lumis

2022

Le, Kevin T.; Yuan, Zhouyuan; Syed, Areeb; Ratelle, Devin; Orenstein, Eric C.; Carter, Melissa L.; Strang, Sarah; Kenitz, Kasia M.; Morgado, Pedro; Franks, Peter J. S.; Vasconcelos, Nuno; Jaffe, Jules S.

Benchmarking and Automating the Image Recognition Capability of an In Situ Plankton Imaging System Journal Article

In: Frontiers in Marine Science, vol. 9, 2022, ISBN: 2296-7745.

Abstract | Links | BibTeX

@article{Le2022,

title = {Benchmarking and Automating the Image Recognition Capability of an In Situ Plankton Imaging System},

author = {Le, Kevin T. and Yuan, Zhouyuan and Syed, Areeb and Ratelle, Devin and Orenstein, Eric C. and Carter, Melissa L. and Strang, Sarah and Kenitz, Kasia M. and Morgado, Pedro and Franks, Peter J. S. and Vasconcelos, Nuno and Jaffe, Jules S.},

editor = {Mark C. Benfield},

url = {https://www.frontiersin.org/article/10.3389/fmars.2022.869088},

doi = {10.3389/fmars.2022.869088},

isbn = {2296-7745},

year  = {2022},

date = {2022-06-10},

journal = {Frontiers in Marine Science},

volume = {9},

abstract = {To understand ocean health, it is crucial to monitor photosynthetic marine plankton – the microorganisms that form the base of the marine food web and are responsible for the uptake of atmospheric carbon. With the recent development of in situ microscopes that can acquire vast numbers of images of these organisms, the use of deep learning methods to taxonomically identify them has come to the forefront. Given this, two questions arise: 1) How well do deep learning methods such as Convolutional Neural Networks (CNNs) identify these marine organisms using data from in situ microscopes? 2) How well do CNN-derived estimates of abundance agree with established net and bottle-based sampling? Here, using images collected by the in situ Scripps Plankton Camera (SPC) system, we trained a CNN to recognize 9 species of phytoplankton, some of which are associated with Harmful Algal Blooms (HABs). The CNNs evaluated on 26 independent natural samples collected at Scripps Pier achieved an averaged accuracy of 92%, with 7 of 10 target categories above 85%. To compare abundance estimates, we fit a linear model between the number of organisms of each species counted in a known volume in the lab, with the number of organisms collected by the in situ microscope sampling at the same time. The linear fit between lab and in situ counts of several of the most abundant key HAB species suggests that, in the case of dinoflagellates, there is good correspondence between the two methods. As one advantage of our method, given the excellent correlation between lab counts and in situ microscope counts for key species, the methodology proposed here provides a way to estimate an equivalent volume in which the employed microscope can identify in-focus organisms and obtain statistically robust estimates of abundance.},

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Lindemann Yoav Ben-Zvi Or, Eyal Gal

Coral fluorescence: a prey-lure in deep habitats Journal Article

In: Communications Biology, vol. 5, iss. 1, no. 5, 2022, ISSN: 2399-3642.

Abstract | Links | BibTeX

Pichaya Lertvilai, Jules S. Jaffe

In situ size and motility measurement of aquatic invertebrates with an underwater stereoscopic camera system using tilted lenses Journal Article

In: Methods in Ecology and Evolution, 2022.

Abstract | Links | BibTeX

@article{Lertvilai2022,

title = {In situ size and motility measurement of aquatic invertebrates with an underwater stereoscopic camera system using tilted lenses},

author = {Pichaya Lertvilai, Jules S. Jaffe},

editor = {Marta Vidal Garcia},

url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13855},

doi = {https://doi.org/10.1111/2041-210X.13855},

year  = {2022},

date = {2022-03-28},

urldate = {2022-03-28},

journal = {Methods in Ecology and Evolution},

abstract = {Abstract In situ observation of traits of aquatic organisms, including size and motility, requires three-dimensional measurements that are commonly done with a stereoscopic imaging system. However, to observe traits of small aquatic invertebrates, the imaging system requires relatively high magnification, which results in a small overlapping volume between the two cameras of a conventional stereoscopic system. The provision of a larger shared volume would therefore be of great advantage, especially, when the organism abundance is low. We implement a stereoscopic system that utilizes a tilted lens approach, known as the Scheimpflug principle, to increase the common imaging volume of two cameras. The system was calibrated and tested in the laboratory and then deployed in a saltmarsh to observe water boatmen Trichocorixa californica. Processing of the image data from the field deployments resulted in the simultaneous estimation of the traits of body length and swimming speed of the aquatic insects. Our stereo setup with tilted lenses increased the sampling volume by 3.1 times compared to a traditional stereo setup with the same optical parameters. The in situ data and subsequent processing reveal that the instrument can capture stereoscopic images that resolve both body length and swimming speed of the aquatic insects. Results indicate that the relationship between the body length and the swimming speed of the water boatmen is linear in the log–log space with an exponent of 0.81±0.12$$ 0.81pm 0.12 $$. Furthermore, the insects experience Reynold's number in the range of 100$$ {10}^0 $$–103$$ {10}^3 $$. Our results demonstrated that the system can be used to observe key traits of small aquatic organisms in an ecologically relevant context. This work expands the capability of underwater imaging systems to measure important traits of an individual aquatic invertebrate in its natural environment and aids in providing a trait-based approach to zooplankton ecology.},

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Sauer, Jon S.; Mayer, Kathryn J.; Lee, Christopher; Alves, Michael R.; Amiri, Sarah; Bahaveolos, Cristina J.; Franklin, Emily B.; Crocker, Daniel R.; Dang, Duyen; Dinasquet, Julie; Garofalo, Lauren A.; Kaluarachchi, Chathuri P.; Kilgour, Delaney B.; Mael, Liora E.; Mitts, Brock A.; Moon, Daniel R.; Moore, Alexia N.; Morris, Clare K.; Mullenmeister, Catherine A.; Ni, Chi-Min; Pendergraft, Matthew A.; Petras, Daniel; Simpson, Rebecca M. C.; Smith, Stephanie; Tumminello, Paul R.; Walker, Joseph L.; DeMott, Paul J.; Farmer, Delphine K.; Goldstein, Allen H.; Grassian, Vicki H.; Jaffe, Jules S.; Malfatti, Francesca; Martz, Todd R.; Slade, Jonathan H.; Tivanski, Alexei V.; Bertram, Timothy H.; Cappah, Christopher D.; Prather, Kimberly A.

The Sea Spray Chemistry and Particle Evolution study (SeaSCAPE): overview and experimental methods Journal Article

In: Environmental Science: Processes and Impacts, 2022.

Links | BibTeX

2021

Merz, Ewa; Kozakiewicz, Thea; Reyes, Marta; Ebi, Christian; Isles, Peter; Baity-Jesi, Marco; Roberts, Paul; Jaffe, Jules S.; Dennis, Stuart R.; Hardeman, Thomas; Stevens, Nelson; Lorimer, Tom; Pomati, Francesco

Underwater dual-magnification imaging for automated lake plankton monitoring Journal Article

In: Water Research, vol. 203, no. 117524, 2021.

Abstract | Links | BibTeX

@article{Merz2021,

title = {Underwater dual-magnification imaging for automated lake plankton monitoring},

author = {Ewa Merz and Thea Kozakiewicz and Marta Reyes and Christian Ebi and Peter Isles and Marco Baity-Jesi and Paul Roberts and Jules S. Jaffe and Stuart R. Dennis and Thomas Hardeman and Nelson Stevens and Tom Lorimer and Francesco Pomati},

url = {https://doi.org/10.1016/j.watres.2021.117524},

year  = {2021},

date = {2021-09-15},

urldate = {2021-09-15},

journal = {Water Research},

volume = {203},

number = {117524},

abstract = {The Dual Scripps Plankton Camera (DSPC) is a new approach for automated in-situ monitoring of phyto- and zooplankton communities based on a dual magnification dark-field imaging microscope. Here, we present the DSPC and its associated image processing while evaluating its capabilities in i) detecting and characterizing plankton species of different size and taxonomic categories and ii) measuring their abundance in both laboratory and field applications. In the laboratory, body size and abundance estimates by the DSPC significantly and robustly scaled with measurements derived by microscopy. In the field, a DSPC installed permanently at 3 m depth in Lake Greifensee (Switzerland) delivered images of plankton individuals, colonies, and heterospecific aggregates at hourly timescales without disrupting natural arrangements of interacting organisms, their microenvironment or their behavior. The DSPC was able to track the dynamics of taxa, mostly at the genus level, in the size range between ∼10 μm to ∼ 1 cm, covering many components of the planktonic food web (including parasites and potentially toxic cyanobacteria). Comparing data from the field-deployed DSPC to traditional sampling and microscopy revealed a general overall agreement in estimates of plankton diversity and abundances. The most significant disagreements between traditional methods and the DSPC resided in the measurements of zooplankton community properties. Our data suggest that the DSPC is better equipped to study the dynamics and demography of heterogeneously distributed organisms such as zooplankton, because high temporal resolution and continuous sampling offer more information and less variability in taxa detection and quantification than traditional sampling. Time series collected by the DSPC depicted ecological succession patterns, algal bloom dynamics and diel fluctuations with a temporal frequency and morphological resolution that was never observed by traditional methods. Access to high frequency, reproducible and real-time data of a large spectrum of the planktonic ecosystem expands our understanding of both applied and fundamental plankton ecology. We conclude the DSPC is robust for both research and water quality monitoring and suitable for stable long-term deployments.},

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The Dual Scripps Plankton Camera (DSPC) is a new approach for automated in-situ monitoring of phyto- and zooplankton communities based on a dual magnification dark-field imaging microscope. Here, we present the DSPC and its associated image processing while evaluating its capabilities in i) detecting and characterizing plankton species of different size and taxonomic categories and ii) measuring their abundance in both laboratory and field applications. In the laboratory, body size and abundance estimates by the DSPC significantly and robustly scaled with measurements derived by microscopy. In the field, a DSPC installed permanently at 3 m depth in Lake Greifensee (Switzerland) delivered images of plankton individuals, colonies, and heterospecific aggregates at hourly timescales without disrupting natural arrangements of interacting organisms, their microenvironment or their behavior. The DSPC was able to track the dynamics of taxa, mostly at the genus level, in the size range between ∼10 μm to ∼ 1 cm, covering many components of the planktonic food web (including parasites and potentially toxic cyanobacteria). Comparing data from the field-deployed DSPC to traditional sampling and microscopy revealed a general overall agreement in estimates of plankton diversity and abundances. The most significant disagreements between traditional methods and the DSPC resided in the measurements of zooplankton community properties. Our data suggest that the DSPC is better equipped to study the dynamics and demography of heterogeneously distributed organisms such as zooplankton, because high temporal resolution and continuous sampling offer more information and less variability in taxa detection and quantification than traditional sampling. Time series collected by the DSPC depicted ecological succession patterns, algal bloom dynamics and diel fluctuations with a temporal frequency and morphological resolution that was never observed by traditional methods. Access to high frequency, reproducible and real-time data of a large spectrum of the planktonic ecosystem expands our understanding of both applied and fundamental plankton ecology. We conclude the DSPC is robust for both research and water quality monitoring and suitable for stable long-term deployments.

Ronen, Roi; Attias, Yacov; Schechner, Yoay Y.; Jaffe, Jules S.; Orenstein, Eric C.

Plankton reconstruction through robust statistical optical tomography Journal Article

In: Journal of the Optical Society of America A, vol. 38, no. 9, pp. 1320-1331, 2021.

Abstract | Links | BibTeX

Pagniello, Camille M. L. S.; Butler, Jack; Rosen, Annie; Sherwood, Addison; Roberts, Paul L. D.; Parnell, P. Edward; Jaffe, Jules S.; Sirovic, Ana

An Optical Imaging System for Capturing Images in Low-Light Aquatic Habitats Using Only Ambient Light Journal Article

In: Oceanography Magazine, 2021.

Abstract | Links | BibTeX

@article{Pagniello2021,

title = {An Optical Imaging System for Capturing Images in Low-Light Aquatic Habitats Using Only Ambient Light},

author = {Camille M. L. S. Pagniello and Jack Butler and Annie Rosen and Addison Sherwood and Paul L. D. Roberts and P. Edward Parnell and Jules S. Jaffe and Ana Sirovic},

url = {https://doi.org/10.5670/oceanog.2021.305},

year  = {2021},

date = {2021-07-08},

journal = {Oceanography Magazine},

abstract = {It is preferable that methods for monitoring fish behavior, diversity, and abundance be noninvasive to avoid potential bias. Optical imaging facilitates the noninvasive monitoring of underwater environments and is best conducted without the use of artificial lighting. Here, we describe a custom-designed optical imaging system that utilizes a consumer-grade camera to capture images in situ in ambient light. This diver-deployed system can be used to collect time series of occurrences of animals while concurrently obtaining behavioral observations for two weeks to a month (depending on the sampling rate). It has also been configured to be paired with a passive acoustic system to record time-synchronized image and acoustic data. The system was deployed in a protected kelp forest off southern California and captured >1,500 high-quality images per day over 14 days. The images revealed numerous fish species exhibiting biologically important behaviors as well as daily patterns of presence/absence. The optical imaging system is a cost-effective tool that can be easily fabricated and improves upon many of the limitations of previous systems, including deployment length and image quality in low-light and limited-visibility conditions. The system provides a relatively noninvasive way to monitor shallow marine habitats, including protected areas, and can augment traditional survey methods by providing nearly continuous observations and thus yield increased statistical power.},

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Lertvilai, Pichaya; Roberts, Paul L. D.; Jaffe, Jules S.

In Situ Underwater Average Flow Velocity Estimation Using a Low-Cost Video Velocimeter Journal Article

In: Journal of Atmospheric and Oceanic Technology, vol. 38, no. 6, pp. 1143-1156, 2021.

Abstract | Links | BibTeX

2020

Garwood, Jessica C.; Lucas, Andrew J.; Naughton, Perry; Roberts, Paul L. D.; Jaffe, Jules S; deGelleke, Laura; Franks, Peter J. S.

Larval cross-shore transport estimated from internal waves with a mean flow: the effects of larval vertical position and depth regulation. Journal Article

In: Limnology and Oceanography, 2020.

Abstract | Links | BibTeX

@article{Garwood2020b,

title = {Larval cross-shore transport estimated from internal waves with a mean flow: the effects of larval vertical position and depth regulation.},

author = {Jessica C. Garwood and Andrew J. Lucas and Perry Naughton and Paul L. D. Roberts and Jules S Jaffe and Laura deGelleke and Peter J. S. Franks},

url = {https://doi.org/10.1002/lno.11632},

year  = {2020},

date = {2020-10-26},

journal = {Limnology and Oceanography},

abstract = {Cross‐shore velocities in the coastal ocean typically vary with depth. The direction and magnitude of transport experienced by meroplanktonic larvae will therefore be influenced by their vertical position. To quantify how swimming behavior and vertical position in internal waves influence larval cross‐shore transport in the shallow (~ 20 m), stratified coastal waters off Southern California, we deployed swarms of novel, subsurface larval mimics, the Mini‐Autonomous Underwater Explorers (M‐AUEs). The M‐AUEs were programmed to maintain a specified depth, and were deployed near a mooring. Transport of the M‐AUEs was predominantly onshore, with average velocities up to 14 cm s−1. To put the M‐AUE deployments into a broader context, we simulated > 500 individual high‐frequency internal waves observed at the mooring over a 14‐d deployment; in each internal wave, we released both depth‐keeping and passive virtual larvae every meter in the vertical. After the waves' passage, depth‐keeping virtual larvae were usually found closer to shore than passive larvae released at the same depth. Near the top of the water column (3–5‐m depth), ~ 20% of internal waves enhanced onshore transport of depth‐keeping virtual larvae by ≥ 50 m, whereas only 1% of waves gave similar enhancements to passive larvae. Our observations and simulations showed that depth‐keeping behavior in high‐frequency internal waves resulted in enhanced onshore transport at the top of the water column, and reduced offshore dispersal at the bottom, compared to being passive. Thus, even weak depth‐keeping may allow larvae to reach nearshore adult habitats more reliably than drifting passively.},

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pubstate = {published},

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}

Orenstein, Eric C.; Ratelle, Devin; Briseño-Avena, Christian; Carter, Melissa L; Franks, Peter J. S.; Jaffe, Jules S.; Roberts, Paul L. D.

The Scripps Plankton Camera system: A framework and platform for in situ microscopy Journal Article

In: Limnology and Oceanography: Methods, 2020.

Abstract | Links | BibTeX

Briseño-Avena, Christian; Prairie, Jennifer C.; Franks, Peter J. S.; Jaffe, Jules S.

Comparing Vertical Distributions of Chl-a Fluorescence, Marine Snow, and Taxon-Specific Zooplankton in Relation to Density Using High Resolution Optical Measurements Journal Article

In: Frontiers in Marine Science, 2020.

Abstract | Links | BibTeX

@article{Briseño-Avena2020,

title = {Comparing Vertical Distributions of Chl-a Fluorescence, Marine Snow, and Taxon-Specific Zooplankton in Relation to Density Using High Resolution Optical Measurements},

author = {Christian Briseño-Avena and Jennifer C. Prairie and Peter J. S. Franks and Jules S. Jaffe},

url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.00602/abstract},

doi = {10.3389/fmars.2020.00602},

year  = {2020},

date = {2020-07-28},

journal = {Frontiers in Marine Science},

abstract = {Interactions between predators and their prey are important in shaping planktonic ecosystems. However, these interactions are difficult to assess in situ at the spatial scales relevant to the organisms. This work presents high spatial resolution observations of the nighttime vertical distributions of individual zooplankton, chlorophyll-a fluorescence, and marine snow in stratified coastal waters of the Southern California Bight. Data were obtained using a planar laser imaging fluorometer (PLIF) augmented with a shadowgraph zooplankton imaging system (O-Cam) mounted along with ancillary sensors on a free-descent platform. Fluorometer and PLIF sensors detected two well-defined and distinct peaks: the subsurface chlorophyll maximum (SCM) and a fluorescent particle maximum (FPM) dominated by large marine snow. The O-Cam imaging system allows reliable estimates of concentrations of crustacean and gelatinous zooplankton groups; we found that grazers and their predators had well-structured nighttime distributions in and around the SCM and FPM in ways that suggested potential predator avoidance at the peak of the SCM and immediately above the FPM (where predatory hydromedusae, and to some degree euphausiids, were primarily located). Calanoid copepods were found above the SCM while cyclopoids were associated with the FPM. The locations of predator and grazer concentration peaks suggest that their dynamics may control the vertical gradients defining the SCM and FPM.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

Lertvilai, Pichaya

The In situ Plankton Assemblage eXplorer (IPAX): An inexpensive underwater imaging system for zooplankton study Journal Article

In: Methods in Ecology and Evolution, 2020.

Abstract | Links | BibTeX

@article{Lertvilai2020,

title = {The In situ Plankton Assemblage eXplorer (IPAX): An inexpensive underwater imaging system for zooplankton study},

author = {Pichaya Lertvilai},

url = {https://doi.org/10.1111/2041-210X.13441},

year  = {2020},

date = {2020-06-27},

journal = {Methods in Ecology and Evolution},

abstract = {1. Zooplankton play vital ecological roles that maintain aquatic ecosystems. Imaging instruments have enabled in situ observations of these organisms that can be automated and are less invasive than traditional sampling methods. However, these instruments are often costly and require sophisticated engineering expertise to operate.

2. The In situ Plankton Assemblage eXplorer (IPAX) is an open‐source low‐cost imaging platform for zooplankton studies. The IPAX is a programmable instrument that has powerful LED illumination and a high‐resolution camera that can image zooplankton in situ, while material costs are less than USD $450. The optical performance of the instrument was calibrated in the laboratory using a calibration target and preserved zooplankton. The IPAX was then deployed in the field to observe diversity, emergent patterns and phototactic behaviour of demersal zooplankton at night to demonstrate its practicality.

3. Laboratory calibration indicated that the IPAX can resolve 100 µm features with 70% contrast at the focal plane with 5 cm × 3 cm field of view and 5 mm depth of field. The instrument also resolved fine morphological details of preserved zooplankton when in focus. The field deployment demonstrated capability to resolve the myriad of zooplankton present in addition to the different phototactic behaviour that was elicited and observed from the different colour LEDs.

4. The IPAX enables economical and autonomous surveys of zooplankton in various aquatic habitats. Its low cost facilitates construction and deployment of multiple units that can cover large spatial areas, while its versatility also allows adaptations to many experimental needs for aquatic ecology.},

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Kenitz, Kasia M; Orenstein, Eric C.; Roberts, Paul L D; Franks, Peter J S; Jaffe, Jules S; Carter, Melissa L; Barton, Andrew D

Environmental drivers of population variability in colony‐forming marine diatoms Journal Article

In: Limnology and Oceanography, 2020.

Abstract | Links | BibTeX

@article{Kenitz2020,

title = {Environmental drivers of population variability in colony‐forming marine diatoms},

author = {Kasia M Kenitz and Eric C. Orenstein and Paul L D Roberts and Peter J S Franks and Jules S Jaffe and Melissa L Carter and Andrew D Barton},

editor = {Ilana Berman-Frank},

url = {https://doi.org/10.1002/lno.11468},

year  = {2020},

date = {2020-05-26},

journal = {Limnology and Oceanography},

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.},

keywords = {},

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Campbell, Robert W; Roberts, Paul L D; Jaffe, Jules S

The Prince William Sound Plankton Camera: a profiling in situ observatory of plankton and particulates Journal Article

In: ICES Journal of Marine Science, vol. 77, no. 4, pp. 1440-1455, 2020.

Abstract | Links | BibTeX

Garwood, Jessica C.; Lucas, Andrew J.; Naughton, Perry; Alford, Matthew H.; Roberts, Paul L. D.; Jaffe, Jules S.; Franks, Peter J. S.

A novel cross‐shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field Journal Article

In: Limnology and Oceanography, vol. 65, no. 7, pp. 1456-1470, 2020.

Abstract | Links | BibTeX

@article{Garwood2020,

title = {A novel cross‐shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field},

author = {Jessica C. Garwood and Andrew J. Lucas and Perry Naughton and Matthew H. Alford and Paul L. D. Roberts and Jules S. Jaffe and Peter J. S. Franks},

editor = {Julia Mullarney},

url = {https://doi.org/10.1002/lno.11400},

year  = {2020},

date = {2020-01-13},

journal = {Limnology and Oceanography},

volume = {65},

number = {7},

pages = {1456-1470},

abstract = {Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s−1 vs. cm s−1) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.},

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2019

Franks, Peter J. S.; Garwood, Jessica C.; Ouimet, Michael; Cortes, Jorge; Musgrave, Ruth C.; Lucas, Andrew J.

Stokes drift of plankton in linear internal waves: Cross-shore transport of neutrally buoyant and depth-keeping organisms Journal Article

In: Limnology and Oceanography, no. WOS:000501665500001, 2019, ISBN: 0024-3590.

Abstract | Links | BibTeX

Lombard, Fabien; Boss, Emmanuel; Waite, Anya M.; Vogt, Meike; Uitz, Julia; Stemmann, Lars; Sosik, Heidi M.; Schulz, Jan; Romagnan, Jean-Baptiste; Picheral, Marc; Pearlman, Jay; Ohman, Mark D.; Niehoff, Barbara; Möller, Klas O.; Miloslavich, Patricia; Lara-Lpez, Ana; Kudela, Raphael; Lopes, Rubens M.; Kiko, Rainer; Karp-Boss, Lee; Jaffe, Jules S.; Iversen, Morten H.; Irisson, Jean-Olivier; Fennel, Katja; Hauss, Helena; Guidi, Lionel; Gorsky, Gaby; Giering, Sarah L. C.; Gaube, Peter; Gallager, Scott; Dubelaar, George; Cowen, Robert K.; Carlotti, François; Briseño-Avena, Christian; Berline, Léo; Benoit-Bird, Kelly; Bax, Nicholas; Batten, Sonia; Ayata, Sakina Dorothée; Artigas, Luis Felipe; Appeltans, Ward

Globally Consistent Quantitative Observations of Planktonic Ecosystems Journal Article

In: Frontiers in Marine Science, vol. 6, pp. 196, 2019, ISSN: 2296-7745 .

Abstract | Links | BibTeX

@article{Lombard2019,

title = {Globally Consistent Quantitative Observations of Planktonic Ecosystems},

author = {Fabien Lombard and Emmanuel Boss and Anya M. Waite and Meike Vogt and Julia Uitz and Lars Stemmann and Heidi M. Sosik and Jan Schulz and Jean-Baptiste Romagnan and Marc Picheral and Jay Pearlman and Mark D. Ohman and Barbara Niehoff and Klas O. Möller and Patricia Miloslavich and Ana Lara-Lpez and Raphael Kudela and Rubens M. Lopes and Rainer Kiko and Lee Karp-Boss and Jules S. Jaffe and Morten H. Iversen and Jean-Olivier Irisson and Katja Fennel and Helena Hauss and Lionel Guidi and Gaby Gorsky and Sarah L. C. Giering and Peter Gaube and Scott Gallager and George Dubelaar and Robert K. Cowen and François Carlotti and Christian Briseño-Avena and Léo Berline and Kelly Benoit-Bird and Nicholas Bax and Sonia Batten and Sakina Dorothée Ayata and Luis Felipe Artigas and Ward Appeltans},

url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00196 },

doi = {10.3389/fmars.2019.00196},

issn = {2296-7745 },

year = {2019},

date = {2019-04-25},

journal = {Frontiers in Marine Science},

volume = {6},

pages = {196},

abstract = {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.

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2018

Naughton, Perry; Roux, Philippe; Schurgers, Curt; Kastner, Ryan; Jaffe, Jules S; Roberts, Paul L D

Self-localization of a mobile swarm using noise correlations with local sources of opportunity Journal Article

In: Journal of the Acoustical Society of America, vol. 144, no. WOS:000454102300035, pp. 2811-2823, 2018, ISBN: 0001-4966, (Technical Area Pick for Signal Processing of the Acoustical Society of America in 2019).

Abstract | Links | BibTeX

@article{Naughton2018,

title = {Self-localization of a mobile swarm using noise correlations with local sources of opportunity},

author = {Perry Naughton and Philippe Roux and Curt Schurgers and Ryan Kastner and Jules S Jaffe and Paul L D Roberts },

url = {https://asa.scitation.org/doi/10.1121/1.5070154},

doi = {10.1121/1.5070154},

isbn = {0001-4966},

year  = {2018},

date = {2018-11-16},

journal = {Journal of the Acoustical Society of America},

volume = {144},

number = {WOS:000454102300035},

pages = {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. (C) 2018 Acoustical Society of America.},

note = {Technical Area Pick for Signal Processing of the Acoustical Society of America in 2019},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

2017

Naughton, Perry; Roux, Philippe; Schurgers, Curt; Kastner, Ryan; Jaffe, Jules S.; Roberts, Paul L. D.

Self-localization of a deforming swarm of underwater vehicles using impulsive sound sources of opportunity Journal Article

In: IEEE Access, vol. 6, no. INSPEC Accession Number: 16881600, pp. 1635-1646, 2017.

Links | BibTeX

Briseño-Avena, Christian; Franks, Peter J S; Roberts, Paul L D; Jaffe, Jules S

A diverse group of echogenic particles observed with a broadband, high frequency echosounder Journal Article

In: ICES Journal of Marine Science, vol. 75, pp. 471-482, 2017.

Abstract | Links | BibTeX

Orenstein, Eric C.; Beijbom, Oscar

Transfer learning and deep feature extraction for planktonic image data sets Inproceedings

In: Winter Conference on Applications of Computer Vision, pp. 1082-1088, IEEE 2017.

Links | BibTeX

Jaffe, Jules S; Franks, Peter J S; Roberts, Paul L D; Mirza, Diba; Schurgers, Curt; Kastner, Ryan; Boch, Adrien

A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics Journal Article

In: Nature Communications, vol. 8, no. 14189, 2017, (Article).

Links | BibTeX

2016

Naughton, Perry; Roux, Philippe; Yeakle, Riley; Schurgers, Curt; Kastner, Ryan; Jaffe, Jules S.; Roberts, Paul L. D.

Ambient noise correlations on a mobile, deformable array Journal Article

In: The Journal of the Acoustical Society of America, vol. 140, no. 6, pp. 4260-4270, 2016.

Abstract | Links | BibTeX

Liao, Ran; Roberts, Paul L. D.; Jaffe, Jules S.

Sizing submicron particles from optical scattering data collected with oblique incidence illumination Journal Article

In: Appl. Opt., vol. 55, no. 33, pp. 9440–9449, 2016.

Abstract | Links | BibTeX

@article{Liao:16,

title = {Sizing submicron particles from optical scattering data collected with oblique incidence illumination},

author = {Ran Liao and Paul L. D. Roberts and Jules S. Jaffe},

url = {http://ao.osa.org/abstract.cfm?URI=ao-55-33-9440},

doi = {10.1364/AO.55.009440},

year  = {2016},

date = {2016-11-01},

journal = {Appl. Opt.},

volume = {55},

number = {33},

pages = {9440--9449},

publisher = {OSA},

abstract = {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 μm 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.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

Mullen, Andrew D.; Treibitz, Tali; Roberts, Paul L. D.; Kelly, Emily L. A.; Horwitz, Rael; Smith, Jennifer E.; Jaffe, Jules S.

Underwater microscopy for in situ studies of benthic ecosystems Journal Article

In: Nat Commun, vol. 7, 2016.

Abstract | Links | BibTeX

Orenstein, Eric C.; Haag, Justin M.; Gagnon, Yakir L.; Jaffe, Jules S.

Automated classification of camouflaging cuttlefish Journal Article

In: Methods in Oceanography, pp. -, 2016, ISSN: 2211-1220.

Abstract | Links | BibTeX

Jaffe, Jules S.

To sea and to see: That is the answer Journal Article

In: Methods in Oceanography, pp. -, 2016, ISSN: 2211-1220.

Abstract | Links | BibTeX

2015

Jaffe, J. S.

Underwater Optical Imaging: The Past, the Present, and the Prospects Journal Article

In: Oceanic Engineering, IEEE Journal of, vol. 40, no. 3, pp. 683-700, 2015, ISSN: 0364-9059.

Links | BibTeX

Treibitz, Tali; Neal, Benjamin P.; Kline, David I.; Beijbom, Oscar; Roberts, Paul L. D.; Mitchell, B. Greg; Kriegman, David

Wide Field-of-View Fluorescence Imaging of Coral Reefs Journal Article

In: Scientific Reports, vol. 5, pp. 7694 EP -, 2015, (Article).

Abstract | Links | BibTeX

Briseño-Avena, Christian; Roberts, Paul L. D.; Franks, Peter J. S.; Jaffe, Jules S.

ZOOPS- O2: A broadband echosounder with coordinated stereo optical imaging for observing plankton in situ Journal Article

In: Methods in Oceanography, vol. 12, pp. 36 - 54, 2015, ISSN: 2211-1220.

Abstract | Links | BibTeX

Pepper, Rachel E; Jaffe, Jules S; Variano, Evan; Koehl, MAR

Zooplankton in flowing water near benthic communities encounter rapidly fluctuating velocity gradients and accelerations Journal Article

In: Marine Biology, vol. 162, no. 10, pp. 1939–1954, 2015.

Abstract | Links | BibTeX

@article{pepper2015zooplankton,

title = {Zooplankton in flowing water near benthic communities encounter rapidly fluctuating velocity gradients and accelerations},

author = {Rachel E Pepper and Jules S Jaffe and Evan Variano and MAR Koehl},

url = {http://link.springer.com/article/10.1007%2Fs00227-015-2713-x},

doi = {10.1007/s00227-015-2713-x},

year  = {2015},

date = {2015-01-01},

journal = {Marine Biology},

volume = {162},

number = {10},

pages = {1939--1954},

publisher = {Springer},

abstract = {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 ≤0.5 Kolmogorov length (smallest eddy scale) to accurately capture velocity gradients along trajectories, but coarser resolutions (≤2–6 × Kolmogorov length) are sufficient for velocities, accelerations, and zooplankton trajectories.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

A., Darcy A.; Yakir, Gagnon; R., Wheeler Benjamin; Sönke, Johnsen; Taniguchi, Jaffe Jules S.

Cuttlefish Sepia officinalis Preferentially Respond to Bottom Rather than Side Stimuli When Not Allowed Adjacent to Tank Walls Journal Article

In: PLoS ONE, vol. 10, no. 10, pp. 1-18, 2015.

Abstract | Links | BibTeX

@article{10.1371/journal.pone.0138690,
title = {Cuttlefish Sepia officinalis Preferentially Respond to Bottom Rather than Side Stimuli When Not Allowed Adjacent to Tank Walls},
author = { Darcy A. A. AND Gagnon Yakir AND Wheeler Benjamin R. AND Johnsen Sönke AND Jaffe Jules S. Taniguchi},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0138690},
doi = {10.1371/journal.pone.0138690},
year = {2015},
date = {2015-01-01},
journal = {PLoS ONE},
volume = {10},
number = {10},
pages = {1-18},
publisher = {Public Library of Science},
abstract = {

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.

},
keywords = {},
pubstate = {published},
tppubtype = {article}
}