Terry Maxwell: An Advanced Operation, June 11, 2016

NOAA Teacher at Sea

Terry Maxwell

Aboard RV Hugh R. Sharp

June 6 – June 21, 2017

Mission: Sea Scallop Survey

Geographic Area of Cruise: Northeast Atlantic Ocean

Date: June 11, 2016

Weather Data from the Bridge
Latitude: 42 06.73
Longitude: 67 18.80
Wind Speed 20.9 Knots (24 miles per hour)
Air Temperature 13.3° Celsius (55.9 Fahrenheit)

Science and Technology Log

Upon my first entry into the Hugh R. Sharp, the one thing that really stuck out to me was the amount of visible technology.  In the dry lab alone, there are over 20 computer screens, close to as many hard drives, and Ethernet cords crossing and spanning the entire dry lab area.  In the laboratory van, where much of our species counting and data collection takes place there are three more touchscreen monitors, motion compensated electronic scales (a scale that measures accurately regardless of boat movement), and electronic meter sticks.  It is overwhelming at first, but as I have settled in now for four days it becomes commonplace.

before and after

What is more impressive than the amount of technology in the dry lab, is that the NOAA crew hooks up all the equipment before the mission starts.  The before picture of the room is on the right.

On the 9th we were delayed due to some rough water, and the need to fix some of our equipment.  Specifically, the ramp, which launches our underwater camera, was broken due to some strong waves.  The engineers and technicians of the boat reinforced the ramp quickly on the morning of the 9th and we were headed back out to our location in Georges Bank in short order.  The science crew I am a part of has the noon to midnight shift, so this gave me a chance to talk with one of the NOAA Fisheries experts Nancy McHugh about the technological advancements she has seen in recent years on the NOAA surveys.


Nancy McHugh sorts and identifies fish from a recent dredge station catch.

Nancy has been with NOAA for 26 years, and has been on many survey missions.  In my last blog, I gave an overview of our dredge missions, and how the data were collected during those missions.  During this blog entry I would like to tell you about the technology that makes all this data easier to collect, analyze, and organize than it once was.  This technology has made all the collection of data more accurate, reliable, and accountable.  I have seen first-hand now how serious NOAA Fisheries is about collecting data that is accurate as possible, down to the last and smallest scallop.

In the 1990’s and early 2000’s, the NOAA Fisheries staff used waterproof paper forms and pencil to collect the information from their surveys.  Separate forms were used for each species collected.  To give you an idea of how many different species are collected during a survey, our survey has collected over 50 different species of organisms, and we still have 11 days left.  That means that during this survey would have had 50 different paper charts about the organisms collected.  Each organism collected would be hand tallied onto a chart about the specimen’s length, weight, gender, and if a stomach content examination was performed. Each species was given a code number so that code number could be entered into a database for retrieval at a later date.

old form

Old fisheries survey data form used in the late 90’s.  Much has changed since then.

Once the data for each species was recorded on its own form, the summary of the information about each species was transferred onto a main master form.  All the scallops were hand measured, and length tallies made for the scallop at each millimeter mark.  Once the dredge station survey was complete, someone would hand total all of those numbers to get a total amount.  The total data sets would be sent out to a prison in Kansas, which would be responsible for key punching (entering on a computer).  This data would take around 3 months to get back.  Once the keypunched data was sent back to NOAA Fisheries, it would then have to go through an intensive audit process before it was considered clean and ready for the stock analysts use.

Today NOAA Fisheries relies on a program called Fisheries Scientific Computer System, or FSCS for short (sounds like Fiscus).  NOAA scientists and programmers created this computer program to replace the tedious method of pencil and paper data recording.  My crewmember Nancy was one of the scientist involved in the creation of FSCS.  The FSCS program has helped to create not only a faster more efficient data collection system, but also one that is more accurate and reliable than the old paper and pencil model.  First, the FSCS system is an offshoot of the Scientific Computer System (SCS), which is able to store information about ship board sensors, ship positioning, latitude and longitude, winch data, and depth.  When we are about to start a dredge station, the NOAA scientists start “an event” in the FSCS computer program.  The program then begins to collect a snapshot of information from the SCS system while the dredge is fishing.

lab van

The laboratory van is set up with three touch screen monitors that all run the FSCS program, ichthysticks (electronic measuring sticks), motion compensated scales, and barcode readers to enter data into the FSCS program.  This was a empty room before the mission.  NOAA Fisheries workers set up this room before the start of the Scallop Survey.

Once the process of pulling up the dredge, and collecting of species, and sorting of species has happened the efficiency of FSCS is revealed. There are three stations in the laboratory van; each station containing an “ichthystick,” a small motion compensated scale, a touch screen monitor, a bar code scanner, and a printer.  Each station has science crew members working in teams of two.  At station one in the laboratory van, our watch-chief begins to enter in data from the different species that are collected.  The bucket the specimen is in is scanned; this bucket’s weight has been pre-programmed into a computer.  By having the bucket weight already in the program’s database, that weight is automatically deducted on the digital scale when the specimen bucket is set on the scale.  This tare process once was done manually, by pressing the tare button on the scale.   Once the specimen buckets have been scanned and weighed, many of the specimens are measured for length.  Again, the new technological advancements help with efficiency and accuracy.  NOAA scientists have developed their own “ichthystick” which essentially is an electronic meter stick.  These “ichthysticks” are at each of the three stations in the laboratory van.

icthy board

Measurements made using the icthysticks go straight into the FSCS program. There is no hand transferring of the data. This allows for fast and efficient data collection.

Before a measurement is taken, a scientist selects a specimen from a list in FSCS of possible collected specimens and scans the barcoded bucket tag to ensure the correct species has been chosen.  For this example, if a scientist was examining sea scallops the user simply places a sea scallop on the board up against a block that is at zero mm, and then places a magnet on the other side of the specimen.  The computer will make a sound to indicate the length is acknowledged, and the data is collected in the program.  Here is the cool part: the computer program knows the general ranges of the specimen’s size.  That means if someone accidentally put the magnet down at 350 mm while measuring a sea scallop, the computer would automatically put up a warning message (visually and audibly) noting that the measurement is beyond the known range of expected sea scallop lengths.  This cuts down on accidental measuring errors.

At station 3 where scallops are shucked and examined, all of the information which I discussed in the last blog goes into the FSCS database as it is recorded.  Again, the program checks for errors.  For example, if a meat weight is entered that is too light for the size of the sea scallop being examined, the computer will alert the user that the meat weight is too small for the examined sea scallop.  Then the cutter can ensure that he removed all of the meat properly.

Once all this data is recorded, it is merged with the SCS data for a complete picture of the survey.  The merged data can then be accessed by NOAA Fisheries scientist to analyze the data and create predictive models.  Essentially the NOAA Fisheries survey crew can leave the boat with data that used to take over three months to finalize after a survey had ended.

Personal Log

I don’t want to jinx it, but I think I finally have my “sea legs.”  The waves are pretty rough today, but I’m not really fazed by the motion.  Yesterday we spent a lot of time on the computers, annotating images from the underwater camera, HabCam.  During that time working, I almost forgot I was on a boat.  Part of that is that the water was calmer yesterday.  But today we have much more chop in the water and I still feel okay.

The 9th was a hard day for me, as I missed my son Zebadiah’s birthday.  Happy Birthday Z!  It’s hard to be away from my family, but as I talk to some of the NOAA Fisheries people or the crew that runs this ship I realize how short my time is away from my family.  Some of the NOAA Fisheries crew is out 120 days at sea each year!  The ship crew will work this mission and then head to another mission right after ours is done.  There are some very hard working people that work for NOAA Fisheries, and the crews that run NOAA’s fleet of ships.

It has only been six days since I arrived at Woods Hole, but I’ve seen some amazing sites.  Even though some of the crew is out so often at sea each year, I’m realizing the amazing sunsets never get old to them.  It is an awesome site each night, as is the moon over the water at night.

sun set

Amazing sunsets every night when you are over 100 miles from the coast.  Being aboard the Hugh R Sharp has been a great experience so far.

Did You Know?

Sea Stars are one of the main predators of scallops.  It’s an interesting correlation.  When we have done dredge station surveys there is definitely an inverse relationship between the number of sea stars caught and the number of scallops caught.  Meaning the more star fish that are in a dredge tow, the less scallops and vice versa.  When using the underwater camera (HabCam) to take pictures of the ocean floor, there are sections with sea stars that litter the ocean floor.  Not surprisingly, there are very little scallops in those sections.  Sea stars have suction cup like structures on their arms, which help them latch onto a scallop.  When that happens, the sea star then slowly attempts to pry the shell open.  Some sea stars are then able to push their stomachs out of their body, and digest the externally.  Another interesting ability of the sea stars is their ability to regenerate arms if they are lost.

star eating clam

Sea stars attacking a razor clam shell.  This picture was taken by the underwater camera on board called the HabCam.

star regen

Sea star with two arms regenerating.

huge star

A gigantic sea star out of our dredge collection.  The normal size one is on the right.

Donna Knutson: Atlantic Sea Scallop Research Progressed into Habitat Modeling, June 13, 2016

NOAA Teacher at Sea Donna Knutson
Aboard R/V Hugh R. Sharp
June 8 – June 24, 2016


2016 Mission: Atlantic Scallop/Benthic Habitat Survey
Geographical Area of Cruise: Northeastern U.S. Atlantic Coast
Date: June 13, 2016

Mission and Geographical Area:  

The University of Delaware’s ship, R/V Sharp, is on a NOAA mission to assess the abundance and age distribution of the Atlantic Sea Scallop along the Eastern U.S. coast from Mid Atlantic Bight to Georges Bank.  NOAA does this survey in accordance with Magnuson Stevens Act requirements.

Science and Technology:

Weather Data from the BridgeTas habcam 055 (4) color

Latitude:  40 43.583 N
Longitude:  67 04.072 W
50% cumulous
: 6 nautical miles
Wind: 296 degrees 11 knots at cruise speed of 6.5 knots
Wave Height: 1-3 ft.
Water Temperature:  52 ºF
Air Temperature:  56 ºF
Sea Level Pressure:  29.4 in of Hg
Water Depth: 107 m

Scientific Blog

During the 1970’s fishermen made the observation that the Atlantic sea scallop was becoming hard to find.  Overfishing had depleted the numbers and they were not repopulating at a steady rate.  In the early 1980’s after noticing that nature wasn’t going to be able to keep up with man’s demands of the scallop, programs were set up to monitor the scallop fishing industry and to also set catch limits.

Live video from rear sonar devices

Live video from rear sonar devices

In 1997 NOAA and the New England Fishery Management Council determined that the Atlantic sea scallops were still being overfished and by 1998 a new plan for allowing the scallop to increase their numbers was implemented.

The guidelines for fishermen proved to be useful and the scallop industry had great success.  It was reported that the scallop biomass harvested had increased eighteen times higher than the previous level between 1994 – 2005.

The demand for the Atlantic sea scallop did not decrease.   The sea scallop adductor muscle, the muscle that holds the two shells together and allows the animal to open and close the two shells, is harvested for food.  The muscle is typically 30 – 40 mm in diameter in adult sea scallops.  The demand for this tasty muscle has made the Atlantic sea scallop fishing industry into a very powerful and prosperous billion-dollar industry.

Live forward sonar scanner

Live forward sonar scanner

Fisherman will agree that science is essential to the health of their industry.  It was determined that rotational management was needed for the scallops to replenish, much like crop rotation on land.  After a period of time, areas need to rest without any activity and other areas can be reopened to scallop fishing after a period of time.


What that time period for rest is and what areas need to rest while other areas are opened to fishing is the science behind the industry.  The industry recognizes that the science is essential to keep a healthy population of Atlantic sea scallops and, through a special research set-aside program, invests 25% of the scallops to research.  The market value of the scallop, usually $10 -$14 per pound, determines the funding scientists can invest into research.

Resource management is not a new idea.  Resources are managed at all levels whether they are animals such as scallops or deer, minerals or elements mined such as aluminum or coal, or even plants such as trees. Without management practices in place, there is a good possibility of endangering the resource for later use, and in the case of living animals, endanger their future viability.


Dr. Scott Gallager

Some of the “Research Set-Aside” monies given by the commercial fisherman have allowed the development of a special habitat mapping camera, affectionately called the HabCam.  Dr. Scott Gallager has combined his two areas of expertise, biology and electronics and developed a series of cameras used for studying underwater habitats.  NOAA has contracted Dr. Gallager to oversee the HabCam during the annual sea scallop survey.

While the original HabCam is being used by the commercial fishing industry on scallop vessels, a fourth generation HabCam is used by NOAA on the R/V Sharp to help with the annual Atlantic scallop survey.  It has two sonar devices, one forward and one rear sonar scans a 50 meter swath on each side of the vehicle. It is equipped with four strobe lights that allow two cameras to take photographs.  Each camera takes six pictures a second.  The HabCam has a sensor called the CTD (Conductivity, Temperature, Depth) to measure physical properties such as salinity, temperature, depth, and dissolved oxygen.  Two other sensors are used to measure turbidity, and a device that measures the scattering and absorption of light at that depth.  Measuring absorption allows the computer to make color corrections on the pictures so the true colors of the habitat are seen.  The vehicle is 3700 lbs. and made of stainless steel.  It is actually towed through the water but is “driven” by using the metal jacketed fiber-optic tow cable which pulls it through the water.  The HabCam relays the real-time images and data directly to the ship where it is processed by computers and also people monitoring the pictures. Computer Vision and Image Processing tools are also being developed to count and size scallops automatically from the images as the vehicle is being towed. This will allow managers in the future to use adaptive sampling approaches whereby the sampling track is actually changed as the vehicle is towed to optimize the survey.

HabCam on Right Side

HabCam on Right Side

By analyzing the data from the HabCam and doing dredges over mapped areas of the ocean, scientists can relay their findings to fisherman with suggestions on the best places to harvest Atlantic sea scallops.  It is important to keep in mind the other animals in the area that may be affected by scallop fishing.  The Yellowtail flounder is one such animals that could be better monitored with the aid of the HabCam.  The flounder often is found living in areas that have a high density of sea scallops, but by identifying areas of high scallop and low yellowtail densities, fishermen may be better able to avoid yellowtail bycatch.  Unfortunately, many bycatch fish do not survive the dredging and are often dead upon being returned to the sea.

While scallops and fish are certainly important to the commercial fishing industry, understanding the habitat that supports these organisms is paramount to their effective management. HabCam collects images that contain a huge amount of information on habitat factors such as temperature, salinity, chlorophyll, seafloor roughness, and substrate type (mud, sand, gravel, shells, boulders, etc). Habitat for one organism is not necessarily the same for the next so we need to put together maps of where certain habitats allow each species to exist and where they co-exist to form communities. Understanding this, we can simulate how communities will respond to climate change and other changing environmental factors such as Ocean Acidification (i.e., low ph), which all contribute to habitat.

Dr, Gallager worling on the HabCam

Dr. Gallager working on the HabCam

Because of the success of the HabCam and other habitat monitoring/mapping devices, HabCams I – VI have been built.  There are four different vehicles used now for specialized data collection depending on what the survey priorities are.

HabCam is a unique, and high-end technology, but at the same time is being upgraded to provide habitat data on a variety of sampling platforms such as high speed torpedo-like systems that are towed at 10 kts or greater and on robotic Autonomous Underwater Vehicles (AUV) that will carry the stereo cameras and sonar systems currently on HabCam. The combination of robotics with underwater sampling provides a window into the ocean universe that humans have not been able to effectively explore and sample because of the great pressure and low temperature of the deep sea. Abyssal habitat (deeper than 3000m) is very difficult to sample and more and more oceanographers are looking to develop and use robots to get to where observations and samples need to be taken.

Monitoring the screens for obstacles

While the HabCam was initially developed for the scallop fishing industry, it has clearly made an invaluable contribution to the study of habitats that have so long been inaccessible to us.  There are many cameras throughout the world used to take pictures of the ocean bottom and even animals therein, but the HabCam series that was developed out of Woods Hole Oceanographic Institution (WHOI) is integrating many different data types to develop a more comprehensive understanding of fauna and flora (animals and plants) in their habitats worldwide.  It is an exciting time for oceanic research!

Driving the HabCam

Driving the HabCam


National Marine Fisheries Services (www.nmfo.noaa.gov)

Dr. Scott Gallager PhD, tenured Associate Scientist, Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, Visiting Professor, Okinawa Institute of Science and Technology, Okinawa, Japan.


Personal Blog:

I am feeling great and meeting so many fascinating people!  Dr. Gallager, or Scott to the scientists on board, has taught me so much in the very short time I’ve been on the ship.  He has many great stories as he has been involved in oceanic research for many years.  He was asked to study the teak wood that the Titanic was made of because “Bob” Ballard saw so little of it even though all the decks and ornamentations were made of it.  So Bob asked Scott to study it and Scott wrote a paper on the polychaete worm that was able to break down the tough cellulose tissue.

After our dredging yesterday resulted in many scallops, you will never guess what we are having for our 12:00 p.m. meal.  I said 12:00 p.m. meal because for some of us it is breakfast and for others it is supper.

Dogfish on the bottom of the ocean, Picture taken by the Habcam.

Dogfish on the bottom of the ocean, Picture taken by the Habcam.

Me and the other five scientists are now done with our 12 hour shift and the new group just took over. We were running the HabCam all day and then looking at random still photos from the HabCam to identify the life forms that are present.  Dr. Gallager is working on a computer image recognizing HabCam, but he feels it is important to have humans involved as well.   I am so thankful I am on the same crew as Dr. Gallager.  I am actually getting better with the whole time schedule shock.  Not really a big deal once you try it.  (Like most things in life.)

Skate on the bottom of the ocean. Picture taken by the HaabCam.

Skate on the bottom of the ocean. Picture taken by the HabCam.