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Lombard, F, Boss E, Waite AM, Vogt M, Uitz J, Stemmann L, Sosik HM, Schulz J, Romagnan JB, Picheral M, Pearlman J, Ohman MD, Niehoff B, Moller KM, Miloslavich P, Lara-Lpez A, Kudela R, Lopes RM, Kiko R, Karp-Boss L, Jaffe JS, Iversen MH, Frisson JO, Fennel K, Hauss H, Guidi L, Gorsky G, Giering SLC, Gaube P, Gallager S, Dubelaar G, Cowen RK, Carlotti F, Briseno-Avena C, Berline L, Benoit-Bird K, Bax N, Batten S, Ayata SD, Artigas LF, Appeltans W.  2019.  Globally consistent quantitative observations of planktonic ecosystems. Frontiers in Marine Science. 6   10.3119/fmars.2019.00196   AbstractWebsite

In this paper we review the technologies available to make globally quantitative observations of particles in general-and plankton in particular-in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.

Briseno-Avena, C, Franks PJS, Roberts PLD, Jaffe JS.  2018.  A diverse group of echogenic particles observed with a broadband, high frequency echosounder. Ices Journal of Marine Science. 75:471-482.   10.1093/icesjms/fsx171   AbstractWebsite

In 1980, Holliday and Pieper stated: "Most sound scattering in the ocean volume can be traced to a biotic origin." However, most of the bio-acoustics research in the past three decades has focused on only a few groups of organisms. Targets such as small gelatinous organisms, marine snow, and phytoplankton, e.g. have been generally to be considered relatively transparent to acoustic waves due to their sizes and relatively low sound speed and density contrasts relative to seawater. However, using a broadband system (ZOOPS-O-2) we found that these targets contributed significantly to acoustic returns in the 1.5-2.5 MHz frequency range. Given that phytoplankton and marine snow layers are ubiquitous features of coastal regions; this works suggests that they should be considered as potential sources of backscatter in biological acoustic surveys.

Naughton, P, Roux P, Schurgers C, Kastner R, Jaffe JS, Roberts PLD.  2018.  Self-localization of a deforming swarm of underwater vehicles using impulsive sound sources of opportunity. Ieee Access. 6:1635-1646.   10.1109/access.2017.2779835   AbstractWebsite

There is increasing interest in deploying swarms of underwater vehicles for marine surveys. One of the main challenges when designing these systems is coming up with an appropriate way to localize each vehicle in relation to one another. This paper considers the self-localization of a deforming swarm of subsurface floating vehicles using impulsive sources of opportunity, such as the sounds of snapping shrimp that are present in warm coastal waters. Impulsive sound sources provide high intensity, broadband signals that facilitate accurate arrival time detections across each vehicle. This makes them useful references for a self-localization solution. However, the similarity between different signals presents a significant correspondence problem, which must be solved to provide accurate estimates of the changing geometry of the swarm. A geometric solution to this correspondence problem is shown and an optimization procedure is proposed to track the geometry of a swarm as it changes. The method is verified using a swarm of 17 self-ballasting subsurface floats that independently drifted with currents off of the coast of San Diego, California. The changing geometry of the floats was estimated using both an acoustic localization system and the proposed approach. The two estimates show good agreement, validating our method. We believe that this new localization strategy is useful for high endurance, low power, and multi-vehicle surveys.

Jaffe, JS, Franks PJS, Roberts PLD, Mirza D, Schurgers C, Kastner R, Boch A.  2017.  A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics. Nature Communications. 8:14189.   10.1038/ncomms14189   Abstract

Measuring the ever-changing 3-dimensional (3D) motions of the ocean requires simultaneous sampling at multiple locations. In particular, sampling the complex, nonlinear dynamics associated with submesoscales (<1–10 km) requires new technologies and approaches. Here we introduce the Mini-Autonomous Underwater Explorer (M-AUE), deployed as a swarm of 16 independent vehicles whose 3D trajectories are measured near-continuously, underwater. As the vehicles drift with the ambient flow or execute preprogrammed vertical behaviours, the simultaneous measurements at multiple, known locations resolve the details of the flow within the swarm. We describe the design, construction, control and underwater navigation of the M-AUE. A field programme in the coastal ocean using a swarm of these robots programmed with a depth-holding behaviour provides a unique test of a physical–biological interaction leading to plankton patch formation in internal waves. The performance of the M-AUE vehicles illustrates their novel capability for measuring submesoscale dynamics.

Naughton, P, Roux P, Yeakle R, Schurgers C, Kastner R, Jaffe JS, Roberts PLD.  2016.  Ambient noise correlations on a mobile, deformable array. Journal of the Acoustical Society of America. 140:4260-4270.   10.1121/1.4971172   AbstractWebsite

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. (C) 2016 Acoustical Society of America.

Liao, R, Roberts PLD, Jaffe JS.  2016.  Sizing submicron particles from optical scattering data collected with oblique incidence illumination. Applied Optics. 55:9440-9449.   10.1364/ao.55.009440   AbstractWebsite

As submicron particles play an important role in a variety of ecosystems that include aqueous, terrestrial, and atmospheric, a measurement system to quantify them is highly desirable. In pursuit of formulating and fabricating a system to size them using visible light, a system that collects multi-directional scattered light from individual particles is proposed. A prototype of the system was simulated, built, and tested via calibration with a set of polystyrene spheres in water with known sizes. Results indicate that the system can accurately resolve the size of these particles in the 0.1 to 0.8 mu m range. The system incorporates a design that uses oblique illumination to collect scattered light over a large range of both forward and backward scatter angles. This is then followed by the calculation of a ratio of forward to backscattered light, integrated over a suitably defined range. The monotonic dependence of this ratio upon particle size leads to an accurate estimate of particle size. The method was explored first, using simulations, and followed with a working version. The sensitivity of the method to a range of relative refractive index was tested using simulations. The results indicate that the technique is relatively insensitive to this parameter and thus of potential use in the analysis of particles from a variety of ecosystems. The paper concludes with a discussion of a variety of pragmatic issues, including the required dynamic range as well as further research needed with environmentally relevant specimens to create a pragmatic instrument. (C) 2016 Optical Society of America

Mullen, AD, Treibitz T, Roberts PLD, Kelly ELA, Horwitz R, Smith JE, Jaffe JS.  2016.  Underwater microscopy for in situ studies of benthic ecosystems. Nature Communications. 7: Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.   10.1038/ncomms12093   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.

Yi, JW, Mirza D, Kastner R, Schurgers C, Roberts P, Jaffe J.  2015.  ToA-TS: Time of arrival based joint time synchronization and tracking for mobile underwater systems. Ad Hoc Networks. 34:211-223.   10.1016/j.adhoc.2014.10.010   AbstractWebsite

Time synchronization and localization are key requirements for distributed underwater systems consisting of numerous low-cost submersibles. In these systems, submersibles are highly resource constrained and typically have limited acoustic communication capability. We investigate the problem of tracking submersibles that only have the capability of receiving acoustic signals. Traditional Long Base Line (LBL) systems track the location of submersibles by providing a GPS-like infrastructure that consists of a few reference beacons at known locations. In these systems the unknown positions of submersibles are estimated from beacon transmissions using time-difference-of-arrival (TDoA) based localization. As such TDoA makes the key assumption that beacon transmissions occur nearly concurrently in time. While this assumption is ensured in small LBL deployments it does not hold as the size of the system scales up. In this paper we identify scenarios where signals from multiple beacons are significantly lagged in time. We further identify the motion of the submersible between signal arrivals as a key factor that deteriorates the performance of TDoA, when transmissions are not concurrent. To address this problem we propose to track the submersible while performing time-synchronization. Our proposed technique, called Time of Arrival based Tracked Synchronization (ToA-TS) essentially extends GPS like localization for scenarios where beacon transmissions are not concurrent and submersibles are not capable of two-way communication. We show the benefit of our proposed scheme by comparing its performance to other localization techniques using experimentally obtained data. (C) 2014 Elsevier B.V. All rights reserved.

Taniguchi, DAA, Gagnon Y, Wheeler BR, Johnsen S, Jaffe JS.  2015.  Cuttlefish Sepia officinalis preferentially respond to bottom rather than side stimuli when not allowed adjacent to tank walls. Plos One. 10   10.1371/journal.pone.0138690   AbstractWebsite

Cuttlefish are cephalopods capable of rapid camouflage responses to visual stimuli. However, it is not always clear to what these animals are responding. Previous studies have found cuttlefish to be more responsive to lateral stimuli rather than substrate. However, in previous works, the cuttlefish were allowed to settle next to the lateral stimuli. In this study, we examine whether juvenile cuttlefish (Sepia officinalis) respond more strongly to visual stimuli seen on the sides versus the bottom of an experimental aquarium, specifically when the animals are not allowed to be adjacent to the tank walls. We used the Sub Sea Holodeck, a novel aquarium that employs plasma display screens to create a variety of artificial visual environments without disturbing the animals. Once the cuttlefish were acclimated, we compared the variability of camouflage patterns that were elicited from displaying various stimuli on the bottom versus the sides of the Holodeck. To characterize the camouflage patterns, we classified them in terms of uniform, disruptive, and mottled patterning. The elicited camouflage patterns from different bottom stimuli were more variable than those elicited by different side stimuli, suggesting that S. officinalis responds more strongly to the patterns displayed on the bottom than the sides of the tank. We argue that the cuttlefish pay more attention to the bottom of the Holodeck because it is closer and thus more relevant for camouflage.

Pepper, RE, Jaffe JS, Variano E, Koehl MAR.  2015.  Zooplankton in flowing water near benthic communities encounter rapidly fluctuating velocity gradients and accelerations. Marine Biology. 162:1939-1954.   10.1007/s00227-015-2713-x   AbstractWebsite

The fine-scale temporal patterns of water velocities, accelerations, and velocity gradients encountered by individual zooplankters carried in ambient flow can affect their dispersal, behavior, and interaction with other organisms, but have not yet been measured in realistic flow environments. We focused on zooplankton in wavy turbulent boundary layer flow near benthic communities because such flow affects important processes, including larval settlement and prey capture by benthic zooplanktivores. Flow across fouling communities measured in the field was mimicked in a wave flume, where time-varying velocity fields over biofouled surfaces were quantified using particle image velocimetry (PIV). Trajectories of simulated zooplankters seeded into these flow fields were followed to quantify temporal patterns of velocity gradients and accelerations that individuals encountered. We found that such zooplankters are not subjected to steady velocities or velocity gradients, but rather encounter rapidly fluctuating accelerations and velocity gradients with peaks reaching several orders of magnitude above mean values and lasting fractions of a second, much shorter than the wave period. We calculated the proportion of time zooplankters spent affected (e.g., being damaged, changing behavior) by accelerations or velocity gradients and found that a small increase in mean velocity can cause a much larger increase in time affected. Animal reaction threshold and reaction time also changed the fraction of time they were affected by the flow. Using different PIV spatial resolutions showed that inter-vector spacing should be a parts per thousand currency sign0.5 Kolmogorov length (smallest eddy scale) to accurately capture velocity gradients along trajectories, but coarser resolutions (a parts per thousand currency sign2-6 x Kolmogorov length) are sufficient for velocities, accelerations, and zooplankton trajectories.

Jaffe, JS.  2015.  Underwater optical imaging: The past, the present, and the prospects. Ieee Journal of Oceanic Engineering. 40:683-700.   10.1109/joe.2014.2350751   AbstractWebsite

This paper discusses the current state of underwater optical imaging in the context of physics, technology, biology, and history. The paper encompasses not only the history of human's ability to see underwater, but also the adaptations that various organisms living in oceans or lakes have developed. The continued development of underwater imaging systems at military, commercial, and consumer levels portends well for both increased visibility and accessibility by these various segments. However, the fundamental limits imposed by the environment, as currently understood, set the ultimate constraints. Physics, biology, computer modeling, processing, and the development of technology that ranges from simple cameras and lights to more advanced gated and modulated illumination are described. The future prospects for continuing advancements are also discussed.

Briseño-Avena, C, Roberts PLD, Franks PJS, Jaffe JS.  2015.  ZOOPS-O2: A broadband echosounder with coordinated stereo optical imaging for observing plankton in situ. Methods in Oceanography. 12:36-54.   10.1016/j.mio.2015.07.001   Abstract

Here we describe the configuration, calibration, and initial results from the combination of two recently developed underwater instruments that measure acoustic reflectivity and, simultaneously, the location, pose and size of millimeter-sized plankton relative to the sonar beam. The acoustic system, ZOOPS (ZOOPlankton Sonar), uses a broadband chirp signal that operates with a single monostatically configured transducer in the 1.5–2.5 MHz frequency range. We demonstrate that the system can record, with adequate signal-to-noise levels, identifiable reflections from single copepods with lengths as small as 360 μm. To simultaneously identify taxa and measure orientation, a pair of “O-Cam” microscopes were stereoscopically calibrated and geometrically co-registered with the orientation and range-resolved acoustic transmissions of the sonar beam. The system’s capability is demonstrated via the in situ measurement of acoustic reflectivity as a function of orientation for 224 individual pelagic copepods comprising three orders of free-living taxa. Comparison with a well-known model, the Distorted Wave Born Approximation (DWBA), using a spheroidal formulation, yields both differences and similarities between the in situ field data and the model’s predictions.

Haag, JM, Roberts PLD, Papen GC, Jaffe JS, Li L, Stramski D.  2014.  Deep-sea low-light radiometer system. Optics Express. 22:30074-30091.: OSA   10.1364/OE.22.030074   AbstractWebsite

Two single-waveband low-light radiometers were developed to characterize properties of the underwater light field relevant to biological camouflage at mesopelagic ocean depths. Phenomena of interest were vertical changes in downward irradiance of ambient light at wavelengths near 470 nm and 560 nm, and flashes from bioluminescent organisms. Depth profiles were acquired at multiple deep stations in different geographic regions. Results indicate significant irradiance magnitudes at 560 nm, providing direct evidence of energy transfer as described by Raman scattering. Analysis of a night profile yielded multiple examples of bioluminescent flashes. The selection of high-sensitivity, high-speed silicon photomultipliers as detectors enabled measurement of spectrally-resolved irradiance to greater than 400 m depth.

Berdalet, E, McManus MA, Ross ON, Burchard H, Chavez FP, Jaffe JS, Jenkinson IR, Kudela R, Lips I, Lips U, Lucas A, Rivas D, Ruiz-de la Torre MC, Ryan J, Sullivan JM, Yamazaki H.  2014.  Understanding harmful algae in stratified systems: Review of progress and future directions. Deep-Sea Research Part Ii-Topical Studies in Oceanography. 101:4-20.   10.1016/j.dsr2.2013.09.042   AbstractWebsite

The Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program of the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of UNESCO, was created in 1999 to foster research on the ecological and oceanographic mechanisms underlying the population dynamics of harmful algal blooms (HABs). The ultimate goal of this research is to develop observational systems and models that will eventually enable the prediction of HABs and thereby minimize their impact on marine ecosystems, human health and economic activities. In August of 2012, a workshop was held under the umbrella of the GEOHAB program at the Monterey Bay Aquarium Research Institute (MBARI). The over arching goal of this workshop was to review the current understanding of the processes governing the structure and dynamics of HABs in stratified systems, and to identify how best to couple physical/chemical and biological measurements at appropriate spatial and temporal scales to quantify the dynamics of HABs in these systems, paying particular attention to thin layers. This contribution provides a review of recent progress in the field of HAB research in stratified systems including thin layers, and identifies the gaps in knowledge that our scientific community should strive to understand in the next decade. (C) 2013 Elsevier Ltd. All rights reserved.

Haag, JM, Jaffe JS, Sweeney AM.  2013.  Measurement system for marine animal reflectance functions. Opt. Express. 21:3603-3616.: OSA   10.1364/OE.21.003603   AbstractWebsite

Photonic structures in the skin of pelagic fishes and squids evolved specifically for hiding in the complex light field of the open ocean. To understand the principles under which these structures operate, a detailed characterization of their optical properties is required. An optical scatterometer has been developed to measure one important property, the bidirectional reflectance distribution function (BRDF). The instrument was used to collect reflectance functions from the squid Pterygioteuthis microlampas and fish Sternoptyx sp. Although the animals appear very different to a casual observer, the results reveal interesting similarities in their scattering patterns, suggesting a similar optical strategy for hiding in open water.

Jaffe, JS, Roberts PLD.  2011.  Acoustic reflections on marine populations. Physics Today. 64:76-77.   10.1063/PT.3.1260   AbstractWebsite

Armed with a simple diffraction-based model, an acoustic oceanographer can bounce sound off marine animals to learn important information about their size and orientation.

Roberts, PLD, Steinbuck JV, Jaffe JS, Horner-Devine AR, Franks PJS, Simonet F.  2011.  Estimation of in situ 3-D particle distributions from a stereo laser imaging profiler. IEEE Journal of Oceanic Engineering. 36:586-601.   10.1109/joe.2011.2165923   AbstractWebsite

In this paper, an image processing system for estimating 3-D particle distributions from stereo light scatter images is described. The system incorporates measured, three-component velocity data to mitigate particle blur associated with instrument motion. An iterative background estimation algorithm yields a local threshold operator that dramatically reduces bias in particle counts over the full image field. Algorithms are tested on simulated particle distributions and data from an open-ocean profile collected near the Santa Barbara Channel Islands, CA. They yield over a 50% reduction in root-mean-squared error in particle size estimates, and a 30% reduction in the magnitude of the motion blur point spread function. In situ particle distributions are estimated and compared to several models. It is demonstrated that quantitative, 3-D particle distributions can be accurately estimated from these data for particles with diameter larger than 4 pixels (0.8 mm).

Roberts, PLD, Jaffe JS, Trivedi MM.  2011.  Multiview, broadband acoustic classification of marine fish: a machine learning framework and comparative analysis. IEEE Journal of Oceanic Engineering. 36:90-104.   10.1109/joe.2010.2101235   AbstractWebsite

Multiview, broadband, acoustic classification of individual fish was investigated using a recently developed laboratory scattering system. Scattering data from nine different species of saltwater fish were collected. Using custom software, these data were processed and filtered to yield a data set of 36 individuals, and between 200 and 500 echoes per individual. These data were sampled uniformly randomly in fish orientation. Feature-, decision-, and collaborative-fusion algorithms were then developed and tested using support vector machines (SVMs) as the underlying classifiers. Decision fusion was implemented by cascading two levels of support vectors machines. Collaborative fusion was implemented by using SVM outputs to estimate confidence levels and performing weighted averaging of probabilities computed from each view with feedback from other views. Collaborative fusion performed as well or better than the others, and did so without requiring assumptions about view geometry. In addition to a comparison between classification algorithms and feature transformations, two data collection geometries were explored, including random observation geometries. In all cases, combining multiple, broadband views yielded significant reductions in classification error (50%) over single-view methods, for uniformly random fish orientation.

Jaffe, JS, Roberts PLD.  2011.  Estimating fish orientation from broadband, limited-angle, multiview, acoustic reflections. Journal of the Acoustical Society of America. 129:670-680.   10.1121/1.3523430   AbstractWebsite

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 degrees to 17 degrees, 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. (C) 2011 Acoustical Society of America. [DOI: 10.1121/1.3523430]

Prairie, JC, Franks PJS, Jaffe JS, Doubell MJ, Yamazaki H.  2011.  Physical and biological controls of vertical gradients in phytoplankton. Limnology & Oceanography: Fluids & Environments. 1:75-90.   10.1215/21573698-1267403   AbstractWebsite

Small-scale vertical heterogeneity in phytoplankton distributions is common in coastal waters and may be a critical feature influencing trophic coupling in planktonic systems. Here we develop a model to investigate the biological and physical dynamics that control vertical gradients in phytoplankton abundance. The model includes phytoplankton layer formation and layer destruction through mixing and predicts that the local maximum scaled phytoplankton gradient is controlled by the relative strengths of these dynamics. We compare the predictions of this model to highly resolved profiles of phytoplankton concentration and fluorescence collected using a free-falling planar laser imaging fluorometer (FIDO-Φ) and turbulence microstructure profiler data (TurboMAP-L). From these profiles, we estimate the model parameters: the maximum rate of layer formation and minimum possible layer thickness. The maximum rate of layer formation ranged from 0.46 to 0.94 d − 1, which is comparable to maximum reported growth rates of the most common phytoplankton taxa found in our samples. The minimum layer thickness estimated from our data suggests that persistent phytoplankton layers thinner than approximately 0.5 m may be rare in coastal waters. This study provides a mechanistic explanation for some of the underlying dynamics governing phytoplankton layer formation, maintenance, and destruction and will allow us to better predict the magnitude and occurrence of these ecologically important structures in the field.

Prairie, JC, Franks PJS, Jaffe JS.  2010.  Cryptic peaks: Invisible vertical structure in fluorescent particles revealed using a planar laser imaging fluorometer. Limnology and Oceanography. 55:1943-1958.   10.4319/lo.2010.55.5.1943   AbstractWebsite

Small-scale vertical structure in the distribution of phytoplankton could be fundamentally important for zooplankton foraging, trophic coupling, and carbon cycling in planktonic ecosystems. Here, we identify regions of structure in phytoplankton communities that would be undetected by fluorometers by comparing the vertical distribution of chlorophyll fluorescence to the concentration of fluorescent particles over submeter scales. Images acquired with a free-falling planar laser fluorescence imaging system were used to calculate vertical profiles of the concentrations and spatial distributions of fluorescent particles (e.g., eukaryotic phytoplankton, aggregates) and bulk fluorescence. We frequently observed peaks in the concentration of fluorescent particles with no coincident peak in bulk fluorescence: we define these features as cryptic peaks. These cryptic peaks can occur because the integrated fluorescence of the particles that are resolved by the imaging system is a small fraction of the total fluorescence; thus, a dramatic local change in the abundance of fluorescent particles can occur without significantly changing the bulk fluorescence. We also observed bulk fluorescence-only peaks: peaks in bulk fluorescence with no coincident peak in fluorescent particle concentration. These features suggest that peaks in bulk fluorescence or chlorophyll a do not necessarily indicate increases in the concentration of the fluorescent particles resolved by our system, again emphasizing the difference between these two measures of phytoplankton structure. Comparing the relative abundances of two size classes of the fluorescent particles in the images revealed that the size composition of the fluorescent particles also varied over small scales. Phytoplankton less than, 500 mm in length numerically dominated the composition of most (65%) of the cryptic peaks we observed. By comparing vertical profiles of fluorescent particle concentration from two drops separated by less than an hour, we hypothesize that the peaks formed through vertical shearing of existing patches. Cryptic peaks contained almost 20% of the total number of fluorescent particles counted in all drops during our study and thus could represent disproportionately intense regions for important ecological processes relative to the rest of the water column.

Jaffe, JS.  2010.  Enhanced extended range underwater imaging via structured illumination. Optics Express. 18:12328-12340. AbstractWebsite

In this article, the utility of structured illumination in order to enhance the contrast and subsequent range capability of an underwater imaging system is explored. The proposed method consists of transmitting a short pulse of light in a grid like pattern that consists of multiple, narrow, delta-function like beams. The grid pattern can be arranged in either a one-dimensional line or an area as a two-dimensional pattern. Scanning the pattern in time results in the sequential illumination of the entire scene. The receiving system architecture imposes the exact same, grid-like pattern sensitivity on the reflected light with a simple subsequent superposition of the time-sequenced images. The system can be viewed as a parallel implementation of a Laser Line Scan System where multiple beams are projected and received instead of a single one. The performance enhancement over more conventional systems that project either a sheet or an area of light is compared for a challenging underwater environment via computer simulations. The resulting images are analyzed as a function of the spacing between the projected light beams to characterize contrast and resolution. The results indicate that reasonable gains are obtainable for close spacing between the beams while quite significant gains are predicted for larger ones. Structured illumination systems can therefore collect images more rapidly than systems that scan a single beam; however with concomitant trade-offs in contrast and resolution. (C) 2010 Optical Society of America

Li, W, Jaffe JS.  2010.  Sizing homogeneous spherical particles from intensity-only angular scatter. Journal of the Optical Society of America a-Optics Image Science and Vision. 27:151-158. AbstractWebsite

A set of algorithms is proposed to retrieve the size of spherically symmetric particles from the measured intensity of angular scatter data. Of special interest are low-contrast particles whose real part of the index of refraction is between 1.03 and 1.09 and whose size ka is constrained so that pi <= ka <= 16 pi, where k=2 pi/lambda and a is particle radius. Several algorithms are evaluated and compared that are based on either simple matching to the Mie theory predictions or inverse tomography methods. In the tomography methods, a previously proposed algorithm [Opt. Express. 15, 12217 ( 2007)] was used after estimating the phase of the scattered data or adapted to use intensity-only data. In order to ensure stability, all algorithms' performance was evaluated in the presence of moderate noise. The performance varied as a function of particle size, refractive index, and algorithm. Results suggest that a scattering device that collects only the angular scatter that is perpendicular to the polarization of incident light, usually denoted as S(1), can be used to accurately estimate the size of homogeneous, low-contrast, spherical particles whose diameters are close to the wavelength of the incident light. (C) 2010 Optical Society of America

Steinbuck, JV, Roberts PLD, Troy CD, Horner-Devine AR, Simonet F, Uhlman AH, Jaffe JS, Monismith SG, Franks PJS.  2010.  An autonomous open-ocean stereoscopic PIV profiler. Journal of Atmospheric and Oceanic Technology. 27:1362-1380.   10.1175/2010jtecho694.1   AbstractWebsite

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 x 25 cm x 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.

Karakoylu, EM, Franks PJS, Tanaka Y, Roberts PLD, Jaffe JS.  2009.  Copepod feeding quantified by planar laser imaging of gut fluorescence. Limnology and Oceanography-Methods. 7:33-41.   10.4319/lom.2009.7.33   AbstractWebsite

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 x 20 mu m 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.