New Benthic Underwater Microscope Described in the Journal Nature Communications

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:

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Quantification of Internal Wave Processes on Plankton Experiment Completed

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.


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Delivery of new SPC system to NOAA Southwest Fisheries Science Center

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

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

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


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Field work on Little Cayman Island

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


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Scripps Plankton Camera System

Under a generous, anonymous donation to the Scripps Institution of Oceanography, we have built and deployed a new version of our plankton cameras at the end of Scripps Pier. The installation is named the Scripps Plankton Camera System and consists of two in situ, color, darkfield microscopes with complementary magnification and resolution designed to image plankton in the range of 10s of microns up to 10s of millimeters. For more information about the cameras, and to view the hundreds of thousands of plankton imaged each day, please visit or click on the image below.


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Scripps Phytoplankton Camera

Our latest underwater imaging system, the Scripps Phytoplankton Camera (SPC-P), was deployed at the end of Scripps Pier on Sept 19, 2014 and has been running for several weeks collecting over 30,000 images per day. Click on the images below to visit the site:


From the site:

The Scripps Phytoplankton Camera (SPC-P) was developed under a grant from the W. M. Keck Foundation and an anonymous donor to the Scripps Inst. of Oceanograpy, and in cooperation with the Southern California Coastal Ocean Observing System (SCCOOS). The SPC-P is an underwater darkfield microscope with real-time image processing and object detection. It was designed to detect objects from a few microns up to several millimeters. It employs darkfield illumination. Data from the SPC-P are transferred in real-time to a webserver and database that support an interactive web tool for browsing images and exploring image statistics.