The journal article “Measurement system for marine animal reflectance functions” by Justin M. Haag, Jules S. Jaffe, and Alison M. Sweeney has been recently published in Optics Express. This paper presents details of the optical instrument design and calibration for a new version of the OSMAR (optical scatterometer for measurement of angular reflectance) system that was described last year. Also included, are scattering patterns for squid and fish species that show interesting similarities in light scatter from two otherwise quite different animals. The physical explanations and potential ecological implications of the observed scattering from these species, as well as from others not yet presented, is a subject of future work.
Below is a fluorescence image from our scanning benthic microscope prototype showing GFP and Chlorophyll fluorescence from coral polyps over a large depth of field.
Coral Fluorescence Imaged With Benthic Microscope|desc=field of view 3 mm (h) x 1.5 mm (v)
On Monday we completed our first successful test with multiple, free-drifting Mini-AUEs. This is a major milestone for the project as it marks the first time that the vehicles have been deployed and recovered in the field un-tethered. It is also the first time that multiple units have been deployed together. We released two units programmed to hold roughly a 6m depth while drifting for one hour off Torrey Pines Beach. We did three consecutive 1-hour deployments and all of the critical functions of the vehicles worked perfectly every time. Below are a few photos from the deployment and a example of preliminary data.
We completed a variety of sea tests on Tuesday with Mini-AUE unit 1. In general things went quite well and we were able to have the vehicle complete several profiles, receive GPS position data, and recover the vehicle. Below is a photo of Paul Roberts programming the vehicle on the boat (Photo Credit: Rich Walsh).
Below is a map of two tracks inferred from GPS data (0001 and 0002). The map shows the start position (farther off shore) where the vehicle entered the water and the end position (closer to shore) where it surfaced after completing its profile. The vehicle was underwater for 30 minutes during each profile. Although the profiles were performed at different times, we can see from the trajectories that the current direction and velocity was quite consistent and in both cases the vehicle drifted by roughly 300 m towards the shore during the 30 minutes.
Our prototype underwater microscope was deployed in July and is described in this great video from the American Museum of Natural History BioSnapshot
Jules Jaffe made the front page of the Union Tribune Sunday June 10, 2012! Check out the full article by Gary Robbins.
Last month we had a successful inter-calibration cruise with our zooplankton imaging system ZOOPS. We configured the system to record simultaneous stereo images and broadband acoustic reflections from individual zooplankton. After two days of hard work we had over 40,000 image pairs and acoustic reflections. We are now sifting through the data to find records where the animal was in both camera images and the acoustic beam at the same time. We plan to use these to better understand the relationship between taxa, size, shape, and orientation of the animals and their acoustic scattering signatures.
Some examples of the of data we were looking for are shown below. Each image gives a roughly orthogonal view of the animal being insonified while the matched filtered acoustic envelope (the red curve below the left image) shows the scattering strength and range of the animal. We hope to estimate the size and orientation of the animals from the image data and then compare the measured acoustic data to well-established scattering models.
Engineer Rob Glatts getting ready to test the vehicle at our 35′ deep tank
The 1.5 liter Mini-Aue on its maiden test voyage
Dr. Jaffe along with Scripps professor of biological oceanography Peter Franks, and UC San Diego professor of computer science and engineering David Kriegman have recently been awarded a $1 Million grant from the W.M. Keck Foundation to build the first ever 3D, multi-resolution, video, underwater microscope.