Quick Links to Research Projects:

Market squid runs off La Jolla Shores beach

Lately the market squid (Loligo opalescens) have been causing quite the stir in the local dive community here in San Diego. They can be found in large numbers all along La Jolla Canyon off of La Jolla Shores beach. The videos below were taken by a member of Dr. Jaffe’s lab, Justin Haag, using a GoPro camera.

Not only are they interesting to observe, but other animals have also taken an interest.

You can get more information about the squid and watch more videos over at the Southwest Fisheries website.

LUMIS2 returns from successful field work In Bocas del Toro

Last week the CVCE team returned from a very productive trip to Bocas Del Toro in Panama. We worked out of the Smithsonian Tropical Research Institute in Bocas.The field work included a large array of different imaging systems including LUMIS2.


The first few days were devoted to maintaining tags of over 250 corals. After completing the maintenance work, we set out to collect images from all tagged corals, setup new transects, and focus in on nearly 45 targeted corals with six different sample modalities including:

  • White light RGB imaging
  • Fluorescence and reflectance spectrometer data
  • LUMIS and 5D fluorescence imaging
  • PAM data
  • Tissues samples
  • Genetic samples

All told it was a great trip with many successful imaging studies happening in parallel. A big thanks to the whole CVCE team!

Day cruise with OmniCam

On July 7, 2011, the members of Jaffe Lab set sail from MARFAC on the R/V Sproul to deploy the OmniCam in the Pacific Ocean!


To learn more about our omnidirectional imaging system, visit our OmniCam page.



Omnicam with Lights

In preparation for our June 7, 2011 cruise we are testing Omnicam with some high-power LED lights. The video below shows the system recording HD video at 30 FPS with the blue and green lights is it is being lowed to the bottom of the Keck tank at night. The lights were so bright that they illuminated the entire tank. Although not shown in the video, the lights are in fact flashing at 30 Hz in sync with the cameras.

Control Volume Grazing in Coastal Ecosystems

The Jaffe Lab is collaborating with Dr. Stephen Monismith from Stanford University and Dr. Amatzia Genin from the Interuniversity Institute of Marine Science to study Flow and Grazing on Coral and Temperate Rocky Reefs as part of the Control Volume Grazing in Coastal Ecosystems research project. As part of the study, two of our broadband acoustic and optical zooplankton imaging systems are being deployed to estimate zooplankton abundance upstream and downstream in a flow field.


For more information about the program visit the Control Volume Grazing in Coastal Ecosystems website.

For more information about our sonar systems see ZOOPS

LUMIS2 Fluorescence Images

After a series of successful deployments both on SCUBA during the day and snorkeling during the day and night, LUMIS2 has captured some very compelling images of coral and algae fluorescence. Below is a set of frames from our most recent nighttime snorkeling ops. In the left column are the fluorescence frames taken with the blue strobes on LUMIS2 and the right column are the matching white strobe light frames of the same subject taken 50ms later. Each “frame” consists of four separate images arranged as follows:

(Green 510-530)  (Color no filter)

(Red 665-695)     (Orange 568-588)

Note that these images are “raw” uncorrected and that the Orange filter image has twice the gain of the Green and Red images.

Computer Vision Coral Ecology Arrival in Moorea

The CVCE dive team arrived in Moorea today with all instruments intact. After a short ferry ride from Tahiti, we got to work checking and assembling all of our camera systems which are now all up and running. Tomorrow the work begins!


Dr. Jules Jaffe’s photonic tools explore the secrets of the ocean

Dr. Jaffe is featured in the SPIE remote sensing newsroom. Check out the video interview: Watch Jules Jaffe video and the article in the SPIE newsroom: Jules Jaffe’s photonic tools explore the secrets of the ocean.


SPIE Newsroom

Video: Jules Jaffe’s photonic tools explore the secrets of the ocean