identifying up to two successive crop cycles within a year, with a superior performance observed for the seasonal than for the relative threshold method, in terms of consistency and cropland season detection capability. Differences between the time series collections were analyzed by comparing the phenology metrics per crop type and year. Results suggest that L8-S2 combined LAI data streams with GPR led to a more precise detection of the start and end of growing seasons for most crop types, reaching an overall detection of 74% over the total planted crops versus 69% with S2 and 63% with L8 alone. Finally, the phenology mapping allowed us to evaluate the spatial and temporal evolution of the croplands over the agroecosystem in the Nile Delta.

Green LAI Mapping and Cloud Gap-Filling Using Gaussian Process Regression in Google Earth Engine.

For the last decade, Gaussian process regression (GPR) proved to be a competitive machine learning regression algorithm for Earth observation applications, with attractive unique properties such as band relevance ranking and uncertainty estimates. More recently, GPR also proved to be a proficient time series processor to fill up gaps in optical imagery, typically due to cloud cover. This makes GPR perfectly suited for large-scale spatiotemporal processing of satellite imageries into cloud-free products of biophysical variables. With the advent of the Google Earth Engine (GEE) cloud platform, new opportunities emerged to process local-to-planetary scale satellite data using advanced machine learning techniques and convert them into gap-filled vegetation properties products. However, GPR is not yet part of the GEE ecosystem. To circumvent this limitation, this work proposes a general adaptation of GPR formulation to parallel processing framework and its integration into GEE. To demonstrate the functioning and utility of the developed workflow, a GPR model predicting green leaf area index (LAI G ) from Sentinel-2 imagery was imported. Although by running this GPR model into GEE any corner of the world can be mapped into LAI G at a resolution of 20 m, here we show some demonstration cases over western Europe with zoom-ins over Spain. Thanks to the computational power of GEE, the mapping takes place on-the-fly. Additionally, a GPR-based gap filling strategy based on pre-optimized kernel hyperparameters is also put forward for the generation of multi-orbit cloud-free LAI G maps with an unprecedented level of detail, and the extraction of regularly-sampled LAI G time series at a pixel level. The ability to plugin a locally-trained GPR model into the GEE framework and its instant processing opens up a new paradigm of remote sensing image processing.