Optimized and automated estimation of vegetation properties: Opportunities for Sentinel-2

La Biosfera es uno de los principales sistemas que conforman la Tierra. Su estudio permite comprender la relación entre la vegetación y el ciclo del carbono y cómo éste puede ser afectado por los cambios en los niveles de CO2 y los usos de suelo. Para el estudio de estas dinámicas a escala global y local, han sido desarrollados diversos modelos que son representaciones de la realidad en una escala y complejidad más simple. Parte de las variables de entrada de estos modelos son obtenidas mediante medidas de teledetección gracias al Global Climate Observing System (GCOS), que ha determinado un conjunto de 50 variables climáticas esenciales que contribuyen a los estudios de cambio climático que lidera la Convención Marco de las Naciones Unidas y el Panel Intergubernamental del Cambio Climático. En esta lista está incluido el índice de área foliar (LAI).El contenido de clorofila en hoja (LCC) es otro parámetro biofísico clave para los estudios de biosfera. El estudio de las propiedades de la vegetación desde el espacio requiere: (1) Métodos óptimos para el procesamiento y la estimación de la información y, (2) Disponibilidad de datos espaciales. Los métodos de procesado y estimación de parámetros biofísicos son necesarios ya que el sensor solo mide los flujos de energía reflejados por las cubiertas vegetales distribuidos espacialmente. Por ello, han sido desarrollados diversos modelos, que van desde complejos modelos con base física hasta modelos estadísticos o la combinación de los anteriores. En el desarrollo de esta tesis se ha reunido una amplia variedad de ellos. la Agencia Espacial Europea (ESA) ha desarrollado la misión Sentinel-2 que está especialmente diseñada para el monitoreo de las propiedades de la vegetación, con las capacidades operativas que cumplen los requerimientos espectrales, espaciales y temporales. Los datos que proporcionará la misión Sentinel-2 permitirán garantizar la continuidad de las misiones Spot y Landsat, aportando un tiempo de revisita menor, mejora de la amplitud de barrido, mayor resolución espectral y una mejor calibración y calidad de imagen. Para el procesamiento y la extracción de información de parámetros biofísicos han sido desarrollados diferentes paquetes computacionales por diversos grupos de investigación. Esta tesis pretende suministrar un conjunto de herramientas computacionales, dinámicas y flexibles que permitan automatizar y evaluar el potencial de los diferentes métodos que en la actualidad han sido publicados y están disponibles para su libre uso. Presenta los resultados científicos de la evaluación del impacto de diferentes parámetros de ajuste en los principales métodos de estimación de parámetros biofísicos, centrándonos en datos simulados del satélite Sentinel-2, previsto para ser lanzado en 2015. Para dicho trabajo se han reunido los principales métodos de estimación que van desde las simples relaciones espectrales hasta los complejos modelos de transferencia radiativa (RTM). Para esto, hemos implementado un conjunto de herramientas informáticas que permiten el diseño y evaluación de diversas estrategias de regularización como son la normalización de los datos, la sinergia entre datos simulados por RTM y datos de campañas de campo o de laboratorio, adición de modelos de ruido a los datos simulados y un amplio conjunto de métodos de regresión tanto paramétricos como no paramétricos. Este trabajo constituye la continuación de mi trabajo Final del Máster de Teledetección, donde he desarrolló una herramienta informática llamado ARTMO (por sus siglas en inglés Automated Radiative Transfer Models Operator) que reunió los RTM de la familia Prospect, SAIL y FLIGTH. Se implementó el método de estimación por tablas de búsqueda (LUT). Esta tesis presenta la evolución de ARTMO que pasa de ser una herramienta informática rígida que no permitía de manera sencilla la ampliación de sus funciones, a un flexible marco de desarrollo (framework software), donde ARTMO se convierte en una plataforma de soporte de diversos módulos implementados de manera independiente. Esta nueva versión de ARTMO permite a cualquier grupo de investigación desarrollar y compartir nuevas funciones, algoritmos y métodos de estimación de parámetros biofísicos. Además, hemos establecido las bases para la creación de una red tanto de usuarios como de desarrolladores en torno al estudio de las propiedades de la vegetación, sirviendo de apoyo para el estudio de nuevos algoritmos de estimación, diseño de nuevos sensores ópticos o para su uso en el campo de la educación.The biosphere is one of the main components of the Earth’s system since it regulates exchanges of energy and mass fluxes at the soil, vegetation and atmosphere level. To know the links between vegetation and the terrestrial energy, water and carbon cycles, and how these might change due to eco-physiological responses to elevated CO2 and changes in land use is of vital importance for the study of the biosphere. To study these exchanges, several kinds of models (scale and target) have been developed. In view of these models, the Global Climate Observing System (GCOS) aims to provide comprehensive information on the total climate system, involving a multidisciplinary range of physical, chemical and biological properties, and atmospheric, oceanic, hydrological, cryospheric and terrestrial processes. Fifty GCOS Essential Climate Variables (ECVs) are required to support the work of the United Nations Framework Convention on Climate Change (UNFCCC) and the Intergovernmental Panel on Climate Change. In support of these terrestrial models, but also in support of monitoring local-to-global vegetation dynamics, this Thesis focuses on improved estimation of vegetation properties from optical RS data, and more specifically leaf area index (LAI) and leaf chlorophyll content (LCC). Although LCC is currently not considered as an ECV due to the lack of a globally applicable retrieval algorithm, it is a key variable in vegetation studies. Monitoring the distribution and changes of LAI and LCC is important for assessing growth and vigour of vegetation on the planet. The quantification of these essential vegetation properties are fundamentally important in land-atmosphere processes and parametrization in climate models. LAI variable represents the amount of leaf material in ecosystems and controls the links between biosphere and atmosphere through various processes such as photosynthesis, respiration, transpiration and rain interception. LCC provides important information about the physiological status of plants and photosynthetic activity, therefore is related to the nitrogen content, water stress and yield forecasting The European Space Agency (ESA)’s forthcoming Sentinel-2 mission is particularly tailored to the monitoring vegetation properties mapping, with operational monitoring capabilities that goes beyond any existing operational mission. A pair of Sentinel-2 polar-orbiting satellites will provide systematic global acquisitions of high-resolution multispectral imagery (10-60 m) with a high revisit frequency on a free and open data policy basis. With the pair of satellites in operation it has a revisit time of five days at the equator (under cloud-free conditions) and 2–3 days at mid-latitudes. Sentinel-2 images will be used to derive the highly prioritized time series of ECVs such as LAI. Sentinel-2 images will also be used provide various experimental variables, e.g. biochemical variables such as LCC. This Thesis is dedicated to tackle the stated recommendation and turn it into consolidated guidelines. The undertaken road map was to work on both generating scientific outputs, as well on developing software to automate the retrieval routines. All essential tools to deliver a prototype retrieval approach that could be embedded into an operational Sentinel-2 processing scheme have been prepared into a scientific software package called ARTMO (Automated Radiative Transfer Models Operator). Physically-based approaches but also latest statisticallybased methods have been implemented into the software package and systematically evaluated. The retrieval methods have been applied to the estimation of LAI and LCC from simulated Sentinel-2 data, but the majority of investigated methods can essentially be applied to derive any detectable vegetation biochemical or biophysical variable. The fundamentals of ARTMO has been laid during J.P. Rivera’s MSc thesis project and has been further developed during the course of my PhD Thesis. The toolbox is built on a suite of radiative transfer models and image processing modules in a modular graphical user interface (GUI) environment. ARTMO has been mainly developed and tested for processing (simulated) Sentinel-2 data in a semiautomatic way, but in principle data from any optical sensor can be processed

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

Los métodos de regresión no paramétricos son una gran herramienta estadística para obtener parámetros biofísicos a partir de medidas realizadas mediante teledetección. Pero los resultados obtenidos se pueden ver afectados por los datos utilizados en la fase de entrenamiento del modelo. Para asegurarse de que los modelos son robustos, se hace uso de varias técnicas de validación cruzada. Estas técnicas permiten evaluar el modelo con subconjuntos de la base de datos de campo. Aquí, se evalúan dos tipos de validación cruzada en el desarrollo de modelos de regresión no paramétricos: hold-out y k-fold. Los métodos de regresión lineal seleccionados fueron: Linear Regression (LR) y Partial Least Squares Regression (PLSR). Y los métodos no lineales: Kernel Ridge Regression (KRR) y Gaussian Process Regression (GPR). Los resultados de la validación cruzada mostraron que LR ofrece los resultados más inestables, mientras KRR y GPR llevan a resultados más robustos. Este trabajo recomienda utilizar algoritmos de regresión no lineales (como KRR o GPR) combinando con la validación cruzada k-fold con un valor de k igual a 10 para hacer la estimación de una manera robust

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) SCOPE and the atmospheric RTM 6SV. The retrieval models, named to S3-TOA-GPR-1.0, were directly implemented in Google Earth Engine (GEE) to enable the quantification of the traits from TOA data as acquired from the S3 Ocean and Land Colour Instrument (OLCI) sensor. Following good to high theoretical validation results with normalized root mean square error (NRMSE) ranging from 5% (FAPAR) to 19% (LAI), a three fold evaluation approach over diverse sites and land cover types was pursued: (1) temporal comparison against LAI and FAPAR products obtained from Moderate Resolution Imaging Spectroradiometer (MODIS) for the time window 2016–2020, (2) spatial difference mapping with Copernicus Global Land Service (CGLS) estimates, and (3) direct validation using interpolated in situ data from the VALERI network. For all three approaches, promising results were achieved. Selected sites demonstrated coherent seasonal patterns compared to LAI and FAPAR MODIS products, with differences between spatially averaged temporal patterns of only 6.59%. In respect of the spatial mapping comparison, estimates provided by the S3-TOA-GPR-1.0 models indicated highest consistency with FVC and FAPAR CGLS products. Moreover, the direct validation of our S3-TOA-GPR-1.0 models against VALERI estimates indicated good retrieval performance for LAI, FAPAR and FVC. We conclude that our retrieval workflow of spatiotemporal S3 TOA data processing into GEE opens the path towards global monitoring of fundamental vegetation traits, accessible to the whole research community.We gratefully acknowledge the financial support by the European Space Agency (ESA) for airborne data acquisition and data analysis in the frame of the FLEXSense campaign (ESA Contract No. 4000125402/18/NL/NA). The research was also supported by the Action CA17134 SENSECO (Optical synergies for spatiotemporal sensing of scalable ecophysiological traits) funded by COST (European Cooperation in Science and Technology, www.cost.eu, accessed on: 8 January 2022). This publication is also the result of the project implementation: “Scientific support of climate change adaptation in agriculture and mitigation of soil degradation” (ITMS2014+313011W580) supported by the Integrated Infrastructure Operational Programme funded by the ERDF

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 beet and onion) and corresponding top-of-canopy (TOC) reflectance spectra acquired by the hyperspectral HyMap airborne sensor. First, commonly used water content index formulations were analysed and validated for the variety of crops, overall resulting in a R2 lower than 0.6. In an attempt to move towards more generically applicable indices, the two new CWC indices exploit the principal water absorption features in the near-infrared by using multiple bands sensitive to water content. We propose the Water Absorption Area Index (WAAI) as the difference between the area under the null water content of TOC reflectance (reference line) simulated with PROSAIL and the area under measured TOC reflectance between 911 and 1271 nm. We also propose the Depth Water Index (DWI), a simplified four-band index based on the spectral depths produced by the water absorption at 970 and 1200 nm and two reference bands. Both the WAAI and DWI outperform established indices in predicting CWC when applied to heterogeneous croplands, with a R2 of 0.8 and 0.7, respectively, using an exponential fit. However, these indices did not perform well for species with a low fractional vegetation cover (<30%). HyMap CWC maps calculated with both indices are shown for the Barrax region. The results confirmed the potential of using generically applicable indices for calculating CWC over a great variety of crops

Análisis de métodos de fusión de imágenes Landsat 8 sobre coberturas y uso del suelo en el municipio de Bahía de Banderas, Nayarit

The municipality of Bahía de Banderas, has opted to invest in the tourism sector as a way of development, in the last two decades has had an intense tourism development, so is undergoing a process of rapid urban growth and clutter; for this reason it is important to analyze the land use and land cover change by the municipality is happening. To do this, firstly, it's important identify the types of land use and land cover that has Bahía de Banderas, so that to carry out this activity satellite images Landsat 8 will be used, However, given the resolution that present these images, is necessary to optimise the quality of the spectral and space resolution, what with carries to use methods of fusion of images, by which in this work evaluated three methods (color normalized, principal component and Gram Schmidt), by means of the metric of quality: the ERGAS index and the index Q, with the end to determine the best method that facilitate the processes of classification of coverage and use of the floor in the municipality of Bahía de Banderas. It found that the Gram Schmidt which was showed better results spectrally both visually, in contrast to the other two methods, therefore for further work, it was decided to use the image resulting from this fusion method.El municipio de Bahía de Banderas, ha optado por invertir en el sector turístico como medio de desarrollo, en las últimas dos décadas ha tenido un intenso desarrollo turístico, por lo cual está experimentando un proceso de crecimiento urbano acelerado y desordenado; por esta razón es importante analizar los cambios de cobertura y uso del suelo por los que está pasando el municipio. Para ello, se debe, primeramente, identificar los tipos de cobertura y uso del suelo que tiene Bahía de Banderas, de modo que, para llevar a cabo esta actividad se utilizarán imágenes de satélite Landsat 8, sin embargo, dada la resolución que presentan estas imágenes, es necesario optimizar la calidad de la resolución espectral y espacial; lo que con lleva a utilizar métodos de fusión de imágenes, por lo cual en este trabajo se evaluaron tres métodos (color normalizado, componentes principales y Gram Schmidt), por medio de las métricas de calidad: índices ERGAS y el índice Q, con el fin de determinar el mejor método que facilite los procesos de clasificación de cobertura y uso del suelo en el municipio de Bahía de Banderas. Se encontró que el método de Gram Schmidt fue el que mostró mejores resultados tanto visualmente como espectralmente, por el contrario de los otros dos métodos; por la tanto, para trabajos posteriores, se utilizará la imagen resultante de este método de fusión

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 learning regression algorithm, i.e., Gaussian processes regression, and an active learning technique to estimate LAI, CCC and VWC of irrigated winter wheat. The established hybrid models of the three traits were validated against in-situ data of a wheat campaign in the Bonaerense valley, South of the Buenos Aires Province, Argentina, in the year 2020. We obtained good to highly accurate validation results with LAI: R2 = 0.92, RMSE = 0.43 m2 m−2, CCC: R2 = 0.80, RMSE = 0.27 g m−2 and VWC: R2 = 0.75, RMSE = 416 g m−2. The retrieval models were also applied to a series of S2 images, producing time series along the seasonal cycle, which reflected the effects of fertilizer and irrigation on crop growth. The associated uncertainties along with the obtained maps underlined the robustness of the hybrid retrieval workflow. We conclude that processing S2 imagery with optimised hybrid models allows accurate space-based crop traits mapping over large irrigated areas and thus can support agricultural management decisions.Fil: Caballero, Gabriel. Technological University of Uruguay (UTEC). Agri-Environmental Engineering; Uruguay. University of Valencia. Image Processing Laboratory (IPL); EspañaFil: Pezzola, Alejandro. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Hilario Ascasubi; ArgentinaFil: Winschel, Cristina Ines. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Hilario Ascasubi; ArgentinaFil: Casella, Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Clima y Agua; ArgentinaFil: Sanchez Angonova, Paolo Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Hilario Ascasubi; ArgentinaFil: Rivera Caicedo, Juan Pablo. CONACYT-UAN. Secretary of Research and Graduate Studies; MéxicoFil: Berger, Katja. University of Valencia. Image Processing Laboratory (IPL); España. Mantle Labs GmbH; AustriaFil: Verrelst, Jochem. University of Valencia. Image Processing Laboratory (IPL); EspañaFil: Delegido, Jesús. Universidad de Valencia. Image Processing Laboratory (IPL); Españ

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) top-of-atmosphere (TOA) reflectance data into crop traits. To achieve this, a training dataset was generated using the leaf-canopy RTM PROSAIL in combination with the atmospheric model 6SV. Gaussian process regression (GPR) retrieval models were then established for eight essential crop traits namely leaf chlorophyll content, leaf water content, leaf dry matter content, fractional vegetation cover, leaf area index (LAI), and upscaled leaf variables (i.e., canopy chlorophyll content, canopy water content and canopy dry matter content). An important pre-requisite for implementation into GEE is that the models are sufficiently light in order to facilitate efficient and fast processing. Successful reduction of the training dataset by 78% was achieved using the active learning technique Euclidean distance-based diversity (EBD). With the EBD-GPR models, highly accurate validation results of LAI and upscaled leaf variables were obtained against in situ field data from the validation study site Munich-North-Isar (MNI), with normalized root mean square errors (NRMSE) from 6% to 13%. Using an independent validation dataset of similar crop types (Italian Grosseto test site), the retrieval models showed moderate to good performances for canopy-level variables, with NRMSE ranging from 14% to 50%, but failed for the leaf-level estimates. Obtained maps over the MNI site were further compared against Sentinel-2 Level 2 Prototype Processor (SL2P) vegetation estimates generated from the ESA Sentinels' Application Platform (SNAP) Biophysical Processor, proving high consistency of both retrievals (R2 from 0.80 to 0.94). Finally, thanks to the seamless GEE processing capability, the TOA-based mapping was applied over the entirety of Germany at 20 m spatial resolution including information about prediction uncertainty. The obtained maps provided confidence of the developed EBD-GPR retrieval models for integration in the GEE framework and national scale mapping from S2-L1C imagery. In summary, the proposed retrieval workflow demonstrates the possibility of routine processing of S2 TOA data into crop traits maps at any place on Earth as required for operational agricultural applications

Preguntas frecuentes sobre frutales

Esta publicación contribuye solucionar las dudas de productores, técnicos y estudiantes en relación al manejo de los principales frutales del trópico Colombiano como Aguacate, cítricos, granadilla, guanábana, guayaba, mango, maracuya, piña, uchuva, mora, pitahaya y tomate de árbol

Colombian consensus recommendations for diagnosis, management and treatment of the infection by SARS-COV-2/ COVID-19 in health care facilities - Recommendations from expert´s group based and informed on evidence

La Asociación Colombiana de Infectología (ACIN) y el Instituto de Evaluación de Nuevas Tecnologías de la Salud (IETS) conformó un grupo de trabajo para desarrollar recomendaciones informadas y basadas en evidencia, por consenso de expertos para la atención, diagnóstico y manejo de casos de Covid 19. Estas guías son dirigidas al personal de salud y buscar dar recomendaciones en los ámbitos de la atención en salud de los casos de Covid-19, en el contexto nacional de Colombia