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  • 1
    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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  • 2
    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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  • 3
    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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  • 4
    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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  • 5
    In: Acoustics Today, Acoustical Society of America (ASA), Vol. 7, No. 3 ( 2011), p. 35-
    Type of Medium: Online Resource
    ISSN: 1557-0223
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2011
    detail.hit.zdb_id: 2466509-5
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  • 6
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2018
    In:  The Journal of the Acoustical Society of America Vol. 144, No. 5 ( 2018-11-01), p. 2811-2823
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 144, No. 5 ( 2018-11-01), p. 2811-2823
    Abstract: Groups of coordinated underwater vehicles or sensors are powerful tools for monitoring the ocean. A requirement of many coordinated surveys is to determine a spatial reference between each node in a swarm. This work considers the self-localization of a swarm of independently moving vehicles using acoustic noise from a dominating incoherent source recorded by a single hydrophone onboard each vehicle. This method provides an inexpensive and infrastructure-free spatial reference between vehicles. Movement between the vehicles changes the swarm geometry and a self-localization estimate must be generated from data collected on short time scales. This challenges past self-localization approaches for acoustic arrays. To overcome this challenge, the proposed self-localization algorithm jointly estimates the vehicle geometry and the directionality of the ambient noise field, without prior knowledge of either estimate. To demonstrate this method, experimental results are provided when a boat is the main dominating source. The results demonstrate the ability to both estimate the direction of arrival of the boat and the relative positions of the vehicles in the swarm. The approach in this paper is not limited to moving vessels. Simulations are provided to examine three different factors that affect the proposed solution: inter-vehicle motion, vehicle geometry, and the azimuthal variance of the noise field.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2018
    detail.hit.zdb_id: 1461063-2
    detail.hit.zdb_id: 219231-7
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  • 7
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2006
    In:  The Journal of the Acoustical Society of America Vol. 120, No. 5_Supplement ( 2006-11-01), p. 3108-3109
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 120, No. 5_Supplement ( 2006-11-01), p. 3108-3109
    Abstract: The use of multiple-angle acoustic scattering to discriminate between two ecologically important classes of zooplankton’ copepods and euphausiids, is proposed. The distorted wave Born approximation is used to model the multiple-angle scatter from a linear array of transducers designed to be practical for field deployment. Using a large set of noisy training and test data generated from uniformly random length and three-dimensional orientation distributions from each class of scatterers, the performance of classification algorithms in several feature spaces is evaluated. The results show a marked improvement in classification performance as additional angles, and larger angular separations, are included in the classifier. Interestingly, even in the case of uniformly random three-dimensional scatterer orientation, low classification error (∼5%) can be obtained. These results hold promise for substantially improving the classification of fluidlike zooplankton in situ using multiple angle scatter obtained with a simple collection geometry.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2006
    detail.hit.zdb_id: 1461063-2
    detail.hit.zdb_id: 219231-7
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  • 8
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2006
    In:  The Journal of the Acoustical Society of America Vol. 119, No. 5_Supplement ( 2006-05-01), p. 3216-3217
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 119, No. 5_Supplement ( 2006-05-01), p. 3216-3217
    Abstract: An important goal in using active sonar systems to assess underwater animals in situ is the inference of animal dimension. Although 180-deg backscatter provides an estimate of target reflectivity, in many situations the reflected energy is not easily related to animal size. An additional degree of freedom, rarely exploited, is to measure animal scatter at a multiplicity of angles. Although this is more challenging from a technical point of view, the benefit of this additional information can make it worthwhile. The interpretation of multi-angle scatter from marine organisms can be most easily understood in the context of diffraction tomography. Depending upon the details of the scattering process, in fortuitous circumstances a complete set of angular data can be inverted to compute the three-dimensional scattering potential which can ultimately lead to a complete inversion for animal morphology. In cases where it is impractical to collect a complete set of angular data it is often possible to infer characteristic dimensions of the animal from an analysis of the obtainable multi-angle data. The interpretation of multi-angle scatter data in the context of diffraction tomgraphy therefore presents opportunities to infer ecologically significant information about animal populations.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2006
    detail.hit.zdb_id: 1461063-2
    detail.hit.zdb_id: 219231-7
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  • 9
    Online Resource
    Online Resource
    Acoustical Society of America (ASA) ; 2008
    In:  The Journal of the Acoustical Society of America Vol. 124, No. 2 ( 2008-08-01), p. 796-802
    In: The Journal of the Acoustical Society of America, Acoustical Society of America (ASA), Vol. 124, No. 2 ( 2008-08-01), p. 796-802
    Abstract: A broadband, multiple-angle acoustic array was used to classify millimeter to centimeter sized live zooplankton in a laboratory tank. Reflections in the frequency range from 1.5to2.5MHz were recorded from untethered 1–4mm calanoid copepods and 8–12mm mysids over an angular range of 0°–47°. A synchronized, coregistered video system recorded animal location and orientation. To highlight differences between animals, a frequency correlation matrix was computed from the observed wide-band power spectra of the scattered sound. Significant differences in the slopes and shapes of the eigenvalue spectra of this matrix were found for mysids versus copepods. These results support the idea that broadband, multiple-angle scatter can be used to classify organisms of different sizes and shapes.
    Type of Medium: Online Resource
    ISSN: 0001-4966 , 1520-8524
    RVK:
    Language: English
    Publisher: Acoustical Society of America (ASA)
    Publication Date: 2008
    detail.hit.zdb_id: 1461063-2
    detail.hit.zdb_id: 219231-7
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  • 10
    Online Resource
    Online Resource
    Wiley ; 2009
    In:  Limnology and Oceanography: Methods Vol. 7, No. 1 ( 2009-01), p. 33-41
    In: Limnology and Oceanography: Methods, Wiley, Vol. 7, No. 1 ( 2009-01), p. 33-41
    Abstract: We present a new method for quantifying the feeding of individual copepods, using a planar sheet of laser light to stimulate the fluorescence of phytoplankton ingested by the copepod. The fluorescence is imaged with a sensitive CCD camera, giving two‐dimensional images of the copepod's gut with 20 × 20 µm spatial resolution. Using tethered copepods, we have obtained 〉 3 h long time series of copepod gut fluorescence with images every 15–20 s. The same individual copepod can be used for multiple experiments, obviating the problems of individual variability as a source of error. Initial data reveal two distinct patterns of variability as material moves through two functionally different gut compartments. These patterns reflect processes occurring in each compartment. The upper (anterior) mid‐gut shows higher variability and less repeatability than the posterior midgut where undigested material is aggregated into a fecal pellet and evacuated at regular intervals. Variability in the upper mid‐gut is likely due to factors such as intermittence of feeding and relatively complex mixing dynamics. In the posterior mid‐gut, mixing dynamics are much simpler, and the variability of the upper compartment is integrated over the time scale of pellet formation.
    Type of Medium: Online Resource
    ISSN: 1541-5856 , 1541-5856
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2161715-6
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