Search results | Digital Commons of Moss Landing Marine Laboratories

Title: Stray light correction of the marine optical system,
Description: The Marine Optical System is a spectrograph-based sensor used on the Marine Optical Buoy for the vicarious calibration of ocean color satellite sensors. It is also deployed from ships in instruments used to develop bio-optical algorithms that relate the optical properties of the ocean to its biological content. In this work, an algorithm is applied to correct the response of the Marine Optical System for scattered, or improperly imaged, light in the system. The algorithm, based on the measured response of the system to a series of monochromatic excitation sources, reduces the effects of scattered light on the measured source by one to two orders of magnitude. Implications for the vicarious calibration of satellite ocean color sensors and the development of bio-optical algorithms are described. The algorithm is a one-dimensional point spread correction algorithm, generally applicable to nonimaging sensors, but can in principle be extended to higher dimensions for imaging systems. © 2009 American Meteorological Society., Cited By (since 1996):6, Oceanography, CODEN: JAOTE, , , Downloaded from: journals.ametsoc.org/doi/pdf/10.../2008JTECHO597.1 (16 June 2014).
Author: Feinholz, Flora, Yarbrough, Lykke, Brown, Johnson, Clark
Date: 2009-01-01T00:00:00Z

Title: The Marine Optical Buoy (MOBY) radiometric calibration and uncertainty budget for ocean color satellite sensor vicarious calibration,
Description: For the past decade, the Marine Optical Buoy (MOBY), an autonomous radiometric buoy stationed in the waters off Lanai, Hawaii, has been the primary in-water oceanic observatory for the vicarious calibration of U. S. satellite ocean color sensors, including the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and the Moderate Resolution Imaging Spectrometer (MODIS) instruments on the National Aeronautics and Space Administration's (NASA's) Terra and Aqua satellites. The MOBY vicarious calibration of these sensors supports international efforts to develop a global, multi-year time series of consistently calibrated ocean color data products. A critical component of the MOBY program is establishing radiometric traceability to the International System of Units (SI) through standards provided by the U. S. National Institute of Standards and Technology (NIST). A detailed uncertainty budget is a core component of traceable metrology. We present the MOBY uncertainty budget for up-welling radiance and discuss approaches in new instrumentation to reduce the uncertainties in in situ water-leaving radiance measurements., Cited By (since 1996):10, Oceanography, Art. No.: 67441M, CODEN: PSISD, ,
Author: Brown, Flora, Feinholz, Yarbrough, Houlihan, Peters, Yong, Mueller, Johnson, Clark
Date: 2007-01-01T00:00:00Z

Title: Radiometric characterization and absolute calibration of the Marine Optical System (MOS) Bench Unit,
Description: The Marine Optical System (MOS) is a dual charge-coupled device (CCD)-based spectrograph system developed for in-water measurements of downwelling solar irradiance E d and upwelling radiance L u. These measurements are currently used in the calibration and validation of satellite ocean color measurement instruments such as the moderate resolution imaging spectroradiometer (MODIS) and the Sea-viewing Wide Field-of view Sensor (SeaWiFS). MOS was designed to be deployed from a ship for single measurements and also integrated into the Marine Optical Buoy (MOBY) for longer time series datasets. Measurements with the two spectrographs in the MOS systems can be compared in the spectral interval from about 580 to 630 nm. In this spectral range, they give different values for L u or E d at a common wavelength. To better understand the origin of this observation and the sources of uncertainty in the calibration of MOBY, an MOS bench unit was developed for detailed radiometric characterization and calibration measurements in a laboratory setting. In the work reported here, a novel calibration approach is described that uses a tunable laser-based, monochromatic, spatially uniform. Lambertian, large area integrating sphere source (ISS). Results are compared with those obtained by a conventional approach using a lamp-illuminated ISS. Differences in the MOS bench unit responsivity between the two calibration approaches were observed and attributed to stray light. A simple correction algorithm was developed for the lamp-illuminated ISS that greatly improves the agreement between the two techniques. Implications for water-leaving radiance measurements by MOS are discussed., Cited By (since 1996):2, CODEN: JAOTE, , , Downloaded from: journals.ametsoc.org/ (13 June 2014).
Author: Habauzit, Brown, Lykke, Johnson, Feinholz, Yarbrough, Clark
Date: 2003-01-01T00:00:00Z

Title: Effects of shade from multiple kelp canopies on an understory algal assemblage,
Description: We examined the effects of shade from multiple kelp canopy layers (surface Macrocystis pyrifera canopy, understory Pterygophora californica canopy), both individually and in combination, on an understory algal assemblage in a central Californian kelp forest. The removal of both kelp canopies resulted in a dense recruitment of the understory brown alga Desmarestia ligulata that formed a third canopy layer, which significantly decreased bottom light and the abundance of understory red algae. We subsequently created an additional canopy treatment by removing this third canopy layer. In general, the understory red algae fluctuated seasonally with winter swell intensity, changes in kelp canopy cover, and grazing; and although species richness increased significantly with increased bottom light, red algal bottom cover did not respond significantly to the canopy clearings until 2 yr after the canopies were initially cleared. Red algal cover within the Pterygophora canopy treatment was similar to that in the control treatment. In the absence of Pterygophora, the Macrocystis canopy treatment and 'no canopy' treatment were found to have greater red algal cover and species richness. Individual understory species were rare, which resulted in small effects sizes and thus low statistical power. However, when grouped post hoc, according to how they responded to the canopy clearings (i.e. response groups), we were able to detect canopy treatment effects as much as 1 yr earlier. This method identified that some understory red algae adapted to areas of canopy removal (light-adapted), and others adapted to a variety of light regimes (shade-tolerant). We were able to classify the light-adapted algae into 2 subgroups: the high-light species and the intermediate-light species. Although this method of grouping was done post hoc, our results indicate that it may provide the clearest assessment of how understory algae respond to shading from kelp canopies., Cited By (since 1996):40, Seaweeds, CODEN: MESED, ,
Author: Clark, Edwards, Foster
Date: 2004-01-01T00:00:00Z

Title: Ocean optics protocols for satellite ocean color semsor validation, revision 4, Volume VI: Special topics in ocean protocols and appendices,
Description: , , ,
Author: Mueller, Clark, Kuwahara, Lazin, Brown, Fargion, Yarbrough, Feinholz, Flora, Broenkow, Kim, Johnson, Yuen, Strutton, Dickey, Abbott, Letelier, Lewis, McLean, Chavez, Barnard, Morrison, Subramaniam, Manov, Zheng, Harding Jr., Barnes, Lykke
Date: 2003-01-01T00:00:00Z

Title: Validation of a wetland rapid assessment method: Use of EPA's level 1-2-3 framework for method testing and refinement,
Description: Wetland rapid assessment has become popular in a variety of applications. Because rapid assessments rely on observable field indicators as surrogates for direct measures of condition, they must be validated against independent data. Here we present a case study of the validation of the riverine and estuarine modules of the California Rapid Assessment Method (CRAM). We evaluated responsiveness of the method to "good" vs. "poor" wetland condition, ability to represent a range of conditions, internal redundancy, alternative combination rules for constituent metrics, and reproducibility of results. Because no independent, concurrently collected measure of condition directly reflecting the same elements comprising CRAM was available for validation, we demonstrate the use of existing monitoring and assessment data on avian diversity, benthic macroinvertebrate indices, and plant community composition. Results indicate that CRAM is an effective tool for assessing general riverine and estuarine wetland condition based on its correspondence with multiple independent assessments of condition. Reproducibility analysis revealed several problematic metrics where ambiguous language or metric construction led to high inter-team error rates. Addressing these issues improved overall average error to within 5. This study demonstrates that, when validated, rapid assessment methods provide a meaningful and reliable tool for assessing wetland condition. © 2009, The Society of Wetland Scientists., Cited By (since 1996):9, ,
Author: Stein, Fetscher, Clark, Wiskind, Grenier, Sutula, Collins, Grosso
Date: 2009-01-01T00:00:00Z

Title: Simultaneous measurement of up-welling spectral radiance using a fiber-coupled CCD spectrograph,
Description: Determination of the water-leaving spectral radiance using in-water instrumentation requires measurements of the upwelling spectral radiance (L u) at several depths. If these measurements are separated in time, changes in the measurement conditions result in increased variance in the results. A prototype simultaneous multi-track system was developed to assess the potential reduction in the Type A uncertainty in single set, normalized water-leaving radiance achievable if the data were acquired simultaneously. The prototype system employed a spectrograph and multi-track fiber-coupled CCD-detector; in situ in-water tests were performed with the prototype system fiber-coupled to a small buoy. The experiments demonstrate the utility of multi-channel simultaneous data acquisition for in-water measurement applications. An example of the potential impact for tracking abrupt responsivity changes in satellite ocean color sensors using these types of instruments as well as for the satellite vicarious calibration is given., Cited By (since 1996):1, Oceanography, Art. No.: 66800J, CODEN: PSISD, ,
Author: Yarbrough, Flora, Feinholz, Houlihan, Kim, Brown, Johnson, Voss, Clark
Date: 2007-01-01T00:00:00Z

Title: Condensation of the isoprenoid and amino precursors in the biosynthesis of domoic acid
Description: Understanding how environmental signals regulate production of domoic acid in blooms of Pseudo-nitzschia spp. at a molecular level requires description of the biochemical pathway to this kainoid neurotoxin. Precursor feeding studies have suggested domoic acid arises from the condensation of the C 10 isoprenoid geranyl diphosphate with glutamate, but the specific reactions leading to domoic acid from these precursors remain undescribed. Here, we develop a method to derivatize domoic acid with propyl chloroformate that enables gas chromatography-mass spectrometry (GC-MS) analysis to measure incorporation of stable isotopes into domoic acid generated in cultures incubated with isotopically-labeled substrates. We apply this method to demonstrate that both 2H from [1- 2H 2]geraniol are incorporated into domoic acid, suggesting that the condensation of geranyl diphosphate with an amino group occurs by nucleophilic substitution of the diphosphate rather than by oxidation of geraniol to the aldehyde before reaction with an amino group to form an imine. Ultimately, these and similar studies will facilitate the identification of DA biosynthetic enzymes and genes which will enable the study of how environmental factors regulate DA biosynthesis at the molecular level. © 2011 Elsevier Ltd., Seaweeds, CODEN: TOXIA
Author: Savage, Smith, Clark, Saucedo
Date: 2012-01-01T00:00:00Z

Title: An example crossover experiment for testing new vicarious calibration techniques for satellite ocean color radiometry,
Description: Vicarious calibration of ocean color satellites involves the use of accurate surface measurements of waterleaving radiance to update and improve the system calibration of ocean color satellite sensors. An experiment was performed to compare a free-fall technique with the established Marine Optical Buoy (MOBY) measurement. It was found in the laboratory that the radiance and irradiance instruments compared well within their estimated uncertainties for various spectral sources. The spectrally averaged differences between the National Institute of Standards and Technology (NIST) values for the sources and the instruments were<2.5% for the radiance sensors and<1.5% for the irradiance sensors. In the field, the sensors measuring the above-surface downwelling irradiance performed nearly as well as they had in the laboratory, with an average difference of<2%.While the water-leaving radiance L w calculated from each instrument agreed in almost all cases within the combined instrument uncertainties (approximately 7%), there was a relative bias between the two instrument classes/techniques that varied spectrally. The spectrally averaged (400-600 nm) difference between the two instrument classes/techniques was 3.1%. However, the spectral variation resulted in the freefall instruments being 0.2% lower at 450 nm and 5.9% higher at 550 nm. Based on the analysis of one matchup, the bias in L w was similar to that observed for L u(1 m) with both systems, indicating the difference did not come from propagating L u(1 m) to L w. © 2010 American Meteorological Society., Cited By (since 1996):6, Oceanography, CODEN: JAOTE, ,
Author: Voss, Mclean, Lewis, Johnson, Flora, Feinholz, Yarbrough, Trees, Twardowski, Clark
Date: 2010-01-01T00:00:00Z

Title: Validation of ADEOS-II GLI ocean color products using in-situ observations,
Description: The Global Imager (GLI) aboard the Advanced Earth Observing Satellite-II (ADEOS-II) made global observations from 2 April 2003 to 24 October 2003. In cooperation with several institutes and scientists, we obtained quality controlled match-ups between GLI products and in-situ data, 116 for chlorophyll-a concentration (CHLA), 249 for normalized water-leaving radiance (nLw) at 443 nm, and 201 for aerosol optical thickness at 865 nm (Tau_865) and Angstrom exponent between 520 and 865 nm (Angstrom). We evaluated the GLI ocean color products and investigated the causes of errors using the match-ups. The median absolute percentage differences (MedPD) between GLI and in-situ data were 14.1-35.7% for nLws at 380-565 nm, 52.5-74.8% nLws at 625-680 nm, 47.6% for Tau_865, 46.2% for Angstrom, and 46.6% for CHLA, values that are comparable to the ocean-color products of other sensors. We found that some errors in GLI products are correlated with observational conditions; nLw values were underestimated when nLw at 680 nm was high, CHLA was underestimated in absorptive aerosol conditions, and Tau_865 was overestimated in sunglint regions. The error correlations indicate that we need to improve the retrievals of the optical properties of absorptive aerosols and seawater and sea surface reflection for further applications, including coastal monitoring and the combined use of products from multiple sensors. © The Oceanographic Society of Japan/TERRAPUB/Springer 2006., Cited By (since 1996):9, ,
Author: Murakami, Sasaoka, Hosoda, Fukushima, Toratani, Frouin, Mitchell, Kahru, Deschamps, Clark, Flora, Kishino, Saitoh, Asanuma, Tanaka, Sasaki, Yokouchi, Kiyomoto, Saito, Dupouy, Siripong, Matsumura, Ishizaka
Date: 2006-01-01T00:00:00Z

Title: Stray light correction algorithm for multichannel hyperspectral spectrographs,
Description: An algorithm is presented that corrects a multichannel fiber-coupled spectrograph for stray or scattered light within the system. The efficacy of the algorithm is evaluated based on a series of validation measurements of sources with different spectral distributions. This is the first application of a scattered-light correction algorithm to a multichannel hyperspectral spectrograph. The algorithm, based on characterization measurements using a tunable laser system, can be extended to correct for finite point-spread response in imaging systems. © 2012 Optical Society of America., Cited By (since 1996):1, Oceanography, CODEN: APOPA, ,
Author: Feinholz, Flora, Brown, Zong, Lykke, Yarbrough, Johnson, Clark
Date: 2012-01-01T00:00:00Z

Title: Net dextral slip, Neogene San Gregorio-Hosgri fault zone, coastal California: Geologic evidence and tectonic implications,
Description: Reinterpretation of onshore and offshore geologic mapping, examination of a key offshore well core, and revision of cross-fault ties indicate Neogene dextral strike slip of 156 ± 4 km along the San Gregorio-Hosgri fault zone, a major strand of the San Andreas transform system in coastal California. Delineating the full course of the fault, defining net slip across it, and showing its relationship to other major tectonic features of central California helps clarify the evolution of the San Andreas system. San Gregorio-Hosgri slip rates over time are not well constrained, but were greater than at present during early phases of strike slip following fault initiation in late Miocene time. Strike slip took place southward along the California coast from the western flank of the San Francisco Peninsula to the Hosgri fault in the offshore Santa Maria basin without significant reduction by transfer of strike slip into the central California Coast Ranges. Onshore coastal segments of the San Gregorio-Hosgri fault include the Seal Cove and San Gregorio faults on the San Francisco Peninsula, and the Sur and San Simeon fault zones along the flank of the Santa Lucia Range. Key cross-fault ties include porphyritic granodiorite and overlying Eocene strata exposed at Point Reyes and at Point Lobos, the Nacimiento fault contact between Salin- ian basement rocks and the Franciscan Complex offshore within the outer Santa Cruz basin and near Esalen on the flank of the Santa Lucia Range, Upper Cretaceous (Cam- panian) turbidites of the Pigeon Point Formation on the San Francisco Peninsula and the Atascadero Formation in the southern Santa Lucia Range, assemblages of Franciscan rocks exposed at Point Sur and at Point San Luis, and a lithic assemblage of Meso- zoic rocks and their Tertiary cover exposed near Point San Simeon and at Point Sal, as restored for intrabasinal deformation within the onshore Santa Maria basin. Slivering of the Salinian block by San Gregorio-Hosgri displacements elongated its northern end and offset its western margin delineated by the older Nacimiento fault, a sinistral strike-slip fault of latest Cretaceous to Paleocene age. North of its juncture with the San Andreas fault, dextral slip along the San Gregorio-Hosgri fault augments net San Andreas displacement. Alternate restorations of the Gualala block imply that nearly half the net San Gregorio-Hosgri slip was accommodated along the offshore Gualala fault strand lying west of the Gualala block, which is bounded on the east by the current master trace of the San Andreas fault. With San Andreas and San Gregorio-Hosgri slip restored, there remains an unresolved proto-San Andreas mismatch of ~100 km between the offset northern end of the Salinian block and the southern end of the Sierran-Tehachapi block. On the south, San Gregorio-Hosgri strike slip is transposed into crustal shortening associated with vertical-axis tectonic rotation of fault-bounded crustal panels that form the western Transverse Ranges, and with kinematically linked deformation within the adjacent Santa Maria basin. The San Gregorio-Hosgri fault serves as the principal link between transrotation in the western Transverse Ranges and strike slip within the San Andreas transform system of central California. © 2005 Geological Society of America., Cited By (since 1996):2, ,
Author: Dickinson, Ducea, Rosenberg, Greene, Graham, Clark, Weber, Kidder, Brabb, Ernst
Date: 2005-01-01T00:00:00Z

Title: Shift from coral to macroalgae dominance on a volcanically acidified reef
Description: Rising anthropogenic CO2 in the atmosphere is accompanied by an increase in oceanic CO2 and a concomitant decline in seawater pH (ref. 1). This phenomenon, known as ocean acidification (OA), has been experimentally shown to impact the biology and ecology of numerous animals and plants2, most notably those that precipitate calcium carbonate skeletons, such as reef-building corals3. Volcanically acidified water at Maug, Commonwealth of the Northern Mariana Islands (CNMI) is equivalent to near-future predictions for what coral reef ecosystems will experience worldwide due to OA. We provide the first chemical and ecological assessment of this unique site and show that acidification-related stress significantly influences the abundance and diversity of coral reef taxa, leading to the often-predicted shift from a coral to an algae-dominated state4,5. This study provides field evidence that acidification can lead to macroalgae dominance on reefs., Early online view available.
Author: Enochs, Manzello, Donham, Kolodziej, Okano, Johnston, Young, Iguel, Edwards, Fox, Valentino, Johnson, Benavente, Clark, Carlton, Burton, Eynaud, Price
Date: 2015-08-10T00:00:00Z

Title: Results in coastal waters with high resolution in situ spectral radiometry: The Marine Optical System ROV,
Description: The water-leaving spectral radiance is a basic ocean color remote sensing parameters required for the vicarious calibration. Determination of water-leaving spectral radiance using in-water radiometry requires measurements of the upwelling spectral radiance at several depths. The Marine Optical System (MOS) Remotely Operated Vehicle (ROV) is a portable, fiber-coupled, high-resolution spectroradiometer system with spectral coverage from 340 nm to 960 nm. MOS was developed at the same time as the Marine Optical Buoy (MOBY) spectrometer system and is optically identical except that it is configured as a profiling instrument. Concerns with instrument self-shadowing because of the large exterior dimensions of the MOS underwater housing led to adapting MOS and ROV technology. This system provides for measurement of the near-surface upwelled spectral radiance while minimizing the effects of shadowing. A major advantage of this configuration is that the ROV provides the capability to acquire measurements 5 cm to 10 cm below the water surface and is capable of very accurate depth control (1cm) allowing for high vertical resolution observations within the very near-surface. We describe the integrated system and its characterization and calibration. Initial measurements and results from observations of coral reefs in Kaneohe Bay, Oahu, extremely turbid waters in the Chesapeake Bay, Maryland, and in Case 1 waters off Southern Oahu, Hawaii are presented., , ,
Author: Yarbrough, Feinholz, Flora, Houlihan, Johnson, Kim, Murphy, Ondrusek, Clark
Date: 2007-01-01T00:00:00Z

Title: Seasonal blubber testosterone concentrations of male humpback whales (Megaptera novaeangliae)
Description: Export Date: 21 January 2015, Article in Press
Author: Vu, Clark, Catelani, Kellar, Calambokidis

Title: Stray-light correction algorithm for spectrographs,
Description: In this paper, we describe an algorithm to correct a spectrograph's response for stray light. Two recursion relations are developed: one to correct the system response when measuring broad-band calibration sources, and a second to correct the response when measuring sources of unknown radiance. The algorithm requires a detailed understanding of the effect of stray light in the spectrograph on the instrument's response. Using tunable laser sources, a dual spectrograph instrument designed to measure the up-welling radiance in the ocean was characterized for stray light. A stray-light correction algorithm was developed, based on the results of these measurements. The instrument's response was corrected for stray light, and the effects on measured up-welling in-water radiance were evaluated., Cited By (since 1996):27, Oceanography, CODEN: MTRGA, ,
Author: Brown, Johnson, Feinholz, Yarbrough, Flora, Lykke, Clark
Date: 2003-01-01T00:00:00Z