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  • 1
    In: Limnology and Oceanography, Wiley, Vol. 65, No. 10 ( 2020-10), p. 2515-2528
    Abstract: Many aquatic microbes form colonies, yet little is known about their abundance and fitness relative to single‐celled taxa. The formation of diatom chains, in particular, has implications for diatom growth, survival, and carbon transfer. Here, we utilize an autonomous underwater microscope, combined with traditional microscopy, to develop a novel, multiyear record of the abundance of single‐cell and colony‐forming diatoms at Scripps Pier, a coastal location in the Southern California Bight. The total abundance of diatoms was lower during the warmer and more stratified conditions from 2015 to early 2016, but increased in cooler and less stratified conditions in mid‐2016 to late 2017. Diatom blooms were dominated by chain‐forming taxa, whereas solitary diatoms prevailed during low‐biomass conditions. The abundance of dinoflagellates, some of which are important diatom predators, is highest when colonies (chains) are most abundant. These observations of the diatom assemblage are consistent with a trade‐off between resource acquisition and predator defenses. Solitary diatom cells dominated during conditions with weak nutrient supply because they have a greater diffusive catchment area per cell in comparison to cells living in colonies. In contrast, during bloom conditions when nutrient supply is high and predators are abundant, forming a colony may reduce predation losses to quickly growing microzooplankton predators, and afford chains a higher fitness despite the costs of sharing resources with neighboring cells. These results highlight the contrasting ecology of single‐cell and chain‐forming diatoms, and the need to differentiate them in monitoring campaigns and ecological models.
    Type of Medium: Online Resource
    ISSN: 0024-3590 , 1939-5590
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2033191-5
    detail.hit.zdb_id: 412737-7
    SSG: 12
    SSG: 14
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  • 2
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2016
    In:  Nature Communications Vol. 7, No. 1 ( 2016-07-12)
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 7, No. 1 ( 2016-07-12)
    Abstract: Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean’s complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2553671-0
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  • 3
    In: Limnology and Oceanography: Methods, Wiley, Vol. 18, No. 11 ( 2020-11), p. 681-695
    Abstract: The large data sets provided by in situ optical microscopes are allowing us to answer longstanding questions about the dynamics of planktonic ecosystems. To deal with the influx of information, while facilitating ecological insights, the design of these instruments increasingly must consider the data: storage standards, human annotation, and automated classification. In that context, we detail the design of the Scripps Plankton Camera (SPC) system, an in situ microscopic imaging system. Broadly speaking, the SPC consists of three units: (1) an underwater, free‐space, dark‐field imaging microscope; (2) a server‐based management system for data storage and analysis; and (3) a web‐based user interface for real‐time data browsing and annotation. Combined, these components facilitate observations and insights into the diverse planktonic ecosystem. Here, we detail the basic design of the SPC and briefly present several preliminary, machine‐learning‐enabled studies illustrating its utility and efficacy.
    Type of Medium: Online Resource
    ISSN: 1541-5856 , 1541-5856
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2161715-6
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  • 4
    Online Resource
    Online Resource
    American Meteorological Society ; 2010
    In:  Journal of Atmospheric and Oceanic Technology Vol. 27, No. 8 ( 2010-08-01), p. 1362-1380
    In: Journal of Atmospheric and Oceanic Technology, American Meteorological Society, Vol. 27, No. 8 ( 2010-08-01), p. 1362-1380
    Abstract: Over the past decade, a novel free-fall imaging profiler has been under development at the Scripps Institution of Oceanography to observe and quantify biological and physical structure in the upper 100 m of the ocean. The profiler provided the first detailed view of microscale phytoplankton distributions using in situ planar laser-induced fluorescence. The present study examines a recent incarnation of the profiler that features microscale turbulent flow measurement capabilities using stereoscopic particle image velocimetry (PIV). As the profiler descends through the water column, a vertical sheet of laser light illuminates natural particles below the profiler. Two sensitive charge-coupled device (CCD) cameras image a 25 cm × 25 cm × 0.6 cm region at a nominal frame rate of 8 Hz. The stereoscopic camera configuration allows all three components of velocity to be measured in the vertical plane with an average spatial resolution of approximately 3 mm. The performance of the PIV system is evaluated for deployments offshore of the southern California coast. The in situ image characteristics, including natural particle seeding density and imaged particle size, are found to be suitable for PIV. Ensemble-averaged velocity and dissipation of turbulent kinetic energy estimates from the stereoscopic PIV system are consistent with observations from an acoustic Doppler velocimeter and acoustic Doppler current profiler, though it is revealed that the present instrument configuration influences the observed flow field. The salient challenges in adapting stereoscopic PIV for in situ, open-ocean turbulence measurements are identified, including cross-plane particle motion, instrument intrusiveness, and measurement uncertainty limitations. These challenges are discussed and recommendations are provided for future development: improved alignment with the dominant flow direction, mitigation of instrument intrusiveness, and improvements in illumination and imaging resolution.
    Type of Medium: Online Resource
    ISSN: 1520-0426 , 0739-0572
    Language: English
    Publisher: American Meteorological Society
    Publication Date: 2010
    detail.hit.zdb_id: 2021720-1
    detail.hit.zdb_id: 48441-6
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  • 5
    Online Resource
    Online Resource
    Institute of Electrical and Electronics Engineers (IEEE) ; 2018
    In:  IEEE Access Vol. 6 ( 2018), p. 1635-1646
    In: IEEE Access, Institute of Electrical and Electronics Engineers (IEEE), Vol. 6 ( 2018), p. 1635-1646
    Type of Medium: Online Resource
    ISSN: 2169-3536
    Language: Unknown
    Publisher: Institute of Electrical and Electronics Engineers (IEEE)
    Publication Date: 2018
    detail.hit.zdb_id: 2687964-5
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  • 6
    Online Resource
    Online Resource
    Optica Publishing Group ; 2016
    In:  Applied Optics Vol. 55, No. 33 ( 2016-11-20), p. 9440-
    In: Applied Optics, Optica Publishing Group, Vol. 55, No. 33 ( 2016-11-20), p. 9440-
    Type of Medium: Online Resource
    ISSN: 0003-6935 , 1539-4522
    Language: English
    Publisher: Optica Publishing Group
    Publication Date: 2016
    detail.hit.zdb_id: 207387-0
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  • 7
    Online Resource
    Online Resource
    Optica Publishing Group ; 2014
    In:  Optics Express Vol. 22, No. 24 ( 2014-12-01), p. 30074-
    In: Optics Express, Optica Publishing Group, Vol. 22, No. 24 ( 2014-12-01), p. 30074-
    Type of Medium: Online Resource
    ISSN: 1094-4087
    Language: English
    Publisher: Optica Publishing Group
    Publication Date: 2014
    detail.hit.zdb_id: 1491859-6
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  • 8
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2011
    In:  The Journal of the Acoustical Society of America Vol. 129, No. 2 ( 2011-02-01), p. 670-680
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 129, No. 2 ( 2011-02-01), p. 670-680
    Abstract: This article demonstrates that multiview, broadband (635–935 kHz), nearly monostatic, acoustic reflections recorded from lateral views of juvenile fish can be used to infer animal orientation. Calibrated acoustic data were recorded from live fish in a laboratory, while orientation was measured simultaneously via optical images. Using eight animals, two-dimensional data sets of target strength as a function of frequency and orientation were obtained. Fish length, lateral thickness, and dorsoventral thickness ranged from 24 to 48 mm, 3 to 7 mm and 10 to 20 mm, respectively. Preliminary estimates of orientation were computed from the direction of the gradient of the local autocorrelation function in the target strength image. These local estimates were then median-filtered over the full system bandwidth (but still limited-angle) to improve accuracy. Angular estimates were then corrected for systematic bias via a simple, one-dimensional model that approximated the animals’ reflection by that of a bar target. Taken over all orientations, the average absolute error in orientation estimation is 5.6° to 17°, dependent on the data set. Results indicate, for most sets of views, reasonable estimates of lateral orientation can be obtained from broadband, multiview data over a set of limited angular reflections.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2011
    detail.hit.zdb_id: 1461063-2
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  • 9
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2007
    In:  The Journal of the Acoustical Society of America Vol. 121, No. 4 ( 2007-04-01), p. 2060-2070
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 121, No. 4 ( 2007-04-01), p. 2060-2070
    Abstract: The use of multiple angle acoustic scatter to discriminate between two taxa of fluid-like zooplankton, copepods and euphausiids, is explored. Using computer modeling, feature extraction, and subsequent classification, the accuracy in discriminating between the two taxa is characterized via computer simulations. The model applies the distorted wave Born approximation together with a simple system geometry, a linear array, to predict a set of noisy training and test data. Three feature spaces are designed, exploiting the relationship between the shape of the scatterer and angularly varying scattering amplitude, to extract discriminant features from these data. Under the assumption of uniform random length and uniform three-dimensional orientation distributions for each class of scatterers, the performance of several classification algorithms is evaluated. Simulations reveal that the incorporation of multiple angle data leads to a marked improvement in classification performance over single angle methods. The improvement is more substantial using broadband scatter. The simulations indicate that under the stated assumptions, a low classification error can be obtained. The use of multiple angle scatter therefore holds promise to substantially improve the in situ acoustic classification of fluid-like zooplankton using simple observation geometries.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2007
    detail.hit.zdb_id: 1461063-2
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  • 10
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2016
    In:  The Journal of the Acoustical Society of America Vol. 140, No. 6 ( 2016-12-01), p. 4260-4270
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 140, No. 6 ( 2016-12-01), p. 4260-4270
    Abstract: This paper presents a demonstration of ambient acoustic noise processing on a set of free floating oceanic receivers whose relative positions vary with time. It is shown that it is possible to retrieve information that is relevant to the travel time between the receivers. With thousands of short time cross-correlations (10 s) of varying distance, it is shown that on average, the decrease in amplitude of the noise correlation function with increased separation follows a power law. This suggests that there may be amplitude information that is embedded in the noise correlation function. An incoherent beamformer is developed, which shows that it is possible to determine a source direction using an array with moving elements and large element separation. This incoherent beamformer is used to verify cases when the distribution of noise sources in the ocean allows one to recover travel time information between pairs of mobile receivers.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2016
    detail.hit.zdb_id: 1461063-2
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