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1.	Soja-Woźniak, Monika, et al. (författare) A Novel Statistical Approach for Ocean Colour Estimation of Inherent Optical Properties and Cyanobacteria Abundance in Optically Complex Waters 2017 Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 9:4 Tidskriftsartikel (refereegranskat)abstract Eutrophication is an increasing problem in coastal waters of the Baltic Sea. Moreover, algal blooms, which occur every summer in the Gulf of Gdansk can deleteriously impact human health, the aquatic environment, and economically important fisheries, tourism, and recreation industries. Traditional laboratory-based techniques for water monitoring are expensive and time consuming, which usually results in limited numbers of observations and discontinuity in space and time. The use of hyperspectral radiometers for coastal water observation provides the potential for more detailed remote optical monitoring. A statistical approach to develop local models for the estimation of optically significant components from in situ measured hyperspectral remote sensing reflectance in case 2 waters is presented in this study. The models, which are based on empirical orthogonal function (EOF) analysis and stepwise multilinear regression, allow for the estimation of parameters strongly correlated with phytoplankton (pigment concentration, absorption coefficient) and coloured detrital matter abundance (absorption coefficient) directly from reflectance spectra measured in situ. Chlorophyll a concentration, which is commonly used as a proxy for phytoplankton biomass, was retrieved with low error (median percent difference, MPD = 17%, root mean square error RMSE = 0.14 in log(10) space) and showed a high correlation with chlorophyll a measured in situ (R = 0.84). Furthermore, phycocyanin and phycoerythrin, both characteristic pigments for cyanobacteria species, were also retrieved reliably from reflectance with MPD = 23%, RMSE = 0.23, R-2 = 0.77 and MPD = 24%, RMSE = 0.15, R-2 = 0.74, respectively. The EOF technique proved to be accurate in the derivation of the absorption spectra of phytoplankton and coloured detrital matter (CDM), with R-2 (lambda) above 0.83 and RMSE around 0.10. The approach was also applied to satellite multispectral remote sensing reflectance data, thus allowing for improved temporal and spatial resolution compared with the in situ measurements. The EOF method tested on simulated Medium Resolution Imaging Spectrometer (MERIS) or Ocean and Land Colour Instrument (OLCI) data resulted in RMSE = 0.16 for chl-a and RMSE = 0.29 for phycocyanin. The presented methods, applied to both in situ and satellite data, provide a powerful tool for coastal monitoring and management.
2.	Alikas, Krista, et al. (författare) Improved retrieval of Secchi depth for optically-complex waters using remote sensing data 2017 Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 77, s. 218-227 Tidskriftsartikel (refereegranskat)abstract Water transparency is one of the ecological indicators for describing water quality and the underwater light field which determines its productivity. In the European Water Framework Directive (WFD) as well as in the European Marine Strategy Framework Directive (MSFD) water transparency is used for ecological status classification of inland, coastal and open sea waters and it is regarded as an indicator for eutrophication in Baltic Sea management (HELCOM, 2007). We developed and compared different empirical and semi-analytical algorithms for lakes and coastal Nordic waters to retrieve Secchi depth (Z(SD)) from remote sensing data (MERIS, 300 m resolution).The algorithms were developed in water bodies with high coloured dissolved organic matter absorption (a(CNOM)(442) ranging 1.7-4.0 m(-1)), Chl a concentration (0.5-73 mg m(-3)) and total suspended matter (0.7-37.5 g m(-3)) and validated against an independent data set over inland and coastal waters (0.6 m < Z(SD) < 14.8 m). The results indicate that for empirical algorithms, using longer wavelengths in the visible spectrum as a reference band decreases the RMSE and increases the coefficient of determination (R-2). The accuracy increased (R-2 = 0.75, RMSE = 1.33 m, n = 134) when Z(SD) was retrieved via an empirical relationship between Z(SD) and K-d (490). The best agreement with in situ data was attained when Z(SD) was calculated via both the diffuse and the beam attenuation coefficient (R-2 = 0.89, RMSE = 0.77 m, n = 89). The results demonstrate that transparency can be retrieved with high accuracy over various optical water types by the means of ocean color remote sensing, improving both the spatial and temporal coverage. The satellite derived Z(SD) product could be therefore used as an additional source of information for WFD and MSFD reporting purposes.
3.	Alikas, Krista, et al. (författare) Robust remote sensing algorithms to derive the diffuse attenuation coefficient for lakes and coastal waters 2015 Ingår i: Limnology and Oceanography. - : Wiley. - 1541-5856. ; 13:8, s. 402-415 Tidskriftsartikel (refereegranskat)abstract In this study, empirical and semianalytical algorithms are developed and compared for optically complex waters to retrieve the diffuse attenuation coefficient of downwelling irradiance (Kd(lambda)) from satellite data. In the first approach, a band ratio algorithm was used. Various sets of MERIS band ratios were tested to achieve the best estimates for K-d(490) based on the in situ dataset which was measured in Nordic lakes (oligotrophic to eutrophic conditions). In the second approach, K-d(490) was expressed as a function of inherent optical properties which were retrieved from MERIS standard products. The algorithms from both approaches were tested against an independent data set and validated in optically complex coastal waters in the Baltic Sea and in Nordic lakes with high concentrations of coloured dissolved organic matter (0.3 < a(cdom)(442) m(-1) < 4.5), chlorophyll a (Chl a) (0.7< C-Chl a(mg m(-3))< 67.5) and total suspended matter (TSM) (0.5 < C-TSM(g m(-3)) < 26.4). MERIS-derived K-d(490) values showed reliable estimates in case of both methods. The results indicate that for band ratio algorithms, the root mean square error (RMSE) decreases and the coefficient of determination (R-2) increases when using longer wavelengths in the visible spectrum as a reference band. It was found that the best estimates were retrieved from MERIS data when using the ratio of R-rs(490)/R-rs(709) for coastal waters (K-d(490) < 2.5 m(-1)) and the ratio R-rs(560)/R-rs(709) for more turbid inland waters (Kd(490) > 2.5 m(-1)). As a result, a combined band ratio algorithm was developed, which provides a promising approach R-2 = 0.98, RMSE= 17%, N = 34, p < 0.05) for estimating K-d(490) over a wide range of values (0.3-6.1 m(-1)).
4.	Andersson, Agneta, et al. (författare) Influence of allochthonous dissolved organic matter on pelagic basal production in a northerly estuary 2018 Ingår i: Estuarine, Coastal and Shelf Science. - : Elsevier. - 0272-7714 .- 1096-0015. ; 204, s. 225-235 Tidskriftsartikel (refereegranskat)abstract Phytoplankton and heterotrophic bacteria are key groups at the base of aquatic food webs. In estuaries receiving riverine water with a high content of coloured allochthonous dissolved organic matter (ADOM), phytoplankton primary production may be reduced, while bacterial production is favoured. We tested this hypothesis by performing a field study in a northerly estuary receiving nutrient-poor, ADOM-rich riverine water, and analyzing results using multivariate statistics. Throughout the productive season, and especially during the spring river flush, the production and growth rate of heterotrophic bacteria were stimulated by the riverine inflow of dissolved organic carbon (DOC). In contrast, primary production and photosynthetic efficiency (i.e. phytoplankton growth rate) were negatively affected by DOC. Primary production related positively to phosphorus, which is the limiting nutrient in the area. In the upper estuary where DOC concentrations were the highest, the heterotrophic bacterial production constituted almost 100% of the basal production (sum of primary and bacterial production) during spring, while during summer the primary and bacterial production were approximately equal. Our study shows that riverine DOC had a strong negative influence on coastal phytoplankton production, likely due to light attenuation. On the other hand DOC showed a positive influence on bacterial production since it represents a supplementary food source. Thus, in boreal regions where climate change will cause increased river inflow to coastal waters, the balance between phytoplankton and bacterial production is likely to be changed, favouring bacteria. The pelagic food web structure and overall productivity will in turn be altered. (C) 2018 The Authors. Published by Elsevier Ltd.
5.	Andersson, Agneta, et al. (författare) Marked impact of allochthonous dissolved organic matter on estuarine primary and bacterial production Annan publikation (övrigt vetenskapligt/konstnärligt)
6.	Beltrán-Abaunza, José M., et al. (författare) Evaluation of MERIS products from Baltic Sea coastal waters rich in CDOM 2014 Ingår i: Ocean Science. - : Copernicus GmbH. - 1812-0784 .- 1812-0792. ; 10:3, s. 377-396 Tidskriftsartikel (refereegranskat)abstract In this study, retrievals of the medium resolution imaging spectrometer (MERIS) reflectances and water quality products using four different coastal processing algorithms freely available are assessed by comparison against sea-truthing data. The study is based on a pair-wise comparison using processor-dependent quality flags for the retrieval of valid common macro-pixels. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data, such as the Swedish coastal and lake monitoring system (http://vattenkvalitet.se). The results show that the pre-processing with the Improved Contrast between Ocean and Land (ICOL) processor, correcting for adjacency effects, improves the retrieval of spectral reflectance for all processors. Therefore, it is recommended that the ICOL processor should be applied when Baltic coastal waters are investigated. Chlorophyll was retrieved best using the FUB (Free University of Berlin) processing algorithm, although overestimations in the range 18-26.5 %, dependent on the compared pairs, were obtained. At low chlorophyll concentrations (< 2.5 mg m(-3)), data dispersion dominated in the retrievals with the MEGS (MERIS ground segment processor) processor. The lowest bias and data dispersion were obtained with MEGS for suspended particulate matter, for which overestimations in the range of 8-16% were found. Only the FUB retrieved CDOM (coloured dissolved organic matter) correlate with in situ values. However, a large systematic underestimation appears in the estimates that nevertheless may be corrected for by using a local correction factor. The MEGS has the potential to be used as an operational processing algorithm for the Himmerfjarden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in the presence of high CDOM attenuation.
7.	Beltrán-Abaunza, José M., 1971- (författare) Remote sensing in optically complex waters : water quality assessment using MERIS data 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract This PhD study focusses on the use of MEdium Resolution Imaging Spectrometer (MERIS) data for reliable and quantitative water-quality assessment of optically-complex waters (lake, brackish and coastal waters). The thesis is divided into two parts: A. intercalibration of reflectance measurements in different optically-complex water bodies (Paper I), and validation of various satellite processing algorithms for the coastal zone (Paper II). B. Applications: the use of MERIS data in integrated coastal zone management mostly using Himmerfjärden bay as an example.Himmerfjärden bay is one of the most frequently monitored coastal areas in the world and it is also the recipient of a large urban sewage treatment plant, where a number of full-scale nutrient management experiments have been conducted to evaluate the ecological changes due to changes in nutrient schemes in the sewage plant.Paper I describes the development and assessment of a new hyperspectral handheld radiometer for in situ sampling and validation of remote sensing reflectance. The instrument is assessed in comparison with readily available radiometers that are commonly used in validation.Paper II has a focus on the validation of level 2 reflectance and water products derived from MERIS data. It highlights the importance of calibration and validation activities, and the current accuracy and limitations of satellite products in the coastal zone. Bio-optical in situ data is highlighted as one of the key components for assessing the reliability of current and future satellite missions. Besides suspended particulate matter (SPM), the standard MERIS products have shown to be insufficient to assure data quality retrieval for Baltic Sea waters. Alternative processors and methods such as those assessed and developed in this thesis therefore will have to be put in place in order to secure the success of future operational missions, such as Sentinel-3.The two presented manuscripts in the applied part B of the thesis (paper III and IV), showed examples on the combined use of in situ measurements with optical remote sensing to support water quality monitoring programs by using turbidity and suspended particulate matter as coastal indicators (manuscript III). The article also provides a new turbidity algorithm for the Baltic Sea and a robust and cost-efficient method for research and management. A novel approach to improve the quality of the satellite-derived products in the coastal zone was demonstrated in manuscript IV. The analysis included, the correction for adjacency effects from land and an improved pixel quality screening. The thesis provides the first detailed spatio-temporal description of the evolution of phytoplankton blooms in Himmerfjärden bay using quality-assured MERIS data, thus forwarding our understanding of ecological processes in in Swedish coastal waters.It must be noted that monitoring from space is not a trivial matter in these optically-complex waters dominated by the absorption of coloured dissolved organic matter (CDOM). These types of coastal waters are especially challenging for quantitative assessment from space due to their low reflectance. Papers III and IV thus also provide tools for a more versatile use in other coastal waters that are not as optically-complex as the highly absorbing Baltic Sea waters. The benefits of the increased spatial-temporal data coverage by optical remote sensing were presented, and also compared to in situ sampling methods (using chlorophyll-a as indicator).
8.	Beltrán-Abaunza, José M., 1971- (författare) Uncertainty measurements and validation of ocean colour data in optically complex waters 2013 Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract The thesis addresses validation activities associated with the use of in situ and satellite-based radiometers to assess water quality parameters, such as chlorophyll-a (Chl-a), total suspended matter (TSM) and coloured dissolved organic matter (CDOM- also known as yellow substances, YEL) in CDOM-dominated waters. In paper I, an inter-comparison of in situ radiometers is presented. Here, a new hand-held radiometer, the Water Insight Spectrometer (WISP-3) was tested and evaluated for routine water monitoring against other common radiometers used for validation. The WISP-3 measures the reflectance at the surface, and thus also works in shallow depths. The WISP-3 is designed for validation in places where other radiometers are difficult to deploy. As it is hyperspectral it can be used to develop in-water algorithms for the retrieval of water-quality information. In paper II, satellite data from the 3rd reprocessing archives of the MEdium Resolution Imaging Spectrometer (MERIS) sensor on board of ENVISAT is evaluated. MERIS level 2 reflectance and water products are assessed against in situ data. This assessment is required in order to ensure the reliability of monitoring systems based on MERIS data such as the Swedish coastal and lake monitoring system www.vattenkvalitet.se. The evaluation of reflectance data is based on a pair-wise comparison of the standard MEGS processor and three coastal processors that are provided as source free plug-ins for the VISAT BEAM software; all pairs are compared to data measured in situ. The derived water products are evaluated both on a pair-wise comparison of processors as well as on an individual comparison of some processors to sea-truthing data. The studied processors improved the retrievals of MERIS reflectance when used the latest MERIS FR 3rd reprocessing, equalized and “smile” corrected and a land adjacency effects were corrected using the improved contrast between ocean and land (ICOL). The blue spectral bands remain problematic for all processors. Chlorophyll was retrieved best using FUB with an overestimation between 18% - 26.5% (MNB) dependent on the compared pairs. At low chlorophyll < 2.5 mg m-3, random errors dominates the retrievals of MEGS. MEGS showed lower bias and random errors when deriving suspended particulate matter (SPM) with an overestimation in the range 8-16% (MNB). All processors failed to retrieve CDOM correctly, but FUB could at least resolve variations in CDOM, however with a systematic underestimation that may be corrected for by using a local correction factor . MEGS has shown already potential to be used as operational processor in the Himmerfjärden bay and adjacent areas, but it requires further improvement of the atmospheric correction for the blue bands and better definition at relatively low chlorophyll concentrations in presence of CDOM.
9.	Beltrán-Abaunza, José M., et al. (författare) Using MERIS data to assess the spatial and temporal variability of phytoplankton in coastal areas 2017 Ingår i: International Journal of Remote Sensing. - : Informa UK Limited. - 0143-1161 .- 1366-5901. ; 38:7, s. 2004-2028 Tidskriftsartikel (refereegranskat)abstract This study aims to highlight how satellite data can be used for an improved understanding of ecological processes in a narrow coastal bay. The usefulness of the Medium Resolution Imaging Spectrometer (MERIS) data (2003-2011) as a complement to the in situ monitoring in Himmerferdenn (HF) bay is used as an example that can also be applied to other coastal areas. HF bay is one of the most frequently monitored coastal areas in the world, allowing for a rigorous comparison between satellites and ship-based monitoring data. MERIS data was used for the integration of chlorophyll-a (chl-a) over each waterbody in the HF area, following the national waterbody classification by the Swedish Meteorological and Hydrological Institute (SMHI). Chl-a anomaly maps were produced for the bay and its adjacent areas. The maps could be used to show events with high chl-a, both with natural causes (e.g. a Prymnesium polylepis bloom observed in summer 2008) and of anthropogenic causes (e.g. failure in the local sewage treatment plant resulting in a strong spring bloom in 2006). Anomaly maps thereby allow to scan larger coastal stretches to discriminate areas that may require additional sampling by ship, or to identify areas that do not differ much from the median value of the MERIS time series.
10.	Blaschek, Leonard, et al. (författare) Cellular and genetic regulation of coniferaldehyde incorporation in lignin of herbaceous and woody plants by quantitative Wiesner staining Annan publikation (övrigt vetenskapligt/konstnärligt)
11.	Blaschek, Leonard, et al. (författare) Cellular and Genetic Regulation of Coniferaldehyde Incorporation in Lignin of Herbaceous and Woody Plants by Quantitative Wiesner Staining 2020 Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 11 Tidskriftsartikel (refereegranskat)abstract Lignin accumulates in the cell walls of specialized cell types to enable plants to stand upright and conduct water and minerals, withstand abiotic stresses, and defend themselves against pathogens. These functions depend on specific lignin concentrations and subunit composition in different cell types and cell wall layers. However, the mechanisms controlling the accumulation of specific lignin subunits, such as coniferaldehyde, during the development of these different cell types are still poorly understood. We herein validated the Wiesner test (phloroglucinol/HCl) for the restrictive quantitative in situ analysis of coniferaldehyde incorporation in lignin. Using this optimized tool, we investigated the genetic control of coniferaldehyde incorporation in the different cell types of genetically-engineered herbaceous and woody plants with modified lignin content and/or composition. Our results demonstrate that the incorporation of coniferaldehyde in lignified cells is controlled by (a) autonomous biosynthetic routes for each cell type, combined with (b) distinct cell-to-cell cooperation between specific cell types, and (c) cell wall layer-specific accumulation capacity. This process tightly regulates coniferaldehyde residue accumulation in specific cell types to adapt their property and/or function to developmental and/or environmental changes.
12.	Cazzaniga, Ilaria, et al. (författare) Temporal changes in the remote sensing reflectance at Lake Vänern 2023 Ingår i: Journal of Great Lakes research. - : Elsevier BV. - 0380-1330. ; 49:2, s. 357-367 Tidskriftsartikel (refereegranskat)abstract The Aerosol Robotic Network - Ocean Color (AERONET-OC) instrument located at the Pålgrunden site in Lake Vänern provides values of remote sensing spectral reflectance RRS(λ) since 2008. These in situ RRS(λ) indicated a temporal increase from 2015 at center-wavelengths in the green and red spectral regions. To investigate the environmental and climate processes responsible for this increase, water color trends in Lake Vänern were analyzed considering in situ limnological measurements, meteo-climatic quantities and additionally satellite-derived data products from the Moderate Resolution Imaging Spectroradiometer on board the Aqua platform (MODIS-A). Satellite ocean color RRS(λ) data assessed against in situ RRS(λ) from the Pålgrunden site showed satisfactory agreement at a number of spectral bands. Relying on these validation results, comprehensive statistical analysis were performed using MODIS-A RRS(λ). These indicated periodical changes between 2002 and 2021 with clear minima occurring between 2010 and 2013. The complementary analyses of temporal changes characterizing limological and meteo-climatic quantities, and also relationships between these quantities and RRS(λ), indicated the existence of complex and concurrent bio-geochemical processes influencing water color in Lake Vänern. In particular, significant correlations were observed between RRS(λ) and turbidity, and also between RRS(λ) and total biovolume. Additionally, an early warming of Lake Vänern surface waters was identified since spring 2014. This occurrence could potentially affect the vertical mixing and water exchange between turbid coastal and pelagic waters with implications for phytoplankton phenology.
13.	Fan, Yongzhen, et al. (författare) OC-SMART : A machine learning based data analysis platform for satellite ocean color sensors 2021 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 253 Tidskriftsartikel (refereegranskat)abstract We introduce a new platform, Ocean Color - Simultaneous Marine and Aerosol Retrieval Tool (OC-SMART), for analysis of data obtained by satellite ocean color sensors. OC-SMART is a multi-sensor data analysis platform which supports heritage, current, and possible future multi-spectral and hyper-spectral sensors from US, EU, Korea, Japan, and China, including SeaWiFS, Aqua/MODIS, SNPP/VIIRS, ISS/HICO, Landsat8/OLI, DSCOVR/EPIC, Sentinel-2/MSI, Sentinel-3/OLCI, COMS/GOCI, GCOM-C/SGLI and FengYun-3D/MERSI2. The products provided by OC-SMART include spectral normalized remote sensing reflectances (R-rs values), chlorophyll_a (CHL) concentrations, and spectral in-water inherent optical properties (IOPs) including absorption coefficients due to phytoplankton (a(ph)), absorption coefficients due to detritus and Gelbstoff (a(dg)) and backscattering coefficients due to particulates (b(bp)). Spectral aerosol optical depths (AODs) and cloud mask results are also provided by OC-SMART. The goal of OC-SMART is to improve the quality of global ocean color products retrieved from satellite sensors, especially under complex environmental conditions, such as coastal/inland turbid water areas and heavy aerosol loadings. Therefore, the atmospheric correction (AC) and ocean IOP algorithms in OC-SMART are driven by extensive radiative transfer (RT) simulations in conjunction with powerful machine learning techniques. To simulate top of the atmosphere (TOA) radiances, we solve the radiative transfer equation pertinent for the coupled atmosphere-ocean system. For each sensor, we have created about 13 million RT simulations and comprehensive training datasets to support the development of the machine learning AC and in-water IOP algorithms. The results, as demonstrated in this paper, are very promising. Not only does OC-SMART improve the quality of the retrieved water products, it also resolves the negative water-leaving radiance problem that has plagued heritage AC algorithms. The comprehensive training datasets created using multiple atmosphere, aerosol, and ocean IOP models ensure global and generic applicability of OC-SMART. The use of machine learning algorithms makes OC-SMART roughly 10 times faster than NASA's SeaDAS platform. OC-SMART also includes an advanced cloud screening algorithm and is resilient to the contamination by weak to moderate sunglint and cloud edges. It is therefore capable of recovering large amounts of data that are discarded by other algorithms (such as those implemented in NASA's SeaDAS package), especially in coastal areas. OC-SMART is currently available as a standalone Python package or as a plugin that can be installed in ESA's Sentinel Application Platform (SNAP).
14.	Harvey, E. Therese, 1979-, et al. (författare) Relationships between colored dissolved organic matter and dissolved organic carbon in different coastal gradients of the Baltic Sea 2015 Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 44:3, s. 392-401 Tidskriftsartikel (refereegranskat)abstract Due to high terrestrial runoff, the Baltic Sea isrich in dissolved organic carbon (DOC), the light-absorbing fraction of which is referred to as coloreddissolved organic matter (CDOM). Inputs of DOC andCDOM are predicted to increase with climate change,affecting coastal ecosystems. We found that therelationships between DOC, CDOM, salinity, and Secchidepth all differed between the two coastal areas studied; theW Gulf of Bothnia with high terrestrial input and the NWBaltic Proper with relatively little terrestrial input. TheCDOM:DOC ratio was higher in the Gulf of Bothnia,where CDOM had a greater influence on the Secchi depth,which is used as an indicator of eutrophication and henceimportant for Baltic Sea management. Based on the resultsof this study, we recommend regular CDOM measurements in monitoring programmes, to increase the value ofconcurrent Secchi depth measurements.
15.	Harvey, E. Therese, et al. (författare) Satellite-based water quality monitoring for improved spatial and temporal retrieval of chlorophyll-a in coastal waters 2015 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 158, s. 417-430 Tidskriftsartikel (refereegranskat)abstract The coastal zones are the most inhabited areas of the world and are therefore strongly affected by humans, leading to undesirable environmental changes that may alter the ecosystems, such as eutrophication. In order to evaluate changes in the environment an effective water quality monitoring system for the coastal zones must be in place. The chlorophyll-a concentration is commonly used as a proxy for phytoplankton biomass and as indicator for eutrophication and it can be retrieved from ocean colour remote sensing data. Several operational monitoring systems based on remote sensing are in place to monitor the open sea and, to some extent, the coastal zones. However, evaluations of coastal monitoring systems based on satellite data are scarce. This paper compares the chlorophyll-a concentrations retrieved from an operational satellite system based on MERIS (Medium Resolution Imaging Spectrophotometer) data with ship-based monitoring for the productive seasons in 2008 and 2010, in a coastal area in the Baltic Sea. The comparisons showed that the satellite-based monitoring system is reliable and that the estimations of chlorophyll-a concentration are comparable to in situ measurements in terms of accuracy and quantitative retrieval. A very strong correlation was found between measurements from satellite-derived chlorophyll-a compared to in situ measurements taken close in time (0-3 days), with RMSE of 64% and a MNB of 17%. The comparison of the monthly means showed improved RMSE and a MNB of only 8%. Furthermore, this study shows that MERIS is better at capturing spatial dynamics and the extent of phytoplankton blooms than ship-based monitoring, since it has a synoptic view and higher temporal resolution. Satellite-based monitoring also increases the frequency of chlorophyll-a observations considerably, where the degree of improvement is dependent on the sampling frequency of the respective monitoring programme. Our results show that ocean colour remote sensing can, when combined with field sampling, provide an improved basis for more effective monitoring and management of the coastal zone. These results are important for eutrophication assessment and status classifications of water basins and can be applied to a larger extent within national and international agreements considering the coastal zones, e.g. the European Commission's Water Framework Directive.
16.	Harvey, E. Therese, et al. (författare) The Effect of Optical Properties on Secchi Depth and Implications for Eutrophication Management 2019 Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 5, s. 1-19 Tidskriftsartikel (refereegranskat)abstract Successful management of coastal environments requires reliable monitoring methods and indicators. Besides Chlorophyll-a concentration (Chl-a), water transparency measured as Secchi Depth (ZSD) is widely used in Baltic Sea management for water quality assessment as eutrophication indicator. However, in many coastal waters not only phytoplankton but also coloured dissolved organic matter (CDOM) and suspended particulate matter (SPM) influence the under-water light field, and therefore the ZSD. In this study all three main optical variables(CDOM, Chl-a and SPM [organic and inorganic]) as well as ZSD were measured in three Swedish regions: the Bothnian Sea, the Baltic Proper and the Skagerrak in 2010-2014. Regional multiple regressions with Chl-a, CDOM and inorganic SPM as predictors explained the variations in ZSD well (R2adj = 0.53-0.84). Commonality analyses of the regressions indicated considerable differences between regions regarding the contribution of each factor to the variance, R2adj, in ZSD. CDOM explained most of the variance in the Bothnian Sea and the Skagerrak; in general, Chl-a contributed only modestly to the ZSD. In the Baltic Proper the largest contribution was from the interaction of all three variables. As expected, the link between Chl-a and ZSD was much weaker in the Bothnian Sea with high CDOM absorption and SPM concentration. When applying the Swedish EU Water Framework Directive threshold for Good/Moderate Chl-a status in the models it was shown that ZSD is neither a sufficient indicator for eutrophication, nor for changes in Chl-a. Natural coastal gradients in CDOM and SPM influence the reference conditions for ZSD and other eutrophication indicators, such as the depth distribution of macro-algae. Hence, setting targets for these indicators based on reference Chl-a concentrations and simple Chl-a to ZSD relationships might in some cases be inappropriate and misleading due to overestimation of water transparency under natural conditions.
17.	Harvey, Therese, 1979- (författare) Bio-optics, satellite remote sensing and Baltic Sea ecosystems : Applications for monitoring and management 2015 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Earth observation satellites cover large areas with frequent temporal repetition and provide us with new insight into ocean and coastal processes. Ocean colour measurements from satellite remote sensing are linked to the bio-optics, which refers to the light interactions with living organisms and dissolved and suspended constituents in the aquatic environment. Human pressures have changed the aquatic ecosystems, by, for example, the increased input of nutrient and organic matter leading to eutrophication. This thesis aims to study and develop the link between bio-optical data and the remote sensing method to the monitoring and management of the Baltic Sea. The results are applied to the European Union’s Water Directives, and the Baltic Sea Action Plan from the Helsinki commission. In paper I indicators for eutrophication, chlorophyll-a concentration and Secchi depth were evaluated as a link to remote sensing observations. Chlorophyll-a measurements from an operational satellite service (paper I) were compared to conventional ship-based monitoring in paper II and showed high correlations to the in situ data. The results in paper I, II and IV show that the use of remote sensing can improve both the spatial and temporal monitoring of water quality. The number of observations increased when also using satellite data, thus facilitating the assessment of the ecological and environmental status within the European Union’s water directives. The spatial patterns make it possible to study the changes of e.g. algae blooms and terrestrial input on larger scales. Furthermore, the water quality products from satellites can offer a more holistic and easily accessible view of the information to decision makers and end-users. In paper III variable relationships between in situ bio-optical parameters, such as coloured dissolved organic matter (CDOM), dissolved organic carbon, salinity and Secchi depth, were found in different parts of the Baltic Sea. In paper IV an in situ empirical model to retrieve suspended particulate matter (SPM) from turbidity was developed and applied to remote sensing data. The use of Secchi depth as an indicator for eutrophication linked to the concentrations of chlorophyll-a and SPM and CDOM absorption was investigated in paper V. The variations in Secchi depth were affected differently by the mentioned parameters in the different regions. Therefore, one must also consider those when evaluating changes in Secchi depth and for setting target levels for water bodies. This thesis shows good examples on the benefits of incorporating bio-optical and remote sensing data to a higher extent within monitoring and management of the Baltic Sea.
18.	Harvey, Therese, 1979-, et al. (författare) The effect of optical properties on Secchi depth and implications for eutrophication management Annan publikation (övrigt vetenskapligt/konstnärligt)abstract Successful management of coastal environments requires reliable monitoring methods and indicators. Secchi depth and chlorophyll-a concentration (Chl-a) are used as indicators for the assessment of eutrophication, both within the European Commission’s Water Framework and Marine Strategy Directives and the Helsinki commission. Chl-a is a used as a proxy for phytoplankton biomass and Secchi depth is used as a measure of changes in Chl-a. However, Secchi depth is more closely correlated with the light climate, affecting for example benthic vegetation. The public strongly link Secchi depth to the perceived water quality. Due to its simple measurement method Secchi depth is included in many monitoring programmes, often with the longest available time-series. In optically complex waters, Secchi depth is influenced by other factors than Chl-a, such as coloured dissolved organic matter (CDOM) and suspended particulate matter (SPM). In this study we evaluate how much Chl-a, CDOM and inorganic SPM each contribute to the variations in Secchi depth. We collected in situ data from different Swedish coastal gradients in three regions, Bothnian Sea, Baltic proper and Skagerrak during 2010-2014. Two linear multiple regression models for each region, with Chl-a, CDOM and inorganic SPM as predictors, explained the Secchi depth well (R2adj=0.54/0.8 for the Bothnian Sea, R2adj=0.81/0.81 for the Baltic proper and R2adj=0.53/0.64 for the Skagerrak). The slope for inorganic SPM was not significant in all models, but still included in the models, as significant correlations were found, both with Secchi depth and between parameters. The follow-up analysis of the multiple regressions by commonality analyses showed differences between the regions in the unique and common effects of the variables to the variance of the R2adj for Secchi depth. In the Bothnian Sea the unique effects for Chl-a were relatively low, 6% and 20%. The highest unique effect were from CDOM (~46% in summer and 20% in spring), whereas inorganic SPM had no unique contribution in summer but in spring with ~6%. The common effects from CDOM and inorganic SPM were large (71% in spring and 42% in summer). In the Baltic proper the optical variables had a different effect on the Secchi depth, with the largest part from the common effects of all three parameters, explaining up to 42-45% of the variations. The largest unique effects were from inorganic SPM (24%) or from Chl-a (15%). The models in the Skagerrak showed another pattern with CDOM having a very high unique effect, 71% for one model and the almost equally to Chl-a in the other 26% (Chl-a 28%). The common effects between CDOM and Chl-a were also pronounced, ~21% and the inorganic SPM had the lowest effect. The models were used for applying the levels for the reference value and the threshold for good/moderate status for Chl-a within the EU directives. The results showed, that in optically complex waters, Secchi depth is not a sufficient indicator for eutrophication, or as a response to Chl-a changes. Differences in natural processes have an indirect effect on the optical components determining the Secchi depth. For example land and river run-off, resuspension, bottom substrate, hydrography and salinity may explain the differences seen between the regions. The natural coastal gradients in Secchi depth will influence the determination of reference conditions for other eutrophication indicators, such as the depth distribution of macro algae. Hence, setting targets for Secchi depth based on reducing Chl-a might in some cases have no or only limited effect.
19.	Hommersom, Annelies, et al. (författare) Intercomparison in the field between the new WISP-3 and other radiometers (TriOS Ramses, ASD FieldSpec, and TACCS) 2012 Ingår i: Journal of Applied Remote Sensing. - 1931-3195. ; 6 Tidskriftsartikel (refereegranskat)abstract Optical close-range instruments can be applied to derive water quality parameters for monitoring purposes and for validation of optical satellite data. In situ radiometers are often difficult to deploy, especially from a small boat or a remote location. The water insight spectrometer (WISP-3) is a new hand-held radiometer for monitoring water quality, which automatically performs measurements with three radiometers (L-sky, L-u, E-d) and does not need to be connected with cables and electrical power during measurements. The instrument is described and its performance is assessed by an intercomparison to well-known radiometers, under real fieldwork conditions using a small boat and with sometimes windy and cloudy weather. Root mean squared percentage errors relative to those of the TriOS system were generally between 20% and 30% for remote sensing reflection, which was comparable to those of the other instruments included in this study. From this assessment, it can be stated that for the tested conditions, the WISP-3 can be used to obtain reflection spectra with accuracies in the same range as well-known instruments. When tuned with suitable regional algorithms, it can be used for quick scans for water quality monitoring of Chl, SPM, and aCDOM.
20.	Kari, Elina, et al. (författare) Development of under-ice stratification in Himmerfjärden bay, north-western Baltic proper, and their effect on the phytoplankton spring bloom 2018 Ingår i: Journal of Marine Systems. - : Elsevier BV. - 0924-7963 .- 1879-1573. ; 186, s. 85-95 Tidskriftsartikel (refereegranskat)abstract Seasonal sea ice cover reduces wind-driven mixing and allows for under-ice stratification to develop. These under-ice plumes are a common phenomenon in the seasonal sea ice zone. They stabilize stratification and concentrate terrestrial runoff in the top layer, transporting it further offshore than during ice-free seasons. In this study, the effect of sea ice on spring stratification is investigated in Himmerfjärden bay in the NW Baltic Sea. Distinct under-ice plumes were detected during long ice seasons. The preconditions for the development of the under-ice plumes are described as well as the typical spatial and temporal dimensions of the resulting stratification patterns. Furthermore, the effect of the under-ice plume on the timing of the onset and the maximum of the phytoplankton spring bloom were investigated, in terms of chlorophyll-a (Chl-a) concentrations. At the head of the bay, bloom onset was delayed on average by 18 days in the event of an under-ice plume. However, neither the maximum concentration of Chl-a nor the timing of the Chl-a maximum were affected, implying that the growth period was shorter with a higher daily productivity. During this period from spring bloom onset to maximum Chl-a, the diatom biomass was higher and Mesodinium rubrum biomass was lower in years with under-ice plumes compared to years without under-ice plumes. Our results thus suggest that the projected shorter ice seasons in the future will reduce the probability of under-ice plume development, creating more dynamic spring bloom conditions. These dynamic conditions and the earlier onset of the spring bloom seem to favor the M. rubrum rather than diatoms.
21.	Kari, Elina, 1986- (författare) Light conditions in seasonally ice-covered waters : within the Baltic Sea region 2018 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Seasonal ice cover is a major driver of seasonality in aquatic ecosystems in the Baltic Sea region. Ice cover influences the underwater light conditions directly by limiting the light transfer and indirectly by modifying the mixing and circulation under the ice. Light conditions and stratification are key factors controlling the onset of the phytoplankton spring bloom. Therefore, the seasonal ice cover has an important role in setting the time frames for the primary production and in influencing the seasonality of the ecological processes. This thesis investigates the optical properties of the ice cover and the bio-optical substances in the water column.Bio-optical substances, suspended particulate matter (SPM), Coloured dissolved organic matter (CDOM) and Chlorophyll-a (Chl-a), determine the availability and spectral distribution of light. Measuring turbidity is quick and easy compared to the gravimetrical determination of the SPM concentration. Paper I provides a new model to estimate the concentration of SPM from turbidity. The new SPM-turbidity model predicts SPM concentrations well, despite the high CDOM absorption and the optical differences in the coastal northwestern and southeastern Baltic proper. Therefore, the new SPM-turbidity model offers a cost-effective and reliable method to monitor SPM concentration.The light transfer through the snow and ice cover was studied both in freshwater lake ice and in brackish sea ice (Papers II and III). Additionally, the seasonal evolution of light transmission through lake ice was investigated during spring. The crystal structure of the ice cover was analysed both in the coastal fast ice zone and in drift ice in the open Baltic Sea. The snow and ice cover was found not only to reduce the amount of light, but also to change its spectral and directional distribution. The light field under ice depended strongly on the snow cover. In addition, the bio-optical substances were analysed within sea ice and in the underlying water, as well as their effect on the light conditions.The seasonal sea ice cover also limits the wind-driven mixing of the water column. The development of stratification was investigated in a coastal bay in the northwestern Baltic proper (Paper IV). The preconditions for an under-ice plume development were defined along with the spatial and temporal dimensions of the stratification pattern. Furthermore, an under-ice plume was found to cause a delay in the onset of the phytoplankton spring bloom, but the timing of the Chl-a maximum was not affected. The results also show that although diatoms dominate the phytoplankton community with and without under-ice plume, the dynamic conditions without under-ice plume seem to favour the motile photosynthetic ciliate Mesodinium rubrum. Overall, this thesis contributes to better understanding of the current role of seasonal ice cover on the light conditions and consequently on to the ecosystem.
22.	Kari, Elina, et al. (författare) Measurements of light transfer through drift ice and landfast ice in the northern Baltic Sea 2020 Ingår i: Oceanologia. - : Elsevier BV. - 0078-3234. ; 62:3, s. 347-363 Tidskriftsartikel (refereegranskat)abstract The aim of this study was to investigate the light transfer through sea ice with a focus on bio-optical substances both in fast ice and in the drift ice zones in the northern Baltic Sea. The measurements included snow and ice structure, spectral irradiance and photo-synthetically active radiation below the sea ice. We also measured the concentrations of the three main bio-optical substances which are chlorophyll-a, suspended particulate matter, and coloured dissolved organic matter (CDOM). These bio-optical substances were determined for melted ice samples and for the underlying sea water. The present study provides the first spectral light transfer data set for drift ice in the Baltic Sea. We found high CDOM absorption values typical to the Baltic Sea waters also within sea ice. Our results showed that the transmittance through bare ice was lower for the coastal fast ice than for the drift ice sites. Bio-optical substances, in particular CDOM, modified the spectral distribution of light penetrating through the ice cover. Differences in crystal structure and the amount of gas inclusions in the ice caused variation in the light transfer. Snow cover on ice was found to be the dominant factor influencing the light field under ice, confirming previous studies. In conclusion, snow cover dominated the amount of light under the ice, but did not modify its spectral composition. CDOM in the ice absorbs strongly in the short wavelengths. As pure water absorbs most in the long wavelengths, the light transfer through ice was highest in the green (549-585 nm).
23.	Kari, Elina, et al. (författare) Measurements of light transfer through sea ice in the northern Baltic Sea Annan publikation (övrigt vetenskapligt/konstnärligt)
24.	Kari, Elina, et al. (författare) Retrieval of suspended pariculate matter from MERIS data : Algorithm development and validation Annan publikation (övrigt vetenskapligt/konstnärligt)
25.	Kari, Elina, et al. (författare) Retrieval of suspended particulate matter from turbidity - model development, validation, and application to MERIS data over the Baltic Sea 2017 Ingår i: International Journal of Remote Sensing. - : Informa UK Limited. - 0143-1161 .- 1366-5901. ; 38:7, s. 1983-2003 Tidskriftsartikel (refereegranskat)abstract Suspended particulate matter (SPM) causes most of the scattering in natural waters and thus has a strong influence on the underwater light field, and consequently on the whole ecosystem. Turbidity is related to the concentration of SPM which usually is measured gravimetrically, a rather time-consuming method. Measuring turbidity is quick and easy, and therefore also more cost-effective. When derived from remote sensing data the method becomes even more cost-effective because of the good spatial resolution of satellite data and the synoptic capability of the method. Turbidity is also listed in the European Union's Marine Strategy Framework Directive as a supporting monitoring parameter, especially in the coastal zone. In this study, we aim to provide a new Baltic Sea algorithm to retrieve SPM concentration from in situ turbidity and investigate how this can be applied to satellite data. An in situ dataset was collected in Swedish coastal waters to develop a new SPM model. The model was then tested against independent datasets from both Swedish and Lithuanian coastal waters. Despite the optical variability in the datasets, SPM and turbidity were strongly correlated (r = 0.97). The developed model predicts SPM reliably from in situ turbidity (R-2 = 0.93) with a mean normalized bias (MNB) of 2.4% for the Swedish and 14.0% for the Lithuanian datasets, and a relative error (RMS) of 25.3% and 37.3%, respectively. In the validation dataset, turbidity ranged from 0.3 to 49.8 FNU (Formazin Nephelometric Unit) and correspondingly, SPM concentration ranged from 0.3 to 34.0 g m(-3) which covers the ranges typical for Baltic Sea waters. Next, the medium-resolution imaging spectrometer (MERIS) standard SPM product MERIS Ground Segment (MEGS) was tested on all available match-up data (n = 67). The correlation between SPM retrieved from MERIS and in situ SPM was strong for the Swedish dataset with r = 0.74 (RMS = 47.4 and MNB = 11.3%; n = 32) and very strong for the Lithuanian dataset with r = 0.94 (RMS = 29.5% and MNB = -1.5%; n = 35). Then, the turbidity was derived from the MERIS standard SPM product using the new in situ SPM model, but retrieving turbidity from SPM instead. The derived image was then compared to existing in situ data and showed to be in the right range of values for each sub-area. The new SPM model provides a robust and cost-efficient method to determine SPM from in situ turbidity measurements (or vice versa). The developed SPM model predicts SPM concentration with high quality despite the high coloured dissolved organic matter (CDOM) range in the Baltic Sea. By applying the developed SPM model to already existing remote sensing data (MERIS/Envisat) and most importantly to a new generation of satellite sensors (in particular OLCI on board the Sentinel-3), it is possible to derive turbidity for the Baltic Sea.
26.	Kratzer, Susanne, et al. (författare) Improvement of MERIS level 2 products in Baltic Sea coastal areas by applying the Improved Contrast between Ocean and Land processor (ICOL) - data analysis and validation 2010 Ingår i: Oceanologia. - 0078-3234. ; 52:2, s. 211-236 Tidskriftsartikel (refereegranskat)abstract In this paper we compare the following MERIS processors against sea-truthing data: the standard MERIS processor (MEGS 7.4.1), the Case 2 Regional processor (C2R) of the German Institute for Coastal Research (GKSS), and the Case 2 Water Properties processor developed at the Freie Universitat Berlin (FUB). Furthermore, the Improved Contrast between Ocean and Land processor (ICOL), a prototype processor for the correction of adjacency effects from land, was tested on all three processors, and the retrieval of level 2 data was evaluated against sea-truthing data, before and after ICOL processing. The results show that by using ICOL the retrieval of spectral reflectance in the open sea was improved for all processors. After ICOL processing, the FUB showed rather small errors in the blue, but underestimated in the red -34% Mean Normalised Bias (MNB) and 37% Root Mean Square (R,MS). For MEGS the reflectance in the red was underestimated by about -20% MNB and 23% RMS, whereas the reflectance in the other channels was well predicted, even without any ICOL processing. The C2R, underestimated the red with about -27% MNB and 29% RMS and at 412 nm it overestimated the reflectance with about 23% MNB and 29% RMS. At the outer open sea stations ICOL processing did not have a strong effect: the effect of the processor diminishes progressively up to 30 km from land. At the open sea stations the ICOL processor improved chlorophyll retrieval using MEGS from -74% to about 34% MU; and TSM retrieval from -63% to about 22% MNB. Using FUB in combination with ICOL gave even better results for both chlorophyll (25% MNB and 45% RMS) and TSM (-4% MNB and 36% EMS) in the open Baltic Sea. All three processors predicted TSM rather well, but the standard processor gave the best results (-12% MNB and 17% RMS). The C2R had a very low MNB for TSM (1%), but a rather high RMS (54%). The FUB was intermediate with -16% MNB and 31% RMS. In coastal waters, the spectral diffuse attenuation coefficient K-d (490) was well predicted using PUB or MEGS in combination with ICOL (MNB about 12% for FUB and 0.4% for MEGS). Chlorophyll was rather well predicted in the open Baltic Sea using FUB with ICOL (MNB 25%) and even without ICOL processing (MNB about 15%). ICOL-processed MEGS data also gave rather good retrieval of chlorophyll in the coastal areas (MNB of 19% and RMS of 28%). In the open Baltic Sea chlorophyll retrieval gave a MNB of 34% and RMS of 70%, which may be due to the considerable patchiness caused by cyanobacterial blooms. The results presented here indicate that with the MERIS mission, ESA and co-workers are in the process of solving some of the main issues regarding the remote sensing of coastal waters: spatial resolution; land-water adjacency effects; improved level 2 product retrieval in the Baltic Sea, i.e. the retrieval of spectral reflectance and of the water quality products TSM and chlorophyll.
27.	Kratzer, Susanne, et al. (författare) Inherent Optical Properties of the Baltic Sea in Comparison to Other Seas and Oceans 2018 Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 10:3 Tidskriftsartikel (refereegranskat)abstract In order to retrieve geophysical satellite products in coastal waters with high coloured dissolved organic matter (CDOM), models and processors require parameterization with regional specific inherent optical properties (sIOPs). The sIOPs of the Baltic Sea were evaluated and compared to a global NOMAD/COLORS Reference Data Set (RDS), covering a wide range of optical provinces. Ternary plots of relative absorption at 442 nm showed CDOM dominance over phytoplankton and non-algal particle absorption (NAP). At 670 nm, the distribution of Baltic measurements was not different from case 1 waters and the retrieval of Chl a was shown to be improved by red-ratio algorithms. For correct retrieval of CDOM from Medium Resolution Imaging Spectrometer (MERIS) data, a different CDOM slope over the Baltic region is required. The CDOM absorption slope, SCDOM, was significantly higher in the northwestern Baltic Sea: 0.018 (+/- 0.002) compared to 0.016 (+/- 0.005) for the RDS. Chl a-specific absorption and a(d) [SPM]*(442) and its spectral slope did not differ significantly. The comparison to the MERIS Reference Model Document (RMD) showed that the SNAP slope was generally much higher (0.011 +/- 0.003) than in the RMD (0.0072 +/- 0.00108), and that the SPM scattering slope was also higher (0.547 +/- 0.188) vs. 0.4. The SPM-specific scattering was much higher (1.016 +/- 0.326 m(2) g(-1)) vs. 0.578 m(2) g(-1) in RMD. SPM retrieval could be improved by applying the local specific scattering. A novel method was implemented to derive the phase function (PF) from AC9 and VSF-3 data. (b) over tilde was calculated fitting a Fournier-Forand PF to the normalized VSF data. (b) over tilde was similar to Petzold, but the PF differed in the backwards direction. Some of the sIOPs showed a bimodal distribution, indicating different water types-e.g., coastal vs. open sea. This seems to be partially caused by the distribution of inorganic particles that fall out relatively close to the coast. In order to improve remote sensing retrieval from Baltic Sea data, one should apply different parameterization to these distinct water types, i.e., inner coastal waters that are more influenced by scattering of inorganic particles vs. open sea waters that are optically dominated by CDOM absorption.
28.	Kratzer, Susanne, et al. (författare) Inorganic suspended matter as an indicator of terrestrial influence in Baltic Sea coastal areas - Algorithm development and validation, and ecological relevance 2020 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 237 Tidskriftsartikel (refereegranskat)abstract Suspended particulate matter (SPM) consists both of an organic (OSPM) and an inorganic fraction (ISPM) and the latter can be used as an indicator for coastal influence in the Baltic Sea. The concentration of SPM can be derived from particle scatter if the specific scattering properties of the respective water body are known. In this paper we show that likewise, ISPM can be derived reliably from remotely sensed particle scatter. An empirical algorithm between particle scatter (AC9 data) and ISPM concentration (measured gravimetrically) was derived from in-water measurements. This regional algorithm was then applied to the iop_bpart level 2 product (i.e. the particle scatter measured at 443 nm) derived from OLCI data on Sentinel-A (S3A) using the C2RCC neural network and validated against an independent data set. The standard error of the derived OLCI match-up data was 10%, and was thus within the goal of the mission requirements of Sentinel-3. The generated S3 composite images from spring and autumn 2018 show that in the Baltic Sea most of the ISPM falls out rather close to the shore, whereas only a very small proportion of ISPM is carried further off-shore. This is also supported by in situ ISPM transects measured in the coastal zone. The ISPM images clearly highlight the areas that are most strongly influenced by terrestrial matter. Differences between the NE Baltic and the SE Baltic proper can be explained by the difference in hydrology and coastal influence as well as bathymetry and wind-wave stirring. The method is of interest for coastal zone management and for assessing the effect of seasonal changes in terrestrial run-off and wind-driven resuspension of sediments. It can also be used to evaluate the effect of climate change which has led to an increase of extreme storm and flooding events that are usually accompanied by increased erosion and run-off from land. Last but not least, turbidity caused by particles influences the light conditions in inner coastal areas and bays, which has a profound effect on pelagic productivity, the maximum growth of macroalgae as well as fish behaviour.
29.	Kratzer, Susanne, et al. (författare) Inorganic Suspended Matter as an indicator of terrestrial influence in Baltic Sea coastal areas - algorithm development, validation and ecological relevance Annan publikation (övrigt vetenskapligt/konstnärligt)
30.	Kratzer, Susanne, et al. (författare) Integrating mooring and ship-based data for improved validation of OLCI chlorophyll-a products in the Baltic Sea 2021 Ingår i: International Journal of Applied Earth Observation and Geoinformation. - : Elsevier BV. - 1569-8432 .- 1872-826X. ; 94 Tidskriftsartikel (refereegranskat)abstract A Water Quality Monitor (WQM) equipped with a range of oceanographic sensors was deployed from April 2017 to October 2017 in the North Western (NW) Baltic Sea. We assessed here if the data from a moored chlorophyll-a fluorometer can be used to improve satellite validation in coastal waters. Calibrated mooring data and ship-based chlorophyll-a concentrations from 2017 and 2018 were matched with OLCI (Ocean and Land Colour Instrument) data to validate the C2RCC (Case-2 Regional Coast Colour) processor, a locally-adapted version of C2RCC (LA-C2RCC), as well as the POLYMER processor. Using additional mooring data resulted in a substantial increase in paired observations compared to using ship-based data alone (C2RCC; N = 41-63, LA-C2RCC; N = 37-59, POLYMER; N = 108-166). However, the addition of mooring data only reduced the error and bias of the LA-C2RCC (MNB: from 24 % to 22 %, RMSE: from 60 % to 57 %, APD: both 47 %). In contrast, the statistical errors increased with the addition of mooring data both for C2RCC (MNB: -26 % to -33 %, RMSE: 50 %-51 %, APD 84 %-96 %) and for POLYMER (MNB: 26 %-36 %, RMSE: 79 % to 79 %, APD 64 %-64 %). The results indicate that the locally-adapted version of the C2RCC should be used for the area of investigation. These results are most likely also related to the effect of the System Vicarious Calibration (SVC). As opposed to C2RCC, the locally-adapted version had not been vicariously calibrated. The results indicate that SVC is not beneficial for Baltic Sea data and that more work needs to be done to improve SVC for Baltic Sea waters or for other waters with high CDOM absorption. In order to improve the validation capabilities of moored fluorometers in general, they should be strategically placed in waters with representative ranges of chl-a concentrations for the area of research in question.
31.	Kratzer, Susanne, 1966-, et al. (författare) Links between Land Cover and In-Water Optical Properties in Four Optically Contrasting Swedish Bays 2024 Ingår i: Remote Sensing. - 2072-4292. ; 16:1 Tidskriftsartikel (refereegranskat)abstract The optical complexity of coastal waters is mostly caused by the water discharged from land carrying optical components (such as dissolved and particulate matter) into coastal bays and estuaries, and increasing the attenuation of light. This paper aims to investigate the links between in-water optical properties in four Swedish bays (from the northern Baltic proper up to the Bothnian bay) and the land use and land cover (LULC) in the respective catchment of each bay. The optical properties were measured in situ over the last decade by various research and monitoring groups while the LULC in each bay was classified using the Copernicus Land Monitoring Service based on Landsat 8/OLI data. The absorption coefficient of colored dissolve organic matter (CDOM) at 440 nm, aCDOM (440), was significantly correlated to Wetlands which may act as sources of CDOM, while Developed areas (Agricultural and Urban classes) were negatively correlated. The Agriculture class was also negatively related to suspended particulate organic matter (SPOM), whilst Coniferous Forests and Mixed Forests as well as Meadows were positively correlated. SPOM seems thus to mostly originate from Natural classes, possibly due to the release of pollen and other organic matter. Overall, the methods applied here allow for a better understanding of effects of land use and land cover on the bio-optical properties, and thus coastal water quality, on a macroscopic scale.
32.	Kratzer, Susanne, et al. (författare) Synergy of Satellite, In Situ and Modelled Data for Addressing the Scarcity of Water Quality Information for Eutrophication Assessment and Monitoring of Swedish Coastal Waters 2019 Ingår i: Remote Sensing. - : MDPI AG. - 2072-4292. ; 11:17 Tidskriftsartikel (refereegranskat)abstract Monthly CHL-a and Secchi Depth (SD) data derived from the full mission data of the Medium Resolution Imaging Spectrometer (MERIS; 2002-2012) were analysed along a horizontal transect from the inner Braviken bay and out into the open sea. The CHL-a values were calibrated using an algorithm derived from Swedish lakes. Then, calibrated Chl-a and Secchi Depth (SD) estimates were extracted from MERIS data along the transect and compared to conventional monitoring data as well as to data from the Swedish Coastal zone Model (SCM), providing physico-biogeochemical parameters such as temperature, nutrients, Chlorophyll-a (CHL-a) and Secchi depth (SD). A high negative correlation was observed between satellite-derived CHL-a and SD (rho = -0.91), similar to the in situ relationship established for several coastal gradients in the Baltic proper. We also demonstrate that the validated MERIS-based estimates and data from the SCM showed strong correlations for the variables CHL-a, SD and total nitrogen (TOTN), which improved significantly when analysed on a monthly basis across basins. The relationship between satellite-derived CHL-a and modelled TOTN was also evaluated on a monthly basis using least-square linear regression models. The predictive power of the models was strong for the period May-November (R-2: 0.58-0.87), and the regression algorithm for summer was almost identical to the algorithm generated from in situ data in Himmerfjarden bay. The strong correlation between SD and modelled TOTN confirms that SD is a robust and reliable indicator to evaluate changes in eutrophication in the Baltic proper which can be assessed using remote sensing data. Amongst all three assessed methods, only MERIS CHL-a was able to correctly depict the pattern of phytoplankton phenology that is typical for the Baltic proper. The approach of combining satellite data and physio-biogeochemical models could serve as a powerful tool and value-adding complement to the scarcely available in situ data from national monitoring programs. In particular, satellite data will help to reduce uncertainties in long-term monitoring data due to its improved measurement frequency.
33.	Kratzer, Susanne, et al. (författare) The use of ocean color remote sensing in integrated coastal zone management - A case study from Himmerfjärden, Sweden 2013 Ingår i: Marine Policy. - : Elsevier BV. - 0308-597X .- 1872-9460. ; 43, s. 29-39 Tidskriftsartikel (refereegranskat)abstract In this study the use of ocean color data as a diagnostic tool in integrated coastal zone management was investigated as part of the Science Policy Integration for Coastal Systems Assessment (SPICOSA) project. Parallel to this, an operational coastal monitoring system has been set up in close collaboration with end-users. The core work of the bio-optical part in the project was to develop Secchi depth and attenuation of light as indicators for coastal zone management, by linking remote sensing with the socio-economic and ecological model developed in SPICOSA. The article emphasizes the benefits of stakeholder involvement and end-user feedback for efficient and improved system development. Furthermore, conceptual models were developed on how to integrate remote sensing data into coastal zone management and into a physical-biological model of the Baltic Sea. One of the work packages in the SPICOSA project was academic training. In this work package, on-line teaching material in the field of remote sensing and bio-optics was developed and disseminated on the SETnet web page. The article presented here may act as supportive material for training in bio-optics and remote sensing.
34.	Kratzer, Susanne, et al. (författare) Using bio-optics to investigate the extent of coastal waters : A Swedish case study 2009 Ingår i: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 629:1, s. 169-186 Tidskriftsartikel (refereegranskat)abstract In order to develop an optical model to map the extent of coastal waters, the authors analyzed variations in bio-optical constituents and submarine optical properties along a transect from the nutrient-enriched coastal bay, Himmerfjärden, out into the open Baltic Sea. The model is a simple implementation of the “ecosystem approach,” because the optical constituents are proxies for important components of ecosystem state. Yellow substance or colored dissolved organic matter (CDOM) is often a marker for terrestrial freshwater or decay processes in the littoral zone. Phytoplankton pigments, especially chlorophyll a, are used as a proxy for phytoplankton biomass that may be stimulated by fluvial or coastal inputs of anthropogenic nutrients. Suspended particulate matter (SPM) is placed in suspension by tidal or wind-wave stirring of shallow seabeds, and is therefore an indicator for physical forcing. It is the thesis of this article that such constituents, and the optical properties that they control, can be used to provide an ecological definition of the extent of the coastal zone. The spatial distribution of the observations was analyzed using a steady-state model that assumes diffusional transport of bio-optical variables along an axis perpendicular to the coast. According to the model, the resulting distribution along this axis can be described as a low-order polynomial (of order 1–3) when moving from a “source” associated with land to the open-sea “sink.” Order 1 implies conservative mixing, and the higher orders imply significant biological or chemical processes within the gradient. The analysis of the transect data confirmed that the trend of each optical component could be described well using a low-order polynomial. Multiple regression analysis was then used to weigh the contribution of each optical component to the spectral attenuation coefficient K d(490) along the transect. The results showed that in this Swedish Baltic case study, the inorganic fraction of the SPM may be used to distinguish between coastal and open-sea waters, as it showed a clear break between coastal and open-sea waters. Alternative models may be needed for coastal waters in which fronts interrupt the continuity of mixing.
35.	Kratzer, Susanne, et al. (författare) Using MERIS full resolution data to monitor coastal waters : A case study from Himmerfjärden, a fjord-like bay in the northwestern Baltic Sea 2008 Ingår i: Remote Sensing of Environment. - : Elsevier Inc. - 0034-4257 .- 1879-0704. ; 112:5, s. 2284-2300 Tidskriftsartikel (refereegranskat)abstract In this paper we investigate if MERIS full resolution (FR) data (300 m) is sufficient to monitor changes in optical constituents in Himmerfjärden, a fjord-like, north– south facing bay of about 30 km length and 4 km width. The MERIS FR products were derived using a coastal processor (FUB Case-2 Plug-In). We also compared the performance between FUB and standard processor (MEGS 7.4), using reduced resolution (RR) data (1 km resolution) from the open Baltic Sea, and compared the products to sea-truthing data. The optical variables measured for seatruthing were chlorophyll, suspended particulate matter (SPM), as well as coloured dissolved organic matter (CDOM, also termed yellow substances), and the spectral diffuse attenuation coefficient, K d (490). The comparison of the RR data to the sea-truthing data showed that, in the open Baltic Sea, the MERIS standard processor overestimated chlorophyll by about 59%, and SPM by about 28%, and underestimated yellow substance by about 81%, whereas the FUB processor underestimated SPM by about 60%, CDOM by about 78%, and chlorophyll a by about 56%. The FUB processor showed a relatively high precision for all optical components (standard deviation: 6– 18%), whereas the precision for the MEGS 7.4 was rather low (standard deviation: 43– 73%), except for CDOM (standard deviation: 13%). The analysis of the FR data showed that all FR level 2 water products derived from MERIS followed a polynomial decline in concentration when moving off-shore. The distribution of chlorophyll and SPM was best described by a 2nd order polynomial, and the distribution of CDOM by a 3rd order polynomial, verifying the diffusional model described in Kratzer and Tett [Kratzer, S. and Tett, P. (in press). Using bio-optics to investigate the extent of coastal waters— a Swedish case study. Hydrobiologia.]. A new K d (490) and Secchi depth algorithm based on MERIS channel 3 (490 nm) and channel 6 (620 nm) each was derived from radiometric sea-truthing data (TACCS, Satlantic). Applying the K d (490) algorithm to the MERIS FR data over Himmerfjärden, and comparing to sea-truthing data the results showed a strong correlation (r =0.94). When comparing the FR data to the seatruthing data CDOM and K d (490) showed a low accuracy, but a high precision with a rather constant off-set. In summary, one may state that the precision of MERIS data improves by applying the FUB Case-2 processor and the accuracy improves with improved spatial resolution for chlorophyll and SPM. Furthermore, the FUB processor can be used off-the-shelf for open Baltic Sea monitoring, provided one corrects for the respective off-set from sea-truthing data which is most likely caused by an inaccuracy in the atmospheric correction. Additionally, the FR data can be used to derive CDOM, K d (490) and Secchi depth in Himmmerfjärden if one corrects for the respective off-set. We will need to perform more comparisons between sea-truthing and MERIS FR data before the new K d (490) algorithm can be made operational, including also scenes from other times of year. In order to provide a level 2 product that can be used reliably by the Baltic Sea user community, our recommendation to ESA is to include the spectral attenuation coefficient as a MERIS standard product.
36.	Kyryliuk, Dmytro, 1989- (författare) Baltic Sea from Space : The use of ocean colour data to improve our understanding of ecological drivers across the Baltic Sea basin – algorithm development, validation and ecological applications 2019 Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract Coastal areas are the most densely populated areas in the world and thus are under immense anthropogenic pressure. To ensure their function and ecological role, coastal areas require continuous monitoring and management. The rapidly emerging field of satellite remote sensing provides a unique opportunity to monitor both land and oceans from Space. This thesis explores recent developments in ocean colour remote sensing, tests several image processing algorithms, evaluates and maps water quality indicators – both on local and Baltic Sea-wide scale – as well as provides essential monitoring data to complement already existing ship-based monitoring and modelling techniques. The overall aim of the thesis is to broaden our understanding and applicability of ocean colour remote sensing for improved modelling and management of the Baltic Sea and its coastal areas.The thesis deals with four independent research topics. In paper I the spatial distribution of Total Suspended Matter (TSM) during the summer season is evaluated using the European Space Agency’s (ESA) MEdium Resolution Imaging Spectrometer (MERIS). The TSM distribution and concentration is retrieved quantitatively from MERIS data for the HELCOM-defined Baltic Sea sub-basins for the summer seasons 2009, 2010, 2011, and summarized in a 3-year summer composite image. Manuscript II deals with the correspondence between satellite, in situ and modelled data in Bråviken bay, NW Baltic proper, which is optically dominated by Coloured Dissolved Organic Matter (CDOM). Chlorophyll-a (CHL-a) and Secchi depth data are analyzed along a horizontal transects reaching from the inner coastal bay out into the open sea. The study addresses the scarcity of in situ monitoring data in comparison to satellite and modelled data. Further, an empirical relationship is established between modelled total nitrogen and CHL-a derived from satellite, potentially allowing to infer information on the distribution of total nitrogen from satellite data. Paper III evaluates the performance of MERIS’s successor – the Ocean and Land Colour Instrument (OLCI) launched on board Sentinel-3A (S3A) satellite. The water quality products derived from S3A OLCI using the Case-2 Regional CoastColour Processor are evaluated via several dedicated validation campaigns (2016-2018) in the NW Baltic proper. In manuscript IV, the in-water relationship between particle scatter at 440 nm and Inorganic Suspended Particulate Matter (ISPM) is used to develop a novel algorithm to derive ISPM from satellite-derived scatter. This algorithm was applied to OLCI data and tested on an independent dataset. The algorithm allows to map the distribution of ISPM across the Baltic Sea basin and to assess the influence of coastal processes.The key outcome of this thesis are reliable water-quality products generated on a Baltic Sea-wide scale, using state-of-the-art Ocean Colour data. Specifically, the thesis highlights the benefits of using remote sensing to improve our understanding of coastal and dynamical processes, as well as Baltic Sea ecology on a wider scale, which simply is not possible by any other scientific means.
37.	Kyryliuk, Dmytro, et al. (författare) Evaluation of Sentinel-3A OLCI products derived using the Case-2 Regional CoastColour Processor over the Baltic Sea Annan publikation (övrigt vetenskapligt/konstnärligt)
38.	Kyryliuk, Dmytro, et al. (författare) Evaluation of Sentinel-3A OLCI Products Derived Using the Case-2 Regional CoastColour Processor over the Baltic Sea 2019 Ingår i: Sensors. - : MDPI AG. - 1424-8220. ; 19:16 Tidskriftsartikel (refereegranskat)abstract In this study, the Level-2 products of the Ocean and Land Colour Instrument (OLCI) data on Sentinel-3A are derived using the Case-2 Regional CoastColour (C2RCC) processor for the SentiNel Application Platform (SNAP) whilst adjusting the specific scatter of Total Suspended Matter (TSM) for the Baltic Sea in order to improve TSM retrieval. The remote sensing product kd_z90max (i.e., the depth of the water column from which 90% of the water-leaving irradiance are derived) from C2RCC-SNAP showed a good correlation with in situ Secchi depth (SD). Additionally, a regional in-water algorithm was applied to derive SD from the attenuation coefficient K-d(489) using a local algorithm. Furthermore, a regional in-water relationship between particle scatter and bench turbidity was applied to generate turbidity from the remote sensing product iop_bpart (i.e., the scattering coefficient of marine particles at 443 nm). The spectral shape of the remote sensing reflectance (R-rs) data extracted from match-up stations was evaluated against reflectance data measured in situ by a tethered Attenuation Coefficient Sensor (TACCS) radiometer. The L2 products were evaluated against in situ data from several dedicated validation campaigns (2016-2018) in the NW Baltic proper. All derived L2 in-water products were statistically compared to in situ data and the results were also compared to results for MERIS validation from the literature and the current S3 Level-2 Water (L2W) standard processor from EUMETSAT. The Chl-a product showed a substantial improvement (MNB 21%, RMSE 88%, APD 96%, n = 27) compared to concentrations derived from the Medium Resolution Imaging Spectrometer (MERIS), with a strong underestimation of higher values. TSM performed within an error comparable to MERIS data with a mean normalized bias (MNB) 25%, root-mean square error (RMSE) 73%, average absolute percentage difference (APD) 63% n = 23). Coloured Dissolved Organic Matter (CDOM) absorption retrieval has also improved substantially when using the product iop_adg (i.e., the sum of organic detritus and Gelbstoff absorption at 443 nm) as a proxy (MNB 8%, RMSE 56%, APD 54%, n = 18). The local SD (MNB 6%, RMSE 62%, APD 60%, n = 35) and turbidity (MNB 3%, RMSE 35%, APD 34%, n = 29) algorithms showed very good agreement with in situ data. We recommend the use of the SNAP C2RCC with regionally adjusted TSM-specific scatter for water product retrieval as well as the regional turbidity algorithm for Baltic Sea monitoring. Besides documenting the evaluation of the C2RCC processor, this paper may also act as a handbook on the validation of Ocean Colour data.
39.	Kyryliuk, Dmytro, et al. (författare) Summer Distribution of Total Suspended Matter Across the Baltic Sea 2019 Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 5 Tidskriftsartikel (refereegranskat)abstract There are three optical in-water components that, besides water itself, govern the under-water light field: phytoplankton, total suspended matter (TSM), and colored dissolved organic matter (CDOM). In essence, it is the spectral absorption and scattering properties of each optical component that govern the underwater light field, and also the color of the sea that we can perceive, and that can also be measured remotely from space. The Baltic Sea is optically dominated by CDOM, apart from cyanobacteria blooms that often cover most of the Baltic proper during summer. Remote sensing images of TSM reveal large-and mesoscale features and currents, especially in the Southern Baltic, which are influenced both by atmospheric Rossby waves and the Coriolis force. In coastal waters, the optical properties are strongly influenced by inorganic suspended matter, which may originate from coastal erosion and from run-off from land, streams, and rivers. In this paper, we evaluate the distribution of TSM across the Baltic Sea using remote sensing data and statistically compare the TSM loads in the different Helsinki Commission (HELCOM)-defined basins. The total suspended matter (TSM) loads during summer vary substantially in the different basins, with the south-eastern Baltic overall being most influenced by cyanobacteria blooms. The Gdansk basin and the Gulf of Riga were distinguished both by relatively high TSM loads with high standard deviations, indicating strong fluvial input and/or resuspension of sediments. We also evaluate a coastal TSM transect in Himmerfjärden bay, which is located at the Swedish East coast in the Western Gotland Basin. The effect of wind-wave stirring on the distribution of TSM from source (shore) to sink (open sea) can be assessed using satellite data from European Space Agency’s (ESA) MEdium Resolution Imaging Spectrometer (MERIS) mission (2002–2012) with 300 m resolution. The TSM transect data from areas with low wind exposure and a stable thermocline showed a gradient distribution perpendicular to the coast for summer seasons 2009, 2010, 2011, and a 3-year summer composite, confirming a previous bio-optical study from the Western Gotland basin.
40.	Kyryliuk, Dmytro, et al. (författare) Synergy of satellite, in situ and modeled data for addressing the scarcity of water quality information for eutrophication assessment and monitoring of Swedish coastal waters Annan publikation (övrigt vetenskapligt/konstnärligt)
41.	Lavigne, H., et al. (författare) Quality-control tests for OC4, OC5 and NIR-red satellite chlorophyll-a algorithms applied to coastal waters 2021 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 255 Tidskriftsartikel (refereegranskat)abstract Reliable satellite estimates of chlorophyll-a concentration (Chl-a) are needed in coastal waters for applications such as eutrophication monitoring. However, because of the optical complexity of coastal waters, retrieving accurate Chl-a is still challenging. Many algorithms exist and give quite different performance for different optical conditions but there is no clear definition of the limits of applicability of each algorithm and no clear basis for deciding which algorithm to apply to any given image pixel (reflectance spectrum). Poor quality satellite Chl-a data can easily reach end-users. To remedy this and provide a clear decision on when a specific Chl-a algorithm can be used, we propose simple quality control tests, based on MERIS water leaving reflectance (rho(w)) bands, to determine on a pixel-by-pixel basis if any of three popular and complementary algorithms can be used. The algorithms being tested are: 1. the OC4 blue-green band ratio algorithm which was designed for open ocean waters; 2. the OC5 algorithm which is based on look-up tables and corrects OC4 overestimation in moderately turbid waters and 3. a near infrared-red (NIR-red) band ratio algorithm designed for eutrophic waters. Using a dataset of 348 in situ Chl-a/MERIS matchups, the conditions for reliable performance of each of the selected algorithms are determined. The approach proposed here looks for the best compromise between the minimization of the relative difference between In situ measurements and satellite estimations and the number of pixels processed. Conditions for a reliable application of OC4 and OC5 depend on rho(w)412/rho(w)443 and rho(w)560, used as proxies of coloured dissolved organic matter and suspended particulate matter (SPM), as compared to rho(w)560/rho(w)490, used as a proxy for Chl-a. Conditions for reliable application of the NIR-red band ratio algorithm depend on Chl-a and SPM. These conditions are translated into pixel-based quality control (QC) tests with appropriately chosen thresholds. Results show that by removing data which do not pass QC, the performance of the three selected algorithms is significantly improved. After combining these algorithms, 70% of the dataset could be processed with a median absolute percent difference of 30.5%. The QC tests and algorithm merging methodology were then tested on four MERIS images of European waters. The OC5 algorithm was found to be suitable for most pixels, except in very turbid and eutrophic waters along the coasts where the NIR-red band ratio algorithm helps to fill the gap. Finally, a test was performed on an OLCI-S3A image. Although some validations of water reflectance are still needed for the OLCI sensors, results show similar behavior to the MERIS applications which suggests that when applied to OLCI data the present methodology will help to accurately estimate Chl-a in coastal waters for the next decade.
42.	Liu, Huizeng, et al. (författare) Estimating ultraviolet reflectance from visible bands in ocean colour remote sensing 2021 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 258 Tidskriftsartikel (refereegranskat)abstract In recent years, ultraviolet (UV) bands have received increasing attention from the ocean colour remote sensing community, as they may contribute to improving atmospheric correction and inherent optical properties (IOPs) retrieval. However, most ocean colour satellite sensors do not have UV bands, and the accurate retrieval of UV remote sensing reflectance (Rrs) from UV satellite data is still a challenge. In order to address this problem, this study proposes a hybrid approach for estimating UV Rrs from the visible bands. The approach was implemented with two popular ocean colour satellite sensors, i.e. GCOM-C SGLI and Sentinel-3 OLCI. In situ Rrs collected globally and simulated Rrs spectra were used to develop UV Rrs retrieval models, and UV Rrs values at 360, 380 and 400 nm were estimated from visible Rrs spectra. The performances of the established models were evaluated using in situ Rrs and satellite data, and applied to a semi-analytical algorithm for IOPs retrieval. The results showed that: (i) UV Rrs retrieval models had low uncertainties with mean absolute percentage differences (MAPD) less than 5%; (ii) the model assessment with in situ Rrs showed high accuracy (r = 0.92–1.00 and MAPD = 1.11%–10.95%) in both clear open ocean and optically complex waters; (iii) the model assessment with satellite data indicated that model-estimated UV Rrs were more consistent with in situ values than satellite-derived UV Rrs; and (iv) model-estimated UV Rrs may improve the decomposition accuracy of absorption coefficients in semi-analytical IOPs algorithm. Thus, the proposed method has great potentials for reconstructing UV Rrs data and improving IOPs retrieval for historical satellite sensors, and might also be useful for UV-based atmospheric correction algorithms.
43.	Liu, Huizeng, et al. (författare) Evaluation of Ocean Color Atmospheric Correction Methods for Sentinel-3 OLCI Using Global Automatic In Situ Observations 2022 Ingår i: IEEE Transactions on Geoscience and Remote Sensing. - 0196-2892 .- 1558-0644. ; 60 Tidskriftsartikel (refereegranskat)abstract The Ocean and Land Color Instrument (OLCI) on Sentinel-3 is one of the most advanced ocean color satellite sensors for aquatic environment monitoring. However, limited studies have been focused on a comprehensive assessment of atmospheric correction (AC) methods for OLCI. In an attempt to fill the gap, this study evaluated seven different AC methods for OLCI using global automatic in situ observations from Aerosol Robotic Network-Ocean Color (AERONET-OC). Results showed that the POLYnomial-based algorithm applied to MERIS (POLYMER) had the best performance for bands with wavelength ≤ 443 nm, and the SeaDAS method based on 779 and 865 nm was the best for longer spectral bands; however, SeaDAS (SeaWiFS Data Analysis System) processing algorithm based on 779 and 1020 nm, as well as 865 and 1020 nm, obtained degraded AC performance; Case 2 Regional CoastColor (C2RCC) also produced large uncertainties; Baseline AC (BAC) method might be better than SeaDAS method; and simple subtraction method was the worst except for turbid waters. POLYMER and C2RCC underestimated high remote sensing reflectance (Rrs) at red and green bands; SeaDAS method based on 779 and 865 nm held an advantage for clear waters over the other two band combinations, while their difference turned small for turbid waters. AC uncertainties generally impacted the performance of chlorophyll retrievals. POLYMER outperformed other methods for chlorophyll retrieval. This study provides a good reference for selecting a suitable AC method for aquatic environment monitoring with Sentinel-3 OLCI.
44.	Locke, Adam E, et al. (författare) Genetic studies of body mass index yield new insights for obesity biology. 2015 Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 518:7538, s. 197-401 Tidskriftsartikel (refereegranskat)abstract Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in up to 339,224 individuals. This analysis identifies 97 BMI-associated loci (P < 5 × 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for ∼2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for >20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous system in obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
45.	Pahlevan, Nima, et al. (författare) ACIX-Aqua : A global assessment of atmospheric correction methods for Landsat-8 and Sentinel-2 over lakes, rivers, and coastal waters 2021 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 258 Tidskriftsartikel (refereegranskat)abstract 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 NASA - ESA activity, was initiated to enable a thorough evaluation of eight state-of-the-art atmospheric correction (AC) processors available for Landsat-8 and Sentinel-2 data processing. Over 1000 radiometric matchups from both freshwaters (rivers, lakes, reservoirs) and coastal waters were utilized to examine the quality of derived aquatic reflectances ((rho) over cap (w)). This dataset originated from two sources: Data gathered from the international scientific community (henceforth called Community Validation Database, CVD), which captured predominantly inland water observations, and the Ocean Color component of AERONET measurements (AERONET-OC), representing primarily coastal ocean environments. This volume of data permitted the evaluation of the AC processors individually (using all the matchups) and comparatively (across seven different Optical Water Types, OWTs) using common matchups. We found that the performance of the AC processors differed for CVD and AERONET-OC matchups, likely reflecting inherent variability in aquatic and atmospheric properties between the two datasets. For the former, the median errors in (rho) over cap (w)(560) and (rho) over cap (w)(664) were found to range from 20 to 30% for best-performing processors. Using the AERONET-OC matchups, our performance assessments showed that median errors within the 15-30% range in these spectral bands may be achieved. The largest uncertainties were associated with the blue bands (25 to 60%) for best-performing processors considering both CVD and AERONET-OC assessments. We further assessed uncertainty propagation to the downstream products such as near-surface concentration of chlorophyll-a (Chla) and Total Suspended Solids (TSS). Using satellite matchups from the CVD along with in situ Chla and TSS, we found that 20-30% uncertainties in (rho) over cap (w)(490 <= lambda <= 743 nm) yielded 25-70% uncertainties in derived Chla and TSS products for top-performing AC processors. We summarize our results using performance matrices guiding the satellite user community through the OWT-specific relative performance of AC processors. Our analysis stresses the need for better representation of aerosols, particularly absorbing ones, and improvements in corrections for sky- (or sun-) glint and adjacency effects, in order to achieve higher quality downstream products in freshwater and coastal ecosystems.
46.	Pellegrino, Andrea, et al. (författare) Assessing the Accuracy of PRISMA Standard Reflectance Products in Globally Distributed Aquatic Sites 2023 Ingår i: Remote Sensing. - 2072-4292. ; 15:8 Tidskriftsartikel (refereegranskat)abstract PRISMA is the Italian Space Agency’s first proof-of-concept hyperspectral mission launched in March 2019. The present work aims to evaluate the accuracy of PRISMA’s standard Level 2d (L2d) products in visible and near-infrared (NIR) spectral regions over water bodies. For this assessment, an analytical comparison was performed with in situ water reflectance available through the ocean color component of the Aerosol Robotic Network (AERONET-OC). In total, 109 cloud-free images over 20 inland and coastal water sites worldwide were available for the match-up analysis, covering a period of three years. The quality of L2d products was further evaluated as a function of ancillary parameters, such as the trophic state of the water, aerosol optical depth (AOD), observation and illumination geometry, and the distance from the coastline (DC). The results showed significant levels of uncertainty in the L2d reflectance products, with median symmetric accuracies (MdSA) varying from 33% in the green to more than 100% in the blue and NIR bands, with higher median uncertainties in oligotrophic waters (MdSA of 85% for the entire spectral range) than in meso-eutrophic (MdSA of 46%) where spectral shapes were retained adequately. Slight variations in the statistical agreement were then noted depending on AOD values, observation and illumination geometry, and DC. Overall, the results indicate that water-specific atmospheric correction algorithms should be developed and tested to fully exploit PRISMA data as a precursor for future operational hyperspectral missions as the standard L2d products are mostly intended for terrestrial applications.
47.	Philipson, Petra, et al. (författare) Satellite-based water quality monitoring in Lake Vänern, Sweden 2016 Ingår i: International Journal of Remote Sensing. - : Informa UK Limited. - 0143-1161 .- 1366-5901. ; 37:16, s. 3938-3960 Tidskriftsartikel (refereegranskat)abstract Lake Vänern, Sweden, is one of Europe’s largest lakes and has a historical, cultural, ecological as well as economic importance. Lake water quality monitoring is required by national and international legislations and directives, but present programmes are insufficient to meet the requirements. To complement in situ based monitoring, the possibility to obtain reliable information about spatial and temporal water quality trends in Lake Vänern from the ENVISAT mission’s MERIS instrument was evaluated. The complete archive (2002–2012) of MERIS (Medium Resolution Imaging Spectrometer) full resolution data was processed using the water processor developed by Free University Berlin (FUB) to derive aerosol optical thickness (AOT), remote-sensing reflectance (Rrs) and water quality parameters: chlorophyll-a (chl-a) concentration, coloured dissolved organic matter absorption at 443 nm (CDOM), and total suspended matter (TSM) concentration. The objective was to investigate if, either, FUB reflectance products in combination with potential lake-specific band ratio algorithms for water quality estimation, or directly, FUB water quality products, could complement the existing monitoring programme.Application of lake-specific band ratio algorithms requires high-quality reflectance products based on correctly estimated AOT. The FUB reflectance and AOT products were evaluated using Aerosol Robotic Network – Ocean Color (AERONET-OC) match-up data measured at station Pålgrunden in Lake Vänern. The mean absolute percentage differences (MAPDs) of the final reflectance retrievals at 413, 443, 490, 555, and 665 nm were 510%, 48%, 33%, 34%, and 33%, respectively, corresponding to a large positive bias in 413 nm, positive bias in 443–555 nm, and a negative bias in 665 nm. AOT was strongly overestimated in all bands.The FUB water quality products were evaluated using match-up in situ data of chl-a, filtered absorbance (AbsF(420)) and turbidity as AbsF(420) is related to CDOM and turbidity is strongly related to TSM. The in situ data was collected within the Swedish national and regional monitoring programmes. In order to widen the range of water constituents and add more data to the analysis, data from four large Swedish lakes (Vänern, Vättern, Mälaren, and Hjälmaren) was included in the analysis. High correlation (r ≥ 0.85) between in situ data and MERIS FUB derived water quality estimates were obtained, but the absolute levels were over- (chl-a) or under- (CDOM) estimated. TSM was retrieved without bias.Calibration algorithms were established for chl-a and CDOM based on the match-up data from all four lakes. After calibration of the MERIS FUB data, realistic time series could be derived that were well in line with in situ measurements. The MAPDs of the final retrievals of chl-a, AbsF(420) and Turbidity in Lake Vänern were 37%, 15%, and 35%, respectively, corresponding to mean absolute differences (MADs) of 0.9 µg l−1, 0.17 m−1, and 0.32 mg l−1 in absolute values.The partly inaccurate reflectance estimations in combination with both positive and negative bias imply that successful application of band ratio algorithms is unlikely. The high correlation between MERIS FUB water quality products and in situ data, on the other hand, shows a potential to complement present water quality monitoring programmes and improve the understanding and representability of the temporally and spatially sparse in situ observations. The monitoring potential shown in this study is applicable to the Sentinel-3 mission’s OLCI (Ocean Land Colour Instrument), which was launched by the European Space Agency (ESA) in February 2016 as a part of the EC Copernicus programme.
48.	Pierson, Donald C., et al. (författare) Relationship between the attenuation of downwelling irradiance at 490 nm with the attenuation of PAR (400 nm-700 nm) in the Baltic Sea 2008 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 112:3, s. 668-680 Tidskriftsartikel (refereegranskat)abstract The vertical attenuation coefficient of diffuse downwelling irradiance at 490 nm (K-d 490) is a parameter that we routinely derive from SeaWiFS images of the Baltic Sea. Here, through model simulations, we examine the relationship between Kd(490), and the vertical attenuation coefficient of PAR (Kd PAR), as this later coefficient determines the light available for aquatic photosynthesis. A simple semi-analytical model is used to predict Kd(490) and Kd(PAR), as a function of the concentrations of chlorophyll, colored dissolved organic material (CDOM), suspended inorganic, and suspended organic particulate material. A series of model simulations based on variations in these optically significant constituents over a range realistic for the Baltic Sea, are used to define the relationship between the two attenuation coefficients. K-d(PAR) = 0.6677K(d)(490)(0.6763). This relationship was verified, using data collected independently from the data set used to derive model coefficients, and appears robust when applied to the Baltic Sea. Comparison to other studies and model sensitivity analyses suggest that the relationship will be dependent on relatively large regional variations in CDOM absorption. A relationship between K-d(490) and Secchi disk depth was also developed and verified. This relationship while useful was more uncertain. The uncertainty was related to a greater influence of scattering on Secchi disk depth estimates and the corresponding parameterization of scattering in our model.
49.	Sathyendranath, Shubha, et al. (författare) An Ocean-Colour Time Series for Use in Climate Studies : The Experience of the Ocean-Colour Climate Change Initiative (OC-CCI) 2019 Ingår i: Sensors. - : MDPI AG. - 1424-8220. ; 19:19 Tidskriftsartikel (refereegranskat)abstract Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.
50.	Sterckx, S., et al. (författare) SIMilarity Environment Correction (SIMEC) applied to MERIS data over inland and coastal waters 2015 Ingår i: Remote Sensing of Environment. - : Elsevier BV. - 0034-4257 .- 1879-0704. ; 157, s. 96-110 Tidskriftsartikel (refereegranskat)abstract The launch of several new satellites such as Sentinel-2, Sentinel-3, HyspIRI, EnMAP and PRISMA in the very near future, opens new perspectives for the inland and coastal water community. The monitoring of the water quality closer to the coast, within estuaries or small lakes with satellite data will become feasible. However for these inland and nearshore coastal waters, adjacency effects may hamper the correct retrieval of water quality parameters from remotely sensed imagery. Here, we present a sensor-generic adjacency pre-processing method, SIMilarity Environment Correction (SIMEC). The correction algorithm estimates the contribution of the background radiance based on the correspondence with the Near-INfrared (NIR) similarity spectrum. The performance of SIMEC was tested on MERIS FR images both above highly reflecting waters with high SPM loads, as well as dark lake waters with high CDOM absorption. The results show that SIMEC has a positive or neutral effect on the normalized remote sensing reflectance above optically-complex waters, retrieved with the MERIS MEGS or UR processor.

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