Research Projects

Autonomous Underwater Explorers

Autonomous Underwater Explorers

Sponsors: National Science Foundation Project Overview: Currently there are very few ways of simultaneously obtaining  spatial and temporal resolution when collecting ocean data.  Of the existing methods, none are low-cost.  The idea behind the AUE project is to build a system that can give both temporal and special resolution in a cost effective manner.  One of the applications for this type of system is the study of small scale circulation, such as coastal or river circulation, and processes, such as dynamics of planktonic communities, oil spill expansion, and sewage outlets that exist on and are affected by such scales.
Benthic Underwater Microscope

Benthic Underwater Microscope

Sponsors: W. M. Keck Foundation , National Science Foundation Project Overview:  Micro-scale activities drive many important changes in marine ecosystems and ideally such processes should be observed in the natural environment. The Benthic Underwater Microscope (BUM) is a diver operated instrument designed in the Jaffe Lab to take microscopic images and video of seafloor environments such as coral reefs.
Keck In Situ Underwater Microscope

Keck In Situ Underwater Microscope

Sponsors: 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.
Open Source Nano AUV

Open Source Nano AUV

Sponsors:  Jaffe Laboratory for Underwater Imaging and UCSD Mechanical and Aerospace Engineering Project Overview: This project aims to design and build small (around 1 liter volume) inexpensive open source AUVs that can be easily constructed ...
Scripps Plankton Camera System

Scripps Plankton Camera System

Sponsors: Beyster Foundation, Keck Foundation, Anonymous Donation to Scripps Project Overview: There is a growing need in oceanography to augment traditional scalar measurements with image data. Towards this end, the SPC project aims to provide real-time, free-space, in situ, plankton cameras with automated object detection and annotation that can be deployed in a diverse range of environments targeting a broad range of plankton imaging applications.
Automated Classification

Automated Classification

Project Overview: The Scripps Plankton Camera (SPC) system, in all its iterations, generates a huge amount of image data; the system captures thousands to hundreds of thousands of images per day. In the short time the pier system has been deployed, it has revealed episodic blooms of fragile diatom chains, many delicate gelatinous organisms, and a form of parasitism not previously reported in the Pacific. To speed the analysis of data coming from the SPC, automated techniques are being developed to label incoming images. At left is an image of colonial radiolarian taken by the SPC during a sea test on the R/V Sproul in 2014.
Plankton Net Camera

Plankton Net Camera

Sponsors: National Science Foundation Project Overview: The SPC netcam is an adaptation of the original SPC cameras (retired at the end of 2014) to image objects in the water flowing out the end of a plankton net. In many scenarios, the natural density of plankton in key size ranges such as 0.5 to 5 mm is too low to be sampled with high spatial resolution and good sample statistics. One example that motivated the construction of the netcam are the waters off Little Cayman. Towards this end, the netcam aims to concentrate the water imaged by the cameras while maintaining high resolution in the images of millimeter sized plankton.
SPC NOAA Fisheries

SPC NOAA Fisheries

Project Overview: A modified version of the SPC was commissioned by Eric Danner from the NOAA South West Fisheries Science Center  to be used to study the invertebrate populations in the Sacramento river and estuary near San Francisco Bay. It is hypothesized that the ability of the salmon populations in the river to withstand changes in their climate such as fluctuations in the release water temperature is highly influenced by available food. This camera system will help quantify the abundance of these food sources and hopefully lead to a synoptic monitoring program through the river and estuary ecosystem.
SPC Prince William Sound Science Center

SPC Prince William Sound Science Center

Project Overview: A modified version of the SPC was commissioned by Rob Campbell from the Prince William Sounds Science Center in Cordov, AK to be mounted on his profiling mooring in the Prince William Sound. The profiler typically runs several times a day sampling water from the surface down to 60 meters at a profile speed of roughly 30 cm per second. The profiler holds an excellent suite of sensors that provide a host of biological and physical measurements. The custom designed SPC will augment these sensors with high-resolution images of plankton in the size of of 1 mm up to several cm. In order to collect enough samples during the relatively short and infrequent profiles, the SPC was redesigned around a much larger field of view (over 500 mL volume images per frame) and housed in a larger set of tubes with large sapphire optical ports. Working with Wetlabs the SPC was integrated as an additional sensor in the suite of instruments on the profiler.

Sub-micron Particle Sizing

Sponsors: National Science Foundation Project Overview:  There is a great need in many scientific applications to be able to accurately size sub-micron particles. As the particle size decreases to be smaller than the wavelength of light it becomes ...

Underwater Imaging LiDAR

Sponsors: Office of Naval Research Project Overview: To support Navy imaging operations in turbid waters, the Jaffe laboratory has been working for several decades on developing advanced laser imaging systems to improve image contrast and range...