Tuesday, June 14, 2016

Armstrong Cruise - Acoutic calibration (2)

Since this is the first onboard  broadband calibration for the Armstrong’s EK80, each frequency has been tested for different settings. While Andone Lavery performed the calibration, Gareth noted the calibration details. In the meantime senior acousticians, Kenneth Foote and Tim Stanton made valuable comments and contributions.
From left to right: Tim Stanton, Kenneth Foote, Gareth Lawson, Andone Lavery and Jennifer Johnson.

With the new wideband echosounders the frequency response of the target sphere is also tested. There are specific frequencies where, theoretically, the sphere should produce very weak echoes (nulls) due to the phase cancellation.  Since the wideband system uses the entire spectrum of the sound produced by the transducers, it is important to calibrate the full band width of each transducer and nulls observed in the expected location. This is done through comparing the observed frequency response curve relative to the theoretical curve.
The main factor determining the position of the nulls is the water density (temperature and salinity) and the material properties of the target. Andone tells a story how she struggled to get correct curve when she was doing a calibration experiment with sphere which she was initially thought that it was tungsten carbide. Her Fourier transform was not able to fit the nulls into the correct theoretical positions. But after two days of failure, she was happy to find out that the sphere was actually stainless steel. This explains the importance of the material properties in determining the backscattering properties. 

Andone Lavery of the WHOI Applied Ocean Physics and Engineering Lab
Another logistical challenge for the calibration is to find an appropriate location. The dockside in Woods Hole is a good compromise as it is very well sheltered and deep enough for the higher frequencies. However, the downside is the presence of other targets such as fish and the water depth is shallower than the suggestion by Simrad ( 20m for 18 kHz). However, Ken and Tim indicated that the only limitation would be the range where the far field is formed.  They practically calculated the nearfeld depth with the following equation: N=(2D)^2 /λ. where “N” is transition from near field to far field,” D” is the diameter of the transducer and “λ” is the wave length. This corresponds to depth convenient for 18kHz which is available at the dockside. According to Ken, the requirement to keep calibration range at such great depths was due to potential instability of the earlier, relatively primitive transducers and analog time varying gain. However with the highly precise new system there is less reason to worry about the calibration depth. 
Kenneth Foote ( WHOI Applied Ocean Physics and Engineering) , Tim Stanton WHOI Applied Ocean Physics and Engineering), Gareth Lawson (WHOI Biology Department)

Monday, June 13, 2016

Armstrong Cruise - Acoutic calibration (1)

A view from the acoustics lab of the R/V Neil Armstrong
R/V Neil Armstrong is equipped with the cutting edge Simrad EK 80 scientific echosounder running at central frequencies of 18 kHz, 38 kHz, 70 kHz, 120 kHz and 200kHz. This echosounder, using pulse compression technique, produce frequency modulated (i.e., broadband) sound signals and can resolve targets with high precision. Thanks to high signal to noise ratio, it is capable of detecting weakly scattering zooplankton accurately with sizes as small as copepods.

Principally, echosounders are able to produce a high resolution biological profile of the water column continuously, given the acoustic returns interpreted correctly. However, as in the case of all other remote sensing approaches, there are significant uncertainties and therefore ground-truthing is required. As a common approach, this will be performed by the stratified net sampling and optics (Video Plankton Recorder, or VPR).

Some structures other than the living organisms are also able produce echoes such as gas bubbles and physical features (e.g. turbulence or temperature /salinity contrast). The new broadband system enables interpretation of these returns in an accurate way thanks to the very high range resolution and the frequency response information along a wide spectrum. There will be an inter-disciplinary effort among biologist, physical oceanographers and acousticians for interpretation of the acoustic data during the cruise.
Gareth Lawson, Gordon Zhang and Andone Lavery
Calibration of the echosounders is essential for the accuracy of a quantitative estimation. This is done by introducing a target to the echosounder with known target strength and stable scattering properties. Standard metal spheres are used for this purpose (generally made of tungsten carbide or copper). During calibration, the target is placed into the ensonified volume and moved around.

Tungsten carbide sphere was used for the initial calibrations.
The principle idea is to ensure that the echosounder is measuring what it is expected to measure. Traditionally the calibration is done to compare the amplitude of the received signal with respect to the expectation based on the transmitted signal (transducer power gain).
an echogram view during the calibration
Calibration also involves a test for the geometry of the acoustic beam. Most modern echosounders are equipped with a split beam system which means the transducer is divided into quadrants. After the sound transmission, each of these quadrants is able to listen independently. This enables locating the exact position of the targets based on the time delay in received signal between different quadrants. This allows calculation of the angle of the target relative to the transducer. As a result, the shape of the acoustic beam (beam pattern) can be tested accurately.


However, logistically, this is not an easy operation. The important task is to position this small sphere exactly below the transducer. On a huge vessel like Armstrong, this is rather difficult. But, thanks to an automated calibration system developed at the Woods Hole National Marine Fisheries Service lab, the whole process runs very smoothly. Development of this system was led by Mike Jech and the engineers working with him.

Mike Jech

Communication hub
Wireless communication

Once the hardware setup is complete, the whole process can be controlled by the software. Three electrical downriggers are connected to a main hub through wireless communication and this hub is connected to the main computer in the acoustic lab. Once the coordinates of the transducers are entered into the software relative to the sphere’s position, and unless a manual operation is desired, the software takes over the control and moves the sphere based on the desired pattern ( e.g. spiral, starshape or grid).

Jennifer Johnson
operation took time a little longer than expected
Jennifer, the assistant of Mike, is adjusting the length of the lines through the software. She is trying to make sure that the sphere is correctly placed below the transducers. Since this was a dockside calibration there were several obstacles that the monofilament line can get entangled in. So this operation took time a little longer than expected.

The tension was constantly checked during the setting up to make sure that it moves freely

Sunday, June 12, 2016

Armstrong Cruise - Preparations

The sailing date is approaching (Friday 6/17).  The biological sampling in this cruise will involve optics, acoustics and net hauls. In addition to the scientific objectives, a thorough evaluation of the sampling capabilities of the new R/V Neil Armstrong is expected. Therefore it is important to get all the instruments ready for deployment before setting out. After several pre-cruise meetings at WHOI, the preparations are getting more intense as the sailing date approaches. Gareth Lawson, the PI of the survey makes relentless efforts to make sure everything runs smoothly and in line with the calendar.
The brand-new research vessel of the Woods Hole Oceanographic Institution
Gareth describes the aim of this cruise as folows "The overall objective of this cruise is to test and evaluate the R/V Armstrong for inter-disciplinary bio-physical-acoustical research. We therefore plan to collect a variety of acoustic, biological, chemical, and physical data near the Pioneer Array and adjacent survey locations at the New England shelf break and slope. If successful this will allow us to characterize the abundance, distribution, and vertical movements of zooplankton and micronekton concurrent to observations of physical processes and chemical conditions, with particular focus on krill, meso-pelagic fish, and ichthyoplankton (i.e., larval fish)."
Installation of the the MOCNESS frames

For net sampling three different systems will be used including mid-water trawl and ring net and two sizes of MOCNESS. MOCNESS is a multiple zooplankton net with a remotely operated closing mechanism. This net enables stratified sampling with a real-time depth control. It also carries a CTD which provide also real-time measurements that are valuable for decision making during the sampling. The communication with the MOCNESS and data acquisition is made through the cable which is also used to haul the net. Two types of MOCNESS will be tested during the cruise: 1mopening and 10 m2 opening. The large MOCNESS is particularly effective in collecting micro-nekton samples. During the first and second week of the June, these nets were installed and tested at the dock prior to embarking. Peter Wiebe, a senior scientist at WHOI, meticulously led the preparations of these net systems
Christy and Alex are  tightening the bolts.
See the details in the video below.
Peter worked enthusiastically during the installation of the MOCNESS and taught the essentials to Christy, Alex and Serdar. Although Alex is not joining to the cruise, he kindly helped for the installation of the 1mMOCNESS. He used this net for collecting his Pteropods in earlier cruises (see the earlier blog posts!) that he attended for his PhD project.

Friday, June 10, 2016

R/V Armstrong Science Verification Cruise - June 17-23, 2016

Hi! This is Serdar, new postdoctoral fellow from Turkey. I will be contributing to the updates of this blog during the Armstrong cruise. I am in Woods Hole as of June 1st, 2016 and I will be working with Gareth Lawson (and  the greater acoustic team here). I have a scholarship from TUBITAK (the NSF equivalent in Turkey ) for one year. My interest is on understanding the acoustic scattering properties of the zooplankton. 

Different aspects of acoustics have been described earlier in this blog as a method for observing the zooplankton. I will be focusing on material properties of these organisms as a scattering parameter. Zooplankton generally found in dense layers of swarms or aggregations. Acoustic returns from these layers are integrated to estimate the density. However, to numerically quantify these densities, the scattering potential from single individual has to be known. Unfortunately, the small organisms like copepods cannot be resolved individually with the fisheries echosounders.  Instead, physical models can be used for estimation. For this, the body mass composition of an organism is an important scattering parameter and are accounted for in such models (e.g. DWBA). But this property can change from species to species as well as depending on the life stage of the species, the season or geographical locations.

A large Calanus copepod. The lipid content inside a copepod can vary greatly, hence, alter its scattering properties. 

During this cruise I am planning to do such measurements together with Dr. Dezhang Chu  who has great experience and personally developed techniques. This is a great chance and it will be a valuable experience for me.

Wednesday, July 9, 2014

Glass squid video

This is a short video of a glass squid that was brought up in a MOCNESS tow from the deepest net, 800-1000 meters, on 2 September 2012 in the NE Pacific at station 7 (47.02172N  144.61145W).  It got a bit damaged during the slow ride to the surface but was still alive.  Notice the huge eyes, necessary for gathering light at great depths where it's pitch black.

Glass Squid in aquarium on board the RV/New Horizon

Wednesday, September 19, 2012

Cruise Complete!

Gareth here. We arrived today in Port Hueneme, California, just north of LA. The cruise was an enormous success. We managed to survey a total of 34 stations, out of a planned 31! The success of the cruise wouldn't have been possible without the outstanding efforts of Captain Ian Lawrence and the New Horizon's crew, as well as our Scripps Institution of Oceanography Resident Technicians Meghan Donohue and John Calderwood (and Dan Schuller for Leg I), and we are very appreciative of their efforts.

Wire and plastic cages in the van [Photo: P. Wiebe]
Installing the VPR into the van [Photo: P. Wiebe]

After a few days of packing while in transit, our gear will soon be en route for Woods Hole: a truck picked up our storage van, our ethanol-preserved samples are traveling via refrigerated truck, some frozen samples are headed via cryo-pack, and some seawater samples are being driven up to Santa Barbara for nutrient analysis. The science party will soon be dispersing, heading to their various homes.

From left to right: Gareth Lawson, Peter Wiebe, Taylor Crockford, Liza Roger, Amy Maas, Leo Blanco Bercial, Nancy Copley, Aleck Wang, Nick Tuttle, Katherine Hoering, Sophie Chu, Alex Bergan, Tom Bolmer, Elliott Roberts, Meghan Donohue, Kelly Knorr. [Photo: John Calderwood]

We all feel an enormous sense of accomplishment and I am very proud of our team. A few numbers to put the magnitude of this project in perspective:

Distance we traveled: 5269 nautical miles (6063 conventional miles)
Amount of fuel we burned: 40,476 gallons
Number of days we spent at sea: 34 days
Approximate cost of that shiptime: Somewhere around $800,000
Number of blog hits: 5,348

I'll sign off for now with a very nice movie Liza Roger made of a Cavolinia uncinata. This pteropod was about 1 1/2 cm long. You can see by how it moves why they're called sea butterflies, and hopefully can see why we find these animals so charismatic.

Tune in again soon for our next field effort!

Monday, September 17, 2012

SEA Alumni are Everywhere!

On a research vessel you are bound to get scientists, crew, engineers, and technicians from all over the world on a cruise.  There is this special subset of people who sometimes come out on our research vessels, SEA Alumni.  SEA, Sea Education Association, is a unique study abroad program operating since 1971 that combines oceanography and traditional tall ships sailing (think of square rig or pirate ships).  It is still rare to get more than one SEA alumnus on a single cruise.   Gareth and Peter, however, put together an impressive science party for this pteropod study.  We have not one…not two…not three, but FOUR SEA alumni on this cruise.   We comprise both the old and new alumni.  We represent the following classes Westward 28, Westward 178, and Corwith Cramer 223.

Left to Right: Meghan Donohue (W178), Tom (W28), Katherine Hoering (C223), and Nick Tuttle (C223) on the bow of R/V New Horizon owned by Scripps Institution of Oceanography. [Photo: P. Wiebe]
Once you've sailed with SEA you can never take the sea out of us. Katherine, Nick, and Tom all work for WHOI. Meghan works for SIO. The four of us share a very special bond allowing us to instantly trust each other's knowledge and capabilities both on deck and in the lab. For one we all know how to tie a bowline behind our back. Can you?

Thanks SEA for making us lifelong oceanographers and sailors. www.sea.edu

- Meghan Donohue