FLEX (Fluorescence Explorer) mission: Observation fluorescence as a new remote sensing technique to study the global terrestrial vegetation state

Revista oficial de la Asociación Española de Teledetección[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 methods for the estimation of classical biophysical parameters, and by introducing a new one: fluorescence. This paper presents the current status of FLEX mission in A/B1 phase and the different ongoing studies, campaigns and projects carried out in support of the FLEX mission.[ES] La misión FLEX (FLuorescence EXplorer) candidata del programa “Earth Explorer” de la ESA, es la primera misión espacial diseñada específicamente para la estimación de la fluorescencia de la vegetación a escala global. La propuesta incluye que FLEX vuele en tándem con el futuro Sentinel-3 de la ESA. La información proporcionada por los sensores de Sentinel-3 será complementada con la proporcionada por FLORIS (FLuORescence Imaging Spectrometer) a bordo de FLEX, que medirá la radiancia entre 500 y 800 nm con una anchura de bandas entre 0,1 nm y 2 nm, proporcionando imágenes con un ancho de barrido de 150 km y tamaño de pixel de 300 m. Esta información permitirá el estudio detallado de la vegetación con métodos mejorados para la estimación de parámetros biofísicos clásicos y la introducción de nuevos parámetros biofísicos como la fluorescencia. En este trabajo se muestra el estado actual de la misión FLEX en fase A/B1 y de los distintos estudios, campañas y proyectos que se están llevando a cabo en torno a la misión FLEX.Este trabajo ha sido posible gracias al Proyecto AYA2010-21432-C02-01 (BIOFLEX) subvencionado por el Ministerio de Economía y Competitividad de España.Moreno, J.; Alonso, L.; Delegido, J.; Rivera, J.; Ruiz-Verdú, A.; Sabater, N.; Tenjo, C.... (2014). Misión FLEX (Fluorescence Explorer): Observación de la fluorescencia por teledetección como nueva técnica de estudio del estado de la vegetación terrestre a escala global. Revista de Teledetección. (41):111-119. https://doi.org/10.4995/raet.2014.2296SWORD11111941Meroni, M., Rossini, M., Guanter, L., Alonso, L., Rascher, U., Colombo, R., & Moreno, J. (2009). Remote sensing of solar-induced chlorophyll fluorescence: Review of methods and applications. Remote Sensing of Environment, 113(10), 2037-2051. doi:10.1016/j.rse.2009.05.003Van der Tol, C., Verhoef, W., Timmermans, J., Verhoef, A., & Su, Z. (2009). An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance. Biogeosciences, 6(12), 3109-3129. doi:10.5194/bg-6-3109-200

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 signal distortions must be accounted for, and a high-precision true vegetation reflectance must be resolved. ESA's upcoming Fluorescence Explorer aims to deliver such novel products thanks to technological and instrumental advances, and by sophisticated approaches that will enable a deeper understanding of the mechanics of energy transfer underlying the photosynthetic process in plant canopies and ecosystems

Chapter “Flex 2018” Cruise: an opportunity to assess phytoplankton chlorophyll fluorescence retrieval at different observative scales

The “FLEX 2018” cruise, organized by the CNR-ISMAR in frame of the ESA “FLEXSense Campaign 2018” and CMEMS project, provided a ground station for several bio-optical instruments that investigated the coastal waters of the Tyrrhenian Sea in June 2018. The field measurements were performed in time synergy with Sentinel 3A and Sentinel 3B satellites and HyPlant airborne imaging spectrometer. Active and passive fluorescence were investigated at different scales in coastal waters to support preparatory activities of the FLuorescence EXplorer (FLEX) satellite mission

Design of a generic end-to-end mission performance simulator and application to the performance analysis of the FLEX/Sentinel-3 mission

La Observación de la Tierra mediante técnicas de teledetección con instrumentos ópticos en satélite tiene como objetivo monitorizar los procesos bio-geofísicos en la superficie y atmósfera terrestre, adquiriendo datos a diferentes longitudes de onda del espectro electromagnético. Con el fin de asegurar el mantenimiento de las observaciones y las capacidades para entender el sistema Tierra, nuevas misiones satelitales están siendo desarrolladas por agencias espaciales nacionales e internacionales así como organizaciones de investigación. En este contexto, los simuladores de misiones espaciales (E2ES por sus siglas en inglés, End-to-End Mission Performance Simulator) ofrecen a los científicos e ingenieros un marco único para entender el impacto de la configuración del instrumento en los productos finales de la misión y, por tanto, acelerar el desarrollo de una misión desde la fase conceptual hasta el lanzamiento. Al mismo tiempo, estas herramientas permiten definir una metodología para la consolidación de los requisitos y la evaluación de la actuación de estas misiones satelitales, estableciendo criterios para la selección de una misión por las diferentes agencias espaciales. Mientras que el concepto de un E2ES es simple, el diseño de nuevos E2ES y la evolución de los ya existentes tienen una falta de guias y metodología estandarizadas, lo cual se traduce en un caro y complejo proceso de re-ingeniería. Esta tesis cubre dos objetivos principales. Por un lado, se pretende armonizar el trabajo hecho en el campo de los E2ES durante las últimas décadas y proponer una serie de guias y metodologías para desarrollas E2ES para misiones satelitales futuras con instrumentos ópticos pasivos. El primer objetivo es por tanto "Diseñar un simulador de misión genérico que pueda ser fácilmente adaptado para reproducir la mayoría de misiones satelitales, presentes y futuras, con sensores ópticos pasivos". Por otro lado, la misión FLEX/Sentinel-3 de la ESA se usa para validar, a través de la implementación de su propio E2ES, el diseño de la arquitectura genérica tratada en el punto anterior. De este modo, el E2ES para la misión FLEX permite evaluar la actuación de la misión para la obtención de la fluorescencia inducida por radiación solar emitida por la vegetación terrestre. La misión FLEX/Sentinel-3 es una candidata óptima para esta tarea de validación dada la complejidad de la misión (p.ej. vuelo en tandem, multi-plataforma/-instrumento, múltiples rangos y resoluciones espectrales, observaciones multi-angulares, sinergia de productos). El segundo objetivo de esta tesis es por tanto "Evaluar la misión FLEX para la la observación de la emisión de fluorescencia emitida por la vegetación usando un E2ES desarrollado de acuerdo con una arquitectura genérica". La razón fundamental tras esta Tesis es promocionar el uso de una arquitectura genérica común para los E2ES que permita comparar misiones satelitales en procesos de selección competitiva como los Earth Explorer de la ESA así como acelerar el análisis de los requisitos técnicos y el rendimiento de la misión a nivel científico. Particularmente, esto se muestra mediante la implementación de esta arquitectura genérica para el caso específico de la misión FLEX/Sentinel-3 demostrando que: (1) la misión es capaz de obtener con la precisión requerida la emisión de fluorescencia por la vegetación ; y (2) el concepto de esta arquitectura genérica es apto para reproducir la complejidad de la misión FLEX/Sentinel-3 y por tanto se espera que esta metodología pueda ser también aplicable para un gran abanico de misiones ópticas pasivas. Esta base lógica se consigue a partir de una categorización de varias misiones satelitales y la identificación y análisis de los elementos principales que afectan en el rendimiento de la misión e impactan en la arquitectura de un simulador de misión. La arquitectura genérica para E2ES propuesta se valida mediante la implementación del E2ES de la misión FLEX/Sentinel-3 de la ESA teniendo en cuenta ambos satélites, sus instrumentos, y evaluando con este E2ES el rendimiento de la misión FLEX. En esta Tesis, los capítulos 1 y 2 introducen los principales temas de esta Tesis y definen los conceptos básicos. Los capítulos 3 al 5 describe el diseño de la arquitectura genérica para los E2ES en misiones ópticas pasivas. Finalmente, el capítulo 6 resume los principales resultados y las conclusiones derivadas de esta Tesis.Earth observation by satellite optical remote sensing aims to monitor bio-geophysical processes happening in the Earth surface and the atmosphere by acquiring data at different wavelengths of the electromagnetic spectrum. In order to ensure sustained observations and capabilities to fill scientific gaps in our current understanding of the Earth system, new satellite missions are being developed by national and international space agencies and research organisations. In this context, End-to-End Mission Performance Simulator (E2ES) tools offer scientists and engineers a unique framework to understand the impact of instrument configuration in the final mission products and to accelerate the mission development from concept to deployment. At the same time, these cost-effective and flexible tools are capable of defining a methodology for the consolidation of requirements and performance assessment of these new satellite missions, setting the criteria for mission selection by the various space agencies’ programme boards. While the concept of an E2ES is simple, the design of new E2ES and the evolution of existing ones lack from a standard methodology and guidelines, which translates into a complex and costly re-engineering process. This Thesis covers two main objectives. On the one hand, it aims to harmonize the work done in the field of E2ES during the last decades and to propose a set of guidelines or methodology to develop E2ES for future remote sensing satellite passive optical missions. The first main objective, therefore, is: ’To design a generic end-to-end mission performance simulator that can be easily adapted to reproduce most present or future passive optical spaceborne instruments’. On the other hand, the ESA’s FLEX/Sentinel-3 tandem mission is used to validate, through the implementation of its E2ES, the designed generic E2ES architecture and to evaluate the performance of the FLEX mission for the retrieval of Sun-induced fluorescence. The FLEX/Sentinel- 3 mission is optimally suitable for this validation task due to the complexity of the mission (e.g. tandem flight, multi-platform/-instrument mission, multiple spectral ranges and resolutions, multi-angular observations, synergy of products). The second main objective, therefore, is: ’To evaluate the FLEX mission for Sun-induced fluorescence retrievals using a newly developed E2ES in agreement with the designed generic E2ES architecture.’. The rationale behind this Thesis is promoting the use of a common generic E2ES architecture that allows comparing missions in competitive selection process (e.g., ESA’s Earth Explorers) and speeding-up the analysis of the mission technical requirements and scientific performances. Particularly, this is shown by implementing this generic E2ES architecture for the specific case of FLEX/Sentinel-3 mission demonstrating that: (1) the mission is capable of retrieving Sun-induced fluorescence within the required accuracy; and (2) the conceptual generic E2ES architecture is suitable toreproduce the complexity of the FLEX/Sentinel-3 tandem mission and thus it is expected to be also applicable for a wide range of passive optical missions. This rationale is achieved by categorising several satellite missions to identify and analyse the main elements that affect the mission performance and impact the simulator architecture. The proposed generic E2ES architecture is validated by implementing the ESA’s FLEX/Sentinel-3 E2ES, both satellites and their instruments, and testing it through the performance assessment of the FLEX mission products. In this Thesis, Chapters 1 and 2 introduce the main research questions and sets the background concepts. Then Chapters 3–5 describe the design of a generic E2ES architecture for passive optical missions. Finally, Chapter 6 summarizes the main results and conclusions derived in this Thesis

Sentinel-3/FLEX Biophysical Product Confidence Using Sentinel-2 Land-Cover Spatial Distributions

The estimation of biophysical variables from remote sensing data raises important challenges in terms of the acquisition technology and its limitations. In this way, some vegetation parameters, such as chlorophyll fluorescence, require sensors with a high spectral resolution that constrains the spatial resolution while significantly increasing the subpixel land-cover heterogeneity. Precisely, this spatial variability often makes that rather different canopy structures are aggregated together, which eventually generates important deviations in the corresponding parameter quantification. In the context of the Copernicus program (and other related Earth Explorer missions), this article proposes a new statistical methodology to manage the subpixel spatial heterogeneity problem in Sentinel-3 (S3) and FLuorescence EXplorer (FLEX) by taking advantage of the higher spatial resolution of Sentinel-2 (S2). Specifically, the proposed approach first characterizes the subpixel spatial patterns of S3/FLEX using inter-sensor data from S2. Then, a multivariate analysis is conducted to model the influence of these spatial patterns in the errors of the estimated biophysical variables related to chlorophyll which are used as fluorescence proxies. Finally, these modeled distributions are employed to predict the confidence of S3/FLEX products on demand. Our experiments, conducted using multiple operational S2 and simulated S3 data products, reveal the advantages of the proposed methodology to effectively measure the confidence and expected deviations of different vegetation parameters with respect to standard regression algorithms. The source codes of this work will be available at https://github.com/rufernan/PixelS3

IEEE

Sentinel missions provide widespread opportunities of exploiting inter-sensor synergies to improve the operational monitoring of terrestrial photosynthetic activity and canopy structural variations using vegetation indices (VI). In this context, continuous and consistent temporal data are logically required to rapidly detect vegetation changes across sensors. Nonetheless, the existing temporal limitations inherent to satellite orbits, cloud occlusions, data degradation, and many other factors may severely constrain the availability of data involving multiple satellites. In response, this letter proposes a novel deep 3-D convolutional regression network (3CRN) for temporally enhancing Sentinel-3 (S3) VI by taking advantage of inter-sensor Sentinel-2 (S2) observations. Unlike existing regression and deep learning-based methods, the proposed approach allows convolutional kernels to slide across the temporal dimension to exploit not only the higher spatial resolution of the S2 instrument but also its own temporal evolution to better estimate time-resolved VI in S3. To validate the proposed approach, we built a database made of multiple day-synchronized S2 and S3 operational products from a study area in Extremadura (Spain). The conducted experimental comparison, including multiple state-of-the-art regression and deep learning models, shows the statistically significant advantages of the presented framework. The codes of this work will be made available at https://github.com/rufernan/3CRN

Development of atmospheric correction algorithms for very high spectral and spatial resolution images: application to SEOSAT and the FLEX/Sentinel-3 missions

Advanced high spectral and spatial resolution imager spectrometers on board new generation of Earth Observation missions bring new exciting opportunities to the remote sensing scientific community. However, this progress goes hand in hand with new challenges. The exploitation of data acquired from these family of advanced instruments requires new processing algorithms able to deal with these particularities. As part of this evolution, atmospheric correction algorithms - a mandatory processing step applied prior to the Earth surface reflectance data exploitation - must be adapted or reformulated, thereby paying special attention to how atmospheric effects disturb the acquired signal in the spectral and spatial domains. For these reasons, this Thesis aims to develop new atmospheric correction strategies to be applied over very high spectral and spatial resolution data. Following this goal, this Thesis was conducted in the framework of two missions during their development phase: (1) the FLEX/Sentinel–3 tandem space mission (for high spectral resolution data) and, (2) the Ingenio/SEOsat space mission (for high spatial resolution data). In the context of these missions, an additional challenge is introduced when acquiring proximal remote sensing data for their validation. This is especially relevant for the FLEX mission, which is dedicated to monitor the weak Solar Induced Chlorophyll Fluorescence (SIF) signal. Following this motivation, the main objectives of this Thesis are threefold: The first objective involved to analyse atmospheric effects on the Ingenio/SEOsat high spatial and low spectral resolution satellite mission and to propose a new atmospheric correction strategy. This strategy was called Hybrid and combines: (1) a per–pixel atmospheric radiative transfer model inversion technique making use of auxiliary data to characterize the atmospheric state, followed by (2) an image deconvolution technique modelling the atmospheric MTF to correct for atmospheric spatial effects. The Hybrid method was applied to Sentinel–2 data, particularly over bands acquired at 10 m resolution due to its similarities with the Ingenio/SEOsat mission. The second objective involved to define a novel atmospheric correction strategy for the FLEX/Sentinel-3 tandem mission. The proposed strategy is a two-steps method where information from Sentinel-3 instruments, OLCI and SLSTR, is first used in synergy to characterize the aerosol and water vapour presence. The high spectral resolution of FLEX data is subsequently exploited to refine the previously aerosol characterization. As part of this objective, the suitability of all the approximations assumed in the formulation proposed for the atmospheric inversion of FLEX data was validated against the FLEX mission requirements. The third objective involved to develop a strategy that deals with the atmospheric correction of very high spectral and spatial resolution data acquired at lower atmospheric scales such as Unmanned Aerial Vehicles or systems mounted on towers. In this Thesis, it was demonstrated that even when acquiring the signal at proximal remote sensing scale, i.e., few meters from the target oxygen absorption must be compensated to properly estimate SIF within these spectral regions. For this reason, a strategy to compensate for the oxygen absorption while properly dealing with the instrumental spectral response function convolution was presented and tested using simulated data. Altogether, this work identified challenges associated to atmospheric correction when applying to high spatial and especially to very high spectral resolution data. In this Thesis, adequate formulations have been developed to resolve these difficulties, and successful methodologies have been designed for the particular cases of SEOsat (high spatial resolution) and FLEX (high spectral resolution); two future remote sensing space missions that will be launched in the forthcoming years

OLCI-A/B tandem phase: evaluation of FLuorescence EXplorer (FLEX)-like radiances and estimation of systematic differences between OLCI-A and OLCI-FLEX

During the tandem phase of Sentinel-3A and Sentinel-3B in summer 2018 the Ocean and Land Colour Imager (OLCI) mounted on the Sentinel-3B satellite was reprogrammed to mimics ESA's eighth Earth Explorer, the FLuorescence EXplorer (FLEX). The OLCI in FLEX configuration (OLCI-FLEX) had 45 spectral bands between 500 and 792 nm. The new data set with high-spectral-resolution measurements (bandwidth: 1.7–3.7 nm) serves as preparation for the FLEX mission. Spatially co-registered measurements of both instruments are used for the atmospheric correction and the retrieval of surface parameters, e.g. the fluorescence or the leaf area index. For such combined products, it is essential that both instruments are radiometrically consistent. We developed a transfer function to compare radiance measurements from different optical sensors and to monitor their consistency. In the presented study, the transfer function shifts information gained from high-resolution “FLEX-mode” settings to information convolved with the spectral response of the normal (lower) spectral resolution of the OLCI sensor. The resulting reconstructed low-resolution radiance is representative of the high-resolution data (OLCI-FLEX), and it can be compared with the measured low-resolution radiance (OLCI-A measurements). This difference is used to quantify systematic differences between the instruments. Applying the transfer function, we could show that OLCI-A is about 2 % brighter than OLCI-FLEX for most bands of the OLCI-FLEX spectral domain. At the longer wavelengths (> 770 nm) OLCI-A is about 5 % darker. Sensitivity studies showed that the parameters affecting the quality of the comparison of OLCI-A and OLCI-FLEX with the transfer function are mainly the surface reflectance and secondarily the aerosol composition. However, the aerosol composition can be simplified as long as it is treated consistently in all steps in the transfer function. Generally, the transfer function enables direct comparison of instruments with different spectral responses even with different observation geometries or different levels of observation. The method is sensitive to measurement biases and errors resulting from the processing. One application could be the quality control of the FLEX mission; presently it is also useful for the quality control of the OLCI-FLEX data

Using Sentinel-2-Based Metrics to Characterize the Spatial Heterogeneity of FLEX Sun-Induced Chlorophyll Fluorescence on Sub-Pixel Scale

Current and upcoming Sun-Induced chlorophyll Fluorescence (SIF) satellite products (e.g., GOME, TROPOMI, OCO, FLEX) have medium-to-coarse spatial resolutions (i.e., 0.3–80 km) and integrate radiances from different sources into a single ground surface unit (i.e., pixel). However, intrapixel heterogeneity, i.e., different soil and vegetation fractional cover and/or different chlorophyll content or vegetation structure in a fluorescence pixel, increases the challenge in retrieving and quantifying SIF. High spatial resolution Sentinel-2 (S2) data (20 m) can be used to better characterize the intrapixel heterogeneity of SIF and potentially extend the application of satellite-derived SIF to heterogeneous areas. In the context of the COST Action Optical synergies for spatiotemporal SENsing of Scalable ECOphysiological traits (SENSECO), in which this study was conducted, we proposed direct (i.e., spatial heterogeneity coefficient, standard deviation, normalized entropy, ensemble decision trees) and patch mosaic (i.e., local Moran’s I) approaches to characterize the spatial heterogeneity of SIF collected at 760 and 687 nm (SIF760 and SIF687, respectively) and to correlate it with the spatial heterogeneity of selected S2 derivatives. We used HyPlant airborne imagery acquired over an agricultural area in Braccagni (Italy) to emulate S2-like top-of-the-canopy reflectance and SIF imagery at different spatial resolutions (i.e., 300, 20, and 5 m). The ensemble decision trees method characterized FLEX intrapixel heterogeneity best (R2 > 0.9 for all predictors with respect to SIF760 and SIF687). Nevertheless, the standard deviation and spatial heterogeneity coefficient using k-means clustering scene classification also provided acceptable results. In particular, the near-infrared reflectance of terrestrial vegetation (NIRv) index accounted for most of the spatial heterogeneity of SIF760 in all applied methods (R2 = 0.76 with the standard deviation method; R2 = 0.63 with the spatial heterogeneity coefficient method using a scene classification map with 15 classes). The models developed for SIF687 did not perform as well as those for SIF760, possibly due to the uncertainties in fluorescence retrieval at 687 nm and the low signal-to-noise ratio in the red spectral region. Our study shows the potential of the proposed methods to be implemented as part of the FLEX ground segment processing chain to quantify the intrapixel heterogeneity of a FLEX pixel and/or as a quality flag to determine the reliability of the retrieved fluorescence

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

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)) for a combination of off-the-shelf commercial spectrometers. Secondly, we evaluated how an erroneous implementation of the retrieval methods increases the uncertainty in the estimated SIF values. Results show that the SFM approach applied to highresolution spectra provided the most reliable SIF retrieval with a relative error (RE) ≤6% and <5% for F687 and F760, respectively. Furthermore, although the SFM was the least affected by an inaccurate definition of the absorption spectral window (RE = 5%) and/or interpolation strategy (RE = 15%– 30%), we observed a sensitivity of the SIF retrieval for the simulated training data underlying the SFM model implementation