Comparison of Crop Trait Retrieval Strategies Using UAV-Based VNIR Hyperspectral Imaging.

Hyperspectral cameras onboard unmanned aerial vehicles (UAVs) have recently emerged for monitoring crop traits at the sub-field scale. Different physical, statistical, and hybrid methods for crop trait retrieval have been developed. However, spectra collected from UAVs can be confounded by various issues, including illumination variation throughout the crop growing season, the effect of which on the retrieval performance is not well understood at present. In this study, four retrieval methods are compared, in terms of retrieving the leaf area index (LAI), fractional vegetation cover (fCover), and canopy chlorophyll content (CCC) of potato plants over an agricultural field for six dates duri…

FLEX End-to-End Mission Performance Simulator

The FLuorescence EXplorer (FLEX) mission, selected as the European Space Agency's eighth Earth Explorer, aims to globally measure the sun-induced-chlorophyll-fluorescence spectral emission from terrestrial vegetation. In the frame of the FLEX mission, several industrial and scientific studies have analyzed the instrument design, image processing algorithms, or modeling aspects. At the same time, a common tool is needed to address the overall FLEX mission performance by combining all these features. For this reason, an end-to-end mission performance simulator has been developed for the FLEX mission (FLEX-E). This paper describes the FLEX-E software design, which combines the generation of co…

Replacing radiative transfer models by surrogate approximations through machine learning

Physically-based radiative transfer models (RTMs) help in understanding the processes occurring on the Earth's surface and their interactions with vegetation and atmosphere. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. They are advantageous in real practice because of the computational efficiency and excellent accuracy and flexibility for extrapolation. We here present an ‘Emulator toolbox’ that enables analyzing three multi-output machine learning regress…

Brown and green LAI mapping through spectral indices

Abstract When crops senescence, leaves remain until they fall off or are harvested. Hence, leaf area index (LAI) stays high even when chlorophyll content degrades to zero. Current LAI approaches from remote sensing techniques are not optimized for estimating LAI of senescent vegetation. In this paper a two-step approach has been proposed to realize simultaneous LAI mapping over green and senescent croplands. The first step separates green from brown LAI by means of a newly proposed index, ‘Green Brown Vegetation Index (GBVI)’. This index exploits two shortwave infrared (SWIR) spectral bands centred at 2100 and 2000 nm, which fall right in the dry matter absorption regions, thereby providing…

Variability and Uncertainty Challenges in Scaling Imaging Spectroscopy Retrievals and Validations from Leaves Up to Vegetation Canopies

Imaging spectroscopy of vegetation requires methods for scaling and generalizing optical signals that are reflected, transmitted and emitted in the solar wavelength domain from single leaves and observed at the level of canopies by proximal sensing, airborne and satellite spectroradiometers. The upscaling embedded in imaging spectroscopy retrievals and validations of plant biochemical and structural traits is challenged by natural variability and measurement uncertainties. Sources of the leaf-to-canopy upscaling variability and uncertainties are reviewed with respect to: (1) implementation of retrieval algorithms and (2) their parameterization and validation of quantitative products through…

Neural Network Emulation of Synthetic Hyperspectral Sentinel-2-Like Imagery With Uncertainty

Hyperspectral satellite imagery provides highly-resolved spectral information for large areas and can provide vital information. However, only a few imaging spectrometer missions are currently in operation. Aiming to generate synthetic satellite-based hyperspectral imagery potentially covering any region, we explored the possibility of applying statistical learning, i.e. emulation. Based on the relationship of a Sentinel-2 (S2) scene and a hyperspectral HyPlant airborne image, this work demonstrates the possibility to emulate a hyperspectral S2-like image. We tested the role of different machine learning regression algorithms (MLRA) and varied the image-extracted training dataset size. We f…

Eco-Friendly Estimation of Heavy Metal Contents in Grapevine Foliage Using In-Field Hyperspectral Data and Multivariate Analysis

Heavy metal monitoring in food-producing ecosystems can play an important role in human health safety. Since they are able to interfere with plants’ physiochemical characteristics, which influence the optical properties of leaves, they can be measured by in-field spectroscopy. In this study, the predictive power of spectroscopic data is examined. Five treatments of heavy metal stress (Cu, Zn, Pb, Cr, and Cd) were applied to grapevine seedlings and hyperspectral data (350−2500 nm), and heavy metal contents were collected based on in-field and laboratory experiments. The partial least squares (PLS) method was used as a feature selection technique, and multiple linear regressions (…

Statistical biophysical parameter retrieval and emulation with Gaussian processes

Abstract Earth observation from satellites poses challenging problems where machine learning is being widely adopted as a key player. Perhaps the most challenging scenario that we are facing nowadays is to provide accurate estimates of particular variables of interest characterizing the Earth's surface. This chapter introduces some recent advances in statistical bio-geophysical parameter retrieval from satellite data. In particular, we will focus on Gaussian process regression (GPR) that has excelled in parameter estimation as well as in modeling complex radiative transfer processes. GPR is based on solid Bayesian statistics and generally yields efficient and accurate parameter estimates, a…

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegeta…

Global Sensitivity Analysis of Leaf-Canopy-Atmosphere RTMs: Implications for Biophysical Variables Retrieval from Top-of-Atmosphere Radiance Data.

Knowledge of key variables driving the top of the atmosphere (TOA) radiance over a vegetated surface is an important step to derive biophysical variables from TOA radiance data, e.g., as observed by an optical satellite. Coupled leaf-canopy-atmosphere Radiative Transfer Models (RTMs) allow linking vegetation variables directly to the at-sensor TOA radiance measured. Global Sensitivity Analysis (GSA) of RTMs enables the computation of the total contribution of each input variable to the output variance. We determined the impacts of the leaf-canopy-atmosphere variables into TOA radiance using the GSA to gain insights into retrievable variables. The leaf and canopy RTM PROSAIL was coupled with…

Seasonal Mapping of Irrigated Winter Wheat Traits in Argentina with a Hybrid Retrieval Workflow Using Sentinel-2 Imagery

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 learni…

Remote sensing algorithms for estimation of fractional vegetation cover using pure vegetation index values: A review

Abstract Green fractional vegetation cover ( f c ) is an important phenotypic factor in the fields of agriculture, forestry, and ecology. Spatially explicit monitoring of f c via relative vegetation abundance (RA) algorithms, especially those based on scaled maximum/minimum vegetation index (VI) values, has been widely investigated in remote sensing research. Although many studies have explored the effectiveness of RA algorithms over the past 30 years, a literature review summarizing the corresponding theoretical background, issues, current state-of-the-art techniques, challenges, and prospects has not yet been published. The overall objective of the present study was to accomplish a compre…

Biomass Assessment of Agricultural Crops Using Multi-temporal Dual-Polarimetric TerraSAR-X Data

The biomass of three agricultural crops, winter wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and canola (Brassica napus L.), was studied using multi-temporal dual-polarimetric TerraSAR-X data. The radar backscattering coefficient sigma nought of the two polarization channels HH and VV was extracted from the satellite images. Subsequently, combinations of HH and VV polarizations were calculated (e.g. HH/VV, HH + VV, HH × VV) to establish relationships between SAR data and the fresh and dry biomass of each crop type using multiple stepwise regression. Additionally, the semi-empirical water cloud model (WCM) was used to account for the effect of crop biomass on radar backscatter …

Evaluation of Sentinel-2 Red-Edge Bands for Empirical Estimation of Green LAI and Chlorophyll Content

ESA’s upcoming satellite Sentinel-2 will provide Earth images of high spatial, spectral and temporal resolution and aims to ensure continuity for Landsat and SPOT observations. In comparison to the latter sensors, Sentinel-2 incorporates three new spectral bands in the red-edge region, which are centered at 705, 740 and 783 nm. This study addresses the importance of these new bands for the retrieval and monitoring of two important biophysical parameters: green leaf area index (LAI) and chlorophyll content (Ch). With data from several ESA field campaigns over agricultural sites (SPARC, AgriSAR, CEFLES2) we have evaluated the efficacy of two empirical methods that specifically make use of the…

A Comparison of Advanced Regression Algorithms for Quantifying Urban Land Cover

Quantitative methods for mapping sub-pixel land cover fractions are gaining increasing attention, particularly with regard to upcoming hyperspectral satellite missions. We evaluated five advanced regression algorithms combined with synthetically mixed training data for quantifying urban land cover from HyMap data at 3.6 and 9 m spatial resolution. Methods included support vector regression (SVR), kernel ridge regression (KRR), artificial neural networks (NN), random forest regression (RFR) and partial least squares regression (PLSR). Our experiments demonstrate that both kernel methods SVR and KRR yield high accuracies for mapping complex urban surface types, i.e., rooftops, pavements, gras…

Simultaneous retrieval of sugarcane variables from Sentinel-2 data using Bayesian regularized neural network

Assessing Non-Photosynthetic Cropland Biomass from Spaceborne Hyperspectral Imagery

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…

A red-edge spectral index for remote sensing estimation of green LAI over agroecosystems

Abstract Leaf area index (LAI) is a key biophysical parameter for the monitoring of agroecosystems. Conventional two-band vegetation indices based on red and near-infrared relationships such as the normalized difference vegetation index (NDVI) are well known to suffer from saturation at moderate-to-high LAI values (3–5). To bypass this saturation effect, in this work a robust alternative has been proposed for the estimation of green LAI over a wide variety of crop types. By using data from European Space Agency (ESA) campaigns SPARC 2003 and 2004 (Barrax, Spain) experimental LAI values over 9 different crop types have been collected while at the same time spaceborne imagery have been acquir…

Advances in Kernel Machines for Image Classification and Biophysical Parameter Retrieval

Remote sensing data analysis is knowing an unprecedented upswing fostered by the activities of the public and private sectors of geospatial and environmental data analysis. Modern imaging sensors offer the necessary spatial and spectral information to tackle a wide range problems through Earth Observation, such as land cover and use updating, urban dynamics, or vegetation and crop monitoring. In the upcoming years even richer information will be available: more sophisticated hyperspectral sensors with high spectral resolution, multispectral sensors with sub-metric spatial detail or drones that can be deployed in very short time lapses. Besides such opportunities, these new and wealthy infor…

Quantifying mangrove leaf area index from Sentinel-2 imagery using hybrid models and active learning

Mangrove forests provide vital ecosystem services. The increasing threats to mangrove forest extent and fragmentation can be monitored from space. Accurate spatially explicit quantification of key vegetation characteristics of mangroves, such as leaf area index (LAI), would further advance our monitoring efforts to assess ecosystem health and functioning. Here, we investigated the potential of radiative transfer models (RTM), combined with active learning (AL), to estimate LAI from Sentinel-2 spectral reflectance in the mangrove-dominated region of Ngoc Hien, Vietnam. We validated the retrieval of LAI estimates against in-situ measurements based on hemispherical photography and compared aga…

Prototyping Crop Traits Retrieval Models for CHIME: Dimensionality Reduction Strategies Applied to PRISMA 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 photo…

Quantifying Irrigated Winter Wheat LAI in Argentina Using Multiple Sentinel-1 Incidence Angles

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 d…

A Survey on Gaussian Processes for Earth-Observation Data Analysis: A Comprehensive Investigation

Gaussian processes (GPs) have experienced tremendous success in biogeophysical parameter retrieval in the last few years. GPs constitute a solid Bayesian framework to consistently formulate many function approximation problems. This article reviews the main theoretical GP developments in the field, considering new algorithms that respect signal and noise characteristics, extract knowledge via automatic relevance kernels to yield feature rankings automatically, and allow applicability of associated uncertainty intervals to transport GP models in space and time that can be used to uncover causal relations between variables and can encode physically meaningful prior knowledge via radiative tra…

Spectral band selection for vegetation properties retrieval using Gaussian processes regression

Abstract With current and upcoming imaging spectrometers, automated band analysis techniques are needed to enable efficient identification of most informative bands to facilitate optimized processing of spectral data into estimates of biophysical variables. This paper introduces an automated spectral band analysis tool (BAT) based on Gaussian processes regression (GPR) for the spectral analysis of vegetation properties. The GPR-BAT procedure sequentially backwards removes the least contributing band in the regression model for a given variable until only one band is kept. GPR-BAT is implemented within the framework of the free ARTMO's MLRA (machine learning regression algorithms) toolbox, w…

Partitioning net carbon dioxide fluxes into photosynthesis and respiration using neural networks

Abstract The eddy covariance (EC) technique is used to measure the net ecosystem exchange (NEE) of CO2 between ecosystems and the atmosphere, offering a unique opportunity to study ecosystem responses to climate change. NEE is the difference between the total CO2 release due to all respiration processes (RECO), and the gross carbon uptake by photosynthesis (GPP). These two gross CO2 fluxes are derived from EC measurements by applying partitioning methods that rely on physiologically based functional relationships with a limited number of environmental drivers. However, the partitioning methods applied in the global FLUXNET network of EC observations do not account for the multiple co‐acting…

Assessment of workflow feature selection on forest LAI prediction with sentinel-2A MSI, landsat 7 ETM+ and Landsat 8 OLI

The European Space Agency (ESA)’s Sentinel-2A (S2A) mission is providing time series that allow the characterisation of dynamic vegetation, especially when combined with the National Aeronautics and Space Administration (NASA)/United States Geological Survey (USGS) Landsat 7 (L7) and Landsat 8 (L8) missions. Hybrid retrieval workflows combining non-parametric Machine Learning Regression Algorithms (MLRAs) and vegetation Radiative Transfer Models (RTMs) were proposed as fast and accurate methods to infer biophysical parameters such as Leaf Area Index (LAI) from these data streams. However, the exact design of optimal retrieval workflows is rarely discussed. In this study, the impact of…

Hybrid retrieval of crop traits from multi-temporal PRISMA hyperspectral imagery

The recently launched and upcoming hyperspectral satellite missions, featuring contiguous visible-to-shortwave infrared spectral information, are opening unprecedented opportunities for the retrieval of a broad set of vegetation traits with enhanced accuracy through novel retrieval schemes. In this framework, we exploited hyperspectral data cubes collected by the new-generation PRecursore IperSpettrale della Missione Applicativa (PRISMA) satellite of the Italian Space Agency to develop and test a hybrid retrieval workflow for crop trait mapping. Crop traits were mapped over an agricultural area in north-east Italy (Jolanda di Savoia, FE) using PRISMA images collected during the 2020 and 202…

Oxygen transmittance correction for solar-induced chlorophyll fluorescence measured on proximal sensing: Application to the NASA-GSFC fusion tower

Since oxygen (O 2 ) absorption of light becomes more pronounced at higher pressure levels, even a few meters distance between the target and the sensor can strongly affect canopy-leaving Solar-Induced chlorophyll Fluorescence (SIF) retrievals. This study was conducted to quantify the consequent error propagation and the impact of ignoring oxygen absorption effects on proximal sensing SIF measurements based on the O 2 -A absorption band with field-acquired and simulated data. It was demonstrated that the uncorrected oxygen transmittance between target and sensor distance of 10 m can lead to SIF relative errors ranging from 66% to higher than 100% when using a Spectral Fitting (SF) technique …

Analysis of Biophysical Variables in an Onion Crop (Allium cepa L.) with Nitrogen Fertilization by Sentinel-2 Observations

The production of onions bulbs (Allium cepa L.) requires a high amount of nitrogen. Ac cording to the demand of sustainable agriculture, the information-development and communication technologies allow for improving the efficiency of nitrogen fertilization. In the south of the province of Buenos Aires, Argentina, between 8000 and 10,000 hectares per year−1 are cultivated in the districts of Villarino and Patagones. This work aimed to analyze the relationship of biophysical variables: leaf area index (LAI), canopy chlorophyll content (CCC), and canopy cover factor (fCOVER), with the nitrogen fertilization of an intermediate cycle onion crop and its effects on yield. A field trial study with …

Systematic Assessment of MODTRAN Emulators for Atmospheric Correction

Atmospheric radiative transfer models (RTMs) simulate the light propagation in the Earth's atmosphere. With the evolution of RTMs, their increase in complexity makes them impractical in routine processing such as atmospheric correction. To overcome their computational burden, standard practice is to interpolate a multidimensional lookup table (LUT) of prestored simulations. However, accurate interpolation relies on large LUTs, which still implies large computation times for their generation and interpolation. In recent years, emulation has been proposed as an alternative to LUT interpolation. Emulation approximates the RTM outputs by a statistical regression model trained with a low number …

Hybrid inversion of radiative transfer models based on high spatial resolution satellite reflectance data improves fractional vegetation cover retrieval in heterogeneous ecological systems after fire

In forest landscapes affected by fire, the estimation of fractional vegetation cover (FVC) from remote sensing data using radiative transfer models (RTMs) enables to evaluate the ecological impact of such disturbance across plant communities at different spatio-temporal scales. Even though, when landscapes are highly heterogeneous, the fine-scale ground spatial variation might not be properly captured if FVC products are provided at moderate or coarse spatial scales, as typical of most of operational Earth observing satellite missions. The objective of this study was to evaluate the potential of a RTM inversion approach for estimating FVC from satellite reflectance data at high spatial reso…

Gradient-based Automatic Look-Up Table Generator for Atmospheric Radiative Transfer Models

Atmospheric correction of Earth Observation data is one of the most critical steps in the data processing chain of a satellite mission for successful remote sensing applications. Atmospheric Radiative Transfer Models (RTM) inversion methods are typically preferred due to their high accuracy. However, the execution of RTMs on a pixel-per-pixel basis is impractical due to their high computation time, thus large multi-dimensional look-up tables (LUTs) are precomputed for their later interpolation. To further reduce the RTM computation burden and the error in LUT interpolation, we have developed a method to automatically select the minimum and optimal set of nodes to be included in a LUT. We pr…

Gaussian processes retrieval of crop traits in Google Earth Engine based on Sentinel-2 top-of-atmosphere data.

The unprecedented availability of optical satellite data in cloud-based computing platforms, such as Google Earth Engine (GEE), opens new possibilities to develop crop trait retrieval models from the local to the planetary scale. Hybrid retrieval models are of interest to run in these platforms as they combine the advantages of physically-based radiative transfer models (RTM) with the flexibility of machine learning regression algorithms. Previous research with GEE primarily relied on processing bottom-of-atmosphere (BOA) reflectance data, which requires atmospheric correction. In the present study, we implemented hybrid models directly into GEE for processing Sentinel-2 (S2) Level-1C (L1C)…

Potential retrieval of biophysical parameters from FLORIS, S3-OLCI and its synergy

The main objective of FLEX is the measurement of vegetation chlorophyll fluorescence (Fs) from space and the exploitation of this signal to better understand the carbon cycle. FLuORescence Imaging Spectrometer (FLORIS) is the main instrument of the FLEX mission concept. ESA's Earth Science Advisory Committee recommended the investigation of the FLEX concept as an in-orbit demonstrator to be flown as a tandem mission with Sentinel-3 (S-3). S-3 is amongst others equipped with the Ocean Land Colour Instrument (OLCI). When flown in tandem these instruments are expected to provide an accurate characterization of key atmospheric and surface parameters to facilitate Fs retrieval for FLORIS. In thi…

Multi-sensor spectral synergies for crop stress detection and monitoring in the optical domain: A review

Retrieval of aboveground crop nitrogen content with a hybrid machine learning method

Abstract 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-base…

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

Abstract 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 …

Introducing ARTMO's Machine-Learning Classification Algorithms Toolbox: Application to Plant-Type Detection in a Semi-Steppe Iranian Landscape.

Accurate plant-type (PT) detection forms an important basis for sustainable land management maintaining biodiversity and ecosystem services. In this sense, Sentinel-2 satellite images of the Copernicus program offer spatial, spectral, temporal, and radiometric characteristics with great potential for mapping and monitoring PTs. In addition, the selection of a best-performing algorithm needs to be considered for obtaining PT classification as accurate as possible . To date, no freely downloadable toolbox exists that brings the diversity of the latest supervised machine-learning classification algorithms (MLCAs) together into a single intuitive user-friendly graphical user interface (GUI). To…

Quantifying the Robustness of Vegetation Indices through Global Sensitivity Analysis of Homogeneous and Forest Leaf-Canopy Radiative Transfer Models

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 heterogeneit…

Vegetation Types Mapping Using Multi-Temporal Landsat Images in the Google Earth Engine Platform

Vegetation Types (VTs) are important managerial units, and their identification serves as essential tools for the conservation of land covers. Despite a long history of Earth observation applications to assess and monitor land covers, the quantitative detection of sparse VTs remains problematic, especially in arid and semiarid areas. This research aimed to identify appropriate multi-temporal datasets to improve the accuracy of VTs classification in a heterogeneous landscape in Central Zagros, Iran. To do so, first the Normalized Difference Vegetation Index (NDVI) temporal profile of each VT was identified in the study area for the period of 2018, 2019, and 2020. This data revealed strong se…

Quantifying Fundamental Vegetation Traits over Europe Using the Sentinel-3 OLCI Catalogue in Google Earth Engine

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) SC…

Towards Quantifying Non-Photosynthetic Vegetation for Agriculture Using Spaceborne Imaging Spectroscopy

Non-photosynthetic vegetation (NPV) has been identified as priority variable in the context of new spaceborne imaging spectroscopy missions. In this study we provide a first attempt to quantify NPV biomass from these unprecedented data streams to be provided by multiple recently launched or planned instruments. A hybrid workflow is proposed including Gaussian process regression (GPR) trained over radiative transfer model (RTM) simulations and applying active learning strategies. A soybean field data set including two dates with NPV measurements on yellow and senescent (brown) plant organs was used for model validation, resulting in relative errors of 13.4%. This prototype retrieval model wa…

Hyperspectral response of agronomic variables to background optical variability: Results of a numerical experiment

Understanding how biophysical and biochemical variables contribute to the spectral characteristics of vegetation canopies is critical for their monitoring. Quantifying these contributions, however, remains difficult due to extraneous factors such as the spectral variability of canopy background materials, including soil/crop-residue moisture, soil-type, and non-photosynthetic vegetation (NPV). This study focused on exploring the spectral response of two important agronomic variables (1) leaf chlorophyll content (Cab ) and (2) leaf area index (LAI) under various canopy backgrounds through a global sensitivity analysis of wheat-like canopy spectra simulated using the physically-based PROSAIL …

FLEX/S3 Tandem Mission Performance Assessment: Evolution of the End-to-End Simulator Flex-E

An End-to-end simulator (E2ES) is a tool to evaluate the performance of a satellite mission. Once a mission is approved for operation, E2ES evolves during Phase C/D to become a supporting tool for the development and validation of the ground data processor, as well as for simulating data sets to test the Prototype and Operational Processors. FLEX-E is the E2ES of the FLEX/Sentinel-3 tandem mission, which was selected in 2015 as ESA's eighth Earth Explorer. The FLEX-E evolution implies the consolidation of all the retrieval algorithms (e.g. fluorescence, reflectance, biophysical variables), the implementation of new scientific developments, as well the improvement of the co-registration proc…

Misión FLEX (Fluorescence Explorer): Observación de la fluorescencia por teledetección como nueva técnica de estudio del estado de la vegetación terrestre a escala global

[EN] FLEX (Fluorescence EXplorer) is a candidate for the 8th ESA’s Earth Explorer mission. Is the first space mission specifically designed for the estimation of vegetation fluorescence on a global scale. The mission is proposed to fly in tandem with the future ESA´s Sentinel-3 satellite. It is foreseen that the information obtained by Sentinel-3 will be supplemented with that provided by FLORIS (Fluorescence Imaging Spectrometer) onboard FLEX. FLORIS will measure the radiance between 500 and 800 nm with a bandwidth between 0.1 nm and 2 nm, providing images with a 150 km swath and 300 m pixel size. This information will allow a detailed monitoring of vegetation dynamics, by improving the me…

Design of a Generic 3-D Scene Generator for Passive Optical Missions and Its Implementation for the ESA’s FLEX/Sentinel-3 Tandem Mission

During the design phase of a satellite mission, end-to-end mission performance simulator (E2ES) tools allow scientists and engineers evaluating the mission concept, consolidating system technical requirements and analyzing the suitability of the implemented technical solutions and data processing algorithms. The generation of synthetic scenes is one of the core parts of an E2ES, providing scenes (ground truth) as would be observed by satellite instruments and used as reference against simulated retrieved mission products. An appropriate generation of the scene also allows assessing the performance of the ground data processing chain replacing real instrument data before the mission is in or…

Mapping Vegetation Density in a Heterogeneous River Floodplain Ecosystem Using Pointable CHRIS/PROBA Data

River floodplains in the Netherlands serve as water storage areas, while they also have the function of nature rehabilitation areas. Floodplain vegetation is therefore subject to natural processes of vegetation succession. At the same time, vegetation encroachment obstructs the water flow into the floodplains and increases the flood risk for the hinterland. Spaceborne pointable imaging spectroscopy has the potential to quantify vegetation density on the basis of leaf area index (LAI) from a desired view zenith angle. In this respect, hyperspectral pointable CHRIS data were linked to the ray tracing canopy reflectance model FLIGHT to retrieve vegetation density estimates over a heterogeneous…

Optimal Spectral Wavelengths for Discriminating Orchard Species Using Multivariate Statistical Techniques

Sustainable management of orchard fields requires detailed information about the tree types, which is a main component of precision agriculture programs. To this end, hyperspectral imagery can play a major role in orchard tree species mapping. Efficient use of hyperspectral data in combination with field measurements requires the development of optimized band selection strategies to separate tree species. In this study, field spectroscopy (350 to 2500 nm) was performed through scanning 165 spectral leaf samples of dominant orchard tree species (almond, walnut, and grape) in Chaharmahal va Bakhtiyari province, Iran. Two multivariable methods were employed to identify the optimum wavelengths:…

Optimizing LUT-based radiative transfer model inversion for retrieval of biophysical parameters using hyperspectral data

Inversion of radiative transfer models using a lookup-table (LUT) approach against hyperspectral data streams leads to retrievals of biophysical parameters such as chlorophyll content (Chl), but necessary optimization strategies are not consolidated yet. Here, various regularization options have been evaluated to the benefit of improved Chl retrieval from hyperspectral CHRIS data, being: i) the role of added noise, ii) the role of multiple best solutions, and iii) the role of applied cost functions in LUT-based inversion. By using data from the ESA-led field campaign SPARC (Barrax, Spain), it was found that introducing noise and opting for multiple best solutions in the inversion considerab…

Urban Heat Island Monitoring and Impacts on Citizen's General Health Status in Isfahan Metropolis: A Remote Sensing and Field Survey Approach.

Urban heat islands (UHIs) are one of the urban management challenges, especially in metropolises, which can affect citizens’ health and well-being. This study used a combination of remote sensing techniques with field survey to investigate systematically the effects of UHI on citizens’ health in Isfahan metropolis, Iran. For this purpose, the land surface temperature (LST) over a three-year period was monitored by Landsat-8 satellite imagery based on the split window algorithm. Then, the areas where UHI and urban cold island (UCI) phenomena occurred were identified and a general health questionnaire-28 (GHQ-28) was applied to evaluate the health status of 800 citizens in terms o…

Gaussian Processes Retrieval of LAI from Sentinel-2 Top-of-Atmosphere Radiance Data

Abstract Retrieval of vegetation properties from satellite and airborne optical data usually takes place after atmospheric correction, yet it is also possible to develop retrieval algorithms directly from top-of-atmosphere (TOA) radiance data. One of the key vegetation variables that can be retrieved from at-sensor TOA radiance data is leaf area index (LAI) if algorithms account for variability in atmosphere. We demonstrate the feasibility of LAI retrieval from Sentinel-2 (S2) TOA radiance data (L1C product) in a hybrid machine learning framework. To achieve this, the coupled leaf-canopy-atmosphere radiative transfer models PROSAIL-6SV were used to simulate a look-up table (LUT) of TOA radi…

Statistical Learning for End-to-End Simulations

End-to-end mission performance simulators (E2ES) are suitable tools to accelerate satellite mission development from concet to deployment. One core element of these E2ES is the generation of synthetic scenes that are observed by the various instruments of an Earth Observation mission. The generation of these scenes rely on Radiative Transfer Models (RTM) for the simulation of light interaction with the Earth surface and atmosphere. However, the execution of advanced RTMs is impractical due to their large computation burden. Classical interpolation and statistical emulation methods of pre-computed Look-Up Tables (LUT) are therefore common practice to generate synthetic scenes in a reasonable…

Global sensitivity analysis of the SCOPE model : what drives simulated canopy - leaving sun - induced fluorescence?

This study provides insight into the key variables that drive sun-induced chlorophyll fluorescence (SIF) emanating from vegetation canopies, based on a global sensitivity analysis (GSA) of the Soil-Canopy Observation of Photosynthesis and Energy (SCOPE) balance model. An updated version of the SCOPE model was used here (v1.53) which contains novel leaf physiological modules for determination of the steady state fluorescence yield: a photosynthesis model coupled with (a) submodels having empirically derived relationships, identified as TB12 for unstressed and TB12-D for drought conditions and (b) a mechanistic (MD12) submodel based on theoretical relationships. By inspecting Sobol's total or…

Spectrodirectional Minnaert-kretrieval using CHRIS-PROBA data

We report on a detailed analysis of hyperspectral and multidirectional remote sensing data acquired using the Compact High Resolution Imaging Spectrometer (CHRIS) mounted onboard the Project for On-Board Autonomy (PROBA) spacecraft. This instrument is capable of sampling reflected radiation over the visible and near-infrared (NIR) region of the solar spectrum at a spatial resolution (approx. 17 m) intermediary between sensors traditionally used in land applications (such as Landsat and Satellite Pour l’Observation de la Terre (SPOT), 30 m–50 m) and the latest instruments delivering a nominal resolution of 1 m or less. The spectral anisotropic signature of an Alpine coniferous forest during …

Top-of-Atmosphere Retrieval of Multiple Crop Traits Using Variational Heteroscedastic Gaussian Processes within a Hybrid Workflow.

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. Establishe…

Análisis de métodos de validación cruzada para la obtención robusta de parámetros biofísicos

[EN] Non-parametric regression methods are powerful statistical methods to retrieve biophysical parameters from remote sensing measurements. However, their performance can be affected by what has been presented during the training phase. To ensure robust retrievals, various cross-validation sub-sampling methods are often used, which allow to evaluate the model with subsets of the field dataset. Here, two types of cross-validation techniques were analyzed in the development of non-parametric regression models: hold-out and k-fold. Selected non-parametric linear regression methods were least squares Linear Regression (LR) and Partial Least Squares Regression (PLSR), and nonlinear methods were…

Gaussian processes retrieval of leaf parameters from a multi-species reflectance, absorbance and fluorescence dataset.

Abstract: Biochemical and structural leaf properties such as chlorophyll content (Chl), nitrogen content (N), leaf water content (LWC), and specific leaf area (SLA) have the benefit to be estimated through nondestructive spectral measurements. Current practices, however, mainly focus on a limited amount of wavelength bands while more information could be extracted from other wavelengths in the full range (400-2500 nm) spectrum. In this research, leaf characteristics were estimated from a field-based multi-species dataset, covering a wide range in leaf structures and Chl concentrations. The dataset contains leaves with extremely high Chl concentrations (>100 mu g cm(-2)), which are seldom es…

Crop Phenology Retrieval Through Gaussian Process Regression

Monitoring crop phenology significantly assists agricultural managing practices and plays an important role in crop yield predictions. Multi-temporal satellite-based observations allow analyzing vegetation seasonal dynamics over large areas by using vegetation indices or deriving biophysical variables. This study presents a framework for automatic corn phenology characterization based on high spatial and temporal resolution time series. By using the Difference Vegetation Index (DVI) estimated from Sentinel-2 data over Iowa (US), independent phenological models were optimized using Gaussian Processes regression. Their respective performances were assessed based on simulated phenological indi…

SCOPE-Based Emulators for Fast Generation of Synthetic Canopy Reflectance and Sun-Induced Fluorescence Spectra

Progress in advanced radiative transfer models (RTMs) led to an improved understanding of reflectance (R) and sun-induced chlorophyll fluorescence (SIF) emission throughout the leaf and canopy. Among advanced canopy RTMs that have been recently modified to deliver SIF spectral outputs are the energy balance model SCOPE and the 3D models DART and FLIGHT. The downside of these RTMs is that they are computationally expensive, which makes them impractical in routine processing, such as scene generation and retrieval applications. To bypass their computational burden, a computationally effective technique has been proposed by only using a limited number of model runs, called emulation. The idea …

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 …

Estimating soil moisture content under grassland with hyperspectral data using radiative transfer modelling and machine learning

The monitoring of soil moisture content (SMC) at very high spatial resolution (10m) using unmanned aerial systems (UAS) is of high interest for precision agriculture and the validation of large scale SMC products. Data-driven approaches are the most common method to retrieve SMC with UAS-borne data at water limited sites over non-disturbed agricultural crops. A major disadvantage of data-driven algorithms is the limited transferability in space and time and the need of a high number of ground reference samples. Physically-based approaches are less dependent on the amount of samples and are transferable in space and time. This study explores the potential of (1) a hybrid method targeting the…

Retrieval of canopy water content of different crop types with two new hyperspectral indices: Water Absorption Area Index and Depth Water Index

Crop canopy water content (CWC) is an essential indicator of the crop’s physiological state. While a diverse range of vegetation indices have earlier been developed for the remote estimation of CWC, most of them are defined for specific crop types and areas, making them less universally applicable. We propose two new water content indices applicable to a wide variety of crop types, allowing to derive CWC maps at a large spatial scale. These indices were developed based on PROSAIL simulations and then optimized with an experimental dataset (SPARC03; Barrax, Spain). This dataset consists of water content and other biophysical variables for five common crop types (lucerne, corn, potato, sugar …

Upward and downward solar-induced chlorophyll fluorescence yield indices of four tree species as indicators of traffic pollution in Valencia

Abstract: Passive steady-state chlorophyll fluorescence (Fs) provides a direct diagnosis of the functional status of vegetation photosynthesis. With the prospect of mapping Fs using remote sensing techniques, field measurements are mandatory to understand to which extent Fs allows detecting plant stress in different environments. Trees of four common species in Valencia were classified in either a low or a high local traffic exposure class based on their leaf magnetic value. Upward and downward hyperspectral fluorescence yield (FY) and indices based on the two Fs peaks (at 687 and 741 nm) were calculated. FY indices of P. canariensis and P. x acerifolia were significantly different between …

Synergy of Sentinel-1 and Sentinel-2 Time Series for Cloud-Free Vegetation Water Content Mapping with Multi-Output Gaussian Processes

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 Senti…

Retrieving and Validating Leaf and Canopy Chlorophyll Content at Moderate Resolution: A Multiscale Analysis with the Sentinel-3 OLCI Sensor

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 cam…

An Emulator Toolbox to Approximate Radiative Transfer Models with Statistical Learning

Physically-based radiative transfer models (RTMs) help in understanding the processes occurring on the Earth’s surface and their interactions with vegetation and atmosphere. When it comes to studying vegetation properties, RTMs allows us to study light interception by plant canopies and are used in the retrieval of biophysical variables through model inversion. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. Emulators are advantageous in real practice because…

Retrieval of Crop Variables from Proximal Multispectral UAV Image Data Using PROSAIL in Maize Canopy

Mapping crop variables at different growth stages is crucial to inform farmers and plant breeders about the crop status. For mapping purposes, inversion of canopy radiative transfer models (RTMs) is a viable alternative to parametric and non-parametric regression models, which often lack transferability in time and space. Due to the physical nature of RTMs, inversion outputs can be delivered in sound physical units that reflect the underlying processes in the canopy. In this study, we explored the capabilities of the coupled leaf–canopy RTM PROSAIL applied to high-spatial-resolution (0.015 m) multispectral unmanned aerial vehicle (UAV) data to retrieve the leaf chlorophyll content (LC…

Biophysical parameter retrieval with warped Gaussian processes

This paper focuses on biophysical parameter retrieval based on Gaussian Processes (GPs). Very often an arbitrary transformation is applied to the observed variable (e.g. chlorophyll content) to better pose the problem. This standard practice essentially tries to linearize/uniformize the distribution by applying non-linear link functions like the logarithmic, the exponential or the logistic functions. In this paper, we propose to use a GP model that automatically learns the optimal transformation directly from the data. The so-called warped GP regression (WGPR) presented in [1] models output observations as a parametric nonlinear transformation of a GP. The parameters of such prior model are…

Chlorophyll content mapping of urban vegetation in the city of Valencia based on the hyperspectral NAOC index

Abstract: Spatially distributed chlorophyll content of urban vegetation provides an important indicator of a plant's health status, which might depend on the habitat quality of the specific urban environment. Recent advances in optical remote sensing led to improved methodologies to monitor vegetation properties. The hyperspectral index NAOC (Normalized Area Over reflectance Curve) is one of these new tools that can be used for mapping chlorophyll content. In this paper we present the work done to quantify vegetation chlorophyll content over the city of Valencia (Spain) based on chlorophyll measurements of four representative tree species: the London plane tree (Platanus x. acerifolia), the…

Mapping landscape canopy nitrogen content from space using PRISMA data

Abstract 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 …

Emulation of Sun-Induced Fluorescence from Radiance Data Recorded by the HyPlant Airborne Imaging Spectrometer

The retrieval of sun-induced fluorescence (SIF) from hyperspectral radiance data grew to maturity with research activities around the FLuorescence EXplorer satellite mission FLEX, yet full-spectrum estimation methods such as the spectral fitting method (SFM) are computationally expensive. To bypass this computational load, this work aims to approximate the SFM-based SIF retrieval by means of statistical learning, i.e., emulation. While emulators emerged as fast surrogate models of simulators, the accuracy-speedup trade-offs are still to be analyzed when the emulation concept is applied to experimental data. We evaluated the possibility of approximating the SFM-like SIF output directly based…

Optimizing Gaussian Process Regression for Image Time Series Gap-Filling and Crop Monitoring

Image processing entered the era of artificial intelligence, and machine learning algorithms emerged as attractive alternatives for time series data processing. Satellite image time series processing enables crop phenology monitoring, such as the calculation of start and end of season. Among the promising algorithms, Gaussian process regression (GPR) proved to be a competitive time series gap-filling algorithm with the advantage of, as developed within a Bayesian framework, providing associated uncertainty estimates. Nevertheless, the processing of time series images becomes computationally inefficient in its standard per-pixel usage, mainly for GPR training rather than the fitting step. To…

First Results of Hyperspectral Scene Generation in Preparation of the Chime Imaging Spectrometer Mission

End-To-End mission performance simulators (E2Es) are software tools developed to support satellite mission preparatory activities. For passive remote sensing missions, E2Es generate synthetic scenes simulating the interaction of the solar radiation between the atmosphere and the surface; therefore allowing the estimation of the mission performance before its launch. In this paper, we present the CHIME Scene Generator Module (SGM) as part of CHIME E2Es, with state-of-the-art parallelization and optimization that give a performance allowing to obtain a whole year of daily worldwide Top-Of-Atmosphere radiance images in a matter of hours. The CHIME SGM generates 100x200km hyperspectral scenes w…

Crop Nitrogen Retrieval Methods for Simulated Sentinel-2 Data Using In-Field Spectrometer Data.

Nitrogen (N) is one of the key nutrients supplied in agricultural production worldwide. Over-fertilization can have negative influences on the field and the regional level (e.g., agro-ecosystems). Remote sensing of the plant N of field crops presents a valuable tool for the monitoring of N flows in agro-ecosystems. Available data for validation of satellite-based remote sensing of N is scarce. Therefore, in this study, field spectrometer measurements were used to simulate data of the Sentinel-2 (S2) satellites developed for vegetation monitoring by the ESA. The prediction performance of normalized ratio indices (NRIs), random forest regression (RFR) and Gaussian processes regression (GPR) f…

Bidirectional sun-induced chlorophyll fluorescence emission is influenced by leaf structure and light scattering properties : a bottom-up approach

Abstract Sun-induced chlorophyll fluorescence (SIF) at leaf level is emitted in both upward and downward directions in the red and far-red part of the spectrum (650–850 nm) when a leaf is illuminated from the upper leaf surface. Hence, total SIF is represented by the sum of the upward and downward emission components. Nevertheless, the downward component of leaf SIF is often not considered despite that downward fluorescence yield (↓FY) can amount up to 40% of the total fluorescence yield (FYtot). Downward SIF is mainly emitted in the far-red, since this part of fluoresced light is highly scattered within leaves, unlike red Chl fluorescence, which is mostly reabsorbed. While total FY can be …

A sun-induced vegetation fluorescence retrieval method from top of atmosphere radiance for the FLEX/Sentinel-3 TanDEM mission

A new fluorescence retrieval method is proposed to support ESA's 8th Earth Explorer FLuorescence EXplorer/Sentinel-3 (FLEX-S3) candidate tandem mission. FLEX is the first mission specially dedicated to measure the Sun-Induced vegetation chlorophyll fluorescence (SIF) strongly related with the vegetation photosynthetic activity. Most hyperspectral fluorescence retrieval algorithms available in the literature are very sensitive to true reflectance modelization and/or they assume the atmospheric status as known. The proposed algorithm delivers the retrieval of full fluorescence spectrum at canopy level by using only Top Of Atmosphere (TOA) radiances from S3 and FLEX as input. Once the spatial …

A fluorescence retrieval method for the flex sentinel-3 tandem mission

A new fluorescence retrieval method is proposed to support ESA's 8th Earth Explorer Fluorescence EXplorer (FLEX) candidate mission. Most hyperspectral fluorescence retrieval algorithms available in the literature are very sensitive to true reflectance modelization and/or they assume the atmospheric status as known. The proposed algorithm delivers the retrieval of full fluorescence spectrum at canopy level by using only Top Of Atmosphere (TOA) radiances as input. The proposed method starts with (1) the atmospheric correction of TOA radiances, characterizing the state of the atmosphere without assuming any a-priori classification on aerosols models, (2) performing a first estimation of fluore…

Exploring the spatial relationship between airborne-derived red and far-red sun-induced fluorescence and process-based GPP estimates in a forest ecosystem

International audience; Terrestrial gross primary productivity (GPP) plays an essential role in the global carbon cycle, but the quantification of the spatial and temporal variations in photosynthesis is still largely uncertain. Our work aimed to investigate the potential of remote sensing to provide new insights into plant photosynthesis at a fine spatial resolution. This goal was achieved by exploiting high-resolution images acquired with the FLuorescence EXplorer (FLEX) airborne demonstrator HyPlant. The sensor was flown over a mixed forest, and the images collected were elaborated to obtain two independent indicators of plant photosynthesis. First, maps of sun-induced chlorophyll fluore…

Gradient-Based Automatic Lookup Table Generator for Radiative Transfer Models

Physically based radiative transfer models (RTMs) are widely used in Earth observation to understand the radiation processes occurring on the Earth’s surface and their interactions with water, vegetation, and atmosphere. Through continuous improvements, RTMs have increased in accuracy and representativity of complex scenes at expenses of an increase in complexity and computation time, making them impractical in various remote sensing applications. To overcome this limitation, the common practice is to precompute large lookup tables (LUTs) for their later interpolation. To further reduce the RTM computation burden and the error in LUT interpolation, we have developed a method to automaticall…

Remote Estimation of Canopy Water Content in Different Crop Types with New Hyperspectral Indices

A diverse range of vegetation indices have earlier been developed for the remote estimation of canopy water content (CWC), but most of them are not universally applicable. The aim of this study is to define new indices valid for a wide variety of crop types, that allow to obtain CWC maps at a large spatial scale. These indices were developed based on PROSAIL simulations and then optimized with an experimental dataset (SPARC03; Barrax, Spain), which consists of field data including water content and other biophysical parameters collected for 6 different crops (lucerne, corn, potato, sugar beet, garlic and onion) and associated TOC reflectance spectra acquired by the HyMap airborne sensor. Sp…

Global sensitivity analysis of the A-SCOPE model in support of future FLEX fluorescence retrievals

In support of ESA's Earth Explorer 8 candidate mission FLEX (FLuorescence EXplorer), a Photosynthesis Study has been initiated to quantitatively link fluorescence to photosynthesis. This led to the development of A-SCOPE, a graphical user interface software package that integrates multiple biochemical models into the soil-vegetation-atmosphere-transfer model SCOPE. Its latest version (v1.53) has been successfully verified and was subsequently evaluated through a global sensitivity analysis. By using the method of Saltelli [4], the relative importance of each input variable to model outputs was quantified through first order and total effect sensitivity indices. Variations in leaf area index…

Active Learning Methods for Efficient Hybrid Biophysical Variable Retrieval

Kernel-based machine learning regression algorithms (MLRAs) are potentially powerful methods for being implemented into operational biophysical variable retrieval schemes. However, they face difficulties in coping with large training data sets. With the increasing amount of optical remote sensing data made available for analysis and the possibility of using a large amount of simulated data from radiative transfer models (RTMs) to train kernel MLRAs, efficient data reduction techniques will need to be implemented. Active learning (AL) methods enable to select the most informative samples in a data set. This letter introduces six AL methods for achieving optimized biophysical variable estimat…

Compensation of Oxygen Transmittance Effects for Proximal Sensing Retrieval of Canopy–Leaving Sun–Induced Chlorophyll Fluorescence

Estimates of Sun–Induced vegetation chlorophyll Fluorescence (SIF) using remote sensing techniques are commonly determined by exploiting solar and/or telluric absorption features. When SIF is retrieved in the strong oxygen (O 2 ) absorption features, atmospheric effects must always be compensated. Whereas correction of atmospheric effects is a standard airborne or satellite data processing step, there is no consensus regarding whether it is required for SIF proximal–sensing measurements nor what is the best strategy to be followed. Thus, by using simulated data, this work provides a comprehensive analysis about how atmospheric effects impact SIF estimations on proximal sensing, regarding: (…

Estimating the phenological dynamics of irrigated rice leaf area index using the combination of PROSAIL and Gaussian Process Regression

The growth of rice is a sequence of three different phenological phases. This sequence of change in rice phenology implies that the condition of the plant during the vegetative phase relates directly to the health of leaves functioning during the reproductive and ripening phases. As such, accurate monitoring is important towards understanding rice growth dynamics. Leaf Area Index (LAI) is an important indicator of rice yields and the availability of this information during key phenological phases can support more informed farming decisions. Satellite remote sensing has been adopted as a proxy to field measurements of LAI and with the launch of freely available high resolution Satellite imag…

Intelligent Sampling for Vegetation Nitrogen Mapping Based on Hybrid Machine Learning Algorithms

Upcoming satellite imaging spectroscopy missions will deliver spatiotemporal explicit data streams to be exploited for mapping vegetation properties, such as nitrogen (N) content. Within retrieval workflows for real-time mapping over agricultural regions, such crop-specific information products need to be derived precisely and rapidly. To allow fast processing, intelligent sampling schemes for training databases should be incorporated to establish efficient machine learning (ML) models. In this study, we implemented active learning (AL) heuristics using kernel ridge regression (KRR) to minimize and optimize a training database for variational heteroscedastic Gaussian processes regression (V…

Gaussian processes uncertainty estimates in experimental Sentinel-2 LAI and leaf chlorophyll content retrieval

Abstract ESA’s upcoming Sentinel-2 (S2) Multispectral Instrument (MSI) foresees to provide continuity to land monitoring services by relying on optical payload with visible, near infrared and shortwave infrared sensors with high spectral, spatial and temporal resolution. This unprecedented data availability leads to an urgent need for developing robust and accurate retrieval methods, which ideally should provide uncertainty intervals for the predictions. Statistical learning regression algorithms are powerful candidats for the estimation of biophysical parameters from satellite reflectance measurements because of their ability to perform adaptive, nonlinear data fitting. In this paper, we f…

Approximating Empirical Surface Reflectance Data through Emulation: Opportunities for Synthetic Scene Generation

Collection of spectroradiometric measurements with associated biophysical variables is an essential part of the development and validation of optical remote sensing vegetation products. However, their quality can only be assessed in the subsequent analysis, and often there is a need for collecting extra data, e.g., to fill in gaps. To generate empirical-like surface reflectance data of vegetated surfaces, we propose to exploit emulation, i.e., reconstruction of spectral measurements through statistical learning. We evaluated emulation against classical interpolation methods using an empirical field dataset with associated hyperspectral spaceborne CHRIS and airborne HyMap reflectance spectra…

Multi-sensor spectral synergies for crop stress detection and monitoring in the optical domain: A review

Remote detection and monitoring of the vegetation responses to stress became relevant for sustainable agriculture. Ongoing developments in optical remote sensing technologies have provided tools to increase our understanding of stress-related physiological processes. Therefore, this study aimed to provide an overview of the main spectral technologies and retrieval approaches for detecting crop stress in agriculture. Firstly, we present integrated views on: i) biotic and abiotic stress factors, the phases of stress, and respective plant responses, and ii) the affected traits, appropriate spectral domains and corresponding methods for measuring traits remotely. Secondly, representative result…

Leaf reflectance variation along a vertical crown gradient of two deciduous tree species in a Belgian industrial habitat

Abstract: The reflectometry of leaf asymmetry is a novel approach in the bio-monitoring of tree health in urban or industrial habitats. Leaf asymmetry responds to the degree of environmental pollution and reflects structural changes in a leaf due to environmental pollution. This paper describes the boundary conditions to scale up from leaf to canopy level reflectance, by describing the variability of adaxial and abaxial leaf reflectance, hence leaf asymmetry, along the crown height gradients of two tree species. Our findings open a research pathway towards bio-monitoring based on the airborne remote sensing of tree canopies and their leaf asymmetric properties. (C) 2015 Elsevier Ltd. All ri…

A Survey of Active Learning for Quantifying Vegetation Traits from Terrestrial Earth Observation Data

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…

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…

Hyperspectral dimensionality reduction for biophysical variable statistical retrieval

Abstract Current and upcoming airborne and spaceborne imaging spectrometers lead to vast hyperspectral data streams. This scenario calls for automated and optimized spectral dimensionality reduction techniques to enable fast and efficient hyperspectral data processing, such as inferring vegetation properties. In preparation of next generation biophysical variable retrieval methods applicable to hyperspectral data, we present the evaluation of 11 dimensionality reduction (DR) methods in combination with advanced machine learning regression algorithms (MLRAs) for statistical variable retrieval. Two unique hyperspectral datasets were analyzed on the predictive power of DR + MLRA methods to ret…

A field study on solar-induced chlorophyll fluorescence and pigment parameters along a vertical canopy gradient of four tree species in an urban environment

Abstract: To better understand the potential uses of vegetation indices based on the sun-induced upward and downward chlorophyll fluorescence at leaf and at canopy scales, a field study was carried out in the city of Valencia (Spain). Fluorescence yield (FY) indices were derived for trees at different traffic intensity locations and at three canopy heights. This allowed investigating within-tree and between-tree variations of FY indices for four tree species. Several FY indices showed a significant (p < 0.05) and important effect of tree location for the species Morus alba (white mulberry) and Phoenix canariensis (Canary Island date palm). The upward FY parameters of M. alba, and the upward…

Emulation as an Accurate Alternative to Interpolation in Sampling Radiative Transfer Codes

Computationally expensive radiative transfer models (RTMs) are widely used to realistically reproduce the light interaction with the earth surface and atmosphere. Because these models take long processing time, the common practice is to first generate a sparse look-up table (LUT) and then make use of interpolation methods to sample the multidimensional LUT input variable space. However, the question arise whether common interpolation methodsperform most accurate. As an alternative to interpolation, this paper proposes to use emulation, i.e., approximating the RTM output by means of the statistical learning. Two experiments were conducted to assess the accuracy in delivering spectral outputs…

Optimizing LUT-Based RTM Inversion for Semiautomatic Mapping of Crop Biophysical Parameters from Sentinel-2 and -3 Data: Role of Cost Functions

Inversion of radiative transfer models (RTM) using a lookup-table (LUT) approach against satellite reflectance data can lead to concurrent retrievals of biophysical parameters such as leaf chlorophyll content (Chl) and leaf area index (LAI), but optimization strategies are not consolidated yet. ESA's upcoming satellites Sentinel-2 (S2) and Sentinel-3 (S3) aim to ensure continuity of old generation satellite sensors by providing superspectral images of high spatial and temporal resolution. This unprecedented data availability leads to an urgent need for developing robust, accurate, and operational retrieval methods. For three simulated Sentinel settings (S2-10 m: 4 bands, S2-20 m: 8 bands an…

Optical remote sensing and the retrieval of terrestrial vegetation bio-geophysical properties – A review

Abstract: Forthcoming superspectral satellite missions dedicated to land monitoring, as well as planned imaging spectrometers, will unleash an unprecedented data stream. The processing requirements for such large data streams involve processing techniques enabling the spatio-temporally explicit quantification of vegetation properties. Typically retrieval must be accurate, robust and fast. Hence, there is a strict requirement to identify next-generation bio-geophysical variable retrieval algorithms which can be molded into an operational processing chain. This paper offers a review of state-of-the-art retrieval methods for quantitative terrestrial bio-geophysical variable extraction using op…

Mapping a-priori defined plant associations using remotely sensed vegetation characteristics

Abstract Incorporation of a priori defined plant associations into remote sensing products is a major challenge that has only recently been confronted by the remote sensing community. We present an approach to map the spatial distribution of such associations by using plant indicator values (IVs) for salinity, moisture and nutrients as an intermediate between spectral reflectance and association occurrences. For a 12 km 2 study site in the Netherlands, the relations between observed IVs at local vegetation plots and visible and near-infrared (VNIR) and short-wave infrared (SWIR) airborne reflectance data were modelled using Gaussian Process Regression (GPR) (R 2 0.73, 0.64 and 0.76 for sali…

Multiple Cost Functions and Regularization Options for Improved Retrieval of Leaf Chlorophyll Content and LAI through Inversion of the PROSAIL Model

Abstract: Lookup-table (LUT)-based radiative transfer model inversion is considered a physically-sound and robust method to retrieve biophysical parameters from Earth observation data but regularization strategies are needed to mitigate the drawback of ill-posedness. We systematically evaluated various regularization options to improve leaf chlorophyll content (LCC) and leaf area index (LAI) retrievals over agricultural lands, including the role of (1) cost functions (CFs); (2) added noise; and (3) multiple solutions in LUT-based inversion. Three families of CFs were compared: information measures, M-estimates and minimum contrast methods. We have only selected CFs without additional parame…

Estimation of leaf area index using PROSAIL based LUT inversion, MLRA-GPR and empirical models: Case study of tropical deciduous forest plantation, North India

Abstract Forests play a vital role in biological cycles and environmental regulation. To understand the key processes of forest canopies (e.g., photosynthesis, respiration and transpiration), reliable and accurate information on spatial variability of Leaf Area Index (LAI), and its seasonal dynamics is essential. In the present study, we assessed the performance of biophysical parameter (LAI) retrieval methods viz. Look-Up Table (LUT)-inversion, MLRA-GPR (Machine Learning Regression Algorithm- Gaussian Processes Regression) and empirical models, for estimating the LAI of tropical deciduous plantation using ARTMO (Automated Radiative Transfer Models Operator) tool and Sentinel-2 satellite im…

Improving the remote estimation of soil organic carbon in complex ecosystems with Sentinel-2 and GIS using Gaussian processes regression

Abstract Background and aims The quantitative retrieval of soil organic carbon (SOC) storage, particularly for soils with a large potential for carbon sequestration, is of global interest due to its link with the carbon cycle and the mitigation of climate change. However, complex ecosystems with good soil qualities for SOC storage are poorly studied. Methods The interrelation between SOC and various vegetation remote sensing drivers is understood to demonstrate the link between the carbon stored in the vegetation layer and SOC of the top soil layers. Based on the mapping of SOC in two horizons (0–30 cm and 30–60 cm) we predict SOC with high accuracy in the complex and mountainous heterogene…

Retrieval of carbon content and biomass from hyperspectral imagery over cultivated areas

A Global Sensitivity Analysis Toolbox to Quantify Drivers of Vegetation Radiative Transfer Models

Abstract Global sensitivity analysis (GSA) enables to gain insight into the functioning of radiative transfer models (RTMs) by identifying the driving input variables of RTM spectral outputs such as reflectance, fluorescence, or radiance. This contribution introduces automated radiative transfer models operator's (ARTMO’s) new GSA toolbox. With the GSA toolbox the majority of ARTMO’s available RTMs can be decomposed into its driving variables. For a selected RTM output, a GSA identifies the most influential and noninfluential input variables according to Sobol' first-order and total-order indices. The toolbox can process RTM spectral outputs for any kind of optical sensor setting within the…

Scenario-based discrimination of common grapevine varieties using in-field hyperspectral data in the western of Iran

Abstract Field spectroscopy is an accurate, rapid and nondestructive technique for monitoring of agricultural plant characteristics. Among these, identification of grapevine varieties is one of the most important factors in viticulture and wine industry. This study evaluated the discriminatory ability of field hyperspectral data and statistical techniques in case of five common grapevine varieties in the western of Iran. A total of 3000 spectral samples were acquired at leaf and canopy levels. Then, in order to identify the best approach, two types of hyperspectral data (wavelengths from 350 to 2500 nm and 32 spectral indices), two data reduction methods (PLSR and ANOVA-PCA) and two classif…

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

Abstract 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 regula…

Crop type discrimination using Geo-Stat Endmember extraction and machine learning algorithms

Denoising AVIRIS-NG Data for Generation of New Chlorophyll Indices

The availability of Airborne Visible and Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) data has enormous possibilities for quantification of Leaf Chlorophyll Content (LCC). The present study used the AVIRIS-NG campaign site of Western India for generation and validation of new chlorophyll indices by denoising the AVIRIS-NG data. For validation, concurrent to AVIRIS-NG flight overpass, field samplings were performed. The acquired AVIRIS-NG was subjected to Spectral Angle Mapper (SAM) classifier for discriminating the crop types. Three smoothing techniques i.e., Fast-Fourier Transform (FFT), Mean and Savitzky-Golay filters were evaluated for their denoising capability. Raw and fil…

Experimental Sentinel-2 LAI estimation using parametric, non-parametric and physical retrieval methods – A comparison

Abstract Given the forthcoming availability of Sentinel-2 (S2) images, this paper provides a systematic comparison of retrieval accuracy and processing speed of a multitude of parametric, non-parametric and physically-based retrieval methods using simulated S2 data. An experimental field dataset (SPARC), collected at the agricultural site of Barrax (Spain), was used to evaluate different retrieval methods on their ability to estimate leaf area index (LAI). With regard to parametric methods, all possible band combinations for several two-band and three-band index formulations and a linear regression fitting function have been evaluated. From a set of over ten thousand indices evaluated, the …

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…

Sensitivity of scope modelled GPP and fluorescence for different plant functional types

This study addresses the question which factors are responsible for reported positive correlations between solar induced fluorescence (SIF) and gross primary production (GPP). A sensitivity analysis of the model SCOPE, which simulates photosynthesis, fluorescence emission and radiative transfer in canopies, has been carried out for four different plant functional types (PFT): tropical rainforest, C4 crops, C3 crops, and tundra, located in distinct climate zones: tropical everwet (Af), tropical with seasonal drought (savannah, Aw), temperate (Cf), and continental tundra (Dfd). Literature values for structural and physiological parameters and climate reanalysis data were used as input. The ef…

Transboundary Basins Need More Attention: Anthropogenic Impacts on Land Cover Changes in Aras River Basin, Monitoring and Prediction.

Changes in land cover (LC) can alter the basin hydrology by affecting the evaporation, infiltration, and surface and subsurface flow processes, and ultimately affect river water quantity and quality. This study aimed to monitor and predict the LC composition of a major, transboundary basin contributing to the Caspian Sea, the Aras River Basin (ARB). To this end, four LC maps of ARB corresponding to the years 1984, 2000, 2010, and 2017 were generated using Landsat satellite imagery from Armenia and the Nakhchivan Autonomous Republic. The LC gains and losses, net changes, exchanges, and the spatial trend of changes over 33 years (1984–2017) were investigated. The most important drivers of the…

Fusing optical and SAR time series for LAI gap filling with 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…

Machine learning regression algorithms for biophysical parameter retrieval: Opportunities for Sentinel-2 and -3

Abstract ESA's upcoming satellites Sentinel-2 (S2) and Sentinel-3 (S3) aim to ensure continuity for Landsat 5/7, SPOT-5, SPOT-Vegetation and Envisat MERIS observations by providing superspectral images of high spatial and temporal resolution. S2 and S3 will deliver near real-time operational products with a high accuracy for land monitoring. This unprecedented data availability leads to an urgent need for developing robust and accurate retrieval methods. Machine learning regression algorithms may be powerful candidates for the estimation of biophysical parameters from satellite reflectance measurements because of their ability to perform adaptive, nonlinear data fitting. By using data from …

Monitoring Cropland Phenology on Google Earth Engine Using Gaussian Process Regression

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 seri…

Evaluating the predictive power of sun-induced chlorophyll fluorescence to estimate net photosynthesis of vegetation canopies: A SCOPE modeling study

Abstract Progress in imaging spectroscopy technology and data processing can enable derivation of the complete sun-induced chlorophyll fluorescence (SIF) emission spectrum. This opens up opportunities to fully exploit the use of the SIF spectrum as an indicator of photosynthetic activity. Simulations performed with the coupled fluorescence–photosynthesis model SCOPE were used to determine how strongly canopy-leaving SIF can be related to net photosynthesis of the canopy (NPC) for various canopy configurations. Regression analysis between SIF retrievals and NPC values produced the following general findings: (1) individual SIF bands that were most sensitive to NPC were located around the fir…

Classification of Plant Ecological Units in Heterogeneous Semi-Steppe Rangelands: Performance Assessment of Four Classification Algorithms.

Plant Ecological Unit’s (PEUs) are the abstraction of vegetation communities that occur on a site which similarly respond to management actions and natural disturbances. Identification and monitoring of PEUs in a heterogeneous landscape is the most difficult task in medium resolution satellite images datasets. The main objective of this study is to compare pixel-based classification versus object-based classification for accurately classifying PEUs with four selected different algorithms across heterogeneous rangelands in Central Zagros, Iran. We used images of Landsat-8 OLI that were pan-sharpened to 15 m to classify four PEU classes based on a random dataset collected in the field (40%). …

Sun-induced fluorescence - a new probe of photosynthesis: First maps from the imaging spectrometer HyPlant.

Variations in photosynthesis still cause substantial uncertainties in predicting photosynthetic CO2 uptake rates and monitoring plant stress. Changes in actual photosynthesis that are not related to greenness of vegetation are difficult to measure by reflectance based optical remote sensing techniques. Several activities are underway to evaluate the sun-induced fluorescence signal on the ground and on a coarse spatial scale using space-borne imaging spectrometers. Intermediate-scale observations using airborne-based imaging spectroscopy, which are critical to bridge the existing gap between small-scale field studies and global observations, are still insufficient. Here we present the first …

Potential use of grapevine cv Askari for heavy metal phytoremediation purposes at greenhouse scale

Grapevine varieties possess desirable characteristics for phytoremediation purposes. We investigated the potential of grapevine cv Askari in phytoremediation of heavy metal (HM) pollutions. In total 80 grapevine seedlings were exposed to four levels of HM stress (mild, low, moderate, and severe) in greenhouse condition during two growing years (2018 and 2019). The HM concentrations (Zn, Cu, Cd, Cr, and Pb) were subsequently determined in the soils, roots, and grapevine aboveground parts (AGPs), and then phytoextraction and phytostabilization potential assessment indices, i.e., biological absorption coefficient (BAC), bioconcentration factor (BCF), and translocation factor (TF), were calcula…

Crop nitrogen monitoring: Recent progress and principal developments in the context of imaging spectroscopy missions

Abstract Nitrogen (N) is considered as one of the most important plant macronutrients and proper management of N therefore is a pre-requisite for modern agriculture. Continuous satellite-based monitoring of this key plant trait would help to understand individual crop N use efficiency and thus would enable site-specific N management. Since hyperspectral imaging sensors could provide detailed measurements of spectral signatures corresponding to the optical activity of chemical constituents, they have a theoretical advantage over multi-spectral sensing for the detection of crop N. The current study aims to provide a state-of-the-art overview of crop N retrieval methods from hyperspectral data…

Urban morphology detection and it's linking with land surface temperature: A case study for Tehran Metropolis, Iran

Abstract Expansion of urban areas and alteration of natural land cover exacerbate the local climate change. To find out the effect of land cover changes on the local climate, in this study, the Local Climate Zone (LCZ) concept was utilized to detect urban morphology in Tehran Metropolis. LCZ and Land Surface Temperature (LST) can be identified and classified based on available remote sensing products. Firstly, LCZ maps of Tehran metropolis were extracted using Landsat imagery, and secondly, relationships between LCZ and LST were explored for three years (1990, 2004, and 2018). We found that Tehran urban structure has 13 LCZs based on imagery from Landsat 5 and 14 LCZs based on images for La…

Evaluation of Hybrid Models to Estimate Chlorophyll and Nitrogen Content of Maize Crops in the Framework of the Future CHIME Mission

In the next few years, the new Copernicus Hyperspectral Imaging Mission (CHIME) is foreseen to be launched by the European Space Agency (ESA). This mission will provide an unprecedented amount of hyperspectral data, enabling new research possibilities within several fields of natural resources, including the &ldquo;agriculture and food security&rdquo; domain. In order to efficiently exploit this upcoming hyperspectral data stream, new processing methods and techniques need to be studied and implemented. In this work, the hybrid approach (HYB) and its variant, featuring sampling dimensionality reduction through active learning heuristics (HAL), were applied to CHIME-like data to evaluate the…

Assessment of maize nitrogen uptake from PRISMA hyperspectral data through hybrid modelling

Alg: a Toolbox for the Generation of Look-Up tables Based on Atmospheric Radiative Transfer Models

Atmospheric radiative transfer models (RTMs) are software tools describing the radiation processes occurring on the Earth’s atmosphere. While the evolution of these tools have achieved better representations of the light-atmosphere interactions, the increase of complexity, interpretability and computation time bears implications towards practical applications in Earth observation. Despite of existing RTM-specific graphical user interfaces, none of these tools allow common streamlining model setup for a wide variety of atmospheric RTMs. In addition, the automatic generation of atmospheric look-up tables (LUTs) can hardly be done with the use of these graphical tools. This paper presents the …

Learning Structures in Earth Observation Data with Gaussian Processes

Gaussian Processes (GPs) has experienced tremendous success in geoscience in general and for bio-geophysical parameter retrieval in the last years. GPs constitute a solid Bayesian framework to formulate many function approximation problems consistently. This paper reviews the main theoretical GP developments in the field. We review new algorithms that respect the signal and noise characteristics, that provide feature rankings automatically, and that allow applicability of associated uncertainty intervals to transport GP models in space and time. All these developments are illustrated in the field of geoscience and remote sensing at a local and global scales through a set of illustrative exa…

On the semi-automatic retrieval of biophysical parameters based on spectral index optimization

Abstract: Regression models based on spectral indices are typically empirical formulae enabling the mapping of biophysical parameters derived from Earth Observation (EO) data. Due to its empirical nature, it remains nevertheless uncertain to what extent a selected regression model is the most appropriate one, until all band combinations and curve fitting functions are assessed. This paper describes the application of a Spectral Index (SI) assessment toolbox in the Automated Radiative Transfer Models Operator (ARTMO) package. ARTMO enables semi-automatic retrieval and mapping of biophysical parameters from optical remote sensing observations. The SI toolbox facilitates the assessment of biop…

Multi-fidelity Gaussian Process Emulation for Atmospheric Radiative Transfer Models

This repository contains several datasets of spectral atmospheric transfer functions (i.e. path radiance, transmittances, spherical albedo) simulated with MODTRAN6 atmospheric radiative transfer model. The simulations are stored in hdf5 files using the Atmospheric Look-up table Generator (ALG) toolbox (https://doi.org/10.5194/gmd-13-1945-2020). Each dataset has an associated .xml file that includes the configuration of ALG/MODTRAN6 executions. All datasets include the input atmospheric/geometric variables that are summarized in the following table. Each dataset file has a random distribution (based on latin hypercube sampling) these input variables with varying number of points (e.g. train5…