Stefan G. H. Simis

Stefan G. H. Simis
Plymouth Marine Laboratory | PML · Earth Observation Science and Applications

PhD, Docent

About

84
Publications
27,544
Reads
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3,080
Citations
Citations since 2016
47 Research Items
2056 Citations
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Introduction
Now working on inland and coastal water quality remote sensing at the Plymouth Marine Laboratory. Check out GloboLakes http://www.globolakes.ac.uk for which we are producing time-series of satellite observations for 1000 lakes worldwide! I still have some Baltic Sea work in the pipeline and I'm keeping an eye on Rflex for automated hyperspectral shipborne reflectance (http://sourceforge.net/projects/rflex/).
Additional affiliations
November 2014 - present
Plymouth Marine Laboratory
Position
  • GloboLakes: Global Observatory of Lake Responses to Environmental Change
Description
  • GloboLakes is a 5-yr research programme investigating the state of lakes and their response to climatic and other environmental drivers of change at a global scale... see http://www.globolakes.ac.uk
November 2014 - present
Plymouth Marine Laboratory
Position
  • Earth Observation Scientist (Inland Waters)
September 2014 - October 2014
University of Helsinki
Position
  • Aquatic Optics
Description
  • Aquatic Optics course for MSc and PhD students (2 cr)
Education
June 2014 - June 2014
University of Helsinki
Field of study
  • Docent in Aquatic Sciences
May 2002 - May 2006
Koninklijke Nederlandse Akademie van Wetenschappen
Field of study
  • Microbial Ecology, Bio-optics, Remote Sensing
September 1996 - April 2002
University of Amsterdam
Field of study
  • Biodiversity and Ecosystem Dynamics

Publications

Publications (84)
Article
Full-text available
Optical-biogeochemical relationships of particulate and dissolved organic matter are presented in support of remote sensing of the Baltic Sea pelagic. This system exhibits strong seasonality in phytoplankton community composition and wide gradients of chromophoric dissolved organic matter (CDOM), properties which are poorly handled by existing remo...
Article
Full-text available
We studied the loadings of dissolved organic matter (DOM) and nutrients from the Neva River into the Eastern Gulf of Finland, as well as their distribution within the salinity gradient. Concentrations of dissolved organic carbon (DOC) ranged from 390 to 840 μM, and were related to absorption of colored DOM (CDOM) at 350 nm, aCDOM(350), ranging from...
Article
Full-text available
Phytoplankton spring bloom phenology was derived from a 15-year time series (2000–2014) of ship-of-opportunity chlorophyll a fluorescence observations collected in the Baltic Sea through the Alg@line network. Decadal trends were analysed against inter-annual variability in bloom timing and intensity, and environmental drivers (nutrient concentratio...
Article
Full-text available
Satellite remote sensing of chlorophyll-a concentration (chla) in oligotrophic and mesotrophic lakes faces uncertainties from sources such as atmospheric correction, complex inherent optical property compositions, and imperfect algorithmic retrieval. To improve chla estimation in oligo- and mesotrophic lakes, we developed Bayesian probabilistic neu...
Article
Full-text available
Remote sensing product uncertainties for phytoplankton chlorophyll-a (chla) concentration in oligotrophic and mesotrophic lakes and reservoirs were characterised across 13 existing algorithms using an in situ dataset of water constituent concentrations, inherent optical properties (IOPs) and remote-sensing reflectance spectra Rrsλ collected from 53...
Article
Full-text available
Consumer cameras, especially on smartphones, are popular and effective instruments for above-water radiometry. The remote sensing reflectance R rs is measured above the water surface and used to estimate inherent optical properties and constituent concentrations. Two smartphone apps, HydroColor and EyeOnWater, are used worldwide by professional and...
Article
Full-text available
Compared to other methods to monitor and detect cyanobacteria in phytoplankton populations, fluorometry gives rapid, robust and reproducible results and can be used in situ. Fluorometers capable of providing biomass estimates and physiological information are not commonly optimized to target cyanobacteria. This study provides a detailed overview of...
Article
Full-text available
In situ hyperspectral remote-sensing reflectance (Rrs(λ)) is used to derive water quality products and perform autonomous monitoring of aquatic ecosystems. Conventionally, above-water Rrs(λ) is estimated from three spectroradiometers which measure downwelling planar irradiance (Ed(λ)), sky radiance (Ls(λ)), and total upwelling radiance (Lt(λ)), wit...
Article
Estimating the concentration of water constituents by optical remote sensing assumes absorption and scattering processes to be uniform over the observation depth. Using hyperspectral reflectance, we present a method to direct the retrieval of the backscattering coefficient (bb(λ)) from reflectance (> 600 nm) towards wavebands where absorption by wa...
Article
Full-text available
Constructing multi-source satellite-derived water quality (WQ) products in inland and nearshore coastal waters from the past, present, and future missions is a long-standing challenge. Despite inherent differences in sensors' spectral capability, spatial sampling, and radiometric performance, research efforts focused on formulating, implementing, a...
Article
Satellite remote sensing data are important to the study of environment problems at a global scale. The GloboLakes project aimed to use satellite remote sensing data to investigate the response of the major lakes on Earth to environmental conditions and change. The main challenge to statistical modelling is the identification of the spatial structu...
Article
Full-text available
Ocean colour (OC) remote sensing is an important tool for monitoring phytoplankton in the global ocean. In optically complex waters such as the Baltic Sea, relatively efficient light absorption by substances other than phytoplankton increases product uncertainty. Sentinel-3 OLCI-A, Suomi-NPP VIIRS and MODIS-Aqua OC radiometric products were assesse...
Article
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Satellite remote sensing can provide indicative measures of environmental variables that are crucial to understanding the environment. The spatial and temporal coverage of satellite images allows scientists to investigate the changes in environmental variables in an unprecedented scale. However, identifying spatiotemporal patterns from such images...
Article
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Retrieval of the phycocyanin concentration (PC), a characteristic pigment of, and proxy for, cyanobacteria biomass, from hyperspectral satellite remote sensing measurements is challenging due to uncertainties in the remote sensing reflectance (∆R rs) resulting from atmospheric correction and instrument radiometric noise. Although several individual...
Article
Full-text available
Satellite product uncertainty estimates are critical for the further development and evaluation of remote sensing algorithms, as well as for the user community (e.g., modelers, climate scientists, and decision-makers). Optical remote sensing of water quality is affected by significant uncertainties stemming from correction for atmospheric effects a...
Article
High resolution imaging spectrometers are prerequisite to address significant data gaps in inland optical water quality monitoring. In this work, we provide a data-driven alignment of chlorophyll-a and turbidity derived from the Sentinel-2 MultiSpectral Imager (MSI) with corresponding Sentinel-3 Ocean and Land Colour Instrument (OLCI) products. For...
Article
Full-text available
Cyanobacterial harmful algal blooms are an increasing threat to coastal and inland waters. These blooms can be detected using optical radiometers due to the presence of phycocyanin (PC) pigments. The spectral resolution of best-available multispectral sensors limits their ability to diagnostically detect PC in the presence of other photosynthetic p...
Article
Full-text available
Phytoplankton photosynthetic physiology can be investigated through single-turnover variable chlorophyll fluorescence (ST-ChlF) approaches, which carry unique potential to autonomously collect data at high spatial and temporal resolution. Over the past decades, significant progress has been made in the development and application of ST-ChlF methods...
Preprint
Full-text available
Phytoplankton photosynthetic physiology can be investigated through single-turnover variable chlorophyll fluorescence (ST-ChlF) approaches, which carry unique potential to autonomously collect data at high spatial and temporal resolution. Over the past decades, significant progress has been made in the development and application of ST-ChlF methods...
Article
Full-text available
Common aquatic remote sensing algorithms estimate the trophic state (TS) of inland and nearshore waters through the inversion of remote sensing reflectance (Rrs (λ)) into chlorophyll-a (chla) concentration. In this study we present a novel method that directly inverts Rrs (λ) into TS without prior chla retrieval. To successfully cope with the optic...
Article
Full-text available
Atmospheric correction over inland and coastal waters is one of the major remaining challenges in aquatic remote sensing, often hindering the quantitative retrieval of biogeochemical variables and analysis of their spatial and temporal variability within aquatic environments. The Atmospheric Correction Intercomparison Exercise (ACIX-Aqua), a joint...
Article
Full-text available
Nutrient pollution causes frequent blooms of potentially harmful cyanobacteria in Lake Peipsi (Estonia/Russia). Although external nutrient loading has reduced since the 1990s, lake water quality has barely improved, and eutrophication is still considered a threat to lake biota and water usage. To understand the recovery dynamics of the lake it is n...
Data
Matchups between AERONET-OC and OLI/Landsat-8, processed with ACOLITE as presented in Vanhellemont (2019). They were used in the present study to extract spectra of AC errors for ACOLITE-OLI and are made available for similar use in other studies. Block of columns per wavelength are: AERONET-OC, ACOLITE-OLI Exponential algorithm, ACOLITE-OLI DSF a...
Data
The following is available: Section S1: Analytical composite contra-band retrieval, Figure S1: Performance of retrieval of the analytical composite band, Section S2: Application of the current OLI orange contra-band algorithm to clear waters, Figure S2: Performance of retrieval of the current OLI orange contra-band with clear waters, Section S3: Ad...
Article
Full-text available
The Operational Land Imager (OLI) onboard Landsat 8 has found successful application in inland and coastal water remote sensing. Its radiometric specification and high spatial resolution allows quantification of water-leaving radiance while resolving small water bodies. However, its limited multispectral band set restricts the range of water qualit...
Article
Full-text available
Aquaculture increasingly contributes to global seafood production, requiring new farm sites for continued growth. In France, oyster cultivation has conventionally taken place in the intertidal zone, where there is little or no further room for expansion. Despite interest in moving production further offshore, more information is needed regarding th...
Technical Report
Full-text available
Executive summary and recommendations The EU Water Framework Directive 1 (WFD) is an ambitious legislation framework to achieve good ecological and chemical status for all surface waters and good quantitative and chemical status for groundwater by 2027. A total of 111,062 surface waterbodies are presently reported on under the Directive, 46% of whi...
Technical Report
Full-text available
Space available for aquaculture, in Europe as elsewhere, is in limited supply and high demand. Additional tools are required to support the identification of potential new sites and to assess their suitability and sustainability for various aquaculture segments. In this report, various aquaculture indicators that were derived using satellite Earth...
Poster
Full-text available
This poster presents the results of a validation study on the calculated orange contra-band (613 nm) for OLI/Landsat 8 against the orange band (620 nm) of OLCI/Sentinel-3. The approach forces atmospheric compensation (AC) bias to be equal for each sensor and scene, allowing to compare the retrieved water leaving signal directly. We find that OLI or...
Article
Full-text available
The relatively high spatial resolution, short revisit time and red-edge spectral band (705 nm) of the ESA Sentinel-2 Multi Spectral Imager makes this sensor attractive for monitoring water quality of coastal and inland waters. Reliable atmospheric correction is essential to support routine retrieval of optically active substance concentration from...
Conference Paper
Full-text available
The Operational Land Imager (OLI) onboard Landsat 8 has found successful application in fresh and coastal water remote sensing. Its radiometric specification and high spatial resolution allows to quantify the dim water leaving radiance while resolving small water bodies and the variability in highly heterogeneous systems. However, its specific comb...
Presentation
Full-text available
The potential for and productivity of shellfish aquaculture is strongly influenced by sea surface temperature (SST), and the concentration and nature of suspended particulate matter (SPM), which can both be monitored from space to determine shellfish growth conditions. Phytoplankton is a main food source for suspension-feeding bivalves. In too high...
Presentation
Full-text available
In Europe, oyster production has historically taken place in intertidal zones. Shellfish farms already occupy large extents of intertidal space, and sometimes have for more than a century. The possibility of expanding shellfish aquaculture in intertidal areas is therefore spatially limited, and is also constrained by carrying capacity, water qualit...
Article
Full-text available
Existing remote-sensing algorithms to estimate the phycocyanin (PC) concentration in turbid inland waters have high associated uncertainties, especially at low PC concentrations in diverse phytoplankton communities. This paper provides the theoretical framework for a four-band semi-analytical algorithm (FBA_PC) which isolates PC absorption from sec...
Article
Full-text available
Inland and coastal waterbodies are critical components of the global biosphere. Timely monitoring is necessary to enhance our understanding of their functions, the drivers impacting on these functions and to deliver more effective management. The ability to observe waterbodies from space has led to Earth observation (EO) becoming established as an...
Article
The Baltic Sea is a semi-enclosed sea that is optically dominated by coloured dissolved organic material (CDOM) and has relatively low sun elevation which makes accurate ocean colour remote sensing challenging in these waters. The high absorption, low scattering properties of the Baltic Sea are representative of other optically similar water bodies...
Article
Full-text available
Sky reflectance Rsky is used to correct in situ reflectance measurements in the remote detection of water color. We analyzed the directional and spectral variability in Rsky due to adjacency effects against an atmospheric radiance model. The analysis is based on one year of semi-continuous Rsky observations that were recorded in two azimuth directi...
Article
Full-text available
A three-component reflectance model (3C) is applied to above-water radiometric measurements to derive remote-sensing reflectance Rrs (λ). 3C provides a spectrally resolved offset Δ(λ) to correct for residual sun and sky radiance (Rayleigh- and aerosol-scattered) reflections on the water surface that were not represented by sky radiance measurements...
Poster
Full-text available
The H2020 project EOMORES will develop operational monitoring and reporting services for inland and coastal water quality based on a combination of the most up-to-date satellite data, innovative in situ instruments and ecological models. Lakes, reservoirs and coastal water bodies constitute essential components of the hydrological and biogeochemica...
Data
Optical models resulting from the analyses presented in the paper are provided in detail in the supplementary data (S1-11 Tables) including detailed value distributions and statistics. An extensive dataset of remote-sensing reflectance (R rs , units sr-1) spectra is additionally provided here (S1 Dataset) based on forward modelling of mean concentr...
Article
This study presents the results of the first field application of a flow-through multi-wavelength Fast Repetition Rate fluorometer (FRRF) equipped with two excitation channels (458 and 593 nm). This device aims to improve the measurement of mixed cyanobacteria and algae community's photosynthetic parameters and was designed to be easily incorporate...
Article
Full-text available
Atmospheric correction of remotely sensed imagery of inland water bodies is essential to interpret water-leaving radiance signals and for the accurate retrieval of water quality variables. Atmospheric correction is particularly challenging over inhomogeneous water bodies surrounded by comparatively bright land surface. We present results of AisaFEN...
Article
Full-text available
Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labor intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine mo...
Conference Paper
Full-text available
Many coastal seas and inland waters have water properties which are outside the normal conditions used for ocean colour algorithm design. In the ESA-funded " Case-2 Extreme " project, retrieval methods for OC products in extreme Case-2 waters are developed, tested, implemented, and validated primarily with reference to the capabilities of the Senti...
Article
The toxic dinoflagellate Alexandrium ostenfeldii is the only bioluminescent bloom-forming phytoplankton in coastal waters of the Baltic Sea. We analysed partial luciferase gene (lcf) sequences and bioluminescence production in Baltic A. ostenfeldii bloom populations to assess the distribution and consistency of the trait in the Baltic Sea, and to e...
Article
Full-text available
Phytoplankton spring bloom phenology was derived from a 15-year time-series (2000-2014) of ship-of-opportunity chlorophyll-a fluorescence observations in the Baltic Sea. Decadal trends were analysed against inter-annual variability in bloom timing and intensity, and environmental drivers (nutrient concentration, temperature, radiation level, wind s...
Conference Paper
Full-text available
Poster presented at SmartSound Plymouth Workshop 2015. Recent high spatial resolution Earth observing sensors allow us to observe spatially heterogeneous systems in the near-shore environment. Thus, remote sensing starts to address environmental challenges within the first kilometres from the coastline and of highest relevance to coastal communiti...
Article
Full-text available
Light (20-450 μmol photons m-2 s-1), temperature (3-11°C) and inorganic nutrient composition (nutrient replete and N, P and Si limitation) were manipulated to study their combined influence on growth, stoichiometry (C:N:P:Chl a) and primary production of the cold water diatom Chaetoceros wighamii. During exponential growth, the maximum growth rate...
Article
Full-text available
This study presents a methods evaluation and intercalibration of active fluorescence-based measurements of the quantum yield ( ) and absorption coefficient ( ) of photosystem II (PSII) photochemistry. Measurements of , , and irradiance (E) can be scaled to derive photosynthetic electron transport rates ( ), the process that fuels phytoplankton carb...
Article
Full-text available
Cyanobacterial bloom detection from flow-through optical sensors on ships-of-opportunity (’ferryboxes’) is challenging in periods of strong stratification and due to varying cell physiology and phytoplankton community composition. Wavelet coherence analysis between ferrybox parameters (chlorophyll-a fluorescence, phycocyanin fluorescence, turbidity...