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A. Spinosa

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Doctoral thesis (2026) - A. Spinosa, A.W. Heemink, H.X. Lin, G.Y.H. El Serafy
This thesis investigates how in situ and satellite remote sensing data, combined via statistical and data-driven approaches, can be used to monitor coastal and terrestrial ecosystems in a scalable, cost-efficient, and scientifically robust way. The main objective of this work was to develop tools supporting the assessment and understanding of ecosystem health by exploiting the growing availability of Earth observation data. This thesis work revolves around two main facets: (i) the development of cost-efficient spatially scalable tools and (ii) the investigation of data integration of different data sources.
The research builds on satellite remote sensing data from the Copernicus mission (Sentinel-1 and Sentinel-2 data), complemented by in situ measurements from other open source repositories (such as Integrated Carbon Observation Systems (ICOS) and the European Fluxes Database Cluster) and additional remotely sensed data. All the models and algorithms used or developed during the research are published and available as open source.
The thesis starts by demonstrating the potential of satellite data as a complementary alternative to traditional in situ measurements. This was done by constructing a modeling framework for the retrieval of the shoreline position from Sentinel-1 data. The model is based on the Otsu method, a global thresholding method optimal for the recognition of the water/land interface. The resulting shorelines were validated against video monitoring systems-derived shorelines, showing sub-pixel accuracy. The results highlighted that satellite data may represent a cost-effective and low-maintenance complementary alternative to in situ measurements, especially in areas lacking dense ground-based instrumentation.... ...

Evaluating the versatility of SARIMAX, XGBoost, and LSTM using ICOS FLUXNET and Sentinel-2 data

Journal article (2026) - Anna Spinosa, Karisma Karisma, Marieke A. Eleveld, Mario Alberto Fuentes-Monjaraz, Valeria Mobilia, Ulf Mallast, Johannes Peterseil, Ghada El Serafy
Predicting Gross Primary Productivity (GPP) is key for understanding ecosystem health and quantifying the global carbon cycle. While data-driven models have shown strong performance in capturing GPP dynamics at specific sites, their ability to generalize across ecosystems without site-specific recalibration remains largely untested. This study addresses this gap by evaluating the applicability of XGBoost and LSTM models in estimating GPP across different European ecosystems. We developed a unified (cross-site) modeling framework that integrates in-situ eddy covariance observations and Sentinel-2–derived vegetation indices using incremental learning. Models’ performance was assessed via: (i) site-specific models, developed to capture individual site characteristics, and (ii) cross-site generalization, including evaluation on an independent dataset of unseen ecosystems. SARIMAX is included as a site-specific statistical benchmark for comparison. Our findings indicate that XGBoost consistently outperformed the other models, achieving site-specific R2 values above 0.90 in forest and grassland ecosystems and an average R2 of 0.72 across unseen sites (range 0.66–0.78). LSTM exhibited better accuracy in predicting GPP peaks at site-specific level, particularly in cropland and forest ecosystems. At site-level, SARIMAX showed comparable performance to XGBoost but struggled in capturing the rapid temporal variation of GPP. These findings demonstrate the feasibility of a data-driven framework for cross-site GPP monitoring within European flux-tower networks, making a first step toward transferable GPP prediction without site-specific recalibration. ...
Journal article (2026) - A. Spinosa, More Authors
Artificial Intelligence (AI) is advancing at an unprecedented pace, offering transformative opportunities for marine research, fisheries management, environmental governance and policy development. Particularly in the context of the interconnected data needs of ecosystem management and biodiversity conservation, these technologies can enhance data acquisition, processing and decision support, enabling more integrated approaches to ecosystem management and biodiversity conservation. Yet their adoption in these domains remains limited by the absence of coherent frameworks that ensure transparency, validation and ethical alignment with ecological and socio-economic sustainability goals. This work proposes a comprehensive framework built on three critical pillars for trustworthy AI: socio-economic and legal viability, data governance and technical and scientific robustness. On the one hand it aims to be a guideline for developer teams. On the other hand, it aims to be a guideline for final users (e.g., industry and managers) for designing the requirements and evaluating such systems. The first pillar underscores the need for AI systems that are cost-effective, scalable, environmentally sustainable and legally supported, balancing short-term costs with long-term social and ecological benefits. The second stresses adherence to fair, reliable and ethical access to digital resources, recognising that without strong governance data and algorithms risk becoming fragmented or misused. The third pillar addresses the necessity of rigorous validation across entire AI pipelines, including preprocessing, model evaluation and benchmarking against alternative ground truths, to ensure reliability in real-world applications. Together, these pillars provide a blueprint for developing ethical, reliable and policy-relevant AI systems that can strengthen trust, improve sustainability and guide decision-making across marine science, fisheries, environmental management and European legislation. ...
Conference paper (2024) - Anna Spinosa, Marieke Eleveld, Ulf Mallast, Johannes Peterseil, Valeria Mobilia, Karisma Karisma, Mario Alberto Fuentes-Monjaraz, Ghada El Serafy
This study addresses the challenges posed by climatic changes and biodiversity loss to ecosystem stability, by quantifying gross primary production (GPP) changes. An improved earth observation product is obtained by integrating in-situ and remote sensing data via data-driven models. Employing a user-centered strategy, our methodology builds on users' engagement, ensuring both the identification of user needs and practical product demonstrations. With GEOSS as central and integrated stakeholder, we strive for a broad interoperability and accessibility of generated outcomes. The project outcomes include a curated dataset with FAIR metadata, openly available code, and reports for reproducibility, contributing to the broader Earth Intelligence supply chain. ...
Journal article (2023) - Anna Spinosa, Mario A. Fuentes-Monjaraz, Ghada El Serafy
The conservation, restoration and sustainable use of wetlands is the target of several international agreements, among which are the Sustainable Development Goals (SDGs). Earth Observation (EO) technologies can assist national authorities in monitoring activities and the environmental status of wetlands to achieve these targets. In this study, we assess the capabilities of the Sentinel-2 instrument to model Gross Primary Productivity (GPP) as a proxy for the monitoring of ecosystem health. To estimate the spatial and temporal variation of GPP, we develop an empirical model correlating in situ measurements of GPP, eight Sentinel-2 derived vegetation indexes (VIs), and different environmental drivers of GPP. The model automatically performs an interdependency analysis and selects the model with the highest accuracy and statistical significance. Additionally, the model is upscaled across larger areas and monthly maps of GPP are produced. The study methodology is applied in a marsh ecosystem located in Doñana National Park, Spain. In this application, a combination of the red-edge chlorophyll index (CLr) and rainfall data results in the highest correlation with in situ measurements of GPP and is used for the model formulation. This yields a coefficient of determination (R 2) of 0.93, Mean Absolute Error (MAE) equal to 0.52 gC m −2 day −1, Root Mean Squared Error (RMSE) equal to 0.63 gC m −2 day −1, and significance level p < 0.05. The model outputs are compared with the MODIS GPP global product (MOD17) for reference; an enhancement of the estimation of GPP is found in the applied methodology. ...
Journal article (2021) - Anna Spinosa, Alex Ziemba, Alessandra Saponieri, Leonardo Damiani, Ghada El Serafy
Remote sensing and satellite imagery have become commonplace in efforts to monitor and model various biological and physical characteristics of the Earth. The land/water interface is a continually evolving landscape of high scientific and societal interest, making the mapping and monitoring thereof particularly important. This paper aims at describing a new automated method of shoreline position detection through the utilization of Synthetic Aperture Radar (SAR) images derived from European Space Agency satellites, specifically the operational SENTINEL Series. The resultant delineated shorelines are validated against those derived from video monitoring systems and in situ monitoring; a mean distance of 1 and a maximum of 3.5 pixels is found. ...
Review (2021) - Ghada Y.H. El Serafy, Blake A. Schaeffer, Merrie-Beth Neely, Anna Spinosa, Daniel Odermatt, Kathleen C. Weathers, Theo Baracchini, Damien Bouffard, Laurence Carvalho, More authors...
Water quality measures for inland and coastal waters are available as discrete samples from professional and volunteer water quality monitoring programs and higher-frequency, near-continuous data from automated in situ sensors. Water quality parameters also are estimated from model outputs and remote sensing. The integration of these data, via data assimilation, can result in a more holistic characterization of these highly dynamic ecosystems, and consequently improve water resource management. It is becoming common to see combinations of these data applied to answer relevant scientific questions. Yet, methods for scaling water quality data across regions and beyond, to provide actionable knowledge for stakeholders, have emerged only recently, particularly with the availability of satellite data now providing global coverage at high spatial resolution. In this paper, data sources and existing data integration frameworks are reviewed to give an overview of the present status and identify the gaps in existing frameworks. We propose an integration framework to provide information to user communities through the the Group on Earth Observations (GEO) AquaWatch Initiative. This aims to develop and build the global capacity and utility of water quality data, products, and information to support equitable and inclusive access for water resource management, policy and decision making. ...

An Application for Aquaculture Operations

Journal article (2020) - Nithin Achutha Shettigar, Biswa Bhattacharya, Lörinc Mészáros, Anna Spinosa, Ghada El Serafy
During the past decades, the aquaculture industry has developed rapidly, due to drop in wild fish catch. Water quality variables play major role in aquaculture operations, specifically seawater temperature has major impact on the metabolism of the fish species and therefore on the growth rate too. Since the fish farming business relies on the growth rate of the species to plan and operate the farm, seawater temperature becomes crucial information. With the availability of hydrodynamic modeling tools and global ocean information source such as Copernicus Marine Environment Monitoring Service (CMEMS), seawater temperature can be simulated for practically any coast with dynamic downscaling approach. However, the simulated data needs to be assessed for uncertainties for enabling informed decision making using such model predictions. In this paper, a coastal 3D hydrodynamic model aiming at simulating seawater temperature is developed for the southern Aegean Sea, Greece using the Delft3D Flexible Mesh modeling tool. Seawater temperature is impacted by atmospheric forces; therefore, uncertainties are assessed for seawater temperature using ensemble atmospheric forcing functions of the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5. Spatial analysis of the uncertainty indicates regions of different seawater temperature behavior within the model domain. Seasonal behavior of the vertical temperature gradient suggests that farms need to adapt different operational strategies in different seasons to make best use of the seawater temperature. The application of CMEMS data along with ECMWF ERA5 ensemble atmospheric forcing members proves to be beneficial in analyzing the uncertainties both in spatial and vertical gradient of seawater temperature. ...