Month: December 2023

GEMM Lab 2023: A Year in the Life

Edited by Rachel Kaplan* & Lisa Hildebrand**

* PhD student, OSU College of Earth, Ocean, and Atmospheric Sciences and Department of Fisheries, Wildlife, and Conservation Sciences (FWCS), Geospatial Ecology of Marine Megafauna (GEMM) Lab

** PhD candidate, OSU Department of Fisheries, Wildlife, and Conservation Sciences (FWCS), Geospatial Ecology of Marine Megafauna (GEMM) Lab

Another year has come and gone, and the GEMM Lab has expanded and accomplished in many facets! Every year it gets just a little bit harder to succinctly summarize all of the research, outreach, and successes that the GEMMs accomplish and this year we are trying something a little different for our Year in the Life tradition. Rather than summarizing what the GEMM Lab has been up to thematically, we have decided to let everyone tell you their 2023 recap in their own words. So, snuggle up with your favorite holiday drink and enjoy our 8th edition of the Year in the Life!

Leigh

As the captain at the helm of the GEMM Lab ship, Leigh plays a major role in all of our accomplishments and celebrates them right along with us. She returned to Oregon after a very well-deserved, refreshing and reflective sabbatical in New Zealand, where she spent three months traveling the north and south islands with her family. One highlight of her trip was when Leigh went paddleboarding in Tarakena Bay and was surrounded by common dolphins the whole time, swimming around her and making eye contact! Almost immediately after her sabbatical, Leigh headed to the lagoons in Baja with Clara, which kick-started a busy year of field work as Leigh oversaw six different projects that involved field work throughout the year. In early summer, Leigh hosted her graduate advisor Dr. Andy Read as part of the OSU Hatfield Marine Science Center’s Lavern Weber Visiting Scientist program. Andy spent a jam-packed 10 days in Oregon, which included many meetings with Leigh and each GEMM project team as well as a fantastic first day on the water for the GRANITE project where Andy was introduced to the beloved PCFG gray whales! Another huge accomplishment for 2023 was Leigh’s successful funding application to the National Science Foundation for the SAPPHIRE project with Dawn and KC (more below), which will see the team head off for more blue whale research in New Zealand in January 2024!

Ale

For postdoctoral scholar Alejandro A. Fernández Ajó, a big highlight of 2023 was the 61 fecal samples from 25 individual gray whales collected by the GRANITE team, with most samples originating from known whales that regularly visit the Oregon coast. This presents a unique opportunity to study changes and track these individual whales across seasons and years, allowing us to observe variations in their reproductive health, body condition, and responses to stressors such as vessel noise and entanglements. Currently, Alejandro is back at his graduate institute, Northern Arizona University (NAU), conducting lab work to analyze these fecal samples. Monitoring endocrine biomarkers (hormones) enables us to understand how Pacific Coast Feeding Group (PCFG) whales respond to stressors, providing insights into different aspects of the PCFG gray whale’s biology and physiology. 

In addition, Alejandro led research this year that assessed diagnostic tools for non-invasive pregnancy diagnosis, and proposed a methodological approach for identifying pregnancies in gray whales. He also taught as a guest lecturer in the grad-level course ‘Conservation Physiology’ at NAU and started mentoring Camila Muñoz Moreda, a PhD student in Argentina, investigating stressors impacting Southern Right Whales’ health in Patagonia. Alejandro was also invited and awarded a travel grant to participate in a workshop to be held in Kruger, South Africa, where a group of 20 leading experts will gather to discuss research approaches and resources that are needed for future comparative physiology research in a changing world.

Allison

Master’s student Allison Dawn started the year off by taking two challenging SCUBA courses, first honing skills like underwater navigation and completing a 100 ft dive in the Hood Canal as part of Advanced Diving. Her favorite memory was seeing a Giant Pacific Octopus with dive buddy and fellow MMI marine scientist Kyra Bankhead! Next, Allison passed her Rescue Dive training where she learned best practices for effective rescue & emergency response while working in the water. During this time, she also completed her Master’s thesis, titled “Intermittent upwelling impacts zooplankton and their gray whale predators at multiple scales” which she successfully defended this past June. Afterwards, Allison led another successful field season in Port Orford for the 9th consecutive year of the TOPAZ/JASPER projects, where she mentored two high school students, one undergraduate SCUBA diver, and one NSF REU undergrad. Read their individual blogs and all about the exciting season here! 

Clara

2023 started off with a big data processing milestone for Clara – she finished annotating all seven years of drone footage for her PhD! She started working on this in her first year, so to finally have her completed dataset was momentous – and meant that she could get to work on analysis and writing. While nothing is yet published, her first chapter is under review and the second and third are both underway. She also presented the results of her first chapter, focused on individual specialization in PCFG gray whale foraging behaviors, at the Animal Behavior Society conference in July. In addition, Clara’s former REU intern, Celest Sorrentino, was in attendance, and Clara enjoyed mentoring Celest through her first scientific conference. Actually, Celest came back for the whole summer as a research assistant, processing data from Clara and Leigh’s trip to Baja California Sur, Mexico in March (read about Celest’s summer here). 

Clara also taught her photogrammetry lab for Renee Albertson’s marine megafauna course for the fourth year in a row and gave outreach talks for the American Cetacean Society Oregon Chapter and the Cape Perpetua Land Sea Symposium. And an update wouldn’t be complete without mentioning field work! Clara participated in the GRANITE project’s eighth field season (her fourth). An absolute highlight was her trip to Baja with Leigh where she collected incredible drone footage and crossed paths with a known whale to the GEMM lab, Pacman! As she works through the final year of her PhD, Clara is excited to continue exploring this incredible behavior data set and learning more about these whales!

Dawn

Through the EMERALD project, postdoctoral scholar Dawn Barlow has been busy examining habitat use, distribution, and abundance of gray whales and harbor porpoises in the Northern California Current over three decades. This project has documented long-term hotspots in gray whale habitat, illustrated regional differences in overlap between harbor porpoises and different fish species, and explored the importance of upwelling dynamics for these nearshore cetaceans. Dawn presented findings at the Effects of Climate Change on the World’s Ocean (ECCWO) conference in Bergen, Norway, which was a fruitful opportunity to connect with researchers from around the world and across disciplines. 

More exciting news came in spring 2023, when a GEMM Lab team was granted funding from the National Science Foundation for the project “Marine Predator and Prey Response to Climate Change: Synthesis of Acoustics, Physiology, Prey, and Habitat in a Rapidly Changing Environment (SAPPHIRE)”. Through the SAPPHIRE project, we will examine how changing ocean conditions affect the availability and quality of krill, and thus impact blue whale behavior, health, and reproduction. Dawn and the team are busily preparing to head to Aotearoa New Zealand to find krill and blue whales for our first field season in January!

Throughout 2023, Dawn also had the opportunity to conduct fieldwork here in our Oregon backyard aboard the R/V Pacific Storm for the HALO project, in the skies aboard USCG helicopters for the OPAL project, and as chief scientist of a research cruise for the MOSAIC project. She also had the pleasure of working with undergraduate student Mariam Alsaid to document the occurrence patterns of the little-studied sei whale in Oregon waters. The fifth and final chapter of her PhD was published in early 2023, wrapping up a decade of research on New Zealand blue whales through the OBSIDIAN project. In December, a collaborative study led by Dawn was published comparing blue whale morphology and oceanography of foraging grounds in California, New Zealand, and Chile. As 2023 comes to a close with various projects nearing completion, in full swing, and just beginning, Dawn looks forward to what 2024 will bring!

Kate

For Master’s student Kate Colson, a highlight of 2023 was teaching an introductory science class to first year undergraduate students at University of British Columbia (UBC). After shaping these young minds, she headed south and moved to Newport to be a part of the GRANITE field team and reunite with the PCFG gray whales! Kate spent the summer working to process the season’s CATS tag deployments, and successfully defended her Master’s thesis in August. After spending the fall turning her thesis chapters into manuscripts, she submitted her first scientific paper, and will be ready to submit her second early in the new year! And, after another season of beautiful Oregon beach walks, Kate finally found a trophy agate from the Oregon coast (see photo). Kate recently moved back to the east coast and has started a new research assistant job working with Dtag data, further developing the tag analysis skills she learned in her master’s program. 

KC

This year was productive on many levels for postdoctoral scholar KC Bierlich! He published seven research papers, with an additional three currently in review, and was fortunate enough to receive several funding awards from a) the Marine Mammal Commission, supporting GRANITE fieldwork for the next two years, b) the National Science Foundation, funding the GEMM Lab’s new SAPPHIRE project, and c) the Office of Naval Research. This last grant will support KC launching MMI’s Center of Drone Excellence (CODEX), which focuses on developing analytical tools for processing and analyzing drone imagery, including user-friendly hardware and software. Some early highlights from CODEX includes major updates to the photogrammetry software MorphoMetriX and CollatriX, and the development of LidarBoX, a 3D printed altimeter hardware system that can attach to several types of commercial drones and help improve the accuracy of altitude measurements. 

KC mentored seven students this year (two high school, two masters, and three undergraduates), and was awarded the “Excellence in Undergraduate Research Mentoring by a Postdoc” by OSU. He had a busy summer with another great GRANITE field season, and partnered with the Innovation Lab (iLab) at HMSC to develop a system for dropping tags onto whales using drones. The team successfully tested this tagging system on a stand-up paddle board, and next will employ the tags while studying Pygmy blue whales in January and February for SAPPHIRE. And most importantly, KC became a dad; Caroline Marie Bierlich was born in early September. KC and Colette have been absolutely overjoyed with their new role as parents! 

Lisa

A big milestone was reached by Lisa in the first quarter of 2023 when she successfully passed her written and oral exams, allowing her to advance to PhD candidacy! Her committee members gave Lisa lots of food for thought in the many scientific papers and book chapters assigned to her during her study period, ranging in topic from Bayesian ecological modeling to baleen whale energetics to Pacific Ocean oceanographic dynamics to foundational foraging theory, all of which will help Lisa as she now works to accomplish her proposed PhD research in the next couple of years. Lisa was once again part of the GRANITE field team this summer, providing her the opportunity to spend over 130 magical hours with the beloved (and by now very well known to the team) PCFG gray whales! Together with KC, Lisa greatly enjoyed mentoring two high school interns, Hali Peterson and Isaac Cancino, during the summer as they assisted her with zooplankton identification and sorting. Hali, who lives and goes to school close to Newport, has continued working with Lisa for the GEMM Lab into the fall, helping with a number of tasks. Lisa was involved in five publications this year, of which she is probably most proud of the paper published in Current, the Journal of Marine Education, where together with Leigh and Tracy Crews (the Associate Director for Education at the Oregon Sea Grant’s STEM Hub), she laid out the roadmap, successes, and hurdles associated with JASPER, the STEM component of the paired TOPAZ/JASPER projects in Port Orford, Oregon. The project has graduated a total of 31 students and Lisa is immensely proud to have been part of this project that will forever remain near and dear to her heart.

Marissa 

PhD student Marissa Garcia’s memories of the year take her back to early mornings driving down the Pacific Coast Highway, the Pacific Ocean as the backdrop to her daily commute to the Hatfield Marine Science Center. For Marissa, the highlight of 2023 was the extended stay — or “PhD sabbatical” — she carved out of the routine summer fieldwork for the HALO Project. Following a July crash course in modeling with Dawn, Soléne, and Leigh, Marissa implemented an oceanographic analysis to share at the Acoustics 23 conference in Sydney, Australia in December. Another highlight from her year was co-organizing the oral session “All Ears In: Advancing Ecology and Conservation with Bioacoustics” at the Ecological Society of America conference over the summer. Earlier in the year, Marissa was selected as an NSF GRFP Fellow as well as an Animal Bioacoustics representative for the Acoustical Society of America’s Student Council. Marissa is proud of the skillsets she gained this year: wrangling large acoustic data sets, running click detectors, wading through oceanographic variables, and setting her sights on species distribution modeling. This upcoming year, she looks forward to challenging herself to grow even more!

Nat

Although new PhD student Natalie Chazal is ending this year at Oregon State University, she actually started 2023 at North Carolina State University, where she defended her Master’s thesis in the spring. Over the summer, Nat submitted both of her thesis chapters for publication, and then moved to Oregon, spending a couple weeks in Newport where she got a taste of fieldwork in the GEMM Lab. During the fall term, Nat took Bayesian statistics with MMI professor Josh Stewart, where she dug into zooplankton tow data from the past 3 years of GRANITE work. She also took a few orientation courses that helped her understand the resources available at OSU and how to best prepare for the journey ahead. In between all of her classwork, TA grading, and research, she has explored the Pacific Northwest with hikes to Mount St. Helens and Mount Hood, birding on Mary’s Peak and Yaquina Head Outstanding Natural Area, and visiting waterfalls near Portland and Silver Falls State Park.

Rachel 

2023 was a far-ranging year for PhD student Rachel Kaplan! Skipping out on the beautiful Oregon summer, she instead spent a six-month winter field season at Palmer Station, the smallest of the U.S. research bases in Antarctica. Working with her CEOAS co-advisor Kim Bernard and undergraduate student Abby Tomita, Rachel loved studying Antarctic krill through at-sea fieldwork and long-term experiments, with plenty of crafting and skiing through the long polar night. Now, she is thrilled to be back with her Oregon krill and labmates. Rachel is happy to be closing out the year with the acceptance of her first PhD chapter for publication, and is excited for all that 2024 will hold!

Solène

After almost three years of working remotely as a postdoctoral scholar, Solène Derville finally made it to Oregon! She spent a year in Newport, mainly working on the OPAL and SLATE projects that address the issue of whale entanglements off the coast of Oregon. Solène contributed to several GEMM Lab milestones this year, including finalizing the first phase of OPAL with a publication of a study investigating how the exposure of rorqual whales to Dungeness crab fishing gear varies in time and space (Derville et al. 2023 in Biological Conservation) and publishing an isotope-based analysis of southern right whale feeding ground distribution over the whole Southern Ocean (Derville et al. 2023 in PNAS). Being in Newport in person offered a lot more opportunities to participate in fieldwork (April STEM cruises, September NCC cruise, small-boat rorqual whale biopsy and photo-ID work) and academic life (co-teaching a graduate course on the Spatial Ecology of Marine Megafauna with Leigh and Dawn). She also got to explore the marvels of Oregon’s amazing outdoors… from climbing at Smith Rock, or skiing in the cascades, to hanging out with blue whales… all in the good company of GEMM Lab friends!

Dear reader…

Thank you, dear reader, for taking the time to review the year with us! You have once again been awesome, supportive viewers of our blog, with a whopping 25,893 views of our blog this year!! We wish you all restful, happy, and most importantly, healthy holidays, and hope you will join us again in 2024!

The GEMM Lab with their white elephant gifts during our annual holiday party

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El Niño de Navidad: What is atmospheric Santa Claus bringing to Oregon krill and whales?

By Rachel Kaplan, PhD student, Oregon State University College of Earth, Ocean, and Atmospheric Sciences and Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Early June marked the onset of El Niño conditions in the Pacific Ocean , which have been strengthening through the fall and winter. For Oregonians, this climate event means unseasonably warm December days, less snow and overall precipitation (it’s sunny as I write this!), and the potential for increased wildfires and marine heatwaves next summer.

This phenomenon occurs about every two to seven years as part of the El Niño Southern Oscillation (ENSO), a cyclical rotation of atmospheric and oceanic conditions in the Pacific Ocean that is initiated by departures from and returns to “normal conditions” at the equator. Typically, the trade winds blow warm water west along the equator, and El Niño occurs when these winds weaken or reverse. As a result, the upwelling of cold water at the equator ceases, and warm water flows towards the west coast of the Americas, rather than its typical pathway towards Asia. When the trade winds resume their normal direction, usually after months or a year, the system returns to “normal” conditions – or, it can enter the cool La Niña part of the cycle, in which the trade winds are stronger than normal. “El Niño de Navidad” was named by South American fisherman in the 1600s because this event tends to peak in December – and El Niño is clearly going to be a guest for Christmas this year.

Figure 1. Maps of sea surface temperature anomalies show Pacific Ocean conditions during a strong La Niña (top) and El Niño (bottom). Source: NOAA climate.gov

These events at the equator trigger changes in global atmospheric circulation patterns, and they can shape weather around the world. Teleconnection, the coherence between meteorological and environmental phenomena occurring far apart, is to me one of the most incredible things about the natural world.  This coherence means that the biological community off the Oregon coast is strongly impacted by events initiated at the equator, with consequences that we don’t yet fully understand.

The effects of El Niño are diverse – floods in some places, droughts in others – and their onset can mean wildly different things for Oregon, Peru, Alaska, and beyond. As we tap our fingers waiting to be able to ski and snowboard in Oregon, what does our current El Niño event mean for the life in the waters off our coast?

Figure 2. Anomalous conditions at the equator qualified as an El Niño event in June 2023.

ENSO plays a big role in the variability in our local Northern California Current (NCC) system, and the outcomes of these events can differ based on the strength and how the signal propagates through the ocean and atmosphere (Checkley & Barth, 2009). Large-scale “coastal-trapped” waves flowing alongshore can bring the warm water signal of an El Niño to our ocean backyard in a matter of weeks. One of the first impacts is a deepening of the thermocline, the upper ocean’s steep gradient in temperature, which changes the cycling of important nutrients in the surface ocean. This can result in a decrease in upwelling and primary productivity that sends ramifications through the food web, including consequences for grazers and predators like zooplankton, marine mammals, and seabirds (Checkley & Barth, 2009).

In addition to these ecosystem effects that result from local changes, the ocean community can also receive new visitors from afar, and see others flee . For krill, the shrimp-like whale prey that I spend a lot of my time thinking about, community composition can change as subtropical species typically found off southern and Baja California are displaced by horizontal ocean flow, or as resident species head north (Lilly & Ohman, 2021).

Figure 3. This Euphausia gibboides krill is typically found in offshore subtropical habitats but moves north and inshore during El Niño events, and tends to persist awhile in these new environments, impacting the local zooplankton community. Source: Solvn Zankl

The two main krill species that occur in the NCC, Euphausia pacifica and Thysanoessa spinifera, favor the cool, coastal waters typical off the coast of Oregon. During El Niño events, E. pacifica tends to contract its distribution inshore in order to continue occupying these conditions, increasing its spatial overlap with T. spinifera (Lilly & Ohman, 2021). In addition, both tend to shift their populations north, toward cooler, upwelling waters (Lilly & Ohman, 2021).

These krill species are a favored prey of rorqual whales, and the coast of Oregon is an important foraging ground for humpback, blue, and fin whales. Predators tend to follow their prey, and shifting distributions of these krill species may cause whales to move, too. During the 2014-2015 “Blob” event in the Pacific Ocean, a marine heatwave was exacerbated by El Niño conditions. Humpback whales in central California shifted their distributions inshore in response to sparse offshore krill, increasing their overlap with fishing gear and leading to an increase in entanglement events (Santora et al., 2020). Further north, these conditions even led humpback whales to forage in the Columbia River!

Figure 4. In September 2015, El Niño conditions led humpback whales to follow their prey and forage in the Columbia River.

As El Niño events compound with the impacts of global climate change, we can expect these distributional shifts – and perhaps surprises – to continue. By the year 2100, the west coast habitat of both T. spinifera and E. pacifica will likely be constrained due to ocean warming – and when El Niños occur, this habitat will decrease even further (Lilly & Ohman, 2021). As a result, the abundances of both species are expected to decrease during El Niño events, beyond what is seen today (Lilly & Ohman, 2021). This decline in prey availability will likely present a problem for future foraging whales, which may already be facing increased environmental challenges.

Understanding connections is inherent to the field of ecology, and although these environmental dependencies are part of what makes life so vulnerable, they can also be a source of resilience. Although humans have known about ENSO for over 400 years, the complex interplay between nature, anthropogenic systems, and climate change means that we are still learning the full implications of these events. Just as waiting for Santa Claus always keeps kids guessing, the dynamic ocean keeps surprising us, too.

References

Checkley, D. M., & Barth, J. A. (2009). Patterns and processes in the California Current System. Progress in Oceanography, 83(1–4), 49–64. https://doi.org/10.1016/j.pocean.2009.07.028

Lilly, L. E., & Ohman, M. D. (2021). Euphausiid spatial displacements and habitat shifts in the southern California Current System in response to El Niño variability. Progress in Oceanography, 193, 102544. https://doi.org/10.1016/j.pocean.2021.102544

Santora, J. A., Mantua, N. J., Schroeder, I. D., Field, J. C., Hazen, E. L., Bograd, S. J., Sydeman, W. J., Wells, B. K., Calambokidis, J., Saez, L., Lawson, D., & Forney, K. A. (2020). Habitat compression and ecosystem shifts as potential links between marine heatwave and record whale entanglements. Nat Commun, 11(1), 536. https://doi.org/10.1038/s41467-019-14215-w

Sonar savvy: using echo sounders to characterize zooplankton swarms

By Natalie Chazal, PhD student, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

I’m Natalie Chazal, the GEMM Lab’s newest PhD student! This past spring I received my MS in Biological and Agricultural Engineering with Dr. Natalie Nelson’s Biosystems Analytics Lab at North Carolina State University. My thesis focused on using shellfish sanitation datasets to look at water quality trends in North Carolina and to forecast water quality for shellfish farmers in Florida. Now, I’m excited to be studying gray whales in the GEMM Lab!

Since the beginning of the Fall term, I’ve jumped into a project that will use our past 8 years of sonar data collected using a Garmin echo sounder during the GRANITE project work with gray whales off the Newport, OR coast. Echo sounder data is commonly used recreationally to detect bottom depth and for finding fish and my goal is to use these data to assess relative prey abundance at gray whale sightings over time and space. 

There are also scientific grade echo sounders that are built to be incredibly precise and very exact in the projection and reception of the sonar pulses. Both types of echosounders can be used to determine the depth of the ocean floor, structures within the water column, and organisms that are swimming within the sonar’s “cone” of acoustic sensing. The precision and stability of the scientific grade equipment allows us to answer questions related to the specific species of organisms, the substrate type at the sea floor, and even animal behavior. However, scientific grade echo sounders can be expensive, overly large for our small research vessel, and require expertise to operate. When it comes to generalists, like gray whales, we can answer questions about relative prey abundances without the use of such exact equipment (Benoit-Bird 2016; Brough 2019). 

While there are many variations of echo sounders that are specific to their purpose, commercially available, single beam echo sounders generally function in the same way (Fig. 1). First, a “ping” or short burst of sound at a specific frequency is produced from a transducer. The ping then travels downward and once it hits an object, some of the sound energy bounces off of the object and some moves into the object. The sound that bounces off of the object is either reflected or scattered. Sound energy that is either reflected or scattered back in the direction of the source is then received by the transducer. We can figure out the depth of the signal using the amount of travel time the ping took (SeaBeam Instruments 2000).

Figure 1. Diagram of how sound is scattered, reflected, and transmitted in marine environments (SeaBeam Instruments, 2000).

The data produced by this process is then displayed in real-time, on the screen on board the boat. Figure 2 is an example of the display that we see while on board RUBY (the GEMM Lab’s rigid-hull inflatable research boat): 

Figure 2. Photo of the echo sounder display on board RUBY. On the left is a map that is used for navigation. On the right is the real time feed where we can see the ocean bottom shown as the bright yellow area with the distinct boundary towards the lower portion of the screen. The more orange layer above that, with the  more “cloudy” structure  is a mysid swarm.

Once off the boat, we can download this echo sounder data and process it in the lab to recreate echograms similar to those seen on the boat. The echograms are shown with the time on the x-axis, depth on the y-axis, and are colored by the intensity of sound that was returned (Fig. 3). Echograms give us a sort of picture of what we see in the water column. When we look at these images as humans, we can infer what these objects are, given that we know what habitat we were in. Below (Fig. 3) are some example classifications of different fish and zooplankton swarms and what they look like in an echogram (Kaltenberg 2010).

Figure 3. Panel of echogram examples, from Kaltenberg 2010, for different fish and zooplankton aggregations that have been classified both visually (like we do in real time on the boat) as well as statistically (which we hope to do with the mysid aggregations). 

For our specific application, we are going to focus on characterizing mysid swarms, which are considered to be the main prey target of PCFG whales in our study area. With the echograms generated by the GRANITE fieldwork, we can gather relative mysid swarm densities, giving us an idea of how much prey is available to foraging gray whales. Because we have 8 years of GRANITE echosounder data, with 2,662 km of tracklines at gray whale sightings, we are going to need an automated process. This demand is where image segmentation can come in! If we treat our echograms like photographs, we can train models to identify mysid swarms within echograms, reducing our echogram processing load. Automating and standardizing the process can also help to reduce error. 

We are planning to utilize U-Nets, which are a method of image segmentation where the image goes through a series of compressions (encoders) and expansions (decoders), which is common when using convolutional neural nets (CNNs) for image segmentation. The encoder is generally a pre-trained classification network (CNNs work very well for this) that is used to classify pixels into a lower resolution category. The decoder then takes the low resolution categorized pixels and reprojects them back into an image to get a segmented mask. What makes U-Nets unique is that they re-introduce the higher resolution encoder information back into the decoder process through skip connections. This process allows for generalizations to be made for the image segmentation without sacrificing fine-scale details (Brautaset 2020; Ordoñez 2022; Slonimer 2023; Vohra 2023).

Figure 4. Diagram of the encoder, decoder architecture for U-Nets used in biomedical image segmentation. Note the skip connections illustrated by the gray lines connecting the higher resolution image information on the left, with the decoder process on the right (Ronneberger 2015)

What we hope to get from this analysis is an output image that provides us only the parts of the echogram that contain mysid swarms. Once the mysid swarms are found within the echograms, we can use both the intensity and the size of the swarm in the echogram as a proxy for the relative abundance of gray whale prey. We plan to quantify these estimates across multiple spatial and temporal scales, to link prey availability to changing environmental conditions and gray whale health and distribution metrics. This application is what will make our study particularly unique! By leveraging the GRANITE project’s extensive datasets, this study will be one of the first studies that quantifies prey variability in the Oregon coastal system and uses those results to directly assess prey availability on the body condition of gray whales. 

However, I have a little while to go before the data will be ready for any analysis. So far, I’ve been reading as much as I can about how sonar works in the marine environment, how sonar data structures work, and how others are using recreational sonar for robust analyses. There have been a few bumps in the road while starting this project (especially with disentangling the data structures produced from our particular GARMIN echosounder), but my new teammates in the GEMM Lab have been incredibly generous with their time and knowledge to help me set up a strong foundation for this project, and beyond. 

References

  1. Kaltenberg A. (2010) Bio-physical interactions of small pelagic fish schools and zooplankton prey in the California Current System over multiple scales. Oregon State University, Dissertation. https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/z890rz74t
  2. SeaBeam Instruments. (2000) Multibeam Sonar Theory of Operation. L-3 Communications, East Walpole MA. https://www3.mbari.org/data/mbsystem/sonarfunction/SeaBeamMultibeamTheoryOperation.pdf
  3. Benoit-Bird K., Lawson G. (2016) Ecological insights from pelagic habitats acquired using active acoustic techniques. Annual Review of Marine Science. https://doi.org/10.1146/annurev-marine-122414-034001
  4. Brough T., Rayment W., Dawson S. (2019) Using a recreational grade echosounder to quantify the potential prey field of coastal predators. PLoS One. https://doi.org/10.1371/journal.pone.0217013
  5. Brautaset O., Waldeland A., Johnsen E., Malde K., Eikvil L., Salberg A, Handegard N. (2020) Acoustic classification in multifrequency echosounder data using deep convolutional neural networks. ICES Journal of Marine Science 77, 1391–1400. https://doi.org/10.1093/icesjms/fsz235
  6. Ordoñez A., Utseth I., Brautaset O., Korneliussen R., Handegard N. (2022) Evaluation of echosounder data preparation strategies for modern machine learning models. Fisheries Research 254, 106411. https://doi.org/10.1016/j.fishres.2022.106411
  7. Slonimer A., Dosso S., Albu A., Cote M., Marques T., Rezvanifar A., Ersahin K., Mudge T., Gauthier S., (2023) Classification of Herring, Salmon, and Bubbles in Multifrequency Echograms Using U-Net Neural Networks. IEEE Journal of Oceanic Engineering 48, 1236–1254. https://doi.org/10.1109/JOE.2023.3272393
  8. Ronneberger O., Fischer P., Brox T. (2015) U-Net: Convolutional Networks for Biomedical Image Segmentation. https://doi.org/10.48550/arXiv.1505.04597