Nichia Huxtable: Time to Make a Map, May 8, 2016

Sunset XBT deployment off Shimada

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 8, 2016
Weather Data from the Bridge:

Science and Technology Log

Seafloor in CINMS
Seafloor in the CINMS

In previous posts, I’ve discussed the ME70 multibeam sonar on board Shimada. You’d think that I’ve told you all there is to know about the wondrous data this piece of equipment provides, but oh, no, dear readers, I’ve merely scraped the surface of that proverbial iceberg. In this post, I will explain how the raw data from the ME70 is used to create important seafloor maps. Heck, I’ll even throw in a shipwreck! Everyone loves shipwrecks.

Nichia Huxtable, Diana Watters, ME70, and EK60; aboard Shimada
Nichia Huxtable, Diana Watters, ME70, and EK60; aboard Shimada

Back to the multibeam. As you may remember, the ME70 uses many beams of sonar to capture a 60 degree image of the water column. It collects A LOT of data, one survey line at a time. Lots of data are good, right? Well, if you want to map the bottom of the ocean, you don’t need ALL the data collected by the ME70, you just need some of it. Take, for example, fish. You don’t want big balls of fish obscuring your view of the seafloor, you just want the seafloor! Leave the schools of fish for Fabio.

Kayla Johnson aboard NOAA Ship Bell M. Shimada
Mapping maven Kayla Johnson

The person you need to make your seafloor map is Kayla Johnson. First, she sends the raw data to a program called MatLab. This nifty software separates the bottom data from all the other stuff in the water column and packages it in something called a .gsf file. Next, this .gsf file goes to this huge processing program called CARIS HIPS, where it is converted into an something called HDCS data.

You’d think that all you’d need to make an accurate seafloor map would be data from the multibeam, but it is actually much more complicated than that (of course you knew that! just look at how long this blog post is). Think about it: while you’re running your survey lines and collecting data, the ocean and, therefore, the ship are MOVING. The ship is heaving, rolling, and pitching, it’s travelling in different directions depending on the survey line, the tides are coming in and out, the temperature and salinity of the water varies, etc. etc. All of these variables affect the data collected by the ME70 and, hence, must be accounted for in the CARIS software. Remember how I said it was HUGE? This is why.

Cross-section of the topography found in the CINMS
Cross-section of the topography found in the CINMS

Everyone still with me? Ok, let’s continue processing this data so that Kayla can make our beautiful map. Next up, she’s going to have to load data into CARIS from the POS. POSMV (POSition of Marine Vehicles) is a software interface used on the ship that collects real-time data on where we are in relation to the water (heave, pitch, and roll).  She’s also going to load into CARIS the local tide information, since the ship will be closer to the seafloor at low tide than at high. Not including tidal change is a good way to get a messed-up map! Once the POSMV and tide files are loaded into CARIS, they are applied to the survey line.

Completed map around San Miguel Island
Completed map around San Miguel Island

Next, Kayla has to compute the TPU (Total Propagated Uncertainty). I could spend the next four paragraphs explaining what it is and how it’s computed, but I really don’t feel like writing it and you probably wouldn’t want to read it. Let’s just say that nothing in life is 100% certain, so the TPU accounts for those little uncertainties.

Since the data was collected using multiple beams at a wide angle, there will be beams returning bad data, especially at the edges of the collection zone. Sometime a bad data point could be a fish, but most often bad data happens when there is an abrupt change in seafloor elevation and the beams can’t find the bottom. So, Kayla will need to manually clean out these bad data points in order to get a clean picture of the seafloor.

Almost done! Last, Kayla makes the surface. All the data points are gridded to a certain resolution based on depth (lots of explanation skipped here…you’re welcome), with the end result being a pretty, pretty picture of the bottom of the seafloor. Phew, we made it! These seafloor maps are incredibly important and have numerous applications, including fisheries management, nautical charting, and searching for missing airplanes and shipwrecks (see! I told you there would be a shipwreck!). I’ll be getting into the importance of this mapping cruise to the Channel Islands Marine Sanctuary in my final post, so stay tuned.

Endnote: A word about XBTs                                                                                                      

Deploying an XBT off Shimada
Deploying an XBT off Shimada

 Before all your data are processed, you need to know how fast the sound waves are travelling through the water. When sound is moving through water, changes in temperature and salinity can bend the wave, altering your data. An XBT is an expendable bathythermograph that is sent overboard every four hours. It transmits temperature and salinity readings throughout its quick trip to the ocean bottom, allowing the computer to make data adjustments, as needed.



Did You Know?
Hey, you’ve made it to the bottom of this post! If you are interested in seafloor mapping, have I got an institute of higher learning for you. The College of Charleston has a program called BEAMS, which trains future ocean surveyors and includes a course called Bathymetric Mappings. Three of the hip young scientists on board have taken this course and it seems to be pretty amazing. If you love sailing the high seas AND data processing, you might want to check it out.

Nichia Huxtable: Life on board, you won’t be bored!, May 6, 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 6, 2016

Weather Data from the Bridge: 2-3 ft swells; storm clouds over land, clear at sea

Science and Technology Log

Dismantling the REMUS 600 AUV for its trip home
Goodbye, AUV. Until we meet again.

The AUV is no longer my favorite thing on Shimada. As I write this, it is being dismantled and packed into shipping boxes for its return trip home to Maryland. To keep a long, sad story short, the AUV had a big electrical problem that was fixed, but when the scientists turned it on for a test run, a tiny $6 lithium battery broke open and oozed all over the motherboard. Game over for the AUV. So now my favorite thing on Shimada is the ice cream.

Personal Log

Enough about science and technology for now. I bet you’re really wondering what it’s like day in and day out on board Shimada. Well, my intrepid future NOAA crew members, this blog post is for you! We’ll start what’s most important: the food.

Breakfast, lunch, and dinner are all served at the same time everyday. The food is prepared in the galley and everyone eats in the mess. Beverages, cereal, yogurt, fruit, snacks, the salad bar, and ice cream are available 24 hours a day, so there is no need to ever be hungry. Not all ships are the same, however. In one of the many anecdotes told to me by master storyteller Fabio Campanella, an Italian research ship he once worked on served fresh bread and authentic pizza everyday…sign me up for that cruise!

Unlike the AUV, the ice cream freezer never disappoints

Next, you’re probably wondering where everyone sleeps. Sleeping quarters are called staterooms and most commonly sleep two people, although larger staterooms might sleep four. Each stateroom has its own television and a bathroom, which is called a head. As you can see in the photo, the bunks have these neat curtains that keep out the light in case your roommate needs to get up at 1 a.m. for the night-shift.

Working in the Acoustics Lab on Shimada

The Shimada has lots and lots of work and storage rooms, each serving a different function. There is a wet lab, dry lab, chem lab, and acoustics lab for doing SCIENCE (woohoo!), as well as a tech room for the computer specialist (called an ET), storage lockers for paint, cleaning supplies, and linens, plus other rooms full of gear and machinery. There’s also a laundry room, so you can take care of your stinky socks before your roommate starts to complain!

Trash on board is separated into recyclable bottles and cans, food waste, and trash. The food waste is ground up into tiny pieces and dumped in the ocean outside of the sanctuary, while the trash is INCINERATED! That’s right, it’s set on fire…a really, really, hot fire. Ash from the incinerator is disposed of onshore.

Shimada‘s incinerator

Another important part of the ship is the bridge. Operations occur 24 hours a day, so the ship never sleeps. Officers on the bridge must know what is happening on the ship, what the weather and traffic is like around the ship, and they must make sure to properly pass down this information between watches. The bridge has radar to spot obstacles and other ships, a radio to communicate with other ships, and a radio to communicate with the crew and scientists.

Looking for wildlife on the NOAA Ship Bell M. Shimada
Bridge on the Shimada

Last, but not least, is the lounge that comes complete with surround-sound, a big screen TV, super-comfy recliners, and about 700 movies, including the newest of the new releases.

Wish this was my living room!

Did you know? 

A female elephant seal was once recorded diving underwater for two continuous hours (they usually stay underwater for 1/2 hour); the deepest recorded dive was by a male and was 5,141ft.

Stay tuned for the next post: Multibeam? You Mean Multi-AWESOME!

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.


Nichia Huxtable: AUV, Why Won’t You Work? May 2, 2016

REMUS 600 onboard Shimada

NOAA Teacher at Sea
Nichia Huxtable
Aboard NOAA Ship Bell M. Shimada
April 28-May 9

Mission: CINMS Mapping
Geographical area of cruise: Channel Islands, California
Date: May 2, 2016

Weather Data from the Bridge: 17-20kt winds; clear skies; 0-1ft swells

Science and Technology Log:

Preparing the AUV for deployment

There is a lot of amazing equipment on board Shimada, but my favorite, by far, is the REMUS 600 AUV. Really, it should be everyone’s favorite. What other piece of equipment can you release in the middle of the ocean, have it swim around for a few hours collecting data, then have it ready and waiting for you in the morning? I’m pretty sure my laptop wouldn’t be able to do that if I threw it overboard (although, on a few occasions, I’ve been tempted to try).

On Shimada’s mission, the AUV is used when scientists need detailed, high-resolution imaging of deep water areas or areas of special interest. The ship’s ME70 multibeam sonar can map the seafloor up to 350m deep, whereas the AUV can map as far down as 400m. Now remember, this is an AUTONOMOUS Underwater Vehicle; this means that you are literally dropping it off the side of the boat, leaving it to propel itself along a pre-programmed route, then, hours later, returning to a set location with the hope of seeing your million-dollar robot pop back up to the surface to be retrieved.

The programmed route of the AUV, including satellite and GPS call points (circles) and return location (yellow square)
The AUV has returned to the Shimada!

There is a lot that needs to go right in order for this to happen. In the REMUS 600, there are three separate systems that must all function correctly in order to successfully complete its mission. The navigational system includes an Inertial Measurement Unit (IMU) for pitch, roll, and heading compensation, a Doppler Velocity Log (DVL) for speed over land measurements, GPS for location, and processing software. The communication system includes a micromodem to receive status messages while AUV is up to 1500m away, an Iridium satellite communications system, and, of course, Wi-Fi. The sensors include multibeam sonar, obstacle avoidance sonar, a depth sensor, and a CT (conductivity, temperature) sensor to analyze sound speed for beam formation.


Troubleshooting the AUV
Troubleshooting the AUV

If these systems aren’t working correctly, there’s a good chance you’ll never see this AUV again (which would make a lot of people very unhappy). Basically, all these systems ensure that the AUV stays at a specific height above the seafloor (around 75m), runs a specific course that you programmed, and collects data for you to analyze when it returns. Every hour or so while it’s running its course, the AUV rises to the surface, makes a satellite phone call to check in with Shimada, then goes back down to continue its data collection. When it’s done with its course, it runs in circles (think underwater donuts) until the ship returns and the scientists call it back up to the surface where it can be retrieved.


The inner workings of the REMUS 600
Remember how I said that all the systems must be working correctly in order for the AUV to successfully complete its mission? Well, this first launch and retrieval went off without a hitch, but it turns out something went wrong with the data collection (as in, there were no data collected after the first 45 minutes). The scientists are once again on the phone with customer support to try to figure out what went wrong.


On the bright side, there are far worse things that could have gone wrong: the AUV successfully ran its course, checked in with the ship, and came up to the surface at the time and place it was supposed to. That doesn’t always happen, which is why the AUV has an “If found, please call this number” sticker right on top of it. Just like what’s written on your retainer case…except your retainer didn’t cost one million dollars.

Personal Log:

Even though it seems like the hours are filled with troubleshooting and problem solving, there are still many things going our way. The ME70 and EK60 have been successfully running all day, the weather is fully cooperating with calm seas and beautiful skies, and, last but not least, dolphins decided to play right next to the ship. Bring on tomorrow!

Dolphins around San Miguel Island
Dolphins around San Miguel Island. Always a crowd pleaser!

Words of the DayAUVs and ROVs. Autonomous Underwater Vehicles are pre-programmed and complete their mission without supervision. Remotely Operated Vehicles are connected to the ship by a cable and are directly controlled by a human operator.

Nichia Huxtable: Day 3, April 30, 2016

NOAA Teacher at Sea
Nichia Huxtable
Aboard NOAA Ship Bell M. Shimada
April 28-May 9

Mission: CINMS Mapping
Geographical area of cruise: Channel Islands, California
Date: April 30, 2016

Weather Data from the Bridge: 3-4 foot swells; clear skys; wind at 29kts
Science and Technology Log:
Ah, technology! Nothing illuminates the darkness of ignorance like these modern marvels of human innovation. Except, of course, when they aren’t working correctly…which is where we find ourselves on day three of the mission.

Troubleshooting on the Shimada.

But I’m getting ahead of myself. Let’s start with a review of what the Shimada is doing and why the mission is so important. If you were a biologist studying mountain lions, you would have a pretty good understanding of where they might be found. You could refer to detailed range and habitat maps and would be able to make management decisions based on some pretty accurate information.

Now, let’s say you are a marine biologist studying sharks around the Channel Islands. Your sharks prefer a sandy seafloor, so you pull up a map that has these areas identified…oh, wait, a map like this doesn’t exist.

NOAA Ship Bell M. Shimada

Perhaps you work for the US Navy and would like to lay down a cable with the least amount of habitat damage, so you pull up a map that identifies fragile, deep sea coral habitat…oh, wait, that doesn’t exist, either!

Most of us know the importance of terrestrial topographic, habitat, and species range maps, yet in many marine ecosystems, such as the Channel Islands National Marine Sanctuary, these data are virtually nonexistent. How crazy to think that we don’t even have information critical to making numerous important decisions! For example, this information is crucial to creating safe navigational routes, placement of pipes and cables, and locations of key fish habitats. This is why the Shimada’s mission of mapping areas around the Channel Islands is so important.


Multibeam SONAR
Multibeam SONAR

There are three different pieces of equipment used to make these maps: ME70, EK60, and REMUS-600 AUV. The ME70 is a multibeam echosounder used for seabed and habitat mapping, the EK60 is an echo sounder used to estimate fish stock and species, and the REMUS-600 is used to map areas too deep for the ME70 or the provide higher-resolution imaging of specific areas of interest. The current technological issues revolve around the ME70. The ME70 works by sending out a sonic “ping.” When the ping hits an object, it bounces back to the ship and is recorded by the computer. All sorts of information can be gathered based on the quality of the returned ping (which I will discuss in later posts), but right now the ME70 is not pinging at the correct rate. It is going much too slowly: only 1 ping per second, whereas it should be pinging roughly 5 times per second. Just like when you have an issue with your computer, the scientists on board are using the satellite phone to call the customer support representative for the ME70 company to try to figure out what the problem is. Another problem is that the ME70 and EK60 are not synching, which means that they cannot be used simultaneously because of interference issues. Last night data was collected using only the EK60, while right now data is being collected using only the ME70. The scientists and crew are obviously trying to figure out how to synchronize


the two systems so that both can collect data at the same time. Finally, the AUV has not yet been deployed because of bad weather (not because it cannot be deployed, but because it would be difficult to retrieve). Monday’s forecast, however, looks very promising, so stay tuned to see how these issues resolve!



Personal Log:
I am constantly awed by the amount of teamwork required to complete a scientific mission such as this. The diversity of duties and expertise of the people involved is mind-boggling: everyone from a ship steward to the Chief Scientist has a crucial role to play and, without each, the mission would fall apart.

Shimada survey techs
Running cables and solving problems

For example, the scientific team consists of hydrographers, AUV operators, marine biologists, and physical scientists. The ship’s crew consists of NOAA Corps officers, engineers, deck, stewards, and survey crew. Each person has their specialty, yet everyone has to work together to solve the inevitable problems that arise.
Finally, I suppose I should mention the crazy weather we had on our first day at sea. The San Francisco Bay was beautiful, but as soon as we passed under the Golden Gate Bridge, the waves grew larger and the passengers began to turn various shades of green. Even though I don’t usually get seasick, I took Dramamine just in case (which, as the swells reaches 15-20 feet, turned out to be a very wise decision). I spent a couple of hours on the bridge riding nature’s finest roller coaster, then turned in for the night and slept 11 hours. What a way to start a mission!

Shimada leaving San Fran
Shimada departing San Francisco.

Did You Know?
The Channel Islands National Marine Sanctuary was designated in 1980 and encompasses 1470 square miles.

Word of the Day:
Bathymetry is the measurement of the depths of large bodies of water, including the oceans, rivers, streams, and lakes.



Nichia Huxtable: Preparing to Sail! April 20, 2016

NOAA Teacher at Sea
Nichia Huxtable
(Almost) aboard NOAA Ship Bell M. Shimada
April 28 – May 9, 2016 


Mission: CINMS Survey
Geographical area of cruise: Channel Islands, California
Date: April 20, 2016


Personal Log

Stardate 8130: Well, not really, but isn’t that the way all logs should start? My name is Nichia Huxtable and I teach biology at Fillmore High School in beautiful Ventura County. Fillmore is a wonderful small town with a rich agricultural history and a picturesque downtown. The best part about Fillmore, however, is the absolutely amazing students that I have the pleasure of working with every day. They are friendly, curious, polite, and funny, and are the reason why I am participating this NOAA expedition.

fam pic 2
The husband and offspring

So, you ask, how can a teacher participating in a research expedition benefit the students? Are you taking them with you? Ah, good question! No, I am not taking them with me, although they will be joining me in spirit. First, I will need to learn. The mission of this trip is to create high resolution maps of sections of the Channel Islands National Marine Sanctuary (CINMS). We will be using scientific equipment and techniques that I never even knew existed and I will be interviewing the scientists and crew members to get a better understanding of who they are and what they do. The whole time I will be posting updates and pictures on this very blog, so be sure to check back often!


Second, when I return to Fillmore, I’ll use my newly acquired knowledge to develop classroom lessons that will bring this amazing science back to my students. These lessons will revolve around three learning goals: 1) the ecological importance of marine sanctuaries, 2) methods scientists use to collect, analyze, and share data, and 3) exposure to new career pathways and possibilities. In order to reach as many students as possible, these lessons and activities will also be shared with other teachers in my district and, in fact, any teacher who would like them.

I cannot even explain how excited I am to participate in this research trip! My background is in wildlife biology, so while I have plenty of experience with kangaroo rat and leopard lizard surveys, I am far less familiar with the science of oceanography.

The next time you see me, I will be in the middle of the Pacific Ocean helping to identify what’s under the water surrounding the Channel Islands. See you then!

PS- Please be sure to check the links to the Ship and the Channel Islands National Marine Sanctuary!