2024
Walker, Joseph L.; Zeng, Zheng; Wu, Chengchen L.; Jaffe, Jules S.; Frasier, Kaitlin E.; Sandin, Stuart S.
Underwater Object Detection Under Domain Shift Bachelor Thesis
2024, ISSN: 1558-1691.
@bachelorthesis{Walker2024,
title = {Underwater Object Detection Under Domain Shift},
author = {Walker, Joseph L. and Zeng, Zheng and Wu, Chengchen L. and Jaffe, Jules S. and Frasier, Kaitlin E. and Sandin, Stuart S.},
url = {https://ieeexplore.ieee.org/document/10679365},
doi = {10.1109},
issn = {1558-1691},
year = {2024},
date = {2024-10-12},
journal = {IEEE Journal of Oceanic Engineering},
volume = {49},
number = {4},
pages = {1209-1219},
abstract = {There is increasing interest in using deep learning–based object recognition algorithms to automate the labeling of image data collected from marine surveys. However, underwater object detection is a particularly challenging problem due to changes in scattering and absorption of light, and spotty data collection efforts, which rarely capture the broad variability. Using deep learning–based object detection systems for long-term or multisite marine surveying is further complicated by shifting data distributions between training and testing stages. Using data from the 100 Island Challenge, we investigate how object detection performance is impacted by changes in site characteristics and imaging conditions. We demonstrate that the combined use of data augmentation and unsupervised domain adaptation techniques can mitigate performance drops in the presence of domain shift. The proposed methodologies are broadly applicable to observational data sets in marine and terrestrial environments where a single algorithm needs to adapt to and perform comparably across changing conditions.},
keywords = {},
pubstate = {published},
tppubtype = {bachelorthesis}
}
There is increasing interest in using deep learning–based object recognition algorithms to automate the labeling of image data collected from marine surveys. However, underwater object detection is a particularly challenging problem due to changes in scattering and absorption of light, and spotty data collection efforts, which rarely capture the broad variability. Using deep learning–based object detection systems for long-term or multisite marine surveying is further complicated by shifting data distributions between training and testing stages. Using data from the 100 Island Challenge, we investigate how object detection performance is impacted by changes in site characteristics and imaging conditions. We demonstrate that the combined use of data augmentation and unsupervised domain adaptation techniques can mitigate performance drops in the presence of domain shift. The proposed methodologies are broadly applicable to observational data sets in marine and terrestrial environments where a single algorithm needs to adapt to and perform comparably across changing conditions.
2023
Brian C. Stock, et al
Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery Bachelor Thesis
2023.
@bachelorthesis{Stock2023,
title = {Protected fish spawning aggregations as self-replenishing reservoirs for regional recovery},
author = {Stock, Brian C., et al},
url = {https://royalsocietypublishing.org/doi/abs/10.1098/rspb.2023.0551},
doi = {10.1098/rspb.2023.0551},
year = {2023},
date = {2023-05-10},
urldate = {2023-05-10},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {290},
number = {1998},
abstract = {Dispersal of eggs and larvae from spawning sites is critical to the population dynamics and conservation of marine fishes. For overfished species like critically endangered Nassau grouper (Epinephelus striatus), recovery depends on the fate of eggs spawned at the few remaining aggregation sites. Biophysical models can predict larval dispersal, yet these rely on assumed values of key parameters, such as diffusion and mortality rates, which have historically been difficult or impossible to estimate. We used in situ imaging to record three-dimensional positions of individual eggs and larvae in proximity to oceanographic drifters released into egg plumes from the largest known Nassau grouper spawning aggregation. We then estimated a diffusion–mortality model and applied it to previous years' drifter tracks to evaluate the possibility of retention versus export to nearby sites within 5 days of spawning. Results indicate that larvae were retained locally in 2011 and 2017, with 2011 recruitment being a substantial driver of population recovery on Little Cayman. Export to a nearby island with a depleted population occurred in 2016. After two decades of protection, the population appears to be self-replenishing but also capable of seeding recruitment in the region, supporting calls to incorporate spawning aggregation protections into fisheries management.},
keywords = {},
pubstate = {published},
tppubtype = {bachelorthesis}
}
Dispersal of eggs and larvae from spawning sites is critical to the population dynamics and conservation of marine fishes. For overfished species like critically endangered Nassau grouper (Epinephelus striatus), recovery depends on the fate of eggs spawned at the few remaining aggregation sites. Biophysical models can predict larval dispersal, yet these rely on assumed values of key parameters, such as diffusion and mortality rates, which have historically been difficult or impossible to estimate. We used in situ imaging to record three-dimensional positions of individual eggs and larvae in proximity to oceanographic drifters released into egg plumes from the largest known Nassau grouper spawning aggregation. We then estimated a diffusion–mortality model and applied it to previous years' drifter tracks to evaluate the possibility of retention versus export to nearby sites within 5 days of spawning. Results indicate that larvae were retained locally in 2011 and 2017, with 2011 recruitment being a substantial driver of population recovery on Little Cayman. Export to a nearby island with a depleted population occurred in 2016. After two decades of protection, the population appears to be self-replenishing but also capable of seeding recruitment in the region, supporting calls to incorporate spawning aggregation protections into fisheries management.
Kasia M. Kenitz, et al
Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy Journal Article
In: Limnology and Oceanography, vol. 68, no. 3, pp. 598-615, 2023.
@article{Kenitz2023,
title = {Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy},
author = {Kenitz, Kasia M., et al},
editor = {Bingzhang Chen},
url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.12297},
doi = {12297},
year = {2023},
date = {2023-03-09},
urldate = {2023-03-09},
journal = {Limnology and Oceanography},
volume = {68},
number = {3},
pages = {598-615},
abstract = {Abstract In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet-18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea, Chattonella spp., Dinophysis spp., and Lingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea (R2=0.79±0.06), Chattonella spp. (R2=0.63±0.06), and L. polyedra (R2=0.72±0.08), whereas models for Dinophysis spp. showed lower prediction accuracy (R2=0.24±0.07). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional-scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional-scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real-time HAB abundance forecasts.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abstract In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet-18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea, Chattonella spp., Dinophysis spp., and Lingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea (R2=0.79±0.06), Chattonella spp. (R2=0.63±0.06), and L. polyedra (R2=0.72±0.08), whereas models for Dinophysis spp. showed lower prediction accuracy (R2=0.24±0.07). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional-scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional-scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real-time HAB abundance forecasts.
Kasia M. Kenitz, et al
Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy Bachelor Thesis
2023.
@bachelorthesis{Kenitz2023d,
title = {Environmental and ecological drivers of harmful algal blooms revealed by automated underwater microscopy},
author = {Kenitz, Kasia M., et al},
url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.12297},
doi = {12297},
year = {2023},
date = {2023-01-09},
urldate = {2023-01-09},
journal = {Limnology and Oceanography},
abstract = {Abstract In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet-18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea, Chattonella spp., Dinophysis spp., and Lingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea ({R}^2 = 0.79 ± 0.06 $$), Chattonella spp. ({R}^2 = 0.63 ± 0.06), and L. polyedra ({R}^2 = 0.72 ± 0.08), whereas models for Dinophysis spp. showed lower prediction accuracy ({R}^2 = 0.24 ± 0.07). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional-scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional-scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real-time HAB abundance forecasts.},
keywords = {},
pubstate = {published},
tppubtype = {bachelorthesis}
}
Abstract In recent years, harmful algal blooms (HABs) have increased in their severity and extent in many parts of the world and pose serious threats to local aquaculture, fisheries, and public health. In many cases, the mechanisms triggering and regulating HAB events remain poorly understood. Using underwater microscopy and Residual Neural Network (ResNet-18) to taxonomically classify imaged organisms, we developed a daily abundance record of four potentially harmful algae (Akashiwo sanguinea, Chattonella spp., Dinophysis spp., and Lingulodinium polyedra) and major grazer groups (ciliates, copepod nauplii, and copepods) from August 2017 to November 2020 at Scripps Institution of Oceanography pier, a coastal location in the Southern California Bight. Random Forest algorithms were used to identify the optimal combination of environmental and ecological variables that produced the most accurate abundance predictions for each taxon. We developed models with high prediction accuracy for A. sanguinea ({R}^2 = 0.79 ± 0.06 $$), Chattonella spp. ({R}^2 = 0.63 ± 0.06), and L. polyedra ({R}^2 = 0.72 ± 0.08), whereas models for Dinophysis spp. showed lower prediction accuracy ({R}^2 = 0.24 ± 0.07). Offshore nutricline depth and indices describing climate variability, including El Niño Southern Oscillation, Pacific Decadal Oscillation, and North Pacific Gyre Oscillation, that influence regional-scale ocean circulation patterns and environmental conditions, were key predictor variables for these HAB taxa. These metrics of regional-scale processes were generally better predictors of HAB taxa abundances at this coastal location than the in situ environmental measurements. Ciliate abundance was an important predictor of Chattonella and Dinophysis spp., but not of A. sanguinea and L. polyedra. Our findings indicate that combining regional and local environmental factors with microzooplankton populations dynamics can improve real-time HAB abundance forecasts.
2022
Jaffe, Jules S.
Non-invasive estimation of coral polyp volume and surface area using optical coherence tomography Journal Article
In: Frontiers in Marine Science, vol. 9, 2022, ISSN: 2296-7745.
@article{Jaffe2022,
title = {Non-invasive estimation of coral polyp volume and surface area using optical coherence tomography},
author = {Jaffe, Jules S.},
editor = {Jian Sheng},
url = {https://doi.org/10.3389/fmars.2022.1049440},
doi = {10.3389/fmars.2022.1049440},
issn = {2296-7745},
year = {2022},
date = {2022-12-12},
urldate = {2022-12-12},
journal = {Frontiers in Marine Science},
volume = {9},
abstract = {The surface area (SA) and three-dimensional (3D) morphology of reef-building corals are central to their physiology. A challenge for the estimation of coral SA has been to meet the required spatial resolution as well as the capability to preserve the soft tissue in its native state during measurements. Optical Coherence Tomography (OCT) has been used to quantify the 3D microstructure of coral tissues and skeletons with nearly micron-scale resolution. Here, we develop a non-invasive method to quantify surface area and volume of single coral polyps. A coral fragment with several coral polyps as well as calibration targets of known areal extent are scanned with an OCT system. This produces a 3D matrix of optical backscatter that is analyzed with computer algorithms to detect refractive index mismatches between physical boundaries between the coral and the immersed water. The algorithms make use of a normalization of the depth dependent scatter intensity and signal attenuation as well as region filling to depict the interface between the coral soft tissue and the water. Feasibility of results is judged by inspection as well as by applying algorithms to hard spheres and fish eggs whose volume and SA can be estimated analytically. The method produces surface area estimates in calibrated targets that are consistent with analytic estimates within 93%. The appearance of the coral polyp surfaces is consistent with visual inspection that permits standard programs to visualize both point clouds and 3-D meshes. The method produces the 3-D definition of coral tissue and skeleton at a resolution close to 10 µm, enabling robust quantification of polyp volume to surface area ratios.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The surface area (SA) and three-dimensional (3D) morphology of reef-building corals are central to their physiology. A challenge for the estimation of coral SA has been to meet the required spatial resolution as well as the capability to preserve the soft tissue in its native state during measurements. Optical Coherence Tomography (OCT) has been used to quantify the 3D microstructure of coral tissues and skeletons with nearly micron-scale resolution. Here, we develop a non-invasive method to quantify surface area and volume of single coral polyps. A coral fragment with several coral polyps as well as calibration targets of known areal extent are scanned with an OCT system. This produces a 3D matrix of optical backscatter that is analyzed with computer algorithms to detect refractive index mismatches between physical boundaries between the coral and the immersed water. The algorithms make use of a normalization of the depth dependent scatter intensity and signal attenuation as well as region filling to depict the interface between the coral soft tissue and the water. Feasibility of results is judged by inspection as well as by applying algorithms to hard spheres and fish eggs whose volume and SA can be estimated analytically. The method produces surface area estimates in calibrated targets that are consistent with analytic estimates within 93%. The appearance of the coral polyp surfaces is consistent with visual inspection that permits standard programs to visualize both point clouds and 3-D meshes. The method produces the 3-D definition of coral tissue and skeleton at a resolution close to 10 µm, enabling robust quantification of polyp volume to surface area ratios.
Kevin T. Le, et al
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.
@article{Le2022b,
title = {Benchmarking and Automating the Image Recognition Capability of an In Situ Plankton Imaging System},
author = {Le, Kevin T., et al},
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},
urldate = {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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
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.
@article{Or2022,
title = {Coral fluorescence: a prey-lure in deep habitats},
author = {Ben-Zvi Or, Lindemann Yoav, Eyal Gal, Loya Yossi},
editor = {Anam Akhtar and Christina Karlsson Rosenthal},
url = {https://doi.org/10.1038/s42003-022-03460-3},
doi = {10.1038/s42003-022-03460-3},
issn = {2399-3642},
year = {2022},
date = {2022-06-02},
journal = {Communications Biology},
volume = {5},
number = {5},
issue = {1},
abstract = {Fluorescence is highly prevalent in reef-building corals, nevertheless its biological role is still under ongoing debate. This feature of corals was previously suggested to primarily screen harmful radiation or facilitate coral photosynthesis. In mesophotic coral ecosystems (MCEs; 30-150 m depth) corals experience a limited, blue-shifted light environment. Consequently, in contrast to their shallow conspecifics, they might not be able to rely on photosynthates from their photosymbionts as their main energy source. Here, we experimentally test an alternative hypothesis for coral fluorescence: a prey-lure mechanism for plankton. We show that plankton exhibit preferential swimming towards green fluorescent cues and that compared to other morphs, higher predation rates are recorded in a green fluorescing morph of the mesophotic coral Euphyllia paradivisa. The evidence provided here - that plankton are actively attracted to fluorescent signals - indicates the significant role of fluorescence in amplifying the nutritional sink adjacent to coral reefs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Fluorescence is highly prevalent in reef-building corals, nevertheless its biological role is still under ongoing debate. This feature of corals was previously suggested to primarily screen harmful radiation or facilitate coral photosynthesis. In mesophotic coral ecosystems (MCEs; 30-150 m depth) corals experience a limited, blue-shifted light environment. Consequently, in contrast to their shallow conspecifics, they might not be able to rely on photosynthates from their photosymbionts as their main energy source. Here, we experimentally test an alternative hypothesis for coral fluorescence: a prey-lure mechanism for plankton. We show that plankton exhibit preferential swimming towards green fluorescent cues and that compared to other morphs, higher predation rates are recorded in a green fluorescing morph of the mesophotic coral Euphyllia paradivisa. The evidence provided here - that plankton are actively attracted to fluorescent signals - indicates the significant role of fluorescence in amplifying the nutritional sink adjacent to coral reefs.
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.
@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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
Jon S. Sauer, et al
The Sea Spray Chemistry and Particle Evolution study (SeaSCAPE): overview and experimental methods Journal Article
In: Environmental Science: Processes and Impacts, 2022.
@article{Sauer2022b,
title = {The Sea Spray Chemistry and Particle Evolution study (SeaSCAPE): overview and experimental methods},
author = {Jon S. Sauer, et al},
url = {https://doi.org/10.1039/D1EM00260K},
doi = {https://doi.org/10.1039/D1EM00260K},
year = {2022},
date = {2022-01-20},
urldate = {2022-01-20},
journal = {Environmental Science: Processes and Impacts},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2021
Ewa Merz, et al
Underwater dual-magnification imaging for automated lake plankton monitoring Journal Article
In: Water Research, vol. 203, no. 117524, 2021.
@article{Merz2021,
title = {Underwater dual-magnification imaging for automated lake plankton monitoring},
author = {Ewa Merz, et al},
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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
@article{Ronen2021,
title = {Plankton reconstruction through robust statistical optical tomography},
author = {Roi Ronen and Yacov Attias and Yoay Y. Schechner and Jules S. Jaffe and Eric C. Orenstein},
url = {https://doi.org/10.1364/JOSAA.423037},
year = {2021},
date = {2021-09-01},
urldate = {2021-09-01},
journal = {Journal of the Optical Society of America A},
volume = {38},
number = {9},
pages = {1320-1331},
abstract = {Plankton interact with the environment according to their size and three-dimensional (3D) structure. To study them outdoors, these translucent specimens are imaged in situ. Light projects through a specimen in each image. The specimen has a random scale, drawn from the population’s size distribution and random unknown pose. The specimen appears only once before drifting away. We achieve 3D tomography using such a random ensemble to statistically estimate an average volumetric distribution of the plankton type and specimen size. To counter errors due to non-rigid deformations, we weight the data, drawing from advanced models developed for cryo-electron microscopy. The weights convey the confidence in the quality of each datum. This confidence relies on a statistical error model. We demonstrate the approach on live plankton using an underwater field microscope.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Plankton interact with the environment according to their size and three-dimensional (3D) structure. To study them outdoors, these translucent specimens are imaged in situ. Light projects through a specimen in each image. The specimen has a random scale, drawn from the population’s size distribution and random unknown pose. The specimen appears only once before drifting away. We achieve 3D tomography using such a random ensemble to statistically estimate an average volumetric distribution of the plankton type and specimen size. To counter errors due to non-rigid deformations, we weight the data, drawing from advanced models developed for cryo-electron microscopy. The weights convey the confidence in the quality of each datum. This confidence relies on a statistical error model. We demonstrate the approach on live plankton using an underwater field microscope.
Camille M. L. S. Pagniello, et al
An Optical Imaging System for Capturing Images in Low-Light Aquatic Habitats Using Only Ambient Light Journal Article
In: Oceanography Magazine, 2021.
@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, et al},
url = {https://doi.org/10.5670/oceanog.2021.305},
year = {2021},
date = {2021-07-08},
urldate = {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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
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.
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.
@article{Lertvilai2021,
title = {In Situ Underwater Average Flow Velocity Estimation Using a Low-Cost Video Velocimeter},
author = {Pichaya Lertvilai and Paul L. D. Roberts and Jules S. Jaffe},
url = {https://doi.org/10.1175/JTECH-D-20-0115.1},
doi = {https://doi.org/10.1175/JTECH-D-20-0115.1},
year = {2021},
date = {2021-06-14},
journal = {Journal of Atmospheric and Oceanic Technology},
volume = {38},
number = {6},
pages = {1143-1156},
abstract = {The development of a low-cost Video Velocimeter (VIV) to estimate underwater bulk flow velocity is described. The instrument utilizes a simplified particle image correlation technique to reconstruct an average flow velocity vector from video recordings of ambient particles. The VIV uses a single camera with a set of mirrors that splits the view into two stereoscopic views, allowing estimation of the flow velocity vector. The VIV was validated in a controlled flume using ambient seawater, and subsequently field tested together with an acoustic Doppler velocimeter with both mounted close to the coastal seafloor. When used in nonturbulent flow, the instrument can estimate mean flow velocity parallel to the front face of the instrument with root-mean-squared errors of the main flow within 10% of the ±20 cm s−1 measurement range when compared to an acoustic Doppler velocimeter (ADV). The predominant feature of the VIV is that it is a cost-effective method to estimate flow velocity in complex benthic habitats where velocity parallel to the sea floor is of interest.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The development of a low-cost Video Velocimeter (VIV) to estimate underwater bulk flow velocity is described. The instrument utilizes a simplified particle image correlation technique to reconstruct an average flow velocity vector from video recordings of ambient particles. The VIV uses a single camera with a set of mirrors that splits the view into two stereoscopic views, allowing estimation of the flow velocity vector. The VIV was validated in a controlled flume using ambient seawater, and subsequently field tested together with an acoustic Doppler velocimeter with both mounted close to the coastal seafloor. When used in nonturbulent flow, the instrument can estimate mean flow velocity parallel to the front face of the instrument with root-mean-squared errors of the main flow within 10% of the ±20 cm s−1 measurement range when compared to an acoustic Doppler velocimeter (ADV). The predominant feature of the VIV is that it is a cost-effective method to estimate flow velocity in complex benthic habitats where velocity parallel to the sea floor is of interest.
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.
@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}
}
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.
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.
@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}
}
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.
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.
Briseño-Avena, Christian; Prairie, Jennifer C.; Franks, Peter J. S.; Jaffe, Jules S.
In: Frontiers in Marine Science, 2020.
@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}
}
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.
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.
@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}
}
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.
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.
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.
@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}
}
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.
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.
@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}
}
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%.
Garwood, Jessica C.; Lucas, Andrew J.; Naughton, Perry; Alford, Matthew H.; Roberts, Paul L. D.; Jaffe, Jules S.; Franks, Peter J. S.
In: Limnology and Oceanography, vol. 65, no. 7, pp. 1456-1470, 2020.
@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 = {},
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}
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.
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.
@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}
}
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.
Fabien Lombard, et al
Globally Consistent Quantitative Observations of Planktonic Ecosystems Journal Article
In: Frontiers in Marine Science, vol. 6, pp. 196, 2019, ISSN: 2296-7745 .
@article{Lombard2019,
title = {Globally Consistent Quantitative Observations of Planktonic Ecosystems},
author = {Fabien Lombard, et al},
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},
urldate = {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}
}
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.
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).
@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}
}
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.
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.
@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}
}
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.
@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}
}
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.
Orenstein, Eric C.; Beijbom, Oscar
Transfer learning and deep feature extraction for planktonic image data sets Proceedings Article
In: Winter Conference on Applications of Computer Vision, pp. 1082-1088, IEEE 2017.
@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}
}
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).
@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}
}
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.
@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}
}
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.
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.
@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}
}
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.
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.
@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}
}
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.
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.
@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}
}
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.
Jaffe, Jules S.
To sea and to see: That is the answer Journal Article
In: Methods in Oceanography, pp. -, 2016, ISSN: 2211-1220.
@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}
}
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.
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.
@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}
}
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).
@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}
}
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.
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.
@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}
}
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.
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.
@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},
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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.
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.
@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 = {<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>},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
<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>
2014
Haag, Justin M; Roberts, Paul L. D.; Papen, George C.; Jaffe, Jules S.; Li, Linhai; Stramski, Dariusz
Deep-sea low-light radiometer system Journal Article
In: Opt. Express, vol. 22, no. 24, pp. 30074–30091, 2014.
@article{Haag:14,
title = {Deep-sea low-light radiometer system},
author = {Justin M Haag and Paul L. D. Roberts and George C. Papen and Jaffe, Jules S. and Linhai Li and Dariusz Stramski},
url = {http://www.opticsexpress.org/abstract.cfm?URI=oe-22-24-30074},
doi = {10.1364/OE.22.030074},
year = {2014},
date = {2014-12-01},
journal = {Opt. Express},
volume = {22},
number = {24},
pages = {30074–30091},
publisher = {OSA},
abstract = {Two single-waveband low-light radiometers were developed to characterize properties of the underwater light field relevant to biological camouflage at mesopelagic ocean depths. Phenomena of interest were vertical changes in downward irradiance of ambient light at wavelengths near 470 nm and 560 nm, and flashes from bioluminescent organisms. Depth profiles were acquired at multiple deep stations in different geographic regions. Results indicate significant irradiance magnitudes at 560 nm, providing direct evidence of energy transfer as described by Raman scattering. Analysis of a night profile yielded multiple examples of bioluminescent flashes. The selection of high-sensitivity, high-speed silicon photomultipliers as detectors enabled measurement of spectrally-resolved irradiance to greater than 400 m depth.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Two single-waveband low-light radiometers were developed to characterize properties of the underwater light field relevant to biological camouflage at mesopelagic ocean depths. Phenomena of interest were vertical changes in downward irradiance of ambient light at wavelengths near 470 nm and 560 nm, and flashes from bioluminescent organisms. Depth profiles were acquired at multiple deep stations in different geographic regions. Results indicate significant irradiance magnitudes at 560 nm, providing direct evidence of energy transfer as described by Raman scattering. Analysis of a night profile yielded multiple examples of bioluminescent flashes. The selection of high-sensitivity, high-speed silicon photomultipliers as detectors enabled measurement of spectrally-resolved irradiance to greater than 400 m depth.
Yi, Jinwang; Mirza, Diba; Kastner, Ryan; Schurgers, Curt; Roberts, Paul; Jaffe, Jules
ToA-TS: Time of arrival based joint time synchronization and tracking for mobile underwater systems Journal Article
In: Ad Hoc Networks, vol. 34, no. 2015, pp. 211 - 223, 2014.
@article{yi2014toa,
title = {ToA-TS: Time of arrival based joint time synchronization and tracking for mobile underwater systems},
author = {Jinwang Yi and Diba Mirza and Ryan Kastner and Curt Schurgers and Paul Roberts and Jules Jaffe},
url = {http://www.sciencedirect.com/science/article/pii/S1570870514002261},
doi = {http://dx.doi.org/10.1016/j.adhoc.2014.10.010},
year = {2014},
date = {2014-01-01},
journal = {Ad Hoc Networks},
volume = {34},
number = {2015},
pages = {211 - 223},
publisher = {Elsevier},
abstract = {Time synchronization and localization are key requirements for distributed underwater systems consisting of numerous low-cost submersibles. In these systems, submersibles are highly resource constrained and typically have limited acoustic communication capability. We investigate the problem of tracking submersibles that only have the capability of receiving acoustic signals. Traditional Long Base Line (LBL) systems track the location of submersibles by providing a GPS-like infrastructure that consists of a few reference beacons at known locations. In these systems the unknown positions of submersibles are estimated from beacon transmissions using time-difference-of-arrival (TDoA) based localization. As such TDoA makes the key assumption that beacon transmissions occur nearly concurrently in time. While this assumption is ensured in small LBL deployments it does not hold as the size of the system scales up. In this paper we identify scenarios where signals from multiple beacons are significantly lagged in time. We further identify the motion of the submersible between signal arrivals as a key factor that deteriorates the performance of TDoA, when transmissions are not concurrent. To address this problem we propose to track the submersible while performing time-synchronization. Our proposed technique, called Time of Arrival based Tracked Synchronization (ToA-TS) essentially extends GPS like localization for scenarios where beacon transmissions are not concurrent and submersibles are not capable of two-way communication. We show the benefit of our proposed scheme by comparing its performance to other localization techniques using experimentally obtained data.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Time synchronization and localization are key requirements for distributed underwater systems consisting of numerous low-cost submersibles. In these systems, submersibles are highly resource constrained and typically have limited acoustic communication capability. We investigate the problem of tracking submersibles that only have the capability of receiving acoustic signals. Traditional Long Base Line (LBL) systems track the location of submersibles by providing a GPS-like infrastructure that consists of a few reference beacons at known locations. In these systems the unknown positions of submersibles are estimated from beacon transmissions using time-difference-of-arrival (TDoA) based localization. As such TDoA makes the key assumption that beacon transmissions occur nearly concurrently in time. While this assumption is ensured in small LBL deployments it does not hold as the size of the system scales up. In this paper we identify scenarios where signals from multiple beacons are significantly lagged in time. We further identify the motion of the submersible between signal arrivals as a key factor that deteriorates the performance of TDoA, when transmissions are not concurrent. To address this problem we propose to track the submersible while performing time-synchronization. Our proposed technique, called Time of Arrival based Tracked Synchronization (ToA-TS) essentially extends GPS like localization for scenarios where beacon transmissions are not concurrent and submersibles are not capable of two-way communication. We show the benefit of our proposed scheme by comparing its performance to other localization techniques using experimentally obtained data.
2013
Haag, Justin M; Jaffe, Jules S.; Sweeney, Alison M
Measurement system for marine animal reflectance functions Journal Article
In: Optics Express, vol. 21, pp. 3603-3616, 2013.
@article{2013,
title = {Measurement system for marine animal reflectance functions},
author = { Justin M Haag and Jules S. Jaffe and Alison M Sweeney},
url = {http://www.opticsinfobase.org/oe/abstract.cfm?uri=oe-21-3-3603},
doi = {10.1364/OE.21.003603},
year = {2013},
date = {2013-01-01},
journal = {Optics Express},
volume = {21},
pages = {3603-3616},
abstract = {Photonic structures in the skin of pelagic fishes and squids evolved specifically for hiding in the complex light field of the open ocean. To understand the principles under which these structures operate, a detailed characterization of their optical properties is required. An optical scatterometer has been developed to measure one important property, the bidirectional reflectance distribution function (BRDF). The instrument was used to collect reflectance functions from the squid Pterygioteuthis microlampas and fish Sternoptyx sp. Although the animals appear very different to a casual observer, the results reveal interesting similarities in their scattering patterns, suggesting a similar optical strategy for hiding in open water.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Photonic structures in the skin of pelagic fishes and squids evolved specifically for hiding in the complex light field of the open ocean. To understand the principles under which these structures operate, a detailed characterization of their optical properties is required. An optical scatterometer has been developed to measure one important property, the bidirectional reflectance distribution function (BRDF). The instrument was used to collect reflectance functions from the squid Pterygioteuthis microlampas and fish Sternoptyx sp. Although the animals appear very different to a casual observer, the results reveal interesting similarities in their scattering patterns, suggesting a similar optical strategy for hiding in open water.
Jaffe, J. S.; Franks, P. J. S.; Briseno, C.; Roberts, P. L. D.; Laxton, B.
Advances in underwater fluorometry, from bulk fluorescence to planar laser imaging of individuals Book Chapter
In: Subsea Optics and Imaging, Woodhead Publishing Limited, Cambridge, Woodhead Publishing Limited, Cambridge, 2013.
@inbook{2013b,
title = {Advances in underwater fluorometry, from bulk fluorescence to planar laser imaging of individuals},
author = { J. S. Jaffe and P. J. S. Franks and C. Briseno and P. L. D. Roberts and B. Laxton},
url = {https://www.researchgate.net/publication/286266263_Advances_in_underwater_fluorometry_From_bulk_fluorescence_to_planar_laser_imaging},
doi = {10.1533/9780857093523.3.536},
year = {2013},
date = {2013-01-01},
booktitle = {Subsea Optics and Imaging, Woodhead Publishing Limited, Cambridge},
publisher = {Woodhead Publishing Limited},
address = {Cambridge},
organization = {Woodhead Publishing Limited},
abstract = {Underwater measurements of photosynthetic pigment fluorescence have long been used as a proxy for phytoplankton biomass. While many useful results have been achieved, the usual measurements made on bulk samples restrict the inferences that can be drawn from the sample. Most importantly, there is no spatial resolution of the single measurement. As an alternative, we examine the utility of underwater imaging of phytoplankton via lab experiments and the analysis of field data. A planar laser imaging fluorometry (PLIF) system, assembled from readily available optical components, was used to image individual fluorescent particles in the lab and field. In addition, an underwater microscope was deployed in the field and showed a layer of large (250-300. μm), highly absorptive particles, inferred to be diatoms. These diatoms were also measured concurrently with a standard subsea fluorometer. The two profiles show that the intensity of fluorescence bears little relationship to the community structure of the phytoplankton. Only by the use of imaging can regions of high fluorescence intensity (high phytoplankton biomass) caused by many small phytoplankton, or a few large ones, be distinguished.},
keywords = {},
pubstate = {published},
tppubtype = {inbook}
}
Underwater measurements of photosynthetic pigment fluorescence have long been used as a proxy for phytoplankton biomass. While many useful results have been achieved, the usual measurements made on bulk samples restrict the inferences that can be drawn from the sample. Most importantly, there is no spatial resolution of the single measurement. As an alternative, we examine the utility of underwater imaging of phytoplankton via lab experiments and the analysis of field data. A planar laser imaging fluorometry (PLIF) system, assembled from readily available optical components, was used to image individual fluorescent particles in the lab and field. In addition, an underwater microscope was deployed in the field and showed a layer of large (250-300. μm), highly absorptive particles, inferred to be diatoms. These diatoms were also measured concurrently with a standard subsea fluorometer. The two profiles show that the intensity of fluorescence bears little relationship to the community structure of the phytoplankton. Only by the use of imaging can regions of high fluorescence intensity (high phytoplankton biomass) caused by many small phytoplankton, or a few large ones, be distinguished.
E. Berdalet, et al
Understanding harmful algae in stratified systems: Review of progress and future directions Journal Article
In: Deep Sea Research Part II: Topical Studies in Oceanography, vol. 101, pp. 4-20, 2013, ISSN: 0967-0645.
@article{Berdalet2013,
title = {Understanding harmful algae in stratified systems: Review of progress and future directions},
author = { E. Berdalet, et al},
url = {http://www.sciencedirect.com/science/article/pii/S0967064513003834},
doi = {http://dx.doi.org/10.1016/j.dsr2.2013.09.042},
issn = {0967-0645},
year = {2013},
date = {2013-01-01},
urldate = {2013-01-01},
journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
volume = {101},
pages = {4-20},
abstract = {The Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program of the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of UNESCO, was created in 1999 to foster research on the ecological and oceanographic mechanisms underlying the population dynamics of harmful algal blooms (HABs). The ultimate goal of this research is to develop observational systems and models that will eventually enable the prediction of HABs and thereby minimize their impact on marine ecosystems, human health and economic activities. In August of 2012, a workshop was held under the umbrella of the GEOHAB program at the Monterey Bay Aquarium Research Institute (MBARI). The over arching goal of this workshop was to review the current understanding of the processes governing the structure and dynamics of HABs in stratified systems, and to identify how best to couple physical/chemical and biological measurements at appropriate spatial and temporal scales to quantify the dynamics of HABs in these systems, paying particular attention to thin layers. This contribution provides a review of recent progress in the field of HAB research in stratified systems including thin layers, and identifies the gaps in knowledge that our scientific community should strive to understand in the next decade.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The Global Ecology and Oceanography of Harmful Algal Blooms (GEOHAB) program of the Scientific Committee on Oceanic Research (SCOR) and the Intergovernmental Oceanographic Commission (IOC) of UNESCO, was created in 1999 to foster research on the ecological and oceanographic mechanisms underlying the population dynamics of harmful algal blooms (HABs). The ultimate goal of this research is to develop observational systems and models that will eventually enable the prediction of HABs and thereby minimize their impact on marine ecosystems, human health and economic activities. In August of 2012, a workshop was held under the umbrella of the GEOHAB program at the Monterey Bay Aquarium Research Institute (MBARI). The over arching goal of this workshop was to review the current understanding of the processes governing the structure and dynamics of HABs in stratified systems, and to identify how best to couple physical/chemical and biological measurements at appropriate spatial and temporal scales to quantify the dynamics of HABs in these systems, paying particular attention to thin layers. This contribution provides a review of recent progress in the field of HAB research in stratified systems including thin layers, and identifies the gaps in knowledge that our scientific community should strive to understand in the next decade.
2012
Haag, Justin M; Sweeney, Alison M; Jaffe, Jules S.
Measurement of Marine Animal Reflectance Functions Proceedings
Glasgow, Scotland, UK, 2012.
@proceedings{2012,
title = {Measurement of Marine Animal Reflectance Functions},
author = { Justin M Haag and Alison M Sweeney and Jules S. Jaffe},
year = {2012},
date = {2012-01-01},
journal = {Ocean Optics XXI},
address = {Glasgow, Scotland, UK},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
Haag, Justin M; Sweeney, Alison M; Jaffe, Jules S.
Measurement System for Obtaining Marine Animal Reflectance Functions Proceedings
Glasgow, Scotland, UK, 2012.
@proceedings{2012b,
title = {Measurement System for Obtaining Marine Animal Reflectance Functions},
author = { Justin M Haag and Alison M Sweeney and Jules S. Jaffe},
year = {2012},
date = {2012-01-01},
journal = {Ocean Optics XXI},
address = {Glasgow, Scotland, UK},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
2011
Roberts, Paul L. D.; Steinbuck, J. V.; Jaffe, Jules S.; Horner-Devine, A. R.; Franks, Peter J. S.; Simonet, F.
Estimation of In Situ, Three-Dimensional Particle Distributions from a Stereo Laser Imaging Profiler Journal Article
In: IEEE Journal of Oceanic Engineering, vol. 36, pp. 586 - 601, 2011.
@article{Roberts2009c,
title = {Estimation of In Situ, Three-Dimensional Particle Distributions from a Stereo Laser Imaging Profiler},
author = { Paul L. D. Roberts and J. V. Steinbuck and Jules S. Jaffe and A. R. Horner-Devine and Peter J.S. Franks and F. Simonet},
year = {2011},
date = {2011-01-01},
journal = {IEEE Journal of Oceanic Engineering},
volume = {36},
pages = {586 - 601},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jaffe, Jules S.; Roberts, Paul L. D.
Applying diffraction theory to measure acoustically the in-situ orientation of marine animals Journal Article
In: Acoustics Today, vol. 7, no. 3, pp. 36-37, 2011.
@article{2011,
title = {Applying diffraction theory to measure acoustically the in-situ orientation of marine animals},
author = { Jules S. Jaffe and Paul L. D. Roberts},
year = {2011},
date = {2011-01-01},
journal = {Acoustics Today},
volume = {7},
number = {3},
pages = {36-37},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jaffe, Jules S.; Roberts, Paul L. D.
Estimating fish orientation from broadband, limited-angle, multi-view, acoustic reflections Journal Article
In: Journal of the Acoustical Society of America, pp. 670-680, 2011.
@article{Jaffe2009,
title = {Estimating fish orientation from broadband, limited-angle, multi-view, acoustic reflections},
author = { Jules S. Jaffe and Paul L. D. Roberts},
url = {http://asa.scitation.org/doi/abs/10.1121/1.3523430},
doi = {http://dx.doi.org/10.1121/1.3523430},
year = {2011},
date = {2011-01-01},
journal = {Journal of the Acoustical Society of America},
pages = {670-680},
chapter = {670-680},
abstract = {This article demonstrates that multiview, broadband (635–935 kHz), nearly monostatic, acoustic reflections recorded from lateral views of juvenile fish can be used to infer animal orientation. Calibrated acoustic data were recorded from live fish in a laboratory, while orientation was measured simultaneously via optical images. Using eight animals, two-dimensional data sets of target strength as a function of frequency and orientation were obtained. Fish length, lateral thickness, and dorsoventral thickness ranged from 24 to 48 mm, 3 to 7 mm and 10 to 20 mm, respectively. Preliminary estimates of orientation were computed from the direction of the gradient of the local autocorrelation function in the target strength image. These local estimates were then median-filtered over the full system bandwidth (but still limited-angle) to improve accuracy. Angular estimates were then corrected for systematic bias via a simple, one-dimensional model that approximated the animals’ reflection by that of a bar target. Taken over all orientations, the average absolute error in orientation estimation is 5.6° to 17°, dependent on the data set. Results indicate, for most sets of views, reasonable estimates of lateral orientation can be obtained from broadband, multiview data over a set of limited angular reflections.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This article demonstrates that multiview, broadband (635–935 kHz), nearly monostatic, acoustic reflections recorded from lateral views of juvenile fish can be used to infer animal orientation. Calibrated acoustic data were recorded from live fish in a laboratory, while orientation was measured simultaneously via optical images. Using eight animals, two-dimensional data sets of target strength as a function of frequency and orientation were obtained. Fish length, lateral thickness, and dorsoventral thickness ranged from 24 to 48 mm, 3 to 7 mm and 10 to 20 mm, respectively. Preliminary estimates of orientation were computed from the direction of the gradient of the local autocorrelation function in the target strength image. These local estimates were then median-filtered over the full system bandwidth (but still limited-angle) to improve accuracy. Angular estimates were then corrected for systematic bias via a simple, one-dimensional model that approximated the animals’ reflection by that of a bar target. Taken over all orientations, the average absolute error in orientation estimation is 5.6° to 17°, dependent on the data set. Results indicate, for most sets of views, reasonable estimates of lateral orientation can be obtained from broadband, multiview data over a set of limited angular reflections.
Roberts, Paul L. D.; Jaffe, Jules S.; Trivedi, M. M.
Multiview, Broadband Acoustic Classification of Marine Fish: A Machine Learning Framework and Comparative Analysis Journal Article
In: IEEE Journal of Oceanic Engineering, vol. 36, pp. 90-104, 2011.
@article{Roberts2009b,
title = {Multiview, Broadband Acoustic Classification of Marine Fish: A Machine Learning Framework and Comparative Analysis},
author = { Paul L. D. Roberts and Jules S. Jaffe and M. M. Trivedi},
year = {2011},
date = {2011-01-01},
journal = {IEEE Journal of Oceanic Engineering},
volume = {36},
pages = {90-104},
chapter = {90-104},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Prairie, Jennifer C.; Franks, Peter J. S.; Jaffe, Jules S.; Doubell, Mark J.; Yamazaki, Hidekatsu
Physical and biological controls of vertical gradients in phytoplankton Journal Article
In: Limnology and Oceanography, 2011.
@article{2011b,
title = {Physical and biological controls of vertical gradients in phytoplankton},
author = { Jennifer C. Prairie and Peter J.S. Franks and Jules S. Jaffe and Mark J. Doubell and Hidekatsu Yamazaki},
year = {2011},
date = {2011-01-01},
journal = {Limnology and Oceanography},
chapter = {75-90},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jaffe, Jules S.; Roberts, Paul L. D.
Acoustic reflections on marine populations Journal Article
In: Physics Today, vol. 64, pp. 76, 2011.
@article{2011b,
title = {Acoustic reflections on marine populations},
author = { Jules S. Jaffe and Paul L. D. Roberts},
year = {2011},
date = {2011-01-01},
journal = {Physics Today},
volume = {64},
pages = {76},
keywords = {},
pubstate = {published},
tppubtype = {article}
}