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Recent Publications

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

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

Close

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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  • https://doi.org/10.1002/lno.11632

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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

Limnology and Oceanography: Methods, 2020.

Abstract | Links | BibTeX

@article{Orenstein2020,
title = {The Scripps Plankton Camera system: A framework and platform for in situ microscopy},
author = {Eric C. Orenstein and Devin Ratelle and Christian Briseño-Avena and Melissa L Carter and Peter J. S. Franks and Jules S. Jaffe and Paul L. D. Roberts},
editor = {Malinda Sutor},
url = {https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10394},
doi = {10.1002/lom3.10394},
year = {2020},
date = {2020-10-05},
journal = {Limnology and Oceanography: Methods},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

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.

Close

  • https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.1002/lom3.10394
  • doi:10.1002/lom3.10394

Close

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

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}
}

Close

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.

Close

  • https://www.frontiersin.org/articles/10.3389/fmars.2020.00602/abstract
  • doi:10.3389/fmars.2020.00602

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Lertvilai, Pichaya

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

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

Close

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.

Close

  • https://doi.org/10.1111/2041-210X.13441

Close

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

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

Close

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.

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  • https://doi.org/10.1002/lno.11468

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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

ICES Journal of Marine Science, 77 (4), pp. 1440-1455, 2020.

Abstract | Links | BibTeX

@article{Campbell2020,
title = {The Prince William Sound Plankton Camera: a profiling in situ observatory of plankton and particulates},
author = {Robert W Campbell and Paul L D Roberts and Jules S Jaffe},
url = {https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsaa029/5811106},
year = {2020},
date = {2020-03-24},
journal = {ICES Journal of Marine Science},
volume = {77},
number = {4},
pages = {1440-1455},
abstract = {A novel plankton imager was developed and deployed aboard a profiling mooring in Prince William Sound in 2016–2018. The imager consisted of a 12-MP camera and a 0.137× telecentric lens, along with darkfield illumination produced by an in-line ring/condenser lens system. Just under 2.5 × 106 images were collected during 3 years of deployments. A subset of almost 2 × 104 images was manually identified into 43 unique classes, and a hybrid convolutional neural network classifier was developed and trained to identify the images. Classification accuracy varied among the different classes, and applying thresholds to the output of the neural network (interpretable as probabilities or classifier confidence), improved classification accuracy in non-ambiguous groups to between 80% and 100%.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

A novel plankton imager was developed and deployed aboard a profiling mooring in Prince William Sound in 2016–2018. The imager consisted of a 12-MP camera and a 0.137× telecentric lens, along with darkfield illumination produced by an in-line ring/condenser lens system. Just under 2.5 × 106 images were collected during 3 years of deployments. A subset of almost 2 × 104 images was manually identified into 43 unique classes, and a hybrid convolutional neural network classifier was developed and trained to identify the images. Classification accuracy varied among the different classes, and applying thresholds to the output of the neural network (interpretable as probabilities or classifier confidence), improved classification accuracy in non-ambiguous groups to between 80% and 100%.

Close

  • https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsaa029/581[...]

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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

Limnology and Oceanography, 65 (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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

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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  • https://doi.org/10.1002/lno.11400

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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

Limnology and Oceanography, (WOS:000501665500001), 2019, ISBN: 0024-3590.

Abstract | Links | BibTeX

@article{Franks2019,
title = {Stokes drift of plankton in linear internal waves: Cross-shore transport of neutrally buoyant and depth-keeping organisms},
author = {Peter J. S. Franks and Jessica C. Garwood and Michael Ouimet and Jorge Cortes and Ruth C. Musgrave and Andrew J. Lucas},
url = {https://doi.org/10.1002/lno.11389},
doi = {10.1002/lno.11389},
isbn = {0024-3590},
year = {2019},
date = {2019-12-10},
journal = {Limnology and Oceanography},
number = {WOS:000501665500001},
abstract = {The meroplanktonic larvae of many invertebrate and vertebrate species rely on physical transport to move them across the shelf to their adult habitats. One potential mechanism for cross‐shore larval transport is Stokes drift in internal waves. Here, we develop theory to quantify the Stokes velocities of neutrally buoyant and depth‐keeping organisms in linear internal waves in shallow water. We apply the analyses to theoretical and measured internal wave fields, and compare results with a numerical model. Near the surface and bottom boundaries, both neutrally buoyant and depth‐keeping organisms were transported in the direction of the wave's phase propagation. However, neutrally buoyant organisms were transported in the opposite direction of the wave's phase at mid depths, while depth‐keeping organisms had zero net transport there. Weakly depth‐keeping organisms had Stokes drifts between the perfectly depth‐keeping and neutrally buoyant organisms. For reasonable wave amplitudes and phase speeds, organisms would experience horizontal Stokes speeds of several centimeters per second—or a few kilometers per day in a constant wave field. With onshore‐polarized internal waves, Stokes drift in internal waves presents a predictable mechanism for onshore transport of meroplanktonic larvae and other organisms near the surface, and offshore transport at mid depths.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

The meroplanktonic larvae of many invertebrate and vertebrate species rely on physical transport to move them across the shelf to their adult habitats. One potential mechanism for cross‐shore larval transport is Stokes drift in internal waves. Here, we develop theory to quantify the Stokes velocities of neutrally buoyant and depth‐keeping organisms in linear internal waves in shallow water. We apply the analyses to theoretical and measured internal wave fields, and compare results with a numerical model. Near the surface and bottom boundaries, both neutrally buoyant and depth‐keeping organisms were transported in the direction of the wave's phase propagation. However, neutrally buoyant organisms were transported in the opposite direction of the wave's phase at mid depths, while depth‐keeping organisms had zero net transport there. Weakly depth‐keeping organisms had Stokes drifts between the perfectly depth‐keeping and neutrally buoyant organisms. For reasonable wave amplitudes and phase speeds, organisms would experience horizontal Stokes speeds of several centimeters per second—or a few kilometers per day in a constant wave field. With onshore‐polarized internal waves, Stokes drift in internal waves presents a predictable mechanism for onshore transport of meroplanktonic larvae and other organisms near the surface, and offshore transport at mid depths.

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  • https://doi.org/10.1002/lno.11389
  • doi:10.1002/lno.11389

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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

Frontiers in Marine Science, 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.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

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.

Close

  • https://www.frontiersin.org/article/10.3389/fmars.2019.00196
  • doi:10.3389/fmars.2019.00196

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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

Journal of the Acoustical Society of America, 144 (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}
}

Close

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.

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  • https://asa.scitation.org/doi/10.1121/1.5070154
  • doi:10.1121/1.5070154

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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

IEEE Access, 6 (INSPEC Accession Number: 16881600), pp. 1635-1646, 2017.

Links | BibTeX

@article{Naughton2017,
title = {Self-localization of a deforming swarm of underwater vehicles using impulsive sound 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://ieeexplore.ieee.org/document/8141871},
doi = {10.1109/ACCESS.2017.2779835},
year = {2017},
date = {2017-12-04},
journal = {IEEE Access},
volume = {6},
number = {INSPEC Accession Number: 16881600},
pages = {1635-1646},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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  • https://ieeexplore.ieee.org/document/8141871
  • doi:10.1109/ACCESS.2017.2779835

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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

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

Abstract | Links | BibTeX

@article{Briseño-Avena2017,
title = {A diverse group of echogenic particles observed with a broadband, high frequency echosounder},
author = {Christian Briseño-Avena and Peter J S Franks and Paul L D Roberts and Jules S Jaffe},
editor = {Howard Browman},
url = {https://doi.org/10.1093/icesjms/fsx171},
year = {2017},
date = {2017-09-18},
journal = {ICES Journal of Marine Science},
volume = {75},
pages = {471-482},
abstract = {In 1980, Holliday and Pieper stated: “Most sound scattering in the ocean volume can be traced to a biotic origin.” However, most of the bioacoustics 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-O2) 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

In 1980, Holliday and Pieper stated: “Most sound scattering in the ocean volume can be traced to a biotic origin.” However, most of the bioacoustics 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-O2) 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.

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  • https://doi.org/10.1093/icesjms/fsx171

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Orenstein, Eric C; Beijbom, Oscar

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

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

Links | BibTeX

@inproceedings{OrensteinTransfer2017,
title = {Transfer learning and deep feature extraction for planktonic image data sets},
author = {Eric C. Orenstein AND Oscar Beijbom},
url = {http://ieeexplore.ieee.org/document/7926708/},
doi = {10.1109/WACV.2017.125},
year = {2017},
date = {2017-03-27},
booktitle = {Winter Conference on Applications of Computer Vision},
pages = {1082-1088},
organization = {IEEE},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}

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  • http://ieeexplore.ieee.org/document/7926708/
  • doi:10.1109/WACV.2017.125

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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

Nature Communications, 8 (14189), 2017, (Article).

Links | BibTeX

@article{Jaffe2017,
title = {A swarm of autonomous miniature underwater robot drifters for exploring submesoscale ocean dynamics},
author = {Jules S Jaffe and Peter J S Franks and Paul L D Roberts and Diba Mirza and Curt Schurgers and Ryan Kastner and Adrien Boch},
url = {http://dx.doi.org/10.1038/ncomms14189},
year = {2017},
date = {2017-01-24},
journal = {Nature Communications},
volume = {8},
number = {14189},
publisher = {The Author(s) SN -},
note = {Article},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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  • http://dx.doi.org/10.1038/ncomms14189

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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

The Journal of the Acoustical Society of America, 140 (6), pp. 4260-4270, 2016.

Abstract | Links | BibTeX

@article{doi:10.1121/1.4971172,
title = {Ambient noise correlations on a mobile, deformable array},
author = {Perry Naughton and Philippe Roux and Riley Yeakle and Curt Schurgers and Ryan Kastner and Jules S. Jaffe and Paul L. D. Roberts},
url = {http://dx.doi.org/10.1121/1.4971172},
doi = {10.1121/1.4971172},
year = {2016},
date = {2016-12-15},
journal = {The Journal of the Acoustical Society of America},
volume = {140},
number = {6},
pages = {4260-4270},
abstract = {This paper presents a demonstration of ambient acoustic noise processing on a set of free floating oceanic receivers whose relative positions vary with time. It is shown that it is possible to retrieve information that is relevant to the travel time between the receivers. With thousands of short time cross-correlations (10 s) of varying distance, it is shown that on average, the decrease in amplitude of the noise correlation function with increased separation follows a power law. This suggests that there may be amplitude information that is embedded in the noise correlation function. An incoherent beamformer is developed, which shows that it is possible to determine a source direction using an array with moving elements and large element separation. This incoherent beamformer is used to verify cases when the distribution of noise sources in the ocean allows one to recover travel time information between pairs of mobile receivers.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

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.

Close

  • http://dx.doi.org/10.1121/1.4971172
  • doi:10.1121/1.4971172

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

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

Appl. Opt., 55 (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}
}

Close

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.

Close

  • http://ao.osa.org/abstract.cfm?URI=ao-55-33-9440
  • doi:10.1364/AO.55.009440

Close

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

Nat Commun, 7 , 2016.

Abstract | Links | BibTeX

@article{Mullen2016b,
title = {Underwater microscopy for in situ studies of benthic ecosystems},
author = { Andrew D. Mullen and Tali Treibitz and Paul L. D. Roberts and Emily L. A. Kelly and Rael Horwitz and Jennifer E. Smith and Jules S. Jaffe},
url = {http://dx.doi.org/10.1038/ncomms12093},
year = {2016},
date = {2016-07-12},
journal = {Nat Commun},
volume = {7},
publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

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.

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  • http://dx.doi.org/10.1038/ncomms12093

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

Automated classification of camouflaging cuttlefish Journal Article

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

Abstract | Links | BibTeX

@article{Orenstein2016,
title = {Automated classification of camouflaging cuttlefish},
author = { Eric C. Orenstein and Justin M. Haag and Yakir L. Gagnon and Jules S. Jaffe},
url = {http://www.sciencedirect.com/science/article/pii/S2211122015300220},
doi = {http://dx.doi.org/10.1016/j.mio.2016.04.005},
issn = {2211-1220},
year = {2016},
date = {2016-01-01},
journal = {Methods in Oceanography},
pages = {-},
abstract = {Abstract The automated processing of images for scientific analysis has become an integral part of projects that collect large amounts of data. Our recent study of cuttlefish camouflaging behavior captured ∼12,000 images of the animals’ response to changing visual environments. This work presents an automated segmentation and classification workflow to alleviate the human cost of processing this complex data set. The specimens’ bodies are segmented from the background using a combination of intensity thresholding and Histogram of Oriented Gradients. Subregions are then used to train a texton-based classifier designed to codify traditional, manual methods of cuttlefish image analysis. The segmentation procedure properly selected the subregion from ∼95% of the images. The classifier achieved an accuracy of ∼94% as compared to manual annotation. Together, the process correctly processed ∼90% of the images. Additionally, we leverage the output of the classifier to propose a model of camouflage display that attributes a given display to a superposition of the user-defined classes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

Abstract The automated processing of images for scientific analysis has become an integral part of projects that collect large amounts of data. Our recent study of cuttlefish camouflaging behavior captured ∼12,000 images of the animals’ response to changing visual environments. This work presents an automated segmentation and classification workflow to alleviate the human cost of processing this complex data set. The specimens’ bodies are segmented from the background using a combination of intensity thresholding and Histogram of Oriented Gradients. Subregions are then used to train a texton-based classifier designed to codify traditional, manual methods of cuttlefish image analysis. The segmentation procedure properly selected the subregion from ∼95% of the images. The classifier achieved an accuracy of ∼94% as compared to manual annotation. Together, the process correctly processed ∼90% of the images. Additionally, we leverage the output of the classifier to propose a model of camouflage display that attributes a given display to a superposition of the user-defined classes.

Close

  • http://www.sciencedirect.com/science/article/pii/S2211122015300220
  • doi:http://dx.doi.org/10.1016/j.mio.2016.04.005

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Jaffe, Jules S

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

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

Abstract | Links | BibTeX

@article{Jaffe2016b,
title = {To sea and to see: That is the answer},
author = {Jules S. Jaffe},
url = {http://www.sciencedirect.com/science/article/pii/S2211122016300238},
doi = {http://dx.doi.org/10.1016/j.mio.2016.05.003},
issn = {2211-1220},
year = {2016},
date = {2016-01-01},
journal = {Methods in Oceanography},
pages = {-},
abstract = {Abstract In this article Dr. Jules S. Jaffe chronicles his development as a scientist and engineer. The story starts during his middle school years and continues up until the present day. Dr. Jaffe, as an inventor of technology for ocean exploration has played a role in a number of advances in ocean engineering. These range from the development of a planar laser imaging system for sensing fluorescent microstructure to swarms of underwater autonomous floats, to a current generation of underwater microscopes. The emphasis of the article is on career development and the process rather than the exact, and detailed, documentation of technology. Dr. Jaffe is also the Editor in Chief of Methods in Oceanography and he instituted these autobiographies for exactly this purpose: To give younger, aspiring, professionals an example of a career that has not been “straight through”, but rather a meandering path through a multitude of projects, proposals, and relationships with colleagues, students, and funding agencies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

Abstract In this article Dr. Jules S. Jaffe chronicles his development as a scientist and engineer. The story starts during his middle school years and continues up until the present day. Dr. Jaffe, as an inventor of technology for ocean exploration has played a role in a number of advances in ocean engineering. These range from the development of a planar laser imaging system for sensing fluorescent microstructure to swarms of underwater autonomous floats, to a current generation of underwater microscopes. The emphasis of the article is on career development and the process rather than the exact, and detailed, documentation of technology. Dr. Jaffe is also the Editor in Chief of Methods in Oceanography and he instituted these autobiographies for exactly this purpose: To give younger, aspiring, professionals an example of a career that has not been “straight through”, but rather a meandering path through a multitude of projects, proposals, and relationships with colleagues, students, and funding agencies.

Close

  • http://www.sciencedirect.com/science/article/pii/S2211122016300238
  • doi:http://dx.doi.org/10.1016/j.mio.2016.05.003

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2015

Jaffe, J S

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

Oceanic Engineering, IEEE Journal of, 40 (3), pp. 683-700, 2015, ISSN: 0364-9059.

Links | BibTeX

@article{6930829,
title = {Underwater Optical Imaging: The Past, the Present, and the Prospects},
author = {J. S. Jaffe},
url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6930829&punumber%3D48},
doi = {10.1109/JOE.2014.2350751},
issn = {0364-9059},
year = {2015},
date = {2015-07-01},
journal = {Oceanic Engineering, IEEE Journal of},
volume = {40},
number = {3},
pages = {683-700},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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  • http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6930829&punumber%[...]
  • doi:10.1109/JOE.2014.2350751

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

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

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

Abstract | Links | BibTeX

@article{Treibitz2015,
title = {Wide Field-of-View Fluorescence Imaging of Coral Reefs},
author = {Treibitz, Tali and Neal, Benjamin P. and Kline, David I. and Beijbom, Oscar and Paul L. D. Roberts and Mitchell, B. Greg and Kriegman, David},
url = {http://dx.doi.org/10.1038/srep07694},
doi = {10.1038/srep07694},
year = {2015},
date = {2015-01-01},
journal = {Scientific Reports},
volume = {5},
pages = {7694 EP -},
publisher = {Macmillan Publishers Limited. All rights reserved SN -},
abstract = {Coral reefs globally are declining rapidly because of both local and global stressors. Improved monitoring tools are urgently needed to understand the changes that are occurring at appropriate temporal and spatial scales. Coral fluorescence imaging tools have the potential to improve both ecological and physiological assessments. Although fluorescence imaging is regularly used for laboratory studies of corals, it has not yet been used for large-scale in situ assessments. Current obstacles to effective underwater fluorescence surveying include limited field-of-view due to low camera sensitivity, the need for nighttime deployment because of ambient light contamination, and the need for custom multispectral narrow band imaging systems to separate the signal into meaningful fluorescence bands. Here we describe the Fluorescence Imaging System (FluorIS), based on a consumer camera modified for greatly increased sensitivity to chlorophyll-a fluorescence, and we show high spectral correlation between acquired images and in situ spectrometer measurements. This system greatly facilitates underwater wide field-of-view fluorophore surveying during both night and day, and potentially enables improvements in semi-automated segmentation of live corals in coral reef photographs and juvenile coral surveys.},
note = {Article},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

Close

Coral reefs globally are declining rapidly because of both local and global stressors. Improved monitoring tools are urgently needed to understand the changes that are occurring at appropriate temporal and spatial scales. Coral fluorescence imaging tools have the potential to improve both ecological and physiological assessments. Although fluorescence imaging is regularly used for laboratory studies of corals, it has not yet been used for large-scale in situ assessments. Current obstacles to effective underwater fluorescence surveying include limited field-of-view due to low camera sensitivity, the need for nighttime deployment because of ambient light contamination, and the need for custom multispectral narrow band imaging systems to separate the signal into meaningful fluorescence bands. Here we describe the Fluorescence Imaging System (FluorIS), based on a consumer camera modified for greatly increased sensitivity to chlorophyll-a fluorescence, and we show high spectral correlation between acquired images and in situ spectrometer measurements. This system greatly facilitates underwater wide field-of-view fluorophore surveying during both night and day, and potentially enables improvements in semi-automated segmentation of live corals in coral reef photographs and juvenile coral surveys.

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  • http://dx.doi.org/10.1038/srep07694
  • doi:10.1038/srep07694

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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

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

Abstract | Links | BibTeX

@article{BriseñoAvena201536,
title = {ZOOPS- O2: A broadband echosounder with coordinated stereo optical imaging for observing plankton in situ},
author = {Christian Briseño-Avena and Paul L.D. Roberts and Peter J.S. Franks and Jules S. Jaffe},
url = {http://www.sciencedirect.com/science/article/pii/S2211122015000237},
doi = {http://dx.doi.org/10.1016/j.mio.2015.07.001},
issn = {2211-1220},
year = {2015},
date = {2015-01-01},
journal = {Methods in Oceanography},
volume = {12},
pages = {36 - 54},
abstract = {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 μ m. 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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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 μ m. 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.

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  • http://www.sciencedirect.com/science/article/pii/S2211122015000237
  • doi:http://dx.doi.org/10.1016/j.mio.2015.07.001

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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

Marine Biology, 162 (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}
}

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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.

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  • http://link.springer.com/article/10.1007%2Fs00227-015-2713-x
  • doi:10.1007/s00227-015-2713-x

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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

PLoS ONE, 10 (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}
}

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<p>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 (<italic>Sepia officinalis</italic>) 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 <italic>S</italic>. <italic>officinalis</italic> 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.</p>

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  • http://dx.doi.org/10.1371%2Fjournal.pone.0138690
  • doi:10.1371/journal.pone.0138690

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