Jaffe Laboratory for Underwater Imaging

Scripps Plankton Cameras Featured on CENIC Blog: Identifying Tiny Organisms with Giant Impact on Climate

November 8, 2018 by pldr

The CENIC blog has a nice article about our work using machine learning to automatically identify plankton in the 1 billion images collected thus far by the Scripps Plankton Cameras:

Identifying Tiny Organisms with Giant Impact on Climate

Lens of Time: Growing Against the Odds

June 13, 2018June 13, 2018 by pldr

Our work on developing 3D stereo microscopy has been featured in the California Academy of Sciences bioGraphic Lens of Time: Growing Against the Odds. Check out the video here: https://www.biographic.com/posts/sto/lens-of-time-growing-against-the-odds

Autonomous Underwater Explorers Described in the Journal Nature Communications

January 24, 2017January 24, 2017 by pldr

Today results from our first field deployment with a swarm of Autonomous Underwater Explorers (M-AUEs) were published in the journal Nature Communications. The article describes the deployment of 16 M-AUEs several kilometers off the coast of Torrey Pines State Park. Along with the M-AUEs, a surface array of acoustic pingers was deployed in a pentagon formation and used to track the M-AUEs underwater in three dimensions. The resulting tracks were used to visualize internal waves propagating through the swarm. The article: A Swarm of Autonomous Miniature Underwater Robot Drifters for Exploring Submesoscale Ocean Dynamics was authored by Jules S. Jaffe, Peter J. S. Franks, Paul L. D. Roberts, Diba Mirza, Curt Schurgers, Ryan Kastner and Adrien Boch.

We would like to thank Rich Walsh who provided small boat support during the development of the M-AUEs and the operations performed during these experiments, Devin Ratelle, Eric Orenstein, Phil Bresnahan, Mike Ouimet, and Mike Bianco for assisting in the deployment and recovery during the experiment, and the maintainers of the OAR/Keck Pool at SIO for facilitating countless hours of pool testing leading up to the field work.

Below are videos and articles covering the work.

New Benthic Underwater Microscope Described in the Journal Nature Communications

August 18, 2016July 12, 2016 by pldr

Today results from our work on the Benthic Underwater Microscope (BUM) were published in Nature Communications. The article Underwater microscopy for in situ studies of benthic ecosystems reports on the development of the BUM and its application to studying several important benthic processes in situ. The paper was authored by Jaffe Lab members Andrew D. Mullen, Tali Treibitz, Paul L.D. Roberts, and Jules Jaffe; as well as coral ecologists Emily L.A. Kelly, Rael Horwitz, and Jennifer E. Smith.

We would like to thank Dr. Amatzia Genin who provided support and critical guidance during the studies of coral polyp behavior, which were filmed at the Interuniversity Institute for Marine Sciences in Eilat, Israel. We also thank the Keck Foundation for their support funding the instrument development. Additionally we thank the National Science Foundation, Link Foundation, and Binational Science Foundation for supporting Andrew Mullen’s research.

Below are several videos and articles covering the work.

New York Times:

UCSD interview with Andrew Mullen:

Interview with Jules Jaffe

Nature Video:

NSF Science 360 Video:

https://science360.gov/obj/video/86e00b24-c628-4e9b-9ce0-67edd693dc82/nsf-science-now-episode-45

Quantification of Internal Wave Processes on Plankton Experiment Completed

July 11, 2016June 29, 2016 by pldr

Yesterday we competed the first of hopefully many experiments to study the effect of internal waves on the distribution of plankton in the ocean. The experiment was ambitious, consisting of deploying 16 small autonomous floats multiple times per day, 5 surface pingers, two bottom mounted ADCPs, two thermistor strings, one wirewalker with CTD, optical sensors, acoustic backscatter, and real-time data telemetry, and a dual magnification plankton microscope attached to the end of a plankton net, rapid vertical CTD profiles from a second CTD, and a helikite to observe the surface signal of internal waves. The experiment spanned three weeks and included 100s of autonomous float profiles, 3,564 wirewalker profiles, millions of plankton images, 100s of CTD cast, and close to zero data or instrument loss. A great success! Below are a few images shot over the coarse of the experiment.

QuiPPEndofDay

Delivery of new SPC system to NOAA Southwest Fisheries Science Center

July 11, 2016June 25, 2016 by pldr

Last week Eric Orenstein delivered a new build of the SPC system to Eric Danner’s group at the NOAA Southwest Fisheries Science Center in Santa Cruz, CA. This new build incorporates larger optics to yield a 0.5 L imaged volume, a brightfield illumination to work well even in turbid river and estuary waters, and a custom flow chamber to allow drift nets, pumps, and other methods to collect plankton and pipe them through the imaged volume. More details about the new system can be found on the research page: SPC NOAA Fisheries

UCSD MAE students build Nano AUVs

July 11, 2016June 3, 2016 by pldr

We had two excellent design teams this year work on the problem of building small open source AUVs. They just competed their final projects and have some excellent results. Click on the image below for more details or follow this link: Open Source Nano AUVs

Delivery of new SPC system to Prince William Sound Science Center in Cordova, AK

July 11, 2016April 5, 2016 by pldr

Last week we delivered a brand new build of our SPC system to Rob Campbell at the Prince William Sound Science Center in Cordova, Alaska. The new build features a much larger imaged volume, a new method for attaching the strobe housing to the camera housing, all new electronics including a faster ODROID processor with 8 cores at 2 GHz, and a revised version of our real time object detection software. More details about the system and its application in Rob’s profiling mooring are available on the research projects page: SPC Prince William Sound Science Center

SPCInCordova

Field work on Little Cayman Island

July 11, 2016March 4, 2016 by pldr

We just wrapped up some extensive field work in Little Cayman with two other research groups from Scripps Oceanography, the Semmens Lab, and the Marine Bioacoustics Lab. The goal of the work was to deploy our AUEs, pingers, plankton net camera, and underwater 360 GoPro camera in the midst of the Nasau Grouper spawning event.

We deployed most of the gear in January but got skunked on the spawning event and also lost a few instruments. We then returned with a smaller team last week to complete the mission and were able to collect some great data with the net camera and the 360 GoPro camera.

For more information about the net camera please see the research page: SPC Net Camera

NighinCaymans

Happy Holidays from the Jaffe Lab

July 11, 2016December 26, 2015 by pldr

Holiday_Card_2015-6.preview

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 Forthcoming

IEEE Access, Forthcoming.

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},
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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.

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