Nichia Huxtable: These ARE the Fish You’re Looking For, May 4, 2016

NOAA Teacher at Sea

Nichia Huxtable

Aboard NOAA Ship Bell M. Shimada

April 28 – May 9, 2016

Mission: Mapping CINMS

Geographical area of cruise: Channel Islands, California

Date: May 4, 2016

Weather Data form the Bridge: 0-2ft swells, partly cloudy, slightly hazy

Science and Technology Log:

We’ve been waiting for you, rockfish. We meet again, at last. You might wonder why scientists need to know the location and population densities of rockfish in the Channel Islands National Marine Sanctuary. Well, rockfish are tasty and commercially important, plus they are an important component of healthy marine ecosystems.  To estimate how many there are and where they’re at, you’ll need lots of equipment and fisheries biologist, Fabio Campanella.


Fabio Campanella and Julia Gorton getting some fresh air. Breaks are important to help them stay on target.


Monitor showing the EK60 in action. Your eyes can deceive you…watch out for the acoustic dead zone!

First, let’s start with the equipment. Shimada has an EK60, which is essentially a fish finder: the computer’s transducer sends out sonic “pings” that become a single acoustic “beam” in the water. It covers about 7° at one time, so think of it as taking a cross section of the water column. The beam bounces off any solid object in the water and returns to the transducer. The size and composition of the object it hits will affect the quality of the returning pings, which allows Fabio to discern between seafloor, small plankton, and larger fish, as well as their location in the water column. One drawback of this system is the existence of an acoustic dead zone, which is an area extending above the seafloor where fish cannot be detected (think of them as sonar blind spots).


Do. Or do not. There is no try. Fabio Campanella hard at work in Shimada‘s Acoustic Lab.


Starry rockfish (Sebastes constellatus)

It’s a trap! Nope, it’s a starry rockfish (Sebastes constellatus) found in the CINMS.

Ideally, acoustic data collection is done simultaneously with ground truthing data. Ground truthing is a way to verify what you’re seeing. If you think the EK60 is showing you a school of herring, you can run nets or trawls to verify. If it’s in an area that is untrawlable, you can use ROVs or stationary cameras to identify fish species and habitat type. Species distribution maps are also useful to have when determining possible fish species.


EK60 data shown on the bottom; ME70 data on top right; 3-D visualization of the school on the top left.

EK60 data shown on the bottom; ME70 data on top right; 3-D visualization of the school on the top left. Witness the power of this fully operational Echoview software.

If Fabio finds something especially interesting on the EK60, such as a large school of fish, he can refer to the data simultaneously collected by the ME70 multibeam sonar to get a more detailed 3-D image. Since the ME70 uses multiple beams and collects 60 degrees of data, he can use it to (usually) get a clear picture of the size and shape of the school, helping him identify fish species and density. So why does he use the EK60 first if there is so much more data provided by the multibeam? Well, the amount of data provided by the ME70 is incredibly overwhelming; it would take weeks of data analysis to cover just a tiny section of the marine sanctuary. By using the EK60 to cover large areas and the ME70 to review small areas of specific interest, he is able to create fish distribution and density maps for the largest areas possible.

After collecting data from the two sonars, it needs to be processed. The method you use to process the data depends on your goal: biomass, population densities, and fish locations are all processed differently. Since rockfish are found close to hard, rocky seafloor, data analysis becomes quite complicated, as it becomes difficult to discriminate the fish from the seafloor. Hard bottoms also introduce a lot of bias to the data; for these, and other, reasons there are very few hard bottom studies for Fabio to refer to.


Cleaned data. I’ve got a good feeling about this.

But back to the data analysis. Once data is collected, it is loaded into Echoview software. Fabio then removes the background noise coming from other equipment, averages the data to reduce variability, and manually modifies the seafloor line (rocky bottoms with lots of pinnacles give incorrect bottom data). This last step is crucial in this mission because the focus is on rockfish who live close to the bottom.




School of fish shown on the right of the screen and the frequency response shown on the left. Fish are not lost today. They are found.

The clean echogram is then filtered for frequencies falling in the suitable range for fish with swimbladders (a gas-filled organ used to control their buoyancy). Object with a flat response at all frequencies (or slightly higher at low frequencies) will most likely be fish with swimbladders, whereas a high response to high frequencies will most likely not be fish (but it could be krill, for example). Once Fabio has made the final fish-only echogram, he exports the backscatter and uses it to create biomass or density estimates. All of these steps are necessary to complete the final product: a map showing where rockfish fish are in relation to the habitat.


Krill shown on the right and frequency response shown on the left. Judge them by their size, we do.









The final product. When making accurate maps of rockfish, there is no such thing as luck.

Personal Log:

It seems I overpacked sunscreen…12 hours of my day are spent in the acoustics lab staring at monitors, with brief breaks every so often to look for whales and other wildlife. This mission is so technical. I am grateful for the hours spent asking the scientists questions and having them explain the details of their work. Lately, the big screen TV in the lab has been turned on with some great movies playing. So far we’ve watched, Zootopia, Deadpool, LoTR, and, of course, The Force Awakens. May the 4th be with you…always.

Word of the Day: Holiday.

A holiday is an area in your bathymetry map that does not include any data (think of it as “holes in your data”). It’s like you’ve painted a picture, but left a blank splotch on your canvas.


Avery Marvin: Is it an Island or Just an Ink Blot? July 16, 2013

NOAA Teacher at Sea
Avery Marvin
Aboard NOAA Ship Rainier (NOAA Ship Tracker)
July 8 — 25, 2013 

Mission: Hydrographic Survey
Geographical Area of Cruise: Shumagin Islands, Alaska
Date: July 16, 2013

Current Location: 54° 55.8’ N, 160° 09.5’ W

Weather on board: Overcast skies with a visibility of .5 nautical miles, South wind at 18 knots, Air temperature: 10°C, Sea temperature: 7.2°C, 1-2 foot swell

Science and Technology log: Shoreline Verification

When you think of a shoreline, you might think of a straight or curved “edge” made of sandy beaches that gradually retreat into deeper and deeper water.  In the Shumagin Islands, a sandy cove is a rare occurrence and a place for a beach party! Towering, jagged cliffs patched with Artic moss and blanketed by a creeping fog are the typical “edges” here.  Below the cliffs in the water, lie sporadic toothed rocks and beds of dense rooted bull kelp, swaying with the current. As I sit on the edge of the skiff (small dingy-like boat), which gently trudges along the outside of the protruding rocks, I think to myself “Is this what Ireland is like?” or is this a world unto its own-untouched and solitary? Whatever it is, this place evokes an ethereal mood and you really feel like you are in one of the most remote places in the world.

Rocky shoreline of Nagai Island

Rocky shoreline of Nagai Island

Navigating through Bull Kelp bed

Navigating around Bull Kelp bed

Picture of skiff offshore

Picture of skiff offshore

Remote it is and that is why we are here. These are for the most part, uncharted or poorly documented waters and shorelines and in this post, I am going to talk about the shoreline aspect.  Besides taking bathymetric data (depth data), hydrographic ships like the Rainier must also verify that the shorelines of various land-masses are portrayed accurately and that all necessary “features” are documented correctly on nautical charts.  Features include anything that might be a navigational hazard such as rocks, shoals, ledges, shipwrecks, islets (small islands) and kelp beds. For shoreline verification, a 19 foot skiff is used for maneuverability and shallow water access. This boat will go out during the “shoreline window”, when the tide is the lowest, with the hopes that if there is a dangerous feature present, it will be visible above the water. In the best case scenario, we can investigate the shoreline fully with the skiff before sending in the bigger launches to survey the area with the sonar, so that we know they won’t hit anything.

Shoreline verification crew

Shoreline verification crew. From left: Randy (Coxswain), John (NOAA Corps. Officer), Chief Jacobson (Chief Survey Tech), Avery (Teacher at Sea)

Shoreline verification crew hard at work

Shoreline verification crew hard at work. From left: Randy (Coxswain), John (NOAA Corps. Officer), Chief Jacobson (Chief Survey Tech), Steve (NOAA Corps. Officer)

The main goal of the scientists aboard the skiff is to establish a “navigational area limit line” (NALL). This is a boundary line delineating how far off shore the launch boats should remain when they are surveying.  This boundary line is obtained in one of three ways:

1) presence of a navigational hazard such as a dense kelp bed or several protruding rocks

2) a depth of 4 meters

3) distance of 64 meters to shore

Whichever of these is reached first by the skiff will be the navigational area limit line for the launches.  Here in the Shumagins, kelp beds and rocks have been the boundary line determinant and often these hazards are in water that is deeper than 4 meters because we have been encountering these before we get within 64 meters of the shoreline.

While scientists are determining the NALL, they are also verifying if certain features portrayed on older charts are in fact present and in the correct location. Using navigational software on a waterproof Panasonic Toughbook, they bring up a digitized version of the old chart of a specific survey area. This chart depicts features using various symbols (asterisk=rock above water, small circle=islet). This software also overlays the boat’s movement on top of the old chart, allowing the boat to navigate directly to or above the feature in question.

Shoreline map 1

Shoreline map showing course of skiff, shoreline buffer, and feature for examination.

Shoreline map 2

Shoreline map showing charted location of islet and the actual location of islet determined by the skiff.

If the feature is not visually seen by the human eye or the single beam sonar on the skiff, it will be “disproved” and a picture and depth measurement will be taken of the “blank” location. If the feature IS seen, more data will be recorded (height of feature above the water, time of day observed, picture) to document its existence.  This same verification procedure is used for newfound features that are not present on the old charts.  All of this data is written on a paper copy of the chart and then back in the “dry lab”(computer lab), these hand-written notes are transferred to a digital copy of the chart.

Section of shoreline showing data and notes about specific features in question

Section of shoreline showing data and notes about specific features in question

Digitized version of notes and data taken at field site Note: Kelp buffer are the large shaded red areas and the smaller red circle is the actual position of the islet

Digitized version of notes and data taken at field site. The black box corresponds to the area from the previous picture above.
Note: Kelp buffers are the large shaded red areas and the smaller red circle is the actual position of the islet. The three southernmost rocks (marked by red asterisks) inside the black box were disproved.

On the two shoreline verification adventures I went on, many rocks and islets were disproved and several new features were found. Most of the new features were rocks, islets or large kelp beds.  It is important to note that if scientists find a new feature which is a serious present navigational hazard (ex. Shipwreck, huge jutting rock or shoal far offshore) it will be marked a DTON (Danger to Navigation) and communicated to mariners within a short time frame. Other less significant features take 1-2 years to appear on updated nautical charts.

For some survey areas, the Rainier uses aircraft-acquired LiDAR (Light Detection And Ranging) to get an initial idea of various features and water depths of a shoreline area. (This is a service that is contracted out by NOAA.) LiDAR data is obtained by a plane flying over an area at 120 mph, emitting laser beams to the water below. Like SONAR, LiDAR measures the time it takes for the laser beam to return to its starting point. Using this measured time and the speed of light, the distance the light traveled can be obtained, using the equation distance = speed*time, accounting for the fact that it travels through air and then water.  Because light travels much faster than sound, the plane can travel significantly faster than a boat and a large area can be surveyed faster.  Unfortunately LiDAR can only be used in clear, calm water because light is easily reflected by various solids (silt in the water, floating wood), specific color wavelengths (ex. White foam on ocean surface) and absorbed by biological specimens for photosynthesis (ex. Surface bull kelp).  LiDAR surveys do reduce the time hydrographers spend at a shoreline site thus increasing the safety and efficiency of an operation.  As with any data acquisition method, it must be cross-checked by another method and in this case because of the obvious downsides, it is used as a guide to shoreline verification.

Map of island showing LIDAR data.

Map of island showing LiDAR data. The skiff does shoreline verification outside the orange line that outlines the island. Everything inside this orange island was surveyed by the LIDAR airplane. The three orange features circled in red on the southeast section of the island, need to be re-surveyed by the skiff. Different colors show various depths. (Green is more shallow than light blue.)

After spending several days “disproving” a lot of rocks and islets that were clearly not present in their identified location, we started to wonder why someone would have thought there was a specific feature there. One possibility is that it was just an ink blot on the original chart, made by accident (from a fountain pen), and then interpreted as a rock or islet in the process of digitizing the chart. It’s better to be safe than shipwrecked! Another possibility is that these features were “eyeballed” in their documented location, and thus were present but just in the wrong spot.  Lastly because of limitations previously mentioned, LiDAR occasionally mis-reports features that are not present. Fortunately, our current survey methods use sophisticated navigational technology and several cross-checks to minimize data errors.

After shoreline verification has been completed, launches can survey the ocean floor (using SONAR) outside the boundary (NALL) that was established by the skiff. Each launch will be in charge of surveying specific polygons (labeled by letters and names). The picture above shows the polygon areas which are outlined in light orange (most are rectangles). I will talk more about SONAR and surveying on the launch in my next post. 🙂

Personal log:

I have been on the skiff two times now helping with the shoreline verification process. After the second time around and a chat with the XO Mike Gonsalves, my understanding of this process is more fine-tuned. It feels good to reach this point and it reminds me of the need to be patient, diligent and okay with the unknown when learning something new. I, like my students, often seek answers and a deep understanding of complex topics immediately and if this doesn’t happen I can get frustrated with myself. I have been more self-forgiving aboard the Rainier because I know I will be exposed to the same topic or process once again either in a different format or with a different set of crew members. I am also surrounded by a group of tolerant people who continually answer my questions with grace and peak my interest with new ideas.  This repetition of content and supportive network is crucial for any learning environment, whether it be on a ship or in a classroom.  Additionally, I have been given several small but important tasks which make me feel like a part of this group and complex operation.  This empowerment inspires me to learn more and continue contributing. Building a successful classroom community is no different than what is going on here on the Rainier. All students need to have a stake in their learning and a purpose for coming to class each day.

One of my small tasks aboard the skiff during the shoreline verification was to take pictures of the various features (rocks, islets etc.) that needed to be examined.  In some cases, it was important to photograph specific biological features that had an effect on navigation.  For example, when rounding the SE side of Chernabura Island we came across a large Stellar Sea Lion rookery inhabiting a small rocky islet. The male proudly stood in the center, surrounded by about 50 females.  As seen in the picture, this was a hefty male who easily weighed upwards of 1200 pounds. (Males can get as big as 2,500 pounds.)  During the breeding season (June-August), the male will fast and often won’t leave his reproductive rookery site. His primary focus is to defend his territory and spread his genes! Even though male Stellar Sea Lions are polygamous, they do not force the females into a harem but rather control the boundaries around their physical territory where within, the females reside.  The most successful rookery territories, not surprisingly are small rocky islands which can remain stable and productive for up to two months.

Stellar sea lion reproductive rookery

Stellar sea lion reproductive rookery

After researching about the Stellar Sea Lion, I learned that the western stock which resides in the Aleutian Islands is listed as an endangered species (since the 1970’s populations have declined by 70-80%). The cause for this is complex and has been attributed to a range of factors including: overfishing of sea lion prey (ex. Herring, Pollock), predation by Orca whales, shooting by fisherman, and disease.  Interestingly, a few native Alaskan communities are still permitted to hunt Stellar Sea Lions for subsistence (survival) purposes.

Stellar Sea Lion Range   Note, the two different stocks (Western and Eastern)

Stellar Sea Lion range

Fun factoid: The Stellar Sea Lion was named after the naturalist, George Wilhelm Stellar who first discovered the species in 1741 while part of Bering’s tragic voyage across the uncharted North Pacific.

Beverly Owens: Vacation Cruise – June 13, 2013

NOAA Teacher at Sea
Beverly Owens
Aboard NOAA Ship Henry B. Bigelow
June 10 – 24, 2013

Mission:  Deep-Sea Corals and Benthic Habitat: Ground-Truthing and Exploration in Deepwater Canyons off the Northeastern Coast of the U.S.
Geographical Area: Western North Atlantic
Date: June 13, 2013

Weather Data from the Bridge:
Air temperature: 16.70 oC (62.06 oF)
Wind Speed: 25.17 knots (28.96mph)

Science and Technology Log

Waypoints for TowCam expedition

Waypoints for TowCam expedition

“You get to go on a two-week cruise for vacation!”

This is the misconception that some people had, when I told them initially that I would be participating as a NOAA Teacher at Sea.  On a vacation cruise and a research cruise, participants stay an extended period of time on the ocean, and they receive three meals a day.  That is pretty much the end of the similarities between these types of cruises.  During a scientific research expedition, there is a mission to accomplish. For example, this trip is examining sites that are known or predicted to be deep-sea coral and sponge habitats.

Many multibeam bathymetric maps are consulted to find the most suitable sites to investigate. Bathymetric maps are similar to topographic maps with the exception that bathymetry applies to the topography of the ocean floor. Most of the major structure-forming deep-sea corals are found on hard substrate. Thus, areas of soft sediment are not the most likely places to find the majority of coral species, however many other organisms like brittle stars and anemones, may be found there.

There is a lot of preparation that goes into planning and coordinating a research “cruise.” The Chief Scientist must put in a request for a research vessel, and must assemble a science crew that has the skills and research interests that align with the research mission. In the months leading up to the research trip, the science party will discuss specific science objectives, protocols and potential study sites. Every participant must receive medical clearance, which includes having a TB (tuberculosis) test, and a recent tetanus vaccination.

The Chief Scientist, with input from the science team, determines which areas of the ocean to examine, and what type of technology to use to explore the ocean. Weather and waves may prevent some of the “dives” from taking place. Safety first – the conditions must be safe enough for the TowCam operators and deck crew to be outside during deployment as they lower TowCam safely into the ocean.

This bathymetric map displays the topography of the ocean floor.

This bathymetric map displays the topography of the ocean floor.

During TowCam deployments, many things must be done to make the dive successful. The Chief Scientist selects several points (waypoints) along a survey line within a canyon. These points help guide the ship during the TowCam deployment.  To get TowCam into the water requires a lot of communication and coordination of efforts. The winch operator and deck crew are responsible for getting TowCam into the water. The winch operator is in constant contact with the TowCam pilot and  controls the wire that lowers TowCam into the water. At a certain depth, the control is passed to the TowCam pilot in the lab who uses a joystick to lower the camera to the ocean floor.  The pilot and the Bridge are in constant communication during the dive. The Bridge controls the ship and follows the track for the survey. The TowCam pilot analyzes data displayed on several computer monitors in order to make the most informed decisions as they guide the camera through the water column by moving TowCam and up and down in the water column.  In addition, a variety of data are collected during the deployment.  I have been logging data during the night shift deployments. I help keep track of variables  such as depth, winch wire tension, latitude, longitude, and altimeter readings along the survey track.  All this information will be invaluable to scientists examining the data collected during this research cruise.

 Personal Log

At Crest Middle School, we try to teach our students critical thinking skills: think for themselves, make informed decisions, gather data, predict, and draw conclusions. This research trip is a prime example of how skills that students acquire in school will be beneficial for them in the future. When completing a task such as logging data, I have to decide what the important events are that have occurred in the TowCam dive, and to phrase those items in a way that others will understand.

TAS Beverly Owens logging data

TAS Beverly Owens logging data

 Did You Know?

TowCam is about the size of a refrigerator. It has one large high-resolution camera that takes pictures every 10 seconds. It also has a CTD, which records conductivity (salinity), temperature, and depth. TowCam also carries several Niskin bottles, used for water collection at depth and a slurp pump that pulls sediment from the ocean floor into a container for later analyses.