Omnicam Birch Aquarium

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OLYMPUS DIGITAL CAMERA

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OLYMPUS DIGITAL CAMERA

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OLYMPUS DIGITAL CAMERA

P1010093

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OLYMPUS DIGITAL CAMERA

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OLYMPUS DIGITAL CAMERA

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 Forthcoming

Limnology and Oceanography, Forthcoming.

BibTeX

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

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

Frontiers in Marine Science, Forthcoming.

Links | BibTeX

Lertvilai, Pichaya

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

Methods in Ecology and Evolution, 2020.

Abstract | Links | BibTeX

@article{Lertvilai2020,
title = {The In situ Plankton Assemblage eXplorer (IPAX): An inexpensive underwater imaging system for zooplankton study},
author = {Pichaya Lertvilai},
url = {https://doi.org/10.1111/2041-210X.13441},
year = {2020},
date = {2020-06-27},
journal = {Methods in Ecology and Evolution},
abstract = {1. Zooplankton play vital ecological roles that maintain aquatic ecosystems. Imaging instruments have enabled in situ observations of these organisms that can be automated and are less invasive than traditional sampling methods. However, these instruments are often costly and require sophisticated engineering expertise to operate.
2. The In situ Plankton Assemblage eXplorer (IPAX) is an open‐source low‐cost imaging platform for zooplankton studies. The IPAX is a programmable instrument that has powerful LED illumination and a high‐resolution camera that can image zooplankton in situ, while material costs are less than USD $450. The optical performance of the instrument was calibrated in the laboratory using a calibration target and preserved zooplankton. The IPAX was then deployed in the field to observe diversity, emergent patterns and phototactic behaviour of demersal zooplankton at night to demonstrate its practicality.
3. Laboratory calibration indicated that the IPAX can resolve 100 µm features with 70% contrast at the focal plane with 5 cm × 3 cm field of view and 5 mm depth of field. The instrument also resolved fine morphological details of preserved zooplankton when in focus. The field deployment demonstrated capability to resolve the myriad of zooplankton present in addition to the different phototactic behaviour that was elicited and observed from the different colour LEDs.
4. The IPAX enables economical and autonomous surveys of zooplankton in various aquatic habitats. Its low cost facilitates construction and deployment of multiple units that can cover large spatial areas, while its versatility also allows adaptations to many experimental needs for aquatic ecology.},
keywords = {},
pubstate = {published},
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}

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

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

Limnology and Oceanography, 2020.

Abstract | Links | BibTeX

@article{Kenitz2020,
title = {Environmental drivers of population variability in colony‐forming marine diatoms},
author = {Kasia M Kenitz and Eric C. Orenstein and Paul L D Roberts and Peter J S Franks and Jules S Jaffe and Melissa L Carter and Andrew D Barton},
editor = {Ilana Berman-Frank},
url = {https://doi.org/10.1002/lno.11468},
year = {2020},
date = {2020-05-26},
journal = {Limnology and Oceanography},
abstract = {Many aquatic microbes form colonies, yet little is known about their abundance and fitness relative to single‐celled taxa. The formation of diatom chains, in particular, has implications for diatom growth, survival, and carbon transfer. Here, we utilize an autonomous underwater microscope, combined with traditional microscopy, to develop a novel, multiyear record of the abundance of single‐cell and colony‐forming diatoms at Scripps Pier, a coastal location in the Southern California Bight. The total abundance of diatoms was lower during the warmer and more stratified conditions from 2015 to early 2016, but increased in cooler and less stratified conditions in mid‐2016 to late 2017. Diatom blooms were dominated by chain‐forming taxa, whereas solitary diatoms prevailed during low‐biomass conditions. The abundance of dinoflagellates, some of which are important diatom predators, is highest when colonies (chains) are most abundant. These observations of the diatom assemblage are consistent with a trade‐off between resource acquisition and predator defenses. Solitary diatom cells dominated during conditions with weak nutrient supply because they have a greater diffusive catchment area per cell in comparison to cells living in colonies. In contrast, during bloom conditions when nutrient supply is high and predators are abundant, forming a colony may reduce predation losses to quickly growing microzooplankton predators, and afford chains a higher fitness despite the costs of sharing resources with neighboring cells. These results highlight the contrasting ecology of single‐cell and chain‐forming diatoms, and the need to differentiate them in monitoring campaigns and ecological models.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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

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

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

Abstract | Links | BibTeX

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

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

Limnology and Oceanography, 65 (7), pp. 1456-1470, 2020.

Abstract | Links | BibTeX

@article{Garwood2020,
title = {A novel cross‐shore transport mechanism revealed by subsurface, robotic larval mimics: Internal wave deformation of the background velocity field},
author = {Jessica C. Garwood and Andrew J. Lucas and Perry Naughton and Matthew H. Alford and Paul L. D. Roberts and Jules S. Jaffe and Peter J. S. Franks},
editor = {Julia Mullarney},
url = {https://doi.org/10.1002/lno.11400},
year = {2020},
date = {2020-01-13},
journal = {Limnology and Oceanography},
volume = {65},
number = {7},
pages = {1456-1470},
abstract = {Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s−1 vs. cm s−1) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.},
keywords = {},
pubstate = {published},
tppubtype = {article}
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2019

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

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

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

Abstract | Links | BibTeX

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

Globally Consistent Quantitative Observations of Planktonic Ecosystems Journal Article

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

Abstract | Links | BibTeX

@article{Lombard2019,
title = {Globally Consistent Quantitative Observations of Planktonic Ecosystems},
author = {Fabien Lombard and Emmanuel Boss and Anya M. Waite and Meike Vogt and Julia Uitz and Lars Stemmann and Heidi M. Sosik and Jan Schulz and Jean-Baptiste Romagnan and Marc Picheral and Jay Pearlman and Mark D. Ohman and Barbara Niehoff and Klas O. Möller and Patricia Miloslavich and Ana Lara-Lpez and Raphael Kudela and Rubens M. Lopes and Rainer Kiko and Lee Karp-Boss and Jules S. Jaffe and Morten H. Iversen and Jean-Olivier Irisson and Katja Fennel and Helena Hauss and Lionel Guidi and Gaby Gorsky and Sarah L. C. Giering and Peter Gaube and Scott Gallager and George Dubelaar and Robert K. Cowen and François Carlotti and Christian Briseño-Avena and Léo Berline and Kelly Benoit-Bird and Nicholas Bax and Sonia Batten and Sakina Dorothée Ayata and Luis Felipe Artigas and Ward Appeltans},
url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00196 },
doi = {10.3389/fmars.2019.00196},
issn = {2296-7745 },
year = {2019},
date = {2019-04-25},
journal = {Frontiers in Marine Science},
volume = {6},
pages = {196},
abstract = {In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
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2018

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

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

Journal of the Acoustical Society of America, 144 (WOS:000454102300035), pp. 2811-2823, 2018, ISBN: 0001-4966, (Technical Area Pick for Signal Processing of the Acoustical Society of America in 2019).

Abstract | Links | BibTeX

@article{Naughton2018,
title = {Self-localization of a mobile swarm using noise correlations with local sources of opportunity},
author = {Perry Naughton and Philippe Roux and Curt Schurgers and Ryan Kastner and Jules S Jaffe and Paul L D Roberts },
url = {https://asa.scitation.org/doi/10.1121/1.5070154},
doi = {10.1121/1.5070154},
isbn = {0001-4966},
year = {2018},
date = {2018-11-16},
journal = {Journal of the Acoustical Society of America},
volume = {144},
number = {WOS:000454102300035},
pages = {2811-2823},
abstract = {Groups of coordinated underwater vehicles or sensors are powerful tools for monitoring the ocean. A requirement of many coordinated surveys is to determine a spatial reference between each node in a swarm. This work considers the self-localization of a swarm of independently moving vehicles using acoustic noise from a dominating incoherent source recorded by a single hydrophone onboard each vehicle. This method provides an inexpensive and infrastructure-free spatial reference between vehicles. Movement between the vehicles changes the swarm geometry and a self-localization estimate must be generated from data collected on short time scales. This challenges past self-localization approaches for acoustic arrays. To overcome this challenge, the proposed self-localization algorithm jointly estimates the vehicle geometry and the directionality of the ambient noise field, without prior knowledge of either estimate. To demonstrate this method, experimental results are provided when a boat is the main dominating source. The results demonstrate the ability to both estimate the direction of arrival of the boat and the relative positions of the vehicles in the swarm. The approach in this paper is not limited to moving vessels. Simulations are provided to examine three different factors that affect the proposed solution: inter-vehicle motion, vehicle geometry, and the azimuthal variance of the noise field. (C) 2018 Acoustical Society of America.},
note = {Technical Area Pick for Signal Processing of the Acoustical Society of America in 2019},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

2017

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

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

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

Links | BibTeX

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

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

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

Abstract | Links | BibTeX

Orenstein, Eric C; Beijbom, Oscar

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

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

Links | BibTeX

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

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

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

Links | BibTeX

2016

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

Ambient noise correlations on a mobile, deformable array Journal Article

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

Abstract | Links | BibTeX

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

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

Appl. Opt., 55 (33), pp. 9440–9449, 2016.

Abstract | Links | BibTeX

@article{Liao:16,
title = {Sizing submicron particles from optical scattering data collected with oblique incidence illumination},
author = {Ran Liao and Paul L. D. Roberts and Jules S. Jaffe},
url = {http://ao.osa.org/abstract.cfm?URI=ao-55-33-9440},
doi = {10.1364/AO.55.009440},
year = {2016},
date = {2016-11-01},
journal = {Appl. Opt.},
volume = {55},
number = {33},
pages = {9440--9449},
publisher = {OSA},
abstract = {As submicron particles play an important role in a variety of ecosystems that include aqueous, terrestrial, and atmospheric, a measurement system to quantify them is highly desirable. In pursuit of formulating and fabricating a system to size them using visible light, a system that collects multi-directional scattered light from individual particles is proposed. A prototype of the system was simulated, built, and tested via calibration with a set of polystyrene spheres in water with known sizes. Results indicate that the system can accurately resolve the size of these particles in the 0.1 to 0.8 μm range. The system incorporates a design that uses oblique illumination to collect scattered light over a large range of both forward and backward scatter angles. This is then followed by the calculation of a ratio of forward to backscattered light, integrated over a suitably defined range. The monotonic dependence of this ratio upon particle size leads to an accurate estimate of particle size. The method was explored first, using simulations, and followed with a working version. The sensitivity of the method to a range of relative refractive index was tested using simulations. The results indicate that the technique is relatively insensitive to this parameter and thus of potential use in the analysis of particles from a variety of ecosystems. The paper concludes with a discussion of a variety of pragmatic issues, including the required dynamic range as well as further research needed with environmentally relevant specimens to create a pragmatic instrument.},
keywords = {},
pubstate = {published},
tppubtype = {article}
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Mullen, Andrew D; Treibitz, Tali; Roberts, Paul L D; Kelly, Emily L A; Horwitz, Rael; Smith, Jennifer E; Jaffe, Jules S

Underwater microscopy for in situ studies of benthic ecosystems Journal Article

Nat Commun, 7 , 2016.

Abstract | Links | BibTeX

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

Automated classification of camouflaging cuttlefish Journal Article

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

Abstract | Links | BibTeX

Jaffe, Jules S

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

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

Abstract | Links | BibTeX

2015

Jaffe, J S

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

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

Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

Marine Biology, 162 (10), pp. 1939–1954, 2015.

Abstract | Links | BibTeX

@article{pepper2015zooplankton,
title = {Zooplankton in flowing water near benthic communities encounter rapidly fluctuating velocity gradients and accelerations},
author = {Rachel E Pepper and Jules S Jaffe and Evan Variano and MAR Koehl},
url = {http://link.springer.com/article/10.1007%2Fs00227-015-2713-x},
doi = {10.1007/s00227-015-2713-x},
year = {2015},
date = {2015-01-01},
journal = {Marine Biology},
volume = {162},
number = {10},
pages = {1939--1954},
publisher = {Springer},
abstract = {The fine-scale temporal patterns of water velocities, accelerations, and velocity gradients encountered by individual zooplankters carried in ambient flow can affect their dispersal, behavior, and interaction with other organisms, but have not yet been measured in realistic flow environments. We focused on zooplankton in wavy turbulent boundary layer flow near benthic communities because such flow affects important processes, including larval settlement and prey capture by benthic zooplanktivores. Flow across fouling communities measured in the field was mimicked in a wave flume, where time-varying velocity fields over biofouled surfaces were quantified using particle image velocimetry (PIV). Trajectories of simulated zooplankters seeded into these flow fields were followed to quantify temporal patterns of velocity gradients and accelerations that individuals encountered. We found that such zooplankters are not subjected to steady velocities or velocity gradients, but rather encounter rapidly fluctuating accelerations and velocity gradients with peaks reaching several orders of magnitude above mean values and lasting fractions of a second, much shorter than the wave period. We calculated the proportion of time zooplankters spent affected (e.g., being damaged, changing behavior) by accelerations or velocity gradients and found that a small increase in mean velocity can cause a much larger increase in time affected. Animal reaction threshold and reaction time also changed the fraction of time they were affected by the flow. Using different PIV spatial resolutions showed that inter-vector spacing should be ≤0.5 Kolmogorov length (smallest eddy scale) to accurately capture velocity gradients along trajectories, but coarser resolutions (≤2–6 × Kolmogorov length) are sufficient for velocities, accelerations, and zooplankton trajectories.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

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

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

PLoS ONE, 10 (10), pp. 1-18, 2015.

Abstract | Links | BibTeX

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

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

},
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