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…

Multitemporal fusion of Landsat and MERIS images

Monitoring Earth dynamics from current and future observation satellites is one of the most important objectives for the remote sensing community. In this regard, the exploitation of image time series from sensors with different characteristics provides an opportunity to increase the knowledge about environmental changes, which are needed in many operational applications, such as monitoring vegetation dynamics and land cover/use changes. Many studies in the literature have proven that high spatial resolution sensors like Landsat are very useful for monitoring land cover changes. However, the cloud cover probability of many areas and the 15-days temporal resolution restrict its use to monito…

How Universal Is the Relationship between Remotely Sensed Vegetation Indices and Crop Leaf Area Index? A Global Assessment

This study aims to assess the relationship between Leaf Area Index (LAI) and remotely sensed Vegetation Indices (VIs) for major crops, based on a globally explicit dataset of in situ LAI measurements over a significant set of locations. We used a total of 1394 LAI measurements from 29 sites spanning 4 continents and covering 15 crop types with corresponding Landsat satellite images. Best-fit functions for the LAI-VI relationships were generated and assessed in terms of crop type, vegetation index, level of radiometric/atmospheric processing, method of LAI measurement, as well as the time difference between LAI measurements and satellite overpass. These global LAI-VI relationships were evalu…

Sun-induced chlorophyll fluorescence II: Review of passive measurement setups, protocols, and their application at the leaf to canopy level

Imaging and non-imaging spectroscopy employed in the field and from aircraft is frequently used to assess biochemical, structural, and functional plant traits, as well as their dynamics in an environmental matrix. With the increasing availability of high-resolution spectroradiometers, it has become feasible to measure fine spectral features, such as those needed to estimate sun-induced chlorophyll fluorescence (F), which is a signal related to the photosynthetic process of plants. The measurement of F requires highly accurate and precise radiance measurements in combination with very sophisticated measurement protocols. Additionally, because F has a highly dynamic nature (compared with othe…

Modelling spatial and spectral systematic noise patterns on CHRIS/PROBA hyperspectral data

In addition to typical random noise, remote sensing hyperspectral images are generally affected by non-periodic partially deterministic disturbance patterns due to the image formation process and characterized by a high degree of spatial and spectral coherence. This paper presents a new technique that faces the problem of removing the spatial coherent noise known as vertical stripping (VS) usually found in images acquired by push-broom sensors, in particular for the Compact High Resolution Imaging Spectrometer (CHRIS). The correction is based on the hypothesis that the vertical disturbance presents higher spatial frequencies than the surface radiance. The proposed method introduces a way to…

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…

Towards the quantitative and physically-based interpretation of solar-induced vegetation fluorescence retrieved from global imaging

Due to emerging high spectral resolution, remote sensing techniques and ongoing developments to retrieve the spectrally resolved vegetation fluorescence spectrum from several scales, the light reactions of photosynthesis are receiving a boost of attention for the monitoring of the Earth's carbon balance. Sensor-retrieved vegetation fluorescence (from leaf, tower, airborne or satellite scale) originating from the excited antenna chlorophyll a molecule has become a new quantitative biophysical vegetation parameter retrievable from space using global imaging techniques. However, to retrieve the actual quantum efficiencies, and hence a true photosynthetic status of the observed vegetation, all …

Remote sensing of sunlight-induced chlorophyll fluorescence and reflectance of Scots pine in the boreal forest during spring recovery

A measurement campaign to assess the feasibility of remote sensing of sunlight-induced chlorophyll fluorescence (ChlF) from a coniferous canopy was conducted in a boreal forest study site (Finland). A Passive Multi-wavelength Fluorescence Detector (PMFD) sensor, developed in the LURE laboratory, was used to obtain simultaneous measurements of ChlF in the oxygen absorption bands, at 687 and 760 nm, and a reflectance index, the PRI (Physiological Reflectance Index), for a month during spring recovery. When these data were compared with active fluorescence measurements performed on needles they revealed the same trend. During sunny days fluorescence and reflectance signals were found to be str…

Affine Illumination Compensation on Hyperspectral/Multiangular Remote Sensing Images

The huge amount of information some of the new optical satellites developed nowadays will create demands to quickly and reliably compensate for changes in the atmospheric transmittance and varying solar illumination conditions. In this paper three different forms of affine transformation models (general, particular and diagonal) are considered as candidates for rapid compensation of illumination variations. They are tested on a group of three pairs of CHRISPROBA radiance images obtained in a test field in Barrax (Spain), and where there is a difference in the atmospheric as well as in the geometrical acquisition conditions. Results indicate that the proposed methodology is satisfactory for …

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 method for the surface reflectance retrieval from PROBA/CHRIS data over land: application to ESA SPARC campaigns

The Compact High Resolution Imaging Spectrometer (CHRIS) onboard the Project for On-Board Autonomy (PROBA) platform system provides the first high spatial resolution hyper-spectral/multiangular remote sensing data from a satellite system, what represents a new source of information for Earth Observation purposes. A fully consistent radiative transfer approach is always preferred when dealing with the retrieval of surface reflectance from hyperspectral/multiangular data. However, due to the reported calibration anomalies for CHRIS data, a direct atmospheric correction based on physical radiative transfer modeling is not possible, and the method must somehow compensate for such calibration pr…

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…

Diurnal Cycle Relationships between Passive Fluorescence, PRI and NPQ of Vegetation in a Controlled Stress Experiment

In order to estimate vegetation photosynthesis from remote sensing observations; some critical parameters need to be quantified. From all absorbed light; the plant needs to release any excess that is not used for photosynthesis; by non-photochemical quenching; by fluorescence emission and unregulated thermal dissipation. Non-photochemical quenching (NPQ) processes are controlled photoprotective mechanisms which; once activated; strongly control the dynamics of photochemical efficiency. With illumination conditions increasing and decreasing during a diurnal cycle; photoprotection mechanisms needs to change accordingly. The goal of this work is to quantify dynamic NPQ; measured from active fl…

Predicting year of plantation with hyperspectral and lidar data

This paper introduces a methodology for predicting the year of plantation (YOP) from remote sensing data. The application has important implications in forestry management and inventorying. We exploit hyperspectral and LiDAR data in combination with state-of-the-art machine learning classifiers. In particular, we present a complete processing chain to extract spectral, textural and morphological features from both sensory data. Features are then combined and fed a Gaussian Process Classifier (GPC) trained to predict YOP in a forest area in North Carolina (US). The GPC algorithm provides accurate YOP estimates, reports spatially explicit maps and associated confidence maps, and provides sens…

Remote sensing of solar-induced chlorophyll fluorescence: Review of methods and applications

Interest in remote sensing (RS) of solar-induced chlorophyll fluorescence (F) by terrestrial vegetation is motivated by the link of F to photosynthetic efficiency which could be exploited for large scale monitoring of plant status and functioning. Today, passive RS of F is feasible with different prototypes and commercial ground-based, airborne, and even spaceborne instruments under certain conditions. This interest is generating an increasing number of research projects linking F and RS, such as the development of new F remote retrieval techniques, the understanding of the link between the F signal and vegetation physiology and the feasibility of a satellite mission specifically designed f…

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 …

Synthetic scene simulator for hyperspectral spaceborne passive optical sensors. Application to ESA's FLEX/sentinel-3 tandem mission

The simulation of synthetic images serve scientists and engineers to study the instrument configuration as well as to develop image processing and retrieval strategies for a sensor in development. Despite synthetic scene simulators have been developed in the past in the frame of satellite missions, their functionality and flexibility to create a user-defined scene is limited by their architecture, design and implementation. This paper introduces the design of a generic scene simulator with the flexibility to generate realistic synthetic scenes by configuration of the surface and atmosphere. Following this generic design, a scene simulator is being developed for the ESA's Earth Explorer 8th …

Relating Hyperspectral Airborne Data to Ground Measurements in a Complex and Discontinuous Canopy

The work described in this paper is aimed at validating hyperspectral airborne reflectance data collected during the Regional Experiments For Land-atmosphere EXchanges (REFLEX) campaign. Ground reflectance data measured in a vineyard were compared with airborne reflectance data. A sampling strategy and subsequent ground data processing had to be devised so as to capture a representative spectral sample of this complex crop. A linear model between airborne and ground data was tried and statistically tested. Results reveal a sound correspondence between ground and airborne reflectance data (R2 > 0.97), validating the atmospheric correction of the latter.

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…

Developments for vegetation fluorescence retrieval from spaceborne high-resolution spectrometry in the O2-A and O2-B absorption bands

Solar-induced chlorophyll fluorescence is a weak electromagnetic signal emitted in the red and far-red spectral regions by vegetation chlorophyll under excitation by solar radiation. Chlorophyll fluorescence has been demonstrated to be a close proxy to vegetation physiological functioning. The basis for fluorescence retrieval from passive space measurements is the exploitation of the O2-A and O2-B atmospheric absorption features to isolate the fluorescence signal from the solar radiation reflected by the surface and the atmosphere. High spectral resolution measurements and a precise modeling of the atmospheric radiative transfer in the visible and near-infrared regions are mandatory. Recent…

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…

Atmospheric and Instrumental Effects on the Fluorescence Remote Sensing Retrieval

Accurately disentangling the tiny Solar–Induced Chlorophyll Fluorescence (SIF) from canopy reflected solar irradiance by using passive remote sensing techniques is always challenging. Regardless the scale at which SIF is measured, i.e., proximal sensing, airborne or satellite level; instrumental and atmospheric effects must be accounted for and compensated as part of the SIF retrieval strategy. Regarding the instrumental effects, the use of very high spectral resolution spectrometers makes mandatory an accurate characterization of the Instrument Spectral Response Function (ISRF); and – in the case of imager spectrometers – an accurate characterization of the full instrument response in the …

Evaluation of remote sensing of vegetation fluorescence by the analysis of diurnal cycles

Chlorophyll fluorescence (ChF) emission is a direct indicator of the photosynthetic activity of vegetation, which is a key parameter of the carbon cycle. This paper analyses chlorophyll fluorescence evolution at leaf level during a complete diurnal cycle in simulated and natural conditions, for two species under different stress conditions. Absolute spectral radiance of the ChF emission is obtained allowing a quantitative derivation of the fluorescence yield of the ChF, which correlates well with established fluorescence instruments. The studied cases show that the ChF emission is mainly driven by the photosynthetic active radiation during the whole cycle, but the fluorescence yield is seve…

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…

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…

Angular Dependency of Hyperspectral Measurements over Wheat Characterized by a Novel UAV Based Goniometer

In this study we present a hyperspectral flying goniometer system, based on a rotary-wing unmanned aerial vehicle (UAV) equipped with a spectrometer mounted on an active gimbal. We show that this approach may be used to collect multiangular hyperspectral data over vegetated environments. The pointing and positioning accuracy are assessed using structure from motion and vary from σ = 1° to 8° in pointing and σ = 0.7 to 0.8 m in positioning. We use a wheat dataset to investigate the influence of angular effects on the NDVI, TCARI and REIP vegetation indices. Angular effects caused significant variations on the indices: NDVI = 0.83–0.95; TCARI = 0.04–0.116; REIP = 729–735 nm. Our analysis high…

Sensitivity analysis of the fraunhofer line discrimination method for the measurement of chlorophyll fluorescence using a field spectroradiometer

The Fraunhofer Line Discrimination (FLD) principle is established as a good method for remote sensing of solar induced chlorophyll fluorescence. Some improvements to the method are analysed in order to determine and reduce the sources of error in the estimation of the fluorescence emission. A sensitivity analysis has been performed over simulated data generated from real diurnal cycle measurements.

Sun-induced chlorophyll fluorescence III: benchmarking retrieval methods and sensor characteristics for proximal sensing

[EN] The interest of the scientific community on the remote observation of sun-induced chlorophyll fluorescence (SIF) has increased in the recent years. In this context, hyperspectral ground measurements play a crucial role in the calibration and validation of future satellite missions. For this reason, the European cooperation in science and technology (COST) Action ES1309 OPTIMISE has compiled three papers on instrument characterization, measurement setups and protocols, and retrieval methods (current paper). This study is divided in two sections; first, we evaluated the uncertainties in SIF retrieval methods (e.g., Fraunhofer line depth (FLD) approaches and spectral fitting method (SFM))…

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…

Stray light characterization in a high-resolution imaging spectrometer designed for solar-induced fluorescence

New commercial-off-the-shelf imaging spectrometers promise the combination of high spatial and spectral resolution needed to retrieve solar induced fluorescence (SIF). Imaging at multiple wavelengths for individual plants and even individual leaves from low-altitude airborne or ground-based platforms has applications in agriculture and carbon-cycle science. Data from these instruments could provide insight into the status of the photosynthetic apparatus at scales of space and time not observable with tools based on gas exchange, and could support the calibration and validation activities of current and forthcoming space missions to quantify SIF. High-spectral resolution enables SIF retrieva…

Sun Induced Fluorescence Calibration and Validation for Field Phenotyping

Reliable measurements of Sun Induced Fluorescence (SIF) require a good instrument characterization as well as a complex processing chain. In this paper, we summarize the state of the art SIF retrieval methods and measurements platforms for field phenotyping. Furthermore, we use HyScreen, hyperspectral-imaging system for top of canopy measurements of SIF, as an example of the instrument requirements, data process, and data validation needed to obtain reliable measurements of SIF.

Multitemporal fusion of Landsat/TM and ENVISAT/MERIS for crop monitoring

Abstract Monitoring Earth dynamics using current and future satellites is one of the most important objectives of the remote sensing community. The exploitation of image time series from sensors with different characteristics provides new opportunities to increase the knowledge about environmental changes and to support many operational applications. This paper presents an image fusion approach based on multiresolution and multisensor regularized spatial unmixing. The approach yields a composite image with the spatial resolution of the high spatial resolution image while retaining the spectral and temporal characteristics of the medium spatial resolution image. The approach is tested using …

First results from the PROBA/CHRIS hyperspectral/multiangular satellite system over land and water targets

The Project for On-Board Autonomy (PROBA) platform developed by the European Space Agency was launched on October 22, 2001. The instrument payload includes the Compact High Resolution Imaging Spectrometer (CHRIS). The coupled system provides high spatial resolution hyperspectral/multi-angular data, which represents a new-generation source of information for Earth observation purposes. The first results obtained from the preprocessing (noise removal and geometric/atmospheric correction) of two different datasets, collected over agricultural crops and inland waters, are presented in this letter. In situ measurements are used to assess the quality of the data and to validate the processing alg…

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 …

Estimating chlorophyll content of crops from hyperspectral data using a normalized area over reflectance curve (NAOC)

Abstract The Normalized Area Over reflectance Curve (NAOC) is proposed as a new index for remote sensing estimation of the leaf chlorophyll content of heterogeneous areas with different crops, different canopies and different types of bare soil. This index is based on the calculation of the area over the reflectance curve obtained by high spectral resolution reflectance measurements, determined, from the integral of the red–near-infrared interval, divided by the maximum reflectance in that spectral region. For this, use has been made of the experimental data of the SPARC campaigns, where in situ measurements were made of leaf chlorophyll content, LAI and fCOVER of 9 different crops – thus, …

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…

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…

Red and far-red sun-induced chlorophyll fluorescence as a measure of plant photosynthesis

Remote estimation of Sun-induced chlorophyll fluorescence emitted by terrestrial vegetation can provide an unparalleled opportunity to track spatiotemporal variations of photosynthetic efficiency. Here we provide the first direct experimental evidence that the two peaks of the chlorophyll fluorescence spectrum can be accurately mapped from high-resolution radiance spectra and that the signal is linked to variations in actual photosynthetic efficiency. Red and far red fluorescence measured using a novel airborne imaging spectrometer over a grass carpet treated with an herbicide known to inhibit photosynthesis was significantly higher than the corresponding signal from an equivalent untreated…

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…

Photoprotection dynamics observed at leaf level from fast temporal reflectance changes

Vegetation dynamically reacts to the available photosynthetically active radiation (PAR) by adjusting the photosynthetic apparatus to either a light harvesting or a photoprotective modus. When activating the photoprotection mechanism, either minor or major pigment-protein interactions may occur at the leaf level, resulting in different light absorption and consequently reflectance intensities. The reflectance changes were measured during sudden illumination transients designed to provoke fast adaptation to high irradiance. Different spectral reflectance change features were observed during different stages of photoprotection activation, extending over part of the visible spectral range (i.e…

Gridding artifacts on medium-resolution satellite image time series: MERIS case study

Earth observation satellites provide a valuable source of data which when conveniently processed can be used to better understand the Earth system dynamics. In this regard, one of the prerequisites for the analysis of satellite image time series is that the images are spatially coregistered so that the resulting multitemporal pixel entities offer a true temporal view of the area under study. This implies that all the observations must be mapped to a common system of grid cells. This process is known as gridding and, in practice, two common grids can be used as a reference: 1) a grid defined by some kind of external data set (e.g., an existing land-cover map) or 2) a grid defined by one of t…

Leaf-Level Spectral Fluorescence Measurements : Comparing Methodologies for Broadleaves and Needles

Successful measurements of chlorophyll fluorescence (ChlF) spectral properties (typically in the wavelength range of 650–850 nm) across plant species, environmental conditions, and stress levels are a first step towards establishing a quantitative link between solar-induced chlorophyll fluorescence (SIF), which can only be measured at discrete ChlF spectral bands, and photosynthetic functionality. Despite its importance and significance, the various methodologies for the estimation of leaf-level ChlF spectral properties have not yet been compared, especially when applied to leaves with complex morphology, such as needles. Here we present, to the best of our knowledge, a first comparison of …

Study of the diurnal cycle of stressed vegetation for the improvement of fluorescence remote sensing

Chlorophyll fluorescence (Chf) emission allows estimating the photosynthetic activity of vegetation - a key parameter for the carbon cycle models - in a quite direct way. However, measuring Chf is difficult because it represents a small fraction of the radiance to be measured by the sensor. This paper analyzes the relationship between the solar induced Chf emission and the photosynthetically active radiation (PAR) in plants under water stress condition. The solar induced fluorescence emission is measured at leaf level by means of three different methodologies. Firstly, an active modulated light fluorometer gives the relative fluorescence yield. Secondly, a quantitative measurement of the Ch…

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: (…

Retrieval of sun-induced fluorescence using advanced spectral fitting methods

Abstract The FLuorescence EXplorer (FLEX) satellite mission, candidate of ESA's 8th Earth Explorer program, is explicitly optimized for detecting the sun-induced fluorescence emitted by plants. It will allow consistent measurements around the O2-B (687 nm) and O2-A (760 nm) bands, related to the red and far-red fluorescence emission peaks respectively, the photochemical reflectance index, and the structural-chemical state variables of the canopy. The sun-induced fluorescence signal, overlapped to the surface reflected radiance, can be accurately retrieved by employing the powerful spectral fitting technique. In this framework, a set of fluorescence retrieval algorithms optimized for FLEX ar…

In vivo photoprotection mechanisms observed from leaf spectral absorbance changes showing VIS–NIR slow-induced conformational pigment bed changes

Abstract Regulated heat dissipation under excessive light comprises a complexity of mechanisms, whereby the supramolecular light-harvesting pigment–protein complex (LHC) shifts state from light harvesting towards heat dissipation, quenching the excess of photo-induced excitation energy in a non-photochemical way. Based on whole-leaf spectroscopy measuring upward and downward spectral radiance fluxes, we studied spectrally contiguous (hyperspectral) transient time series of absorbance A(λ,t) and passively induced chlorophyll fluorescence F(λ,t) dynamics of intact leaves in the visible and near-infrared wavelengths (VIS–NIR, 400–800 nm) after sudden strong natural-like illumination exposure. …

CEFLES2: The remote sensing component to quantify photosynthetic efficiency from the leaf to the region by measuring sun-induced fluorescence in the oxygen absorption bands

The CEFLES2 campaign during the Carbo Europe Regional Experiment Strategy was designed to provide simultaneous airborne measurements of solar induced fluorescence and CO<sub>2</sub> fluxes. It was combined with extensive ground-based quantification of leaf- and canopy-level processes in support of ESA's Candidate Earth Explorer Mission of the "Fluorescence Explorer" (FLEX). The aim of this campaign was to test if fluorescence signal detected from an airborne platform can be used to improve estimates of plant mediated exchange on the mesoscale. Canopy fluorescence was quantified from four airborne platforms using a combination of novel sensors: (i) the prototype ai…

FluoCat: A cable-suspended multi-sensor system for the vegetation SIF Cal/Val monitoring and estimation of effective sunlit surface fluorescence

Red and Far-Red Fluorescence Emission Retrieval from Airborne High-Resolution Spectra Collected by the Hyplant-Fluo Sensor

The contribution presents the development and testing of a fluorescence retrieval scheme based on the ESA's FLuorescence EXplorer mission concept. The algorithm employs on a coupled surface-atmosphere forward model at oxygen absorption bands: i) the atmospheric effect is computed by MODTRAN5; ii) the surface reflectance and fluorescence are modeled by means of the Spectral Fitting approach. The algorithm, previously tested on numerical simulations, was further implemented and optimized to process real observations collected by the FLEX airborne demonstrator HyPlant. The retrieval scheme has been tested on a number of flight lines collected in several locations, different ecosystems types, a…

Towards a novel approach for Sentinel-3 synergistic OLCI/SLSTR cloud and cloud shadow detection based on stereo cloud-top height estimation

Abstract Sentinel-3 is an Earth observation satellite constellation launched by the European Space Agency. Each satellite carries two optical multispectral instruments: the Ocean and Land Colour Instrument (OLCI) and the Sea and Land Surface Temperature Radiometer (SLSTR). OLCI and SLSTR sensors produce images covering the visible and infrared spectrum that can be collocated in order to generate synergistic products. In Earth observation, a particular weakness of optical sensors is their high sensitivity to clouds and their shadows. An incorrect cloud and cloud shadow detection leads to mistakes in both land and ocean retrievals of biophysical parameters. In order to exploit both OLCI and S…

Remote sensing of chlorophyll fluorescence for estimation of stress in vegetation. Recommendations for future missions

Vegetation monitoring is a key issue in Earth Observation due to its relation with the global CO2 cycle. Chlorophyll fluorescence (ChF) emitted by the vegetation is an accurate indicator of the plant status and their photosynthetic activity. This work analyses the diurnal evolution of the ChF emission spectrum and the fluorescence yield in order to determine the best conditions for remote sensing of ChF from a satellite platform. The ChF evolution is studied at leaf level during several diurnal cycles, in simulated conditions, for two species under different stress conditions. The analysis of the signal levels gives an estimation of the values of ChF emission which could be observed from a …

Novel leaf-level measurements of chlorophyll fluorescence for photosynthetic efficiency

Solar induced chlorophyll fluorescence (SIF) from vegetation can now be obtained from satellites as well as ground-based field studies, at select wavelengths associated with atmospheric features. At the leaf level, full spectrum (650–800 nm) chlorophyll emissions (ChlF) can be measured using specialized instrumentation to support interpretation of these SIF observations. We found that ChlF spectra differ for leaf bottoms versus upper leaf surfaces, potentially affecting within-canopy radiative scattering. Our ChlF measurements for leaves of eight tree species (n≥125) obtained during fall 2013 senescence at the Duke Forest in North Carolina, USA and the 2014 growing season (n=72) at the USDA…

Remote sensing of sun-induced chlorophyll fluorescence at different scales

In this contribution we present activities and selected results obtained in recent studies and campaigns conducted in the context of the FLuorescence EXplorer (FLEX) mission. FLEX is a candidate mission for the ESA 8th Earth Explorer and large efforts are currently dedicated to the development of an implementation scheme for an accurate mapping of fluorescence from the selected spaceborne sensor and mission configuration. Field and airborne data collected in different experimental campaigns, together with simulated data, have been used to demonstrate the feasibility of fluorescence retrievals and the potential of exploiting high spatial resolution fluorescence maps for a better understandin…

The 2013 FLEX—US Airborne Campaign at the Parker Tract Loblolly Pine Plantation in North Carolina, USA

The first European Space Agency (ESA) and NASA collaboration in an airborne campaign to support ESA’s FLuorescence EXplorer (FLEX) mission was conducted in North Carolina, USA during September–October 2013 (FLEX-US 2013) at the Parker Tract Loblolly Pine (LP) Plantation (Plymouth, NC, USA). This campaign combined two unique airborne instrument packages to obtain simultaneous observations of solar-induced fluorescence (SIF), LiDAR-based canopy structural information, visible through shortwave infrared (VSWIR) reflectance spectra, and surface temperature, to advance vegetation studies of carbon cycle dynamics and ecosystem health. We obtained statistically significant results for fluorescence…

Spatial Variation of Leaf Optical Properties in a Boreal Forest Is Influenced by Species and Light Environment

Leaf Optical Properties (LOPs) convey information relating to temporally dynamic photosynthetic activity and biochemistry. LOPs are also sensitive to variability in anatomically related traits such as Specific Leaf Area (SLA), via the interplay of intra-leaf light scattering and absorption processes. Therefore, variability in such traits, which may demonstrate little plasticity over time, potentially disrupts remote sensing estimates of photosynthesis or biochemistry across space. To help to disentangle the various factors that contribute to the variability of LOPs, we defined baseline variation as variation in LOPs that occurs across space, but not time. Next we hypothesized that there wer…

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…

Plant chlorophyll fluorescence: active and passive measurements at canopy and leaf scales with different nitrogen treatments

Highlight We studied for the first time the temporal and spatial limits within which active and passive chlorophyll fluorescence measurements are comparable.

Early Diagnosis of Vegetation Health From High-Resolution Hyperspectral and Thermal Imagery: Lessons Learned From Empirical Relationships and Radiative Transfer Modelling

[Purpose of Review] We provide a comprehensive review of the empirical and modelling approaches used to quantify the radiation–vegetation interactions related to vegetation temperature, leaf optical properties linked to pigment absorption and chlorophyll fluorescence emission, and of their capability to monitor vegetation health. Part 1 provides an overview of the main physiological indicators (PIs) applied in remote sensing to detect alterations in plant functioning linked to vegetation diseases and decline processes. Part 2 reviews the recent advances in the development of quantitative methods to assess PI through hyperspectral and thermal images.

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…

An Overview of the Regional Experiments for Land-Atmosphere Exchanges 2012 (Reflex 2012) Campaign

The REFLEX 2012 campaign was initiated as part of a training course on the organization of an airborne campaign to support advancement of the understanding of land-atmosphere interaction processes. This article describes the campaign, its objectives and observations, remote as well as in situ. The observations took place at the experimental Las Tiesas farm in an agricultural area in the south of Spain. During the period of ten days, measurements were made to capture the main processes controlling the local and regional land-atmosphere exchanges. Apart from multi-temporal, multi-directional and multi-spatial space-borne and airborne observations, measurements of the local meteorology, energy…

Sun-Induced Chlorophyll Fluorescence I: Instrumental Considerations for Proximal Spectroradiometers

Growing interest in the proximal sensing of sun-induced chlorophyll fluorescence (SIF) has been boosted by space-based retrievals and up-coming missions such as the FLuorescence EXplorer (FLEX). The European COST Action ES1309 &ldquo;Innovative optical tools for proximal sensing of ecophysiological processes&rdquo; (OPTIMISE, ES1309; https://optimise.dcs.aber.ac.uk/) has produced three manuscripts addressing the main current challenges in this field. This article provides a framework to model the impact of different instrument noise and bias on the retrieval of SIF; and to assess uncertainty requirements for the calibration and characterization of state-of-the-art SIF-oriented spectroradiom…

Regularized multiresolution spatial unmixing for ENVISAT/MERIS and landsat/TM image fusion

Earth observation satellites currently provide a large volume of images at different scales. Most of these satellites provide global coverage with a revisit time that usually depends on the instrument characteristics and performance. Typically, medium-spatial-resolution instruments provide better spectral and temporal resolutions than mapping-oriented high-spatial-resolution multispectral sensors. However, in order to monitor a given area of interest, users demand images with the best resolution available, which cannot be reached using a single sensor. In this context, image fusion may be effective to merge information from different data sources. In this letter, an image fusion approach ba…

A RADARSAT-2 Quad-Polarized Time Series for Monitoring Crop and Soil Conditions in Barrax, Spain

An analysis of the sensitivity of synthetic aperture radar (SAR) backscatter (σo) to crop and soil conditions was conducted using 57 RADARSAT-2 C-band quad-polarized SAR images acquired from April to September 2009 for large fields of wheat, barley, oat, corn, onion, and alfalfa in Barrax, Spain. Preliminary results showed that the cross-polarized σHVo was particularly useful for monitoring both crop and soil conditions and was the least sensitive to differences in beam incidence angle. The greatest separability of barley, corn, and onion occurred in spring after the barley had been harvested or in the narrow time window associated with grain crop heading when corn and onion were still imma…

Scene-based spectral calibration assessment of high spectral resolution imaging spectrometers

An accurate knowledge of the spectral calibration of imaging spectrometers is required for optimum data processing and interpretation. The scene-based spectral characterization of imaging spectrometers is frequently necessary to update or replace the pre-flight laboratory-based spectral characterization supplied by the data provider. An automatic method for the estimation of spectral calibration parameters (channel position and bandwidth) at atmospheric absorption regions from high spectral resolution imaging spectrometers (spectral sampling interval below 5 nm) is presented in this contribution. The method has been tested on two commercial instruments with spectral sampling intervals below…

CHRIS/PROBA toolbox for hyperspectral and multiangular data exploitations

The project CHRIS/Proba Toolbox for BEAM (CHRIS-Box) has been developed in order to support users of data from the CHRIS sensor onboard of ESA's Proba platform. BEAM and the CHRIS-Box are user tools which ESA/ESRTN are providing free of charge to the Earth Observation Community. The CHRIS-Box software provides extensions for BEAM that allows accomplishing the following tasks: a) Noise reduction to remove the vertical striping and other noise present in CHRIS response-corrected images; b) Cloud screening to mark cloudy pixels in CHRIS noise-corrected images; the cloud screening algorithm provides cloud probability and abundances for each pixel; c) Atmospheric correction that provides surface…

Cloud detection for CHRIS/Proba hyperspectral images

Accurate and automatic detection of clouds in satellite scenes is a key issue for a wide range of remote sensing applications. With no accurate cloud masking, undetected clouds are one of the most significant source of error in both sea and land cover biophysical parameter retrieval. Sensors with spectral channels beyond 1 um have demonstrated good capabilities to perform cloud masking. This spectral range can not be exploited by recently developed hyperspectral sensors that work in the spectral range between 400- 1000 nm. However, one can take advantage of their high number of channels and spectral resolution to increase the cloud detection accuracy, and to describe properly the detected c…

Estimation of solar-induced vegetation fluorescence from space measurements

[1] A characteristic spectral emission is observed in vegetation chlorophyll under excitation by solar radiation. This emission, known as solar-induced chlorophyll fluorescence, occurs in the red and near infra-red spectral regions. In this paper a new methodology for the estimation of solar-induced chlorophyll fluorescence from spaceborne and airborne sensors is presented. The fluorescence signal is included in an atmospheric radiative transfer scheme so that chlorophyll fluorescence and surface reflectance are retrieved consistently from the measured at-sensor radiance. This methodology is tested on images acquired by the Medium Resolution Imaging Spectrometer (MERIS) on board the ENVIron…

Impact of Structural, Photochemical and Instrumental Effects on Leaf and Canopy Reflectance Variability in the 500–600 nm Range

Current rapid technological improvement in optical radiometric instrumentation provides an opportunity to develop innovative measurements protocols where the remote quantification of the plant physiological status can be determined with higher accuracy. In this study, the leaf and canopy reflectance variability in the PRI spectral region (i.e., 500–600 nm) is quantified using different laboratory protocols that consider both instrumental and experimental set-up aspects, as well as canopy structural effects and vegetation photoprotection dynamics. First, we studied how an incorrect characterization of the at-target incoming radiance translated into an erroneous vegetation reflectance spectru…

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 …

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 …

Correction of systematic spatial noise in push-broom hyperspectral sensors: application to CHRIS/PROBA images

Hyperspectral remote sensing images are affected by different types of noise. In addition to typical random noise, nonperiodic partially deterministic disturbance patterns generally appear in the data. These patterns, which are intrinsic to the image formation process, are characterized by a high degree of spatial and spectral coherence. We present a new technique that faces the problem of removing the spatially coherent noise known as vertical striping, usually found in images acquired by push-broom sensors. The developed methodology is tested on data acquired by the Compact High Resolution Imaging Spectrometer (CHRIS) onboard the Project for On-board Autonomy (PROBA) orbital platform, whi…

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 …