Vegetation indices (VIs) are widely used in optical remote sensing to estimate biophysical variables of vegetated surfaces. With the advent of spectroscopy technology, spectral bands can be combined in numerous ways to extract the desired information. This resulted in a plethora of proposed indices, designed for a diversity of applications and research purposes. However, it is not always clear whether they are sensitive to the variable of interest while at the same time, responding insensitive to confounding factors. Hence, to be able to quantify the robustness of VIs, a systematic evaluation is needed, thereby introducing a widest possible variety of biochemical and structural heterogeneity. Such exercise can be achieved with coupled leaf and canopy radiative transfer models (RTMs), whereby input variables can virtually simulate any vegetation scenario. With the intention of evaluating multiple VIs in an efficient way, this led us to the development of a global sensitivity analysis (GSA) toolbox dedicated to the analysis of VIs on their sensitivity towards RTM input variables. We identified VIs that are designed to be sensitive towards leaf chlorophyll content (LCC), leaf water content (LWC) and leaf area index (LAI) for common sensors of terrestrial Earth observation satellites: Landsat 8, MODIS, Sentinel-2, Sentinel-3 and the upcoming imaging spectrometer mission EnMAP. The coupled RTMs PROSAIL and PROINFORM were used for simulations of homogeneous and forest canopies respectively. GSA total sensitivity results suggest that LCC-sensitive indices respond most robust: for the great majority of scenarios, chlorophyll a + b content (Cab) drives between 75% and 82% of the indices’ variability. LWC-sensitive indices were most affected by confounding variables such as Cab and LAI, although the equivalent water thickness (Cw) can drive between 25% and 50% of the indices’ variability. Conversely, the majority of LAI-sensitive indices are not only sensitive to LAI but rather to a mixture of structural and biochemical variables.

ESA’s Eighth Earth Explorer mission “FLuorescence EXplorer” (FLEX) will be dedicated to the global monitoring of the chlorophyll fluorescence emitted by vegetation. In order to properly interpret the measured fluorescence signal, essential vegetation variables need to be retrieved concomitantly. FLEX will fly in tandem formation with Sentinel-3 (S3), which conveys the Ocean and Land Color Instrument (OLCI) that is designed to characterize the atmosphere and the terrestrial vegetation at a spatial resolution of 300 m. In support of FLEX’s preparatory activities, this paper presents a first validation exercise of OLCI vegetation products against in situ data coming from the 2018 FLEXSense campaign. During this campaign, leaf chlorophyll content (LCC) and leaf area index (LAI) measurements were collected over croplands, while HyPlant DUAL images of the area were acquired at a 3 m spatial resolution. A multiscale validation strategy was pursued. First, estimates of these two variables, together with the combined canopy chlorophyll content (CCC = LCC × LAI), were obtained at the HyPlant spatial resolution and were compared against the in situ measurements. Second, the fine-scale retrieval maps from HyPlant were coarsened to the S3 spatial scale as a reference to assess the quality of the OLCI vegetation products. As an intermediary step, vegetation products extracted from Sentinel-2 data were used to compare retrievals at the in-between spatial resolution of 20 m. For all spatial scales, CCC delivered the most accurate estimates with the smallest prediction error obtained at the 300 m resolution (R${}^2$ of 0.74 and RMSE = 26.8 μg cm${}^{-2}$). Results of a scaling analysis suggest that CCC performs well at the different tested spatial resolutions since it presents a linear behavior across scales. LCC, on the other hand, was poorly retrieved at the 300 m scale, showing overestimated values over heterogeneous pixels. The introduction of a new LCC model integrating mixed reflectance spectra in its training enabled to improve by 16% the retrieval accuracy for this variable (RMSE = 10 μg cm${}^{-2}$ for the new model versus RMSE = 11.9 μg cm${}^{-2}$ for the former model).

Optical Earth observation satellites provide spatially-explicit data that are necessary to study trends in vegetation dynamics. However, more of often than not optical data are discontinuous in time, due to persistent cloud cover and instrumental noises. Hence, the operating constraints of these data require several essential pre-processing steps, especially when aiming to reach towards monitoring of vegetation seasonal trends.  To facilitate this task, here we present an end-to-end processing software framework applied to Sentinel-2 images.To do so, first biophysical retrieval models were generated by means of a trained machine learning regression algorithm (MLRA) using simulated data coming from radiative transfer models. Among various tested MLRAs, the variational heteroscedastic Gaussian process regression (VHGPR) was evaluated as best performing. to train the retrieval model.  The training and retrieval were conducted in the Automated Radiative Transfer Models Operator (ARTMO) software framework.Subsequently, in view of retrieving the phenological parameters from the obtained vegetation products, a novel times series toolbox as part of the ARTMO framework was used, called:  Decomposition and Analysis of Time Series software (DATimeS). DATimeS provides temporal interpolation among other functionalities with several advanced MLRAs for gap filling, smoothing functions and subsequent calculation of phenology indicators. Various MLRAs were tested for gap filling to reconstruct cloud-free maps of biophysical variables at a step of 10 days.A demonstration case is presented involving the retrieval of Leaf area index (LAI), fraction of Absorbed Photosynthetically Active Radiation (FAPAR) from sentinel-2 time series.  A large agricultural Algerian site of 143, 75 km² including Oued Rhiou, Ouarizane, Djidioua (1,345,075 pixels) was chosen for this study.  A reference image was excluded from the time series in order to evaluate the reconstruction accuracy over a 40-day artificial gap.  The reference vs.  Reconstructed maps produced by the gap-filling methods were compared with statistical goodness-of-fit metrics.  Considering both accuracy and processing speed, the fitting algorithms Gaussian process regression (GPR) and Next neighbour interpolation (R²= 0.90 / 0.081 sec per pixel and R²=0.88 / 0.001 sec per pixel respectively) interpolations proved to reconstruct the vegetation products the most efficient, with GPR as more accurate but Next faster by a factor of 70.Finally, we evaluated of the phenology indicators such as start-of-season and end-of-season based on LAI and FAPAR. The obtained maps provide valid information of the vegetation dynamics.  Altogether, the ARTMO-DATimeS software framework enabled seamless processing of all essential steps:  (1) from L2A sentinel-2 images converted to vegetation products, (2) to cloud-free composite products, and finally (3) converted into vegetation phenology indicators.