Keck In Situ Underwater Microscope

2016-03-04 17.19.10Sponsors: W. M. Keck Foundation

Project Overview:

There is a great need in microscopy and especially in situ, underwater microscopy to study behavior and interactions of organisms in a their natural fluid environment. This precludes the use of traditional microscopy techniques that prepare specimens on a slide or image z-stacks through immobilized 3D volumes. To address some of these limitations the Keck In Situ Underwater Microscope  was designed to record video of a 3D volume (a cubic centimeter for example) with sufficient resolution for taxa identification and 3D localization with resolution on the order of microns.

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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.

AUE GPS communication successfully tested at SIO Pier

We made a big step forward in the past weeks with a successful test of the GPS system that is to be used on the Mini-AUEs. The system uses the Global Star Network to transmit the location of the vehicle to a remote server. This information can then notify researchers that the vehicle has returned to the surface and give its precise location to aid in recovery.

The Global Star network has significant advantages over other networks due to much lower cost (single transmission costs are on the order of $0.15) and its widespread use.  However, adapting the RF electronics to work while bobbing around at the ocean surface was a non-trival task. The positive results of this test make us optimistic that the Global Star system will provide a reliable solution to location and recovering these autonomous underwater explorers.

The figure below shows GPS fixes sent from the vehicle over the Global Star network. The upper left corner shows a view of the vehicle in the water.

For more information about the AUE project check out the Autonomous Underwater Explorer Page.

Results from the Global Star test off SIO Pier


iPhone goes to out sea: Testing the iPhone GPS receiver for locating and tracking autonomous underwater vehicles

One of the key components of the Autonomous Underwater Explorers (AUEs) currently under development in our lab is a GPS receiver for locating, tracking, and recovering the AUEs after a deployment. Because the AUEs will be floating right at the surface of the water, there are problems acquiring satellites and getting reliable GPS fixes using conventional receivers.

On a recent cruise, we had the opportunity to test the GPS receiver of the iPhone 3G. The test consisted of putting together a small plastic housing for the iPhone that was weighted to ensure the iPhone was at the surface. Below is a photograph of the components of the housing:


The housing consisted of a set of large washers for ballast, some padding to fill the empty space in a 1 L plastic jar, electrical tape to fix a line to the jar, and the iPhone. The iPhone was then powered on, and a GPS application was started to acquire and log GPS fixes. The parts were then assembled:


IMG_2731 IMG_2736

We then deployed the iPhone off the stern of the ship, payed out about 200 feet of line, and then towed the package behind the ship for a few minutes. After recovering the package, downloading the GPS data and plotting using GPSVisualizer, we obtained a nice GPS track:


Follow this link to explore the GPS track intertactively on

Note that this was recorded by the iPhone while it was partially underwater, bobbing up and down as it was towed behind a ship!

Many GPS receivers fail to work at all when used right at the surface of the ocean. Yet the iPhone not only worked, it worked well! There are several factors to this performance. Perhaps one of the most significant is that the iPhone uses the cellular network to acquire GPS almanacs and therefore can rapidly initialize and start computing GPS coordinates.  Of course without the cellular network, this performance would be reduced, but none the less, the iPhone does provide a solution for acquiring GPS fixes at the surface (perhaps even slightly under water) of the ocean!