Bio-optical properties of east coast Malaysia waters in relation to remote sensing of chlorophyll

Surface water samples collected during the monsoon and inter-monsoon seasons of 2009 off the east coast of Peninsular Malaysia have been analysed for concentrations of total chlorophyll, suspended particulates and coloured dissolved organic matter (CDOM). Spectral absorption coefficients of dissolved and particulate materials have also been measured. Significant seasonal variabilities in concentrations and optical properties were reported with high concentrations of all parameters during the northeast monsoon (NEM) season and low during the southwest monsoon (SWM) and inter-monsoon seasons. Contrary to previous reports on the oligotrophic nature of the waters during the inter-monsoon season, relatively high concentrations of chlorophyll (>3 mg m^?3) were observed at offshore stations in the study area in the spring and fall inter-monsoon months. The chlorophyll-specific absorption spectrum changes with the seasons with the greatest absorption per unit chlorophyll during the SWM and the least during the inter-monsoon seasons, probably in response to seasonal changes in phytoplankton community and cell size structure. The water is classified as optical case 2. At the blue end of the spectrum (440 nm), light absorption by non-phytoplankton materials (CDOM and detritus) accounts for nearly 70% of the total non-water absorption regardless of the season. At the wavelength (676 nm) of the secondary chlorophyll absorption peak in the red part of the spectrum, light absorption by chlorophyll contributes 80–90% to total non-water absorption at most stations and this may provide the basis for remote sensing of phytoplankton chlorophyll in these waters.     

A single probe fibre optic fluorosensor for marine and freshwater measurements of phytoplankton populations

A white light optical fibre fluorosensor for water quality measurements of the phytoplankton population is reported. The excitation light is amplitude modulated and a phase sensitive detection system is employed. The spectral properties of two typical samples of phytoplankton obtained off the coast of Scotland have been characterised and used in laboratory tests of the fluorosensor. Initial results show that this system is capable of resolving fluorescein concentrations in water of 10^?8mol 1^?1 and phytoplankton populations of 0.1 μgl.     

Estimation of phytoplankton pigment concentration in the Gulf of Aqaba (Eilat) by in situ and remote sensing single-wavelength algorithms

Bio-optical relationships between inherent and apparent optical properties, and between optical properties and phytoplankton pigment concentration (C) averaged in a discrete layer, were developed. These relationships were derived from analysis of data collected during the period 1996–1998 in the Gulf of Aqaba (Eilat), a ‘Case 1’ type water body. Parameterization of these relationships was accomplished by combining Gershun's equation, radiative transfer theory for average cosine of underwater light field, and a set of different bio-optical models. An analysis of the asymptotic light field was carried out. Semi-analytical single-wavelength (at λ = 443nm) algorithms for in situ and remote sensing (RS) estimation of mean pigment concentration were developed, and evaluated by sensitivity and error analysis. The advantages of RS single-wavelength algorithms in comparison with current two- and multi-wavelengths RS algorithms are discussed.     

Bio‐optical properties and estimation of the optically active substances in Lake Tianmuhu in summer

Bio‐optical properties in an optically complex and biologically productive region of Lake Tianmuhu were determined in three cruises from June to August 2006. The concentrations of three optically active substances, tripton C _Tripton (calculated from total suspended matter and chlorophyll‐a (Chla) and phaeophytin‐a (Pa)), phytoplankton pigment C _Chla+Pa , and chromophoric dissolved organic matter (CDOM) a _CDOM(440), were predicted from the estimated irradiance reflectance based on in situ measurements and laboratory analyses. The total relative contributions of phytoplankton, tripton, CDOM and pure water over the range of photosynthetically active radiation (PAR) (400–700 nm) were 36.1%, 24.2%, 15.9% and 23.8%, respectively. The dominant contribution of phytoplankton to the total absorption was due to high phytoplankton pigment concentration. The range and variation in irradiance reflectance and diffuse attenuation coefficient derived from a bio‐optical model, based on inherent optical properties, compared well with the measured variability. A reasonably strong relationship (R² = 0.92) was observed between irradiance reflectance at 780 nm R(780) and C _Tripton. For our data set, the best algorithm for C _Chla+Pa used the three‐band reflectance model [R ^?1(688)?R ^?1(717)]×R(747). The a _CDOM(440) could be estimated using the ratio of irradiance reflectance R(682)/R(555). The retrieval accuracy (R²) of tripton, phytoplankton pigment and CDOM was 0.92, 0.87 and 0.91, respectively, while the rms. error was 0.90 mg l^?1 (18.2%), 3.27 µg l^?1 (14.8%) and 0.073 m^?1 (15.3%), respectively. Estimation of the concentrations of the three optically active substances was reasonably accurate based on inherent optical properties measurement.     

Point or pointless – quality of ground data

A method for measuring continuously the inherent optical properties of water together with the salinity and the temperature values was developed and tested at the Division of Geophysics, University of Helsinki. The flow‐through system operates from a moving boat and has been used to collect parameters for optical modelling, coastal zone and inland water studies and to track the path of the fresh water spreading into sea areas. The system was also used in Lake Vänern, Sweden, to calculate the radiance reflectance, R _r, and total back‐scattering efficiency, b _{b eff}, along a transect. An example from the Gulf of Finland is presented, which shows how the spectral behaviour of light changes when moving away from a fresh water source. Data collected from the River Kymijoki estuary showed that the details in a rapidly changing environment were strongly smoothed in a Moderate Resolution Imaging Spectroradiometer (MODIS) data image. The correlation for continuously measured scattering values and MODIS channel 1 data varied between 0.70 and 0.85, n?=?126. Flow‐through measurement datasets can be used to obtain representative sites for vertical profiles or calibration measurements.     

Single-wavelength algorithms for in situ or remote sensing estimation of mean pigment concentration

The bio-optical relationships between inherent and apparent optical properties, and between optical properties and phytoplankton pigment concentration (C) averaged in a layer (ΔZ), were derived from analysis of data collected during the period 1996–1998 in the Gulf of Aqaba (Eilat). Parametrization of these relationships was based on radiative transfer theory, Gershun's equation, minimization of model errors by least-square fitting, and on known optical models relating underwater remote sensed reflectance (R _rsw) with the ratio of backscattering (b _b) to vertical attenuation coefficient (K _d) [or to absorption coefficient (a)]. These relationships explain a frequently used form of remote sensing algorithms for C estimation using ratio of water-leaving radiances measured at two or more wavelengths (λ). In this study, the possibility of using for this purpose a single wavelength in the blue range (λ=443?nm) within the framework of in situ and remote sensing algorithms for Case 1 waters was assessed.     

Sensitivity of the Indian Ocean circulation to phytoplankton forcing using an ocean model

Most ocean general circulation models (OGCMs) do not take into account the effect of space- and time-varying phytoplankton on solar radiation penetration, or do it in a simplistic way using a constant attenuation depth, even though one-dimensional experiments have shown potential significant effect of phytoplankton on mixed-layer dynamics. Since some ocean basins are biologically active, it is necessary for an OGCM to take water turbidity into account, even if it is not coupled with a biological model. Sensitivity experiments carried out with the Massachusetts Institute of Technology (MIT) OGCM with spatially and temporally-varying pigment concentration from Sea-viewing Wide Field-of-view Sensor (SeaWiFS) data during 1998-2003 reveal the effect of ocean turbidity on tropical Indian Ocean circulation. Variations of light-absorbing phytoplankton pigments change the vertical distribution of solar heating in the mixed layer, thereby affecting upper-ocean circulation. A simulation was performed from 1948 to 2003 with a constant minimum pigment concentration of 0.02 mg m^− 3 while another simulation was performed from September 1997 to December 2003 with variable pigment concentration, and the differences between these two simulations allow us to quantify the effects of phytoplankton on solar radiation penetration in the ocean model. Model results from a period of 6 years (1998-2003) show large seasonal variability in the strength of the meridional overturning circulation (MOC), meridional heat transports (MHT), and equatorial under current (EUC). The MOC mass transport changes by 2 to 5 Sv (1 Sv = 10⁶ m³ s^− 1) between boreal winter (January) and boreal summer (July), with a corresponding change in the MHT of ∼ 0.05 PW (1 PW = 10¹⁵ W) in boreal winter, which is close to the expected change associated with a significant climate change [Shell, K., Frouin, R., Nakamoto, S., & Somerville, R.C.J. (2003): Atmospheric response to solar radiation absorbed by phytoplankton. Journal of Geophysical Research, 108(D15), 4445. doi:10.1029/2003JD003440.]. In addition, changes in phytoplankton pigments concentration are associated with a reduction in the EUC by ∼ 3 cm s^− 1. We discuss the possible physical mechanisms behind this variability, and the necessity of including phytoplankton forcing in the OGCM.     

Mapping bottom depth and albedo in coastal waters of the South China Sea islands and reefs using Landsat TM and ETM+ data

Optical models for the retrieval of shallow water bottom depth and albedo using multispectral data usually require in situ water depth data to tune the model parameters. In the South China Sea (SCS), however, such in situ data are often lacking or obsolete (perhaps from half a century ago) for most coastal waters around its islands and reefs. Here, we combine multispectral data collected by MODIS and Landsat to estimate bottom depth and albedo for four coral reef regions in the SCS, with results partially validated by some scarce in situ data. The waters in these remote regions are oligotrophic whose optical properties can be well derived from Moderate Resolution Imaging Spectroradiometer (MODIS) measurements when the waters are optically deep. The MODIS-derived optical properties are used to estimate the water column attenuation to the Landsat measurements over shallow waters, thus eliminating the requirement of model tuning using field measured water depths. The model is applied to four Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) images covering Pratas Atoll, Woody Island, Scarborough Shoal, and North Danger Reefs. The retrieved bathymetry around Pratas Atoll and North Danger Reefs are validated with some in situ data between 1 and 25 m. The relative difference and root mean square difference between the two measurements were 17% and 1.6 m, for Pratas Atoll and 11% and 1.1 m for North Danger Reefs, respectively. These results suggest that the approach developed here may be extended to other shallow, clear waters in the SCS.     

An absorption model to determine phytoplankton size classes from satellite ocean colour

We have developed a model linking phytoplankton absorption to phytoplankton size classes (PSCs) that uses a single variable, the optical absorption by phytoplankton at 443 nm, a_ph(443), which can be derived from the inversion of ocean colour data. The model is based on the observation that the absolute value of a_ph(443) co-varies with the spectral slope of phytoplankton absorption in the range of 443-510 nm, which is also a characteristic of phytoplankton size classes. The model when used for analysis of SeaWiFS global data, showed that picoplankton dominated ~ 79.1% of surface waters, nanoplankton ~ 18.5% and microplankton the remainder (2.3%). The N. and S. Atlantic and the N. and S. Pacific Oceans showed seasonal cycles with both micro and nanoplankton increasing in spring and summer in each hemisphere, while picoplankton, dominant in the oligotrophic gyres, decreased in the summer. The PSCs derived from SeaWiFS data were verified by comparing contemporary 8-day composites with PSCs derived from in situ pigment data from quasiconcurrent Atlantic Meridional Transect cruises.     

Coupled Path Planning,Region Optimization,and Applications in Intensity-modulated Radiation Therapy

In this paper, we consider an optimization problem in discrete geometry, called coupled path planning (CPP). Given a finite rectangular grid and a non-negative function f defined on the horizontal axis of the grid, we seek two non-crossing monotone paths in the grid, such that the vertical difference between the two paths approximates f in the best possible way. This problem arises in intensity-modulated radiation therapy (IMRT), where f represents an ideal radiation dose distribution and the two coupled paths represent the motion trajectories (or control sequence) of two opposing metal leaves of a delivery device for controlling the area exposed to the radiation source. By finding an optimal control sequence, the CPP problem aims to deliver precisely a prescribed radiation dose, while minimizing the side-effects on the surrounding normal tissue. We present efficient algorithms for different versions of the CPP problems. Our results are based on several new ideas and geometric observations, and substantially improve the solutions based on standard techniques. Implementation results show that our CPP algorithms run fast and produce better quality clinical treatment plans than the previous methods.     

Detection and monitoring of algal blooms using SeaWiFS imagery

SeaWiFS (Sea viewing Wide Field of view Sensor) imagery is used to monitor the birth, development and termination of phytoplankton blooms in the north-east Atlantic. Extensive patches of water giving high reflectance of visible light were observed from the beginning of February to the end of July 1998 in the Celtic and Armorican Shelf regions between 45° and 60°?N and interpreted as phytoplankton. Eighteen relatively cloud-free SeaWiFS images have been analysed in order to detect the spatial, temporal and spectral development of the blooms within the two study areas. Consistency of the spectral signature and the very high broadband reflectance leads to the conclusion that these are blooms of the widespread coccolithophore Emiliana huxley, although no in situ data during the study period are available to validate this hypothesis. The utility of SeaWiFS data for studying the life history of phytoplankton blooms is confirmed.     

Analyzing the status of submerged aquatic vegetation using novel optical parameters

The reservoirs constructed throughout Brazil for electrical power generation following its industrial and socioeconomic development now favour abundant aquatic macrophyte growth. Nova Avanhandava Reservoir is fully inhabited by submerged aquatic vegetation (SAV) that poses serious ecological and economic threats. The overall goal of this study was to assess the radiation availability in the water column in the Nova Avanhandava Reservoir and analyse its influence on SAV development and growth. In addition to the diffuse attenuation coefficient (K_d) and euphotic zone depth (Z_EZ), optical parameters such as percentage light through the water (PLW) were computed and analysed to achieve the objective. Nineteen sampling locations were considered for both spectroradiometer measurements and water sampling for analytical determination of total suspended solids (TSS) and chlorophyll-a concentration. Depth, SAV height, and precise position were also collected through hydro-acoustic measurements. The upstream region showed the highest TSS and K_d levels compared to the downstream. SAV heights were found to be lower upstream compared to downstream. The growth of tall SAV was favoured by low PLW, which grew taller to intercept required radiation. Locations with high transparency (lower K_d) also favoured the development of tall SAV compared to areas of high K_d. This may mean that low PLW values favour tall SAV growth if K_d is low enough not to hinder this. An inverse relationship between SAV height and attenuation of photosynthetic active radiation (K_d,PAR) was observed with a coefficient of determination of R² = 0.56 (p < 0.001), demonstrating that SAV height can be estimated using K_d,PAR with significant accuracy.     

Optical models of mesotrophic and eutrophic water bodies

Abstract

Interpretation techniques have been developed to process the spectra of upwelling radiation from water in the visible. Spectral indices to retrieve the concentration of optically active components have been suggested. They make it possible to retrieve the chlorophyll-a concentration with a standard error of less than 2.6mgm^?3, mineral suspended matter concentration less than 4mgl^?l, and dissolved organic matter concentration less than O.5mgCl^?1. The instrumentation is described for measurments of the upwelling radiation as well as for operational determination of the concentrations of phytoplankton chlorophyll-a, mineral suspended matter and dissolved organic matter.     

Retrieval of marine water constituents from AVIRIS data in the Hudson/Raritan Estuary

This paper reports on the validation of bio‐optical models in estuarine and nearshore (case 2) waters of New Jersey–New York to retrieve accurate water leaving radiance spectra and chlorophyll concentration from the NASA Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data complemented with in situ measurements. The study area—Hudson/Raritan Estuary—is a complex estuarine system where tidal and wind‐driven currents are modified by freshwater discharges from the Hudson, Raritan, Hackensack, and Passaic rivers. Over the last century the estuarine water quality has degraded, in part due to eutrophication, which has disrupted the pre‐existing natural balance, resulting in phytoplankton blooms of both increased frequency and intensity, increasing oxygen demand and leading to episodes of hypoxia. During 1999–2001 data acquisitions by NASA AVIRIS field measurements were obtained to establish hydrological optical properties of the Hudson/Raritan Estuary: (1) concurrent above‐ and below‐surface spectral irradiance; (2) sampling for laboratory determination of inherent optical properties; and (3) concentrations of optically‐important water quality parameters. We used a bio‐optical model based on Gordon et al. to predict the sub‐surface irradiance reflectance from optically important water constituents. Modelling of reflectance is a prerequisite for processing remote sensing data to desired thematic maps for input into the geographical information system (GIS) for use as a management tool in water quality assessment. A Radiative Transfer Code—MODTRAN‐4—was applied to remove the effects of the atmosphere so as to infer the water leaving radiance from the AVIRS data. The results of this procedure were not satisfactory, therefore an alternative approach was tested to directly correct the AVIRIS image using modelled spectra based on measured optical characteristics. The atmospherically corrected AVIRIS ratio image was used to calculate a thematic map of water quality parameters (i.e. chlorophyll‐a) concentration, which subsequently were integrated into a GIS for management of water quality purposes.     

Extending one-dimensional models for deep lakes to simulate the impact of submerged macrophytes on water quality

Submerged macrophytes can stabilise clear water conditions in shallow lakes. However, many existing models for deep lakes neglect their impact. Here, we tested the hypothesis that submerged macrophytes can affect the water clarity in deep lakes. A one-dimensional, vertically resolved macrophyte model was developed based on PCLake and coupled to SALMO-1D and GOTM hydrophysics and validated against field data. Validation showed good coherence in dynamic growth patterns and colonisation depths. In our simulations the presence of submerged macrophytes resulted in up to 50% less phytoplankton biomass in the shallowest simulated lake (11 m) and still 15% less phytoplankton was predicted in 100 m deep oligotrophic lakes. Nutrient loading, lake depth, and lake shape had a strong influence on macrophyte effects. Nutrient competition was found to be the strongest biological interaction. Despite a number of limitations, the derived dynamic lake model suggests significant effects of submerged macrophytes on deep lake water quality.     

Estimation of catchment-scale water-balance with a soil-vegetation-atmosphere transfer model

Catchments with a small elevation range and relatively long dry periods in high radiation conditions may be described as an array of vertical one-dimensional pathways for water and energy. Such a representation enhances the ability of SVAT modeling to simulate mass exchanges across the catchment. This note reports on a comparison of a Soil-Vegetation-Atmosphere Transfer (SVAT) model (Braud et al., 1995), a deterministic hydrological model (Dawes and Hatton, 1993) and a stochastic hydrological model (Sivapalan and Woods, 1995; Kalma et al., 1995). The original version of the SVAT model only considers vertical transport and this one-dimensional representation must be aggregated to describe the entire catchment. Therefore, two new versions have been developed: a deterministic SVAT model which sub-divides the catchment into 40 sub-regions linked by surface flow, and a stochastic model which provides a distribution of the output fluxes as related to the spatial distribution of initial water content and/or soil properties. All simulations have been made for a 60-day period.     

Spectral absorption properties of dissolved and particulate matter in Lake Erie

Spectral absorption properties of particulate and dissolved matter were determined for Lake Erie waters in order to investigate the natural variability of the absorption coefficients required as inputs to optical models for converting satellite observations of water colour into water quality information. Particulate absorption measured using the quantitative filter technique yielded absorption spectra containing a fraction that could not be attributed to phytoplankton pigments, living heterotrophs, mineral sediments, or organic detritus but were indicative of additional absorption by a fraction of dissolved organic matter present in colloidal and/or particle-bound form. Erroneously high phytoplankton absorption coefficients measured at short wavelengths using the filter technique suggested that this particle-bound DOM is removed along with phytoplankton pigments during bleaching by sodium hypochlorite and as such is mistakenly incorporated into the phytoplankton absorption signal. Observations suggest that the selective sorption of fractions of DOM onto suspended particles may be responsible for significant variability in the absorption coefficients of particulate and dissolved matter and may be an important contributor to the total spectral absorption signals in Lake Erie waters. This reservoir of coloured organic matter, which to date has not been seriously considered in the optical properties of coastal and inland waters, may produce significant uncertainties in the parameterization of optical models and the interpretation of in situ and remotely sensed aquatic colour signals.     

Absorption characteristics of ocean water in the Arabian Sea during winter bloom from in situ measurements and Oceansat 2 OCM and MODIS data

In the northern Arabian Sea, blooms usually occur during the northeast monsoon (November–January) and inter-monsoon (February–April) periods. After death, these phytoplankton blooms produce massive subsurface zones of low dissolved oxygen levels that have a major impact on the ocean water ecosystem. Many studies have been done to identify the bloom in this region, but those on the optical properties of bloom water are scarce. The present study emphasizes the optical properties (inherent) of the bloom water in the study region using in situ and satellite data. The total absorption coefficient of ocean water was measured from in situ radiance data collected in the northern Arabian Sea from the Sagar Sampada cruise (SS-286) during March 2011. The same data were also derived from the top-of-atmosphere radiance and remote sensing reflectance of the Oceansat 2 Ocean Colour Monitor (OCM-2) and Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) sensors, respectively. A comparison between measured (in situ) and retrieved total absorption coefficients from OCM-2 was made. The measured and retrieved absorption coefficients are in good agreement. Root mean square errors between measured and retrieved absorption coefficients are 0.018 m^?1, 0.026 m^?1, and 0.034 m^?1 for 490 nm, 510 nm, and 555 nm, respectively. An inter-comparison of total absorption properties retrieved from OCM-2 and MODIS data in the region of one degree radius around the stations was also made. A fairly good match was observed on 10, 14, and 16 March 2011 (coefficient of determination, R² = 0.75, 0.87, and 0.62, respectively) for the blue band (490 nm) and (R² = 0.77, 0.79, and 0.71, respectively) the green band (555 nm). The study demonstrates the potential of using remote-sensing optical data for identifying bloom waters.     

A multispectral remote sensing study of coastal waters off Vancouver Island

In March 1996, a multispectral aircraft survey of the coastal waters off Vancouver Island was carried out using a Compact Airborne Spectrographic Imager (CASI). This survey was combined with in situ measurements of water properties (phytoplankton composition, phytoplankton pigments, absorption spectra of phytoplankton, and concentration of dissolved organic carbon, or DOC). Comparison of the phytoplankton absorption data from this experiment with similar data from other regions shows that phytoplankton community has a significant impact on the spectral form and magnitude of absorption spectra, when normalized to unit chlorophyll-a. Concurrent measurements of in situ properties and aircraft data were obtained at eight stations. The in situ measurements of phytoplankton absorption and estimates of downwelling irradiance based on a clear-sky atmospheric-transmission model are used as inputs to a model of water-leaving irradiance. The modelled irradiances are compared with the remotely sensed values of water-leaving radiances. The observed differences between model and observation are used to evaluate the potential influence of DOC on water-leaving radiance. Practical difficulties of separating the phytoplankton signal from that of the coloured component of DOC (also known as yellow substance) are examined. Algorithms for estimation of the concentration of chlorophyll-a (the major phytoplankton pigment) can be based on their absorption or fluorescence properties. The distribution of chlorophyll-a in the study area is estimated using both these approaches, and possible causes for the observed discrepancies are discussed.     

Radiometric and photometric determinations of simulated shallow-water environment

Optical remote sensing is increasingly becoming a preferred economic alternative to the traditional in situ observations and physical sampling for mapping and monitoring habitats. Submersed habitats, such as eelgrass and corals, are especially challenging for field work. Even for remote-sensing work, a priori knowledge of environmental factors is required for highly accurate analysis. Background illumination and water clarity are two key factors that affect the optical remote-sensing imagery, which may vary widely with season, time of year, geographic location, or water depth. This article presents efforts to simulate natural oceanic conditions in a laboratory setting. Solar radiation predicted at different latitudes under varying water clarity conditions and depth were replicated using a 2.5 m deep wave tank at the University of New Hampshire. The goals of the study were: (1) to simulate illumination and water clarity conditions that approximate coastal and oceanic waters, and (2) to quantify the impact of the simulated illumination and water clarity conditions at different depths on the apparent colours that can be observed from an aerial platform. The empirical radiometric measurements included irradiance, radiance, and remote-sensing reflectance from an underwater array of light sources. The results of the study show good correlation (r ²?=?0.89–0.93) between the natural daylight spectrum at the water surface and the irradiance measurements between 350 nm and 590 nm, at 3.5 m from the light array. The colours of the clear and murky water types were photometrically calculated from the radiometric measurements and validated using underwater video imagery. Using this methodology, illumination and water clarity can be replicated under controlled laboratory conditions and used to assist in studying the physical, chemical, and biological processes in habitats, at varied geographic locations and differing environments.