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)

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
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.

Logistics

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

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: 1m² opening 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 1m² MOCNESS. He used this net for collecting his Pteropods in earlier cruises (see the earlier blog posts!) that he attended for his PhD project.

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.

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

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!

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

Pteropods and the Arts II

Gareth here. Dedicated followers of this blog will recall that last year during the first cruise of our Ocean Acidification and Pteropods Study we had just started a collaboration with sculptor Cornelia Kubler Kavanagh. Earlier this year Cornelia's show, The Pteropod Project: charismatic microfauna opened at the Blue Mountain Gallery in NYC. Cornelia carved some of our favorite shelled (thecosome) pteropods, Limacina helicina and Limacina retroversa, as well as the predatory naked (gymnosome) pteropod Clione limacina, which feeds exclusively on its shelled cousins. Cornelia's pieces show via her medium of sculpture how she imagines these animals might respond to the more acidic conditions of the future ocean. This is exactly what we're doing via our project, only through the 'medium' of science. For the show, our group contributed photographs, text, and some 'specimen boards' of actual pteropod shells, to complement the artwork and provide context.

Below are some photographs of the opening reception, the sculptures, and the animals that inspired them. Hopefully you find these animals as charismatic as Cornelia and we do!

Cornelia's Limacina helicina

Cornelia's Limacina retroversa

The Pteropod Project at Blue Mountain Gallery [Photo: D. Allison]

Cornelia's Limacina retroversa installed in Blue Mountain Gallery [Photo: D. Allison]

Opening reception. Left to right: Nicole Smith, Gareth Lawson, Nancy Copley, Cornelia Kavanagh, Unknown gallery visitor. [Photo: R. Schmitt]

Opening reception, Clione limacina in foreground [Photo: R. Schmitt]

One of the specimen boards (with magnifying glass) our group provided for the show [Photo: G. Lawson]

Limacina helicina sampled during our cruise [Photo: L. Roger

Clione limacina sampled during our cruise [Photo: L. Roger]

Where Do the Data Go?

 

Oceanographers normally collect large amounts of data in the course of the work at sea. In the background on most academic research vessels are the sensors deployed to measure meteorological conditions (wind speed and direction, air temperature and barometric pressure, humidity and precipitation, and long and short wave solar radiation) and sea surface conditions (seawater temperature, salinity, and fluorescence) continuously as the ship moves along the trackline from the time it leaves port to when it returns.

The New Horizon's bridge and above it the meteorological sensors. Note the two anemometers on either side, presently measuring winds of 19 knots and out of a direction of 318 degrees relative to the vessel. After correcting for the ship's speed and heading, this corresponds to a true wind speed of 14 knots out of 21 degrees (i.e., just east of north) [Photo: G. Lawson]

On our cruise, additional data are collected continuously by acoustic transducers attached to the hull of the ship to measure backscattering at various frequencies (an indicator of plankton and nekton living in the water column). A hose mounted on the bow pulls in air to measure the partial pressure of CO2 (pCO2) and the water from the uncontaminated seawater line is used to measure pCO2, Dissolved Inorganic Carbon (DIC), and pH continuously. At stations, more data are collected by the instruments deployed over the side of the ship.  The CTD/rosette with the Video Plankton Recorder attached deployed to 1000 m, or the CTD/rosette deployed to 3000 m collects pressure, temperature, salinity, fluorescence, oxygen, and light transmission data, and hundreds of Gigabytes of video pictures of plankton. The MOCNESS towed to 1000 m, measures pressure, temperature, and salinity while collecting zooplankton in 8 depth strata between 1000 m and the surface on the up-portion of the tow, and the HammarHead towed body collects broad-band acoustics data as well as pressure, temperature, salinity, and fluorescence at selected depths. The Reeve Net, used to collect animals for live work and other experimental purposes, also has a time-depth recorder to provide a record of the tow.

In the lab on the ship more experimental data are generated in the analysis of the water samples from the Niskin bottles on the rosette that go to depth open and are closed at specific depths on the way back to the surface. These include pH, alkalinity, nutrients (phosphorus, nitrate, nitrite), pCO2, DIC, and Dissolved Organic Carbon (DOC).  Furthermore, on board, there are the data being generated from physiological, morphological, and genetic studies being conducted on the pteropods. In order to keep track of all of the data being collected, an electronic event log (E-Log) is kept that records the beginning and end of every over the side deployment of the instruments including the instrument name,  time, ship position, depth of the cast, water depth, station number, transect number, and person responsible. On this cruise we have an IPad that can be taken around the ship to where events are happening and used to log the event via a wireless connection to the main event log server. The total amount of data can be in the 100’s of megabytes to a few terabytes, by the time the cruise ends. So what happens to all of these data sets at the end of the cruise and some which are not produced until samples get back to the laboratory for further analyses?

The electronic event logger. This is a web browser-based application running from a server on the ship that can be accessed by any computer on the ship's network. We use it to keep track of when and where each event (e.g., instrument deployments, the ship arriving on station, etc) occurs. This is key to later data analysis.

Gareth Lawson using the IPad to enter a CTD recovery into the E-Log [Photo: P. Wiebe]

The answer is that the research funds come with a requirement for data sharing.  Since this cruise has been funded by the biological oceanography section at the National Science Foundation (NSF), the data must be submitted to an official data repository and made publically available within a two year time period or sooner if possible. The repository these data will be submitted to is the Biological and Chemical Oceanography Data Management Office (BCO-DMO.org) located in Woods Hole, MA. The BCO-DMO has a mandate to serve principal investigators funded by the NSF Geosciences Directorate (GEO), Division of Ocean Sciences (OCE) Biological and Chemical Oceanography Programs, and Office of Polar Programs (OPP) Antarctic Sciences (ANT) Organisms & Ecosystems Program. The BCO-DMO manages a repository where marine biogeochemical and ecological data and information developed in the course of scientific research can easily be stored, protected, and disseminated on short and intermediate time-frames. Ultimately the data will be sent to permanent archives like the National Oceanographic Data Center.

The data (and metadata) in the BCO-DMO repository are readily available to anyone with a computer and web browser via the internet. They are available either in a text-based format or in a graphical map-server form.  Anyone reading this blog can go to the BCO-DMO web site and locate data from this cruise (once they are submitted) or other cruises.  It is important to remember that using other peoples data requires informing them if you intend to use them for some reason.

Researcher's End Game

When all is said and done
And we are long since gone
What will remain to be distributed
Are the data we contributed
With digital identifiers assigned
And our names clearly defined
Our work will be on-line
Until the end-of-time.
- PHW 16 June 2008

- Peter Wiebe

Pteropod Assemblages

In all ecosystems, whether terrestrial or marine, species combine to form assemblages. These assemblages are often specific to various environmental conditions at work in that ecosystem and so as you cross from one ecosystem to another the species assemblage changes. Although the ocean might seem like one big ecosystem made of water, this conception is wrong. The ocean is made of many different ecosystems, each characterized by different parameters such as seawater temperature, salinity, currents...even the exchanges with the atmosphere that occur at the surface can affect the species assemblages.

I described in a previous post how I am out here preserving pteropods for my dissertation work on the structure of pteropod shells. As a preliminary analysis, I decided to plot the number of shells of each species I have preserved so far to see if any assemblages are obvious along the geographical gradient of the first three survey lines (aka transects) we have sailed along. I quickly plotted the numbers of shells sampled at eight 'test stations' along our survey transect 0 (the first run from Newport to the study region) and transect 3 (the second transit out from Newport).

Map showing sea surface temperature (in color) and the location of our sampling stations. The regularly-spaced stations extending from 50N 150W to 35N 135W are our main study region. We also conducted a series of 'test' stations during our transit to the study region, which are the less regularly-spaced stations that together make a line from the survey start to Newport, Oregon, our port of departure.

At each of these stations we sampled with the Reeve net, and caught a few different pteropod species, including Limacina helicina helicina forma pacifica, Limacina helicina helicina forma acuta, Clio pyramidata and one more species labelled below 'AB'. To help you decode this, in Limacina helicina helicina forma pacifica, Limacina is the genus, helicina is the species, the second helicina indicates the sub-species, and pacifica denotes the forma. Formae describe sub-groups within a species where the individuals can be subdivided morphologically and geographically into several related groups that overlap and interbreed.

The morphological difference between pacifica and acuta are easily seen in the pictures below. Acuta is high-whorled, with distinct regular striations on each whorl; pacifica is low-whorled, without striations. These two formae have been found to cross-breed. In the graphs below I've grouped under the label 'AB' all the Limacina helicina helicina shells that do not fit in the forma pacifica or acuta. 'AB' individuals can be a combination of any of the features of acuta or pacifica: low-whorled with regular strations/with irregular striations, high-whorled without stration/with irregular strations.

Forma acuta

Forma pacifica

Clio pyramidata has a totally different shell morphology.

Clio pyramidata shell

So, here are the graphs...

Can you see a pattern? Here are a few hints:
 
-Compare test stations 05 and 02
-Compare test stations 06 and 03
-Compare test stations 07 and 04
 
If you look back at the map you can see the location of each station. Based on the changes in the composition (%) of the catch we can draw a range for each of the three species plotted here, along a geographical gradient going from southeast to northwest. Here is a new map to help you visualize where we crossed into the range of each species.

Map showing the relative abundance of the different pteropod species sampled.

We entered the range of Clio pyramidata near test stations 04 and 07. The pacifica forma of Limacina helicina helicina was present at test stations 02, 05, 03 and 06, with highest abundance at 06 and lowest at 03. This indicates that while we were deep inside its range at T06 we were only on the edge of it at T03. A very sharp change in the abundance could be explained by environmental parameters (seawater temperature, salinity etc).
 
Test station 08 was totally within the range of Limacina helicina helicina forma acuta but no other species or formae were seen there. With acuta being present at every test station we can presume its geographical range is much bigger than that of the other species or formae presented here. From the colors in the background of the map (representing the sea surface temperature) we can also see this forma prefers colder temperatures. 

Well, I hope this has given you a better idea of what we are seeing here. These analyses are very preliminary but already interesting. We hope the MOCNESS depth-stratified samples will help us further determine the species range with regards to geography, bathymetry, and seawater chemistry. Stay tuned!

That's all folks!

- Liza Roger

Arts and Crafts at Sea

Interspersed with deployments, sampling, and data processing, the scientists and crew have been decorating Styrofoam cups to be sent to great depths in the ocean. This is a common tradition among oceanographers and something that is well planned before we leave home -- we make sure to bring numerous cups, sharpies, and mesh bags. In addition, some people bring cups from home that have been colored weeks in advance by friends and family. Yes, we are that serious about this activity!

 

Sophie coloring

Colored cups ready for deployment

The cups are placed in a mesh bag that is then zip tied onto the CTD rosette frame and lowered to 3000m (that’s almost 2 miles below the surface!!!).

Cups in the bag before deployment

Shrunken cups attached to the CTD rosette frame

Pressure increases with depth and forces the air out of the Styrofoam and thus the cups shrink. Shapes and text are deformed and distorted as a once 4 inch tall cup becomes a mere 2 inches!

Shrunken cups that completed the journey

Shrunken cup

With good luck, the cups make the entire 3 hour journey down and back up again. Cups are generally decorated with cruise information and serve as a unique souvenir from our journey.

- Katherine Hoering