The Fish Sound Project: Unraveling the identity of fish sounds in British Columbia, CanadaLatest update January 18, 2019 Started on October 10, 2018
The ocean is full of intriguing sounds! Whales, seals, wind, rain, boats are all important contributors to the ocean soundscape. But did you know that many fishes also make sounds?
A team of scientists is on a journey to discover the sounds produced by the coastal fishes off British Columbia, Canada.
Adding a hook to the Trident
As I mentioned in previous posts, we want to use the Trident to recover our hydrophone and camera array from the seafloor. While planning for the next deployment, I took some time to perform some tests and added a pole at the front of the Trident with a carabiner. After few iterations, I found a reasonable design that does not affect too much the maneuverability of the Trident and is easy to put together (and repair in the field). Once hooked to the mooring, the carabiner detaches itself from the pole and is closed using a simple quick release mechanism. I tested it in shallow water (5m) off a dock nearby and it worked pretty well. The real test will be to use it in deeper water, but things look promising so far.
Our instruments are working again and we are planning to deploy the fish array in the next few days, as soon as the weather calms down. Stay tuned...
Cadboro Bay – recovery
The weather has been absolutely crazy after we deployed the hydrophone array. A severe wind storm caused the cancellation of multiple ferries, delayed many flights, put down a number of trees (causing 1 fatality) and left about 225,000 homes without power across Southern Vancouver Island and the Lower Mainland. Needless to say that I was worried about our mooring, especially with the surface buoy. On the bright side, at least this was a good stress test. If the hydrophone array survived this, I think we could call this deployment a success…
Due to the storm we delayed the recovery trip by a day and went back on the water on Friday morning with Jess and Alex MacGillivray (a good friend and colleague of mine at JASCO) who kindly agreed to come help us. Luckily, the winds had completely died down after the storm and the weather conditions were amazingly good. We couldn’t use the same boat ramp as last time since it was completely blocked off by driftwood that got washed out by the storm (see picture below). Luckily, there is another boat ramp near by that was still accessible. To be honest, at this point, I was prepared to not find the surface buoy and was already thinking about backup plans to get the instruments back. But as we approached the deployment location with the M/V Liber Ero, I could see the orange buoy in the distance. That was a relief… Once at the mooring location, we deployed the Trident to make sure everything was sitting properly on the seafloor and that the lines were not tangled in the PVC frame. It was fairly straightforward to find the hydrophone array on the seafloor. Now that we have more experience with the Trident, I am pretty confident that we will soon be able to deploy the array without a surface buoy and use the Trident to retrieve the instruments. After some heavy lifting, we managed to bring the whole unit back on the boat and go back to shore. Everything looked fine and I was pleased to see that the structure handled very well the harsh conditions of the last few days. Mission accomplished! Time to go back home [...you can imagine myself with a big smile driving my tiny car packed to the roof with all the equipment, plus the big buoy]_
So, that was the good part… now the bad… As soon as I arrived home, I started to download the data. I was excited to see if we had caught any fish on the camera. Unfortunately, my smile and excitement quickly disappeared, and my face progressively turned red. The camera did record video files… but they were all empty. I was devastated. All these efforts to have no video data… Looking at the logs, I saw that all the scripts, battery pack, power management, and buzzer worked well, but there was something wrong with the camera sensor. I am still investigating the exact reason of this failure, but it looks like the camera sensor got damaged during the transit on the boat. As for the acoustics, we collected data on all 6 hydrophones, but one of the channels seems to have issues. Here, again, I am investigating to see how this can get fixed.
To be honest, I was not to keen to write this post and report failure. But I guess it is part of the game. Failure is part of the process. Spending quality time during the Christmas holidays with my loved ones helped me step back and see the positive side of it. Stan, Francis and Rodney were also very supportive. Even though I did not collect good data, this deployment brought to light some issues that need to be fixed to improve the robustness of the system. Overall it was also good to gain experience with the deployment and recovery of the unit. I have more confidence in the structure of the array and in the deployment/recovery process.
Now back to the drawing board to fix all the issues and hopefully we’ll be able to redeploy soon.
Best fishes for 2019!
Cadboro Bay – deployment
Our first deployment site is in Cadboro Bay, close to the University of Victoria. We picked this site because sculpins have been seen there and also because this is a sheltered site. For the first deployment we didn’t really want to go straight in the open ocean. Baby steps.
So, on Monday, Jess Qualley (manager of the Juanes lab and skipper), Katie Inness (Juanes lab assistant), Tristan and I went onboard the M/V Liber Ero to deploy the hydrophone array. The weather was cooperating, and everything went pretty smoothly. One of the challenges was to find out how to fit the array on the tiny boat. It was tight, but we made it work. For this first deployment, we chose to have a surface buoy for the recovery, just to be safe. This might cause some noise if there are big waves, but at this point in the mission we just wanted to make sure we could retrieve the instruments easily. We’ll get braver in a few deployments, once we gain more experience and confidence.
Once everything was deployed, we put the Trident ROV in the water to make sure the array was sitting properly on the seabed. It was only the second time using the Trident (the first time in the ocean). It was neat and reassuring to be able to inspect the array once deployed.
The instruments will stay in the water for 4 days before we come back to pick everything up.
Mission underway !
- Camera system
- Hydrophone array
- PVC frame
- Trident ROV
This is it ! We now have everything we need to start real measurements in the ocean. First deployment planned before Christmas.
First test dive with the Trident
This week I received the Trident from OpenROV. I was not expecting it before January, so it was a nice surprise. After getting familiar with the hardware and making all the necessary software updates, I took it on a test dive. I initially wanted to test it in the ocean right by my house but seeing all the kelp floating around made me a little bit anxious. All I wanted to know for this first dive was how hard/easy it was to control the Trident. Until I knew this, getting tangled in kelp didn’t seem like a good idea. So, I went to Thetis Lake instead, a lake few kilometers away from where I leave. There is nothing too exciting in this lake, but at least there were no big waves or kelp. Good conditions to get started.
After about 15 minutes, I was getting used to the controls and was able to go where I wanted in a relatively smooth fashion. The compass, tilt and depth meters on the cockpit display appeared to be essential for navigation. Without these, it would be very easy to get disoriented. The lights are surprisingly powerful and allow to have a good image even at depth where it is very dark. As I expected, there was nothing too crazy to see in the lake. Only a few cans of beer and branches. But at least now I am more comfortable with controlling the Trident.
Next step, the ocean!
The S.E.E. initiative
Back in September, I started to investigate how the Trident underwater drone could be useful for our expedition. I quickly realized that it would not only be a nice tool to have, but would be a complete game changer! Its amazing technology and portability would allow us to deploy the hydrophone array without requiring divers. This is huge, because divers can be expensive and the few that have all the required certifications at the University of Victoria are already very busy with other projects. So, with the Trident, I would be able to deploy much more often and at more locations. Also, I could not stop thinking about how neat it would be to integrate hydrophones to it and perform the acoustic localization right from the Trident.
Having limited funding, I contacted OpenROV to see if they would be willing to collaborate and lend us a Trident. I agree… it was a long shot, but I had to try. And I am so glad I did. Nicole Guintu from OpenROV nicely replied to me and told me about the Science Exploration Education (S.E.E.) Initiative. An initiative where OpenROV is giving away 1,000 Tridents to citizens, educators, researchers and students to monitor and protect marine environments. Say no more! I barely finished Nicole’s emails, that I started the grant application process. Unlike typical academic research grants, the application for the S.E.E. initiative is largely based on how the science and progress are communicated to the public. Being the only scientist in my family, I appreciate the importance of science outreach, and could totally relate to this approach. This Open Explorer expedition page is in fact the very product of the application process.
Few days ago, I received the results from our S.E.E. application and…. WE GOT IT!! Our application was successful, and we will receive a Trident in the coming weeks! I can’t think of a better way to end the year. I am really thankful to Madeleine Foote from Open Explorer and the OpenROV team for their support! Also, thanks to all the people who support me by following this expedition and posting comments! Now, just like a kid, I am counting the number of sleeps until the Trident arrives…
From the backyard to the ocean
It is time to get real and get things wet. The hydrophone and camera array has been sitting in my backyard for few weeks now and it is time to test everything in the ocean!
There are few things I want to know before we start the expedition “for real”. An important one is to see how portable the system is and how easy it is to assemble and deploy it in the field. The goal is to deploy our array at many different places along the coast of British Columbia. So, we need the system to be transportable in a truck or a car and easy to assemble in remote areas. I also want to know if the structure of the array is noisy underwater. If the PVC frame is squeaking whenever there is some current, this would contaminate our measurements and would obviously be a pretty significant issue.
Thanks to my friend John, I got in touch with Ed Wright and Josh Zotzman who work at the Institute of Ocean Sciences in Sidney and were kind enough to let me deploy the array off the Coast Guard dock there. So here we went. Heloise Frouin-Mouy (a bioacoustician at JASCO specialized in pinnipeds, and also my wife as you might have guessed from her name) and Matt Pine (an acoustician colleague at UVic) came along to help me out. The first challenge was to find a way to make everything fit in my car. Let’s say that I don’t really have a big truck, but rather a tiny European-sized car. Nonetheless, after several iterations, we managed to make everything fit! System portability: Check! After a smooth ride to Sidney, we met with Josh and he escorted us to the Coast Guard dock. It took us about an hour to assemble the PVC frame, install the acoustic recorder, and secure the hydrophones and camera. Not bad for a first time! Ease of assembly: Check! Heloise, Josh and I then lowered the array off the dock in about 10 m of water. It took us some time to find out the best way to do this, but at the end it went pretty smoothly. Few things on the frame need to be modified to make the deployment easier, but overall the PVC frame was sturdy enough to handle the deployment. It is always stressful to put all this electronics in the water… Even if I had double checked everything several times, there is always the worry of having forgotten something. Did I close the pressure case of the camera properly? Wait… did I put the waterproof plug back on? Once we left the dock, I just couldn’t stop looking at all the pictures we took and zoom in on every single detail to check that everything was ok. I spent so much time designing and building this array that I really didn’t want to find everything flooded.
We came back the next day to retrieve the instrument and everything worked fine! The camera worked great, so did the acoustic recorder. That was a relief. We even had the privilege to have a small group of harbor porpoise come say hello. I listened to the acoustic recordings and apart from few crabs chomping away at the legs of the structure, the PVC frame did not generate much noise. Quiet frame: check!
This test deployment was successful, and I am very excited to have everything together and working. I am dealing with some administrative/permitting paperwork right now, but very soon this expedition will be underway! We will finally be able to deploy the array off Victoria and start our fish sound cataloging effort. I can’t wait!
Spying scientists listen in on fish conversations
Here is an interview in the CBC Radio show Quirks and Quarks about our research on fish sounds. Disclaimer: I have been tricked into mimicking cat fish sounds... and yes, you can make fun of me ;-)
Things are progressing ! The first field test of the camera was very beneficial and allowed to identify few issues. So, I spent some time modifying the system so it is more stable and can record for longer periods of time. I also had to design a light PVC frame to hold all the instruments together on the seabed. Something that is easy to assemble, carry and repair in the field. It is now built and is sitting in my backyard which, as you can imagine, attracts the curious neighbors.
Things are coming along and I am hopeful that we will be able to start deploying the system in the water soon !
PS: In the video below you can see a simulated observation of 1 male and 2 juveniles fish swimming beside the hydrophone array ;-)
It was a Tuesday morning when I received that email. I must have misunderstood… It just can’t be right.
Since I started to work in underwater acoustics, I have had the privilege to work with many smart and friendly people. People that influenced not only my career but also my personal life. Callum is one of them. I have met him at the Canadian Healthy Oceans Network conference in Ottawa back in 2017. He was presenting some of the work he was doing for his M.Sc. at Memorial University in Newfoundland. His project was quite interesting. He put together a high definition cinema-grade camera system towed on the seabed to map benthic communities off New Brunswick. He was specifically interested in how the distribution of sea potatoes (Boltenia ovifera) was related to the physical properties of the ocean. If sea potatoes are not your thing, believe me, talk to Callum and he will make them be your new favorite animal! His enthusiasm and passion were contagious. We connected right away. When I explained to him the camera system I was trying to put together I could see sparkles in his eyes. Since that day we started to work together. He brought to me his technical expertise and a wealth of experience on camera systems, and I helped him out with some programming he needed to process his images. He is the one who pointed me towards the 110-degrees camera lens I am using now. He is also the one who introduced me to the Trident ROV. In May 2018, we met again in Montreal for the World Conference on Marine Biodiversity. We even shared a room to keep the travel costs down. He was about to finish his M.Sc., just found a dream job in Newfoundland and was moving soon with his girlfriend.
When I received the email that Tuesday morning with the subject line “Callum Mireault”, I immediately thought that Callum wanted to chat about a script I had just sent him. Then, I read more carefully and realized that the message was not from Callum but from Paul Snelgrove, a professor at Memorial University working with him. I kept reading and re-reading the email trying to find the part that I misunderstood. But no, unfortunately, I understood correctly... Paul was announcing that Callum had a heart attack and passed away. He was not even 30.
Still to this day, I have a very hard time wrapping my head around the loss of Callum. This project would not be where it is now without him. He would certainly have been excited to be part of this expedition.
First test of the video camera
Building an autonomous video camera system that can record continuously for several days has been challenging. But things are coming together. We finally tested our first prototype in the field. Tristan took the system out to Madrona Point, close to Nanaimo. He and Courtney, his diving partner, dove and placed the camera prototype and an acoustic recorder at a site covered in Yelloweye and Quillback rockfish.
The test was very successful ! The camera worked well and we gathered data that will allow us to improve the system. Very encouraging! Also very excited to report that we recorded our first rockfish sounds!
A ROV called Trident
For our expedition, one of the great tools that we plan to use is the Trident Remotely Operated Vehicule (ROV) from OpenROV. This is basically the underwater version of a drone. It "flies" through the water and thanks to its integrated camera, let you see and explore the ocean just like if you were diving. Unlike many ROVs, it is small, very portable and can be controlled from shore or from any type of boats (motor boats, kayaks, etc.). This amazing little instrument will be key for many aspects of our expedition.
Searching for good deployment sites. Once we have selected the general location of our study sites, we need to find the perfect spot to deploy our hydrophone and camera array. It needs to be relatively flat for the structure to be stable and close to fish aggregations, so we can capture their sounds. The Trident will be used before the deployment to identify good locations for the array.
Retrieving the hydrophone array. Deploying the hydrophone array on the ocean floor is easy. We just lower it down from the boat with a line. Once the array is on the bottom, we let go one end of the line and pull on the other end to get it back. To retrieve the array, this is more tricky. We need to find a way to attach the line back to the array. We can't leave a surface float on the array like crab or lobster traps because it would make too much noise that would contaminate our acoustic recordings. So, instead we will use the Trident to hook the line back to the array. Just like the video below. Then, we can pull the array back at the surface from the boat using that line. This retrieval technique is efficient, requires only 2 persons and will allow us to deploy in many places around the BC coast.
Cataloging fish sounds. Many fishes like to hide and hang out in rocks and boulders. Unfortunately, due to its size and shape, our hydrophone and camera array can only be deployed in areas where the bottom is relatively flat. So, we will design a small array of 2 or 3 hydrophones that we will attach to the Trident. These hydrophones combined with the camera from the Trident will allow us to catalog fish sounds in much more complex habitats than with the fixed array. This idea is actually not new. Rodney and Francis have already tried to add hydrophones to ROVs almost 10 years ago (see their paper here). But what they found at the time is that regular ROVs are very noisy and make the recording of fish sounds very challenging. With its much smaller and streamlined design, we are very confident that the Trident won't have that problem.
I am so excited to start playing with this really neat ROV!
Localizing fish sounds in 3D
To catalog fish sounds in their environment, we need hydrophones to record sounds and cameras to visually identify the species making them. But what if a fish is making sounds outside the field of view of the camera ? Well, this could be a problem... When we see a fish on the camera, we need to make sure that it is the one making the sounds. This is where the passive acoustic localization comes in.
Imagine yourself in a busy street of a city. Now close you eyes and listen.... The jack hammer across the street from the construction workers, the siren of the ambulance passing by, the bird chirping away above your head, a baby crying in a stroller behind you. Even though you can't see them, you know precisely where all these sounds come from. And all of this is because your ears are few centimeters apart and don't receive the sounds exactly at the same time. Only few microseconds...but this tiny difference is enough for your brain to find out where the sound comes from. For our fish sounds we can use the same principle, except that we use hydrophones instead of our ears and that we are not limited to 2! The more hydrophones you use, the more accurate the localization.
Earlier this year, we published a proof-of-concept paper just showing that. We used data that Rodney had collected several years ago in Cape Cod with 6 hydrophones and a 2 cameras, and were able to localize sounds in 3D and associate them to a fish called the tautog. For our expedition in British Columbia, we will use the same approach. However we can't use the same instruments. The system used in Cape Cod was cabled to a dock and could only record for 2 or 3 hours. For our expedition we need to record for several days at a time and in places that are too far from shore to use cabled instruments. This looks like a detail, but it is actually a fairly big challenge that has kept me busy for some time. Especially for the video camera. There are no video camera systems on the market that can record autonomously for several days (at least at a reasonable price). So, I have been working away on designing a low-cost camera unit based on raspberry Pi computers. First field test to come soon...
HI, why should we care about fish sounds? Listen to my short introduction to the topic.
Meet the team
From the engineering of the instruments, selection of the study sites, to the analysis and interpretation of the data, this expedition touches on many research fields. Each member of the team brings a unique set of skills that is essential for putting all the pieces of the puzzle together.
Xavier Mouy, MSc
Xavier is a PhD student in acoustics at the University of Victoria, Canada, and a project scientist in the environmental consulting company JASCO Applied Sciences. He is leading this expedition as part of his PhD thesis supervised by Dr. Francis Juanes and Dr. Stan Dosso. Xavier comes with 10 years of experience in the industry developing tools for automatically detecting, classifying and localizing marine mammals sounds. He is keen to help making passive acoustics a viable tool for monitoring fish in British Columbia.
Francis Juanes, PhD
Francis is the Liber Ero Chair for Fisheries Research and a Professor at the University of Victoria. He is a specialist on the behaviour, ecology and evolution of fishes and marine invertebrates. His research also includes the use of marine soundscapes as a tool for conservation. He is at the head of many research projects in British Columbia dealing with the impact of noise on endangered southern resident killer whales and their prey. His wealth of knowledge and experience on fish ecology and biology are key for all the phases of this project.
Stan Dosso, PhD
Stan is a Professor in geophysics and ocean acoustics at the University of Victoria and the director of the School of Earth and Oceans Sciences. He is a worldwide expert in Bayesian inverse methods and has developed state-of-the-art algorithms for geoacoustic inversion. He has worked on many different topics ranging from estimating geoacoustic properties of the ocean bottom in the high Arctic, analysing earthquakes off British Columbia, to tracking bowhead whales and walruses using passive acoustics. Stan’s expertise is fundamental for the analysis of the acoustic data collected by our hydrophones.
Rodney Rountree, PhD
Rodney is an independent fish ecologist based in Cape Cod, Massachusetts and visiting scientist in the biology department at the University of Victoria. He is an expert on fish habitat use, behavior and trophic ecology, but you might also know him as the Fish Listener. He is one of the pioneers in the field of fish bioacoustics and has over 20 years experience in the identification and analysis of fish sounds around the world, from piranhas in the Amazon River to haddock in the Gulf of Maine. Rodney brings his expertise with fish sounds and the application of passive acoustics to fisheries science to the team.
Tristan Blaine, BSc
Tristan is a biologist, commercial diver and field lead with the Central Coast Indigenous Resource Alliance (CCIRA). He has extensive field experience and spends most of his time underwater surveying rockfish, herring and crab habitat. He knows more than anyone else where to find the different species of fish in British Columbia. His knowledge of the coastal waters of British Columbia and his field experience are essential for selecting our study sites and facilitating the logistics of the expedition.
To identify fish sounds to specific species and behavior, we need to have our eyes and ears underwater. We need to know exactly where the sounds come from to pin-point which fish is producing them. Acoustic recorders equipped with hydrophones can be used as our ears and underwater video cameras as ours eye. Using several hydrophones, we can precisely localize the origin of the sounds in three dimensions.
Due to the complexity and the diversity of fish habitats, two different instrument systems will be used. For areas with a relatively flat seafloor, we will use a compact autonomous array composed of 6 hydrophones and 2 underwater cameras. This fixed system will be deployed on the seafloor for up to 1 week at each location. For steep seafloor slopes and complex habitats such as boulders, we will use a Trident ROV equipped with 2 hydrophones. This mobile platform will be employed for short-term missions (few hours).
There are several technical challenges associated with this project. For the fixed observing platform, one of the biggest challenges is that there are no off-the-shelf autonomous camera systems that can record for several days in a row. Consequently, we will design our own using a low-cost Raspberry Pi single board computer. For the mobile platform, the challenges reside in integrating the hydrophones to the Trident ROV.
Currently, we are building a prototype of underwater camera (pressure housing and electronics) and will be testing it in the next few days.
Photo by Tristan Blaine
“Prrrrr… thump… thump… brrrrr…”, these are the sounds you can hear in the coastal waters of British Columbia. Sounds the fish can make to scare away predators or attract mates. Yes, you read correctly, fish make sounds! And it has been known for a very long time. Aristotle was already describing these intriguing sounds in the 4th Century BC. Despite this, we still don’t know very much about the different types of sounds fish make and what they use them for. Currently, we know that about 800 species of fishes worldwide produce sounds. Among the approximately 400 known marine fish species frequenting the waters of British Columbia, only 22 have been reported to produce sounds so far. It is believed that many more of these species produce sounds, but their acoustic repertoires have not been identified yet and this is exactly what this project is about: Exploring the coastal waters of British Columbia to record and identify the sounds produced by the various fish species frequenting these waters.
Why do we care? The fish sound catalog we are building will allow us to monitor fishes over long time periods and large geographic areas in a completely non-intrusive manner, just by listening to the ocean. This will constitute an important tool for marine conservation and fisheries management.
How will we proceed? Fish don’t behave the same in a fish tank as in the wild. This is why we will record fish sounds directly in their natural environment by deploying a combination of hydrophones and underwater cameras. We will use two types of instruments: 1) a compact autonomous array composed of 6 hydrophones (underwater microphones) and 2 underwater video cameras deployed on the ocean floor for several days at a time; and 2) a Trident ROV from OpenROV equipped with 2 hydrophones to perform short term missions. Our expedition will start in the Salish Sea and move progressively northward towards Prince Rupert.
Photo by Tristan Blaine
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