A Master’s odyssey: Decoding gray whale foraging energetics with high-resolution tag data

By: Kate Colson, MSc Oceans and Fisheries, University of British Columbia, Institute for the Oceans and Fisheries, Marine Mammal Research Unit

When I wrote my first blog a year ago, I was just starting to dig into the field work and data analysis I had loftily proposed for my graduate degree. Now I am writing to you as a new Master of Science! A little more than a month ago, I successfully defended my thesis research where I used the data from minimally invasive high-resolution accelerometry suction cup tags deployed by the GEMM Lab to estimate the relative energetic cost of different foraging behaviors (see my first blog) of Pacific Coast Feeding Group (PCFG) gray whales that forage during summer months off the coast of Oregon. I learned a lot of new skills through this research project and am excited to share some of my odyssey with you.

To start, I want to highlight the technology that made this work possible: the high-resolution accelerometry suction cup tags. These suction cup tags not only record fine scale data about the whale’s movement and behavior from inertial sensors like accelerometers, magnetometers and gyroscopes, the tags also incorporate video and audio data to record what the whale is seeing and hearing in its environment. I used the data from these tags to achieve two research objectives relating to 1) describing foraging behavior of PCFG gray whales and 2) estimating the relative energetic cost of these behaviors. 

Through the hard work of the GEMM Lab field team and collaborators John Calambokidis and Dr. Dave Cade, 10 of these high-resolution accelerometry tags were deployed to collect approximately 91.5 hours of data from PCFG gray whales. Excitingly, two of these tags were deployed on a known mother-daughter pair on the same day. The mother and her 8-year-old daughter were even observed foraging together while tagged later in the day and recorded each other while feeding (Figure 1)! 

My first research objective was to quantitatively describe the foraging behaviors of PCFG gray whales. These quantitative descriptions exist for other baleen whale foraging behaviors, such as the lunge feeding behavior of rorqual whales (e.g., humpback, fin, and blue whales) where large mouthfuls of prey are engulfed, or the ram filtration feeding of bowhead and right whales where water is filtered for prey as the whale swims along with its mouth open. High-resolution accelerometry tag data has found that a strong acceleration signal is useful for detecting lunges (Goldbogen et al., 2013) and continuous fluking paired with low swim speeds signal the occurrence of ram filtration feeding (Simon et al., 2009). However, gray whales are the only baleen whales to use suction feeding behavior where the whale rolls to one side and sucks up water to filter for prey. Beyond describing side preferences when performing suction feeding (Woodward & Winn, 2006), this unique foraging behavior of gray whales lacks quantitative descriptions. My thesis works to add quantitative descriptions of gray whale suction feeding to the existing descriptions of baleen whale foraging behavior using high-resolution tag data. Based on previous drone focal follows that qualitatively describe gray whale foraging behaviors (Torres et al., 2018), I hypothesized that body position variables would be important for quantitatively describing PCFG gray whale foraging tactics using tag data. I anticipated that the signals of gray whale suction feeding behavior would be different from the signals of lunge and ram filtration feeding performed by other species of baleen whales (Figure 2).

Figure 1. Snapshots from the video footage of high-resolution accelerometry suction cup tags deployed on a mother-daughter pair of whales foraging together. The top photo is from the tag deployed on the daughter filming the mother, and the bottom photo is from the tag deployed on the mother filming the daughter. 
Figure 2. Quantitative descriptions of foraging behaviors for different baleen whale feeding mechanisms. The left panel indicates the strong acceleration signal used to detect lunges of rorquals (e.g., humpback, fin, and blue whales). The acceleration figure is adapted from Izadi et al., (2022). The middle panel shows the continuous fluking and low swim speed signal for ram filtration feeding of bowheads (Simon et al., 2009). The right panel indicates the hypothesized importance of body position variables when quantitatively describing the unique suction feeding behavior of gray whales (my thesis). 

My second objective was to estimate the relative energetic cost of PCFG gray whale foraging behaviors. Previous research has estimated the energetic cost of gray whale broad state behaviors (e.g., transit, search, and forage) using respiration rates (Sumich, 1986). However, respiration rates are difficult to use when estimating the energetic cost of fine scale behaviors, like the precise foraging tactics performed within a dive. Therefore, I calculated biologging-derived proxies of energy expenditure from the tag data such as stroke rate (i.e., the frequency of the whale’s fluke beats) and Overall Dynamic Body Acceleration (ODBA; i.e., the total body movement of the whale) to estimate the relative energetic cost of three different PCFG gray whale foraging tactics: benthic dig, headstand, and side swim. To put these energy expenditure proxies into a human example, if you were walking, your stroke rate would be the frequency of your steps and your ODBA would be all the acceleration of your body including your legs moving with each step, your swinging arms, and turning head. Stroke rate and ODBA are common proxies of energy expenditure that are easily calculated from biologging tag data and have been linked to metabolic rate in many species, including bottlenose dolphins (Allen et al., 2022) and fur seals (Jeanniard-Du-Dot et al., 2016). 

When comparing these two proxies of energy expenditure between PCFG gray whale foraging tactics, I expected that the benthic dig foraging behavior would be the least energetically costly compared to the other PCFG foraging tactics. Benthic digs occur when the whale is rolled onto its side and plows through the sediment to suction up prey while leaving feeding pits on the seafloor. Benthic digs are assumed to be the primary foraging tactic of the majority of the gray whale population (Nerini, 1984) that feed in the Arctic and sub-Arctic region where gray whales must dive deeper to reach their prey in the bottom sediments, making it likely that a lower energetic cost of foraging motivates the higher use of this foraging tactic. Excitingly, preliminary results indicate that these three gray whale foraging tactics have different energy expenditures, which can potentially help explain patterns of behavior choice and tactic usage between different groups of gray whales. My thesis research is a foundational step toward better understanding gray whale foraging energetics by providing a means to assess prey requirements and inform management policies to reduce threats facing the PCFG gray whales. For example, previous work has shown that vessel disturbance reduces the searching time (Sullivan & Torres, 2018) and increases the stress levels (Lemos et al., 2022) of PCFG gray whales. My work builds on this by demonstrating an elevated energetic cost of some foraging tactics that could be used to support increasing the distance requirements between vessels and feeding PCFG whales as a way to reduce the energetic impact of vessel disturbance (Figure 3). Additionally, differences in energetic cost of foraging behaviors may help inform potential risks posed by changes in prey quality and quantity for gray whales using different foraging tactics.

Figure 3. Snapshot from the video footage of a high-resolution accelerometry suction cup tag deployed on a PCFG gray whale showing the high number of vessels present during a surfacing following a foraging dive. The energetic cost of foraging behaviors found in my thesis might suggest that increasing distance between vessels and forging whales could reduce the energetic impacts of vessel disturbance. 

Overall, I am so grateful for my Master’s experience. I had the opportunity to work with amazing scientists that taught me many valuable skills and lessons that I will take with me as I move onto the next phase of my career. Throughout my degree I’ve had a lot of “firsts” and I am excited to embark on another as I prepare my first manuscripts for publication! 



Allen, A. S., Read, A. J., Shorter, K. A., Gabaldon, J., Blawas, A. M., Rocho-Levine, J., & Fahlman, A. (2022). Dynamic body acceleration as a proxy to predict the cost of locomotion in bottlenose dolphins. Journal of Experimental Biology225(4). https://doi.org/10.1242/jeb.243121

Goldbogen, J. A., Friedlaender, A. S., Calambokidis, J., McKenna, M. F., Simon, M., & Nowacek, D. P. (2013). Integrative approaches to the study of baleen whale diving behavior, feeding performance, and foraging ecology. BioScience63(2), 90–100. https://doi.org/10.1525/bio.2013.63.2.5

Izadi, S., Aguilar de Soto, N., Constantine, R., & Johnson, M. (2022). Feeding tactics of resident Bryde’s whales in New Zealand. Marine Mammal Science, 1–14. https://doi.org/10.1111/mms.12918

Jeanniard-Du-Dot, T., Trites, A. W., Arnould, J. P. Y., Speakman, J. R., & Guinet, C. (2016). Flipper strokes can predict energy expenditure and locomotion costs in free-ranging northern and Antarctic fur seals. Scientific Reports6. https://doi.org/10.1038/srep33912

Lemos, L. S., Haxel, J. H., Olsen, A., Burnett, J. D., Smith, A., Chandler, T. E., Nieukirk, S. L., Larson, S. E., Hunt, K. E., & Torres, L. G. (2022). Effects of vessel traffic and ocean noise on gray whale stress hormones. Scientific Reports12(1). https://doi.org/10.1038/s41598-022-14510-5

Nerini, M. (1984). A review of gray whale feeding ecology. In M. Lou Jones, S. L. Swartz, & S. Leatherwood (Eds.), The gray whale: Eschrichtius robustus (pp. 423–450). Academic Press. https://doi.org/10.1016/B978-0-08-092372-7.50024-8

Simon, M., Johnson, M., Tyack, P., & Madsen, P. T. (2009). Behaviour and kinematics of continuous ram filtration in bowhead whales (Balaena mysticetus). Proceedings of the Royal Society B: Biological Sciences276(1674), 3819–3828. https://doi.org/10.1098/rspb.2009.1135

Sullivan, F. A., & Torres, L. G. (2018). Assessment of vessel disturbance to gray whales to inform sustainable ecotourism. Journal of Wildlife Management82(5), 896–905. https://doi.org/10.1002/jwmg.21462

Sumich, J. L. (1986). Latitudinal distribution, calf growth and metabolism, and reproductive energetics of gray whales, Eschrichtius robustus. Oregon State University.

Torres, L. G., Nieukirk, S. L., Lemos, L., & Chandler, T. E. (2018). Drone up! Quantifying whale behavior from a new perspective improves observational capacity. Frontiers in Marine Science5. https://doi.org/10.3389/fmars.2018.00319

Woodward, B. L., & Winn, J. P. (2006). Apparent lateralized behavior in gray whales feeding off the Central British Columbia coast. Marine Mammal Science22(1), 64–73. https://doi.org/10.1111/j.1748-7692.2006.00006.x

Fantastic beasts and how to measure  them! 

Sagar Karki, Master’s student in the Computer Science Department at Oregon State University 

What beasts? Good question! We are talking about gray whales in this article but honestly we can tweak the system discussed in this blog a little and make it usable for other marine animals too.  

Understanding the morphology, such as body area and length, of wild animals and populations can provide important information on animal  behavior and health (check out postdoc Dr. KC Bierlich’s post on this topic). Since 2015, the GEMM Lab has been flying drones over whales to collect aerial imagery to allow for photogrammetric measurements to gain this important morphological data. This photogrammetry data has shed light on multiple important aspects of gray whale morphology, including the facts that the whales feeding off Oregon are skinnier [1] and shorter [2] than the gray whales that feed in the Arctic region.  But, these surprising conclusions overshadow the immense, time-consuming labor that takes place behind the scenes to move from aerial images to accurate measurements.  

To give you a sense of this laborious process, here is a quick run through of the methods: First the 10 to 15 minute videos must be carefully watched to select the perfect frames of a whale (flat and straight at the surface) for measurement. The selected frames from the drone imagery are then imported into MorphoMetriX, which is a custom software developed for photogrammetry measurement [1]. MorphoMetriX is an interactive application that allows an analyst to manually measure the length by clicking points along the centerline of the whale’s body. Based on this line, the whale is divided into a set of sections perpendicular to the centerline, these are used to then measure widths along the body. The analyst then clicks border points at the edge of the whale’s body to delineate the widths following the whale’s body curve. MorphoMetriX then generates a file containing the lengths and widths of the whale in pixels for each measured image. The length and widths of whales are converted from pixels to metric units using a software called CollatriX [4] and this software also calculates metrics of body condition from the length and width measurements. 

While MorphoMetriX [3] and CollatriX [4] are both excellent platforms to facilitate these photogrammetry measurements, each measurement takes time, a keen eye, and attention to detail. Plus, if you mess up one step, such as an incorrect length or width measurement, you have to start from the first step. This process is a bottleneck in the process of obtaining important morphology data on animals. Can we speed this process up and still obtain reliable data? 

What if we can apply automation using computer vision to extract the frames we need and automatically obtain measurements that are as accurate as humans can obtain? Sounds pretty nice, huh? This is where I come into the picture. I am a Master’s student in the Computer Science Department at OSU, so I lack a solid background in marine science, but bring to the table my skills as a computer programmer. For my master’s project, I have been working in the GEMM Lab for the past year to develop automated methods to obtain accurate photogrammetry measurements of whales.  

We are not the first group to attempt to use computers and AI to speed up and improve the identification and detection of whales and dolphins in imagery. Researchers have used deep learning networks to speed up the time-intensive and precise process of photo-identification of  individual whales and dolphins [5], allowing us to more quickly determine animal location, movements and abundance. Millions of satellite images of the earth’s surface are collected daily and scientists are attempting to utilize these images to  benefit marine life by studying patterns of species occurrence, including detection of gray whales in satellite images using deep learning [6]. There has also been success using computer vision to identify whale species and segment out the body area of the whales  from drone imagery [7]. This process involves extracting segmentation masks of the whale’s body followed by length extraction from the mask. All this previous research shows promise for the application of computer vision and AI to assist with animal research and conservation. As discussed earlier, the automation of image extraction and photogrammetric measurement  from drone videos will help researchers collect vital data more quickly so that decisions that impact  the health of whales can be more responsive and effective.For instance,  photogrammetry data extracted from drone images can diagnose pregnancy of the whales [8], thus automation of this information could speed up our ability to understand population trends. 

Computer vision and natural language processing fields are growing exponentially. There are new foundation models like ChatGPT that can do most of the natural language understanding and processing tasks. Foundational models are also emerging for computer vision tasks, such as “the segment anything model” from Meta. Using these foundation models along with other existing research work in computer vision, we have developed and deployed a system that automates the manual and computational tasks of MorphoMetriX and CollatriX systems.  

This system is currently in its testing and monitoring phase, but we are rapidly moving toward a publication to disseminate all the tools developed, so stay tuned for the research paper that will explain in detail the methodologies followed on data processing, model training and test results. The following images give a sneak peak of results. Each image  illustrates a frame from a drone video that was  identified and extracted through automation, followed by another automation process that identified important points along the whale’s body and curvature.  The user interface of the system aims to make the user experience intuitive and easy to follow. The deployment is carefully designed to run on different hardwares, with easy monitoring and update options using the latest open source frameworks. The user has to do just two things. First, select the videos for analysis. The system then generates potential frames for photogrammetric analysis (you don’t need to watch 15 mins of drone footage!). Second, the user selects the frame of choice for photogrammetric analysis and waits for the system to give you measurements. Simple! Our goal is for these softwares to be a massive time-saver while  still providing vital, accurate body measurements  to the researchers in record time. Furthermore, an advantage of this approach is that researchers can follow the methods in our to-be-soon-published research paper to make  a few adjustments enabling the software to measure other marine species, thus expanding the impact of this work to many other life forms.  

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  1. Torres LG, Bird CN, Rodríguez-González F, Christiansen F, Bejder L, Lemos L, Urban R J, Swartz S, Willoughby A, Hewitt J, Bierlich K (2022) Range-Wide Comparison of Gray Whale Body Condition Reveals Contrasting Sub-Population Health Characteristics and Vulnerability to Environmental Change. Front Mar Sci 910.3389/fmars.2022.867258 
  1. Bierlich KC, Kane A, Hildebrand L, Bird CN, Fernandez Ajo A, Stewart JD, Hewitt J, Hildebrand I, Sumich J, Torres LG (2023) Downsized: gray whales using an alternative foraging ground have smaller morphology. Biol Letters 19:20230043 doi:10.1098/rsbl.2023.0043 
  1. Torres et al., (2020). MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna. Journal of Open Source Software, 5(45), 1825, https://doi.org/10.21105/joss.01825 
  1. Bird et al., (2020). CollatriX: A GUI to collate MorphoMetriX outputs. Journal of Open Source Software, 5(51), 2328, https://doi.org/10.21105/joss.02328 
  1. Patton, P. T., Cheeseman, T., Abe, K., Yamaguchi, T., Reade, W., Southerland, K., Howard, A., Oleson, E. M., Allen, J. B., Ashe, E., Athayde, A., Baird, R. W., Basran, C., Cabrera, E., Calambokidis, J., Cardoso, J., Carroll, E. L., Cesario, A., Cheney, B. J. … Bejder, L. (2023). A deep learning approach to photo–identification demonstrates high performance on two dozen cetacean species. Methods in Ecology and Evolution, 00, 1–15. https://doi.org/10.1111/2041-210X.14167 
  1. Green, K.M., Virdee, M.K., Cubaynes, H.C., Aviles-Rivero, A.I., Fretwell, P.T., Gray, P.C., Johnston, D.W., Schönlieb, C.-B., Torres, L.G. and Jackson, J.A. (2023), Gray whale detection in satellite imagery using deep learning. Remote Sens Ecol Conserv. https://doi.org/10.1002/rse2.352 
  1. Gray, PC, Bierlich, KC, Mantell, SA, Friedlaender, AS, Goldbogen, JA, Johnston, DW. Drones and convolutional neural networks facilitate automated and accurate cetacean species identification and photogrammetry. Methods Ecol Evol. 2019; 10: 1490–1500. https://doi.org/10.1111/2041-210X.13246 
  1. Fernandez Ajó A, Pirotta E, Bierlich KC, Hildebrand L, Bird CN, Hunt KE, Buck CL, New L, Dillon D, Torres LG (2023) Assessment of a non-invasive approach to pregnancy diagnosis in gray whales through drone-based photogrammetry and faecal hormone analysis. Royal Society Open Science 10:230452 

A Journey From Microbiology to Macrobiology

Mariam Alsaid, University of California Berkeley, GEMM Lab REU Intern

My name is Mariam Alsaid and I am currently a 5th year undergraduate transfer student at the University of California, Berkeley. Growing up on the small island of Bahrain, I was always minutes away from the water and was enraptured by the creatures that lie beneath the surface. Despite my long-standing interest in marine science, I never had the opportunity to explore it until just a few months ago. My professional background up until this point was predominantly in soil microbiology through my work with Lawrence Berkeley National Laboratory, and I was anxious about how I would switch directions and finally be able to pursue my main passion. For this reason, I was thrilled by my acceptance into the OSU Hatfield Marine Science Center’s REU program this year, which led to my exciting collaboration with the GEMM Lab. It was kind of a silly transition to go from studying bacteria, one of the smallest organisms on earth, to whales, who are the largest.

My project this summer focused on sei whale acoustic occurrence off the coast of Oregon. “What’s a sei whale?” is a question I heard a lot throughout the summer and is one that I had to Google myself several times before starting my internship. Believe it or not, sei whales are the third largest rorqual in the world but don’t get much publicity because of their small population sizes and secretive behavior. The commercial whaling industry of the 19th and 20th centuries did a number on sei whale populations globally, rendering them endangered. In consequence, little research has been conducted on their global range, habitat use, and behavior since the ban of commercial whaling in 1986 (Nieukirk et al. 2020). Additionally, sei whales are relatively challenging to study because of their physical similarities to the fin whale, and acoustic similarities to other rorqual vocalizations, most notably blue whale D-calls and fin whale 40 Hz calls. As of today, published literature indicates that sei whale acoustic presence in the Pacific Ocean is restricted to Antarctica, Chile, Hawaii, and possibly British Columbia, Canada (Mcdonald et al. 2005; Espanol-Jiminez et al. 2019; Rankin and Barlow, 2012; Burnham et al. 2019). The idea behind this research project was sparked by sparse visual sightings of sei whales by research cruises conducted by the Marine Mammal Institute (MMI) in recent years (Figure 1). This raised questions about if sei whales are really present in Oregon waters (and not just misidentified fin whales) and if so, how often?

Figure 1. Map of sei whale visual sightings off the coast of Oregon, colored by MMI Lab research cruise, and the location of the hydrophone at NH45 (white star).

A hydrophone, which is a fancy piece of equipment that records continuous underwater sound, was deployed 45 miles offshore of Newport, OR between October of 2021 and December of 2022. My role this summer was to use this acoustic data to determine whether sei whales are hanging out in Oregon or not. Acoustic data was analyzed using the software Raven Pro, which allowed me to visualize sound in the form of spectrograms (Fig. 2). From there, my task was to select signals that could potentially be sei whale calls. It was a hurdle familiarizing myself with sei whale vocalizations while also keeping in mind that other species (e.g., blue and fin whales) may produce similar sounding (and looking in the spectrograms) calls. For this reason, I decided to establish confidence levels based on published sei whale acoustic research that would help me classify calls with less bias. Vocalizations produced by sei whales are characterized by low frequency, broadband, downsweeps. Sei whales can be acoustically distinguished from other whales because of their tendency to produce uniform groups of calls (typically in doublets and triplets) in a short timeframe. This key finding allowed me to navigate the acoustic data with more ease.

The majority of the summer was spent slowly scanning through the months of data at 5-minute increments. As you can imagine, excitement varied by day. Some days I would find insanely clear signals of blue, fin, and humpback whales and other days I would find nothing. The major discovery and the light at the end of the tunnel was the SEI WHALES!!! I detected numerous high quality sei whale calls throughout the study period with peaks in October and November (but a significantly higher peak in occurrence in 2022 versus 2021). I also encountered a unique vocalization type in fall of 2022, consisting of a very long series of repeated calls that we called “multiplet”, rather than doublets or triplets that is more typical of sei whales (Fig. 3). Lastly, I found no significant diel pattern in sei whale vocalization, indicating that these animals call at any hour of the day. More research needs to go into this project to better estimate sei whale occurrence and understand their behavior in Oregon but this preliminary work provides a great baseline into what sei whales sound like in this part of the world. In the future, the GEMM lab intends on implementing more hydrophone data and work on developing an automated detection system that would identify sei whale calls automatically.

Figure 2. Spectrogram of typical sei whale calls detected in acoustic data
Figure 3. Spectrogram of unique sei whale multiplet call type
Figure 4. My first time conducting fieldwork! I spent a few mornings assisting Dr. Rachel Orben’s group in surveying murre and cormorant nests (thanks to my good friend Jacque McKay :))

My experience this summer was so formative for me. As someone who has been an aspiring marine biologist for so long, I am so grateful for my experience working with the GEMM Lab alongside incredible scientists who are equally passionate about studying the mysteries of the ocean. This experience has also piqued my interest in bioacoustics and I plan on searching for other opportunities to explore the field in the future. Aside from growing professionally, I learned that I am more capable of tackling and overcoming obstacles than I had thought. I was afraid of entering a field that I knew so little about and was worried about failing and not fitting in. My anxieties were overshadowed by the welcoming atmosphere at Hatfield and I could not have asked for better people to work with. As I was searching for sei whale calls this summer, I suppose that I was also unintentionally searching for my voice as a young scientist in a great, blue field.

Figure 5. My mentor, Dr. Dawn Barlow, and I with my research poster at the Hatfield Marine Science Center Coastal Intern Symposium

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Nieukirk, S. L., Mellinger, D. K., Dziak, R. P., Matsumoto, H., & Klinck, H. (2020). Multi-year occurrence of sei whale calls in North Atlantic polar waters. The Journal of the Acoustical Society of America, 147(3), 1842–1850. https://doi.org/10.1121/10.0000931

McDonald, M. A., Calambokidis, J., Teranishi, A. M., & Hildebrand, J. A. (2001). The acoustic calls of blue whales off California with gender data. The Journal of the Acoustical Society of America, 109(4), 1728–1735. https://doi.org/10.1121/1.1353593

Español-Jiménez, S., Bahamonde, P. A., Chiang, G., & Häussermann, V. (2019). Discovering sounds in Patagonia: Characterizing sei whale (<i>Balaenoptera borealis</i>) downsweeps in the south-eastern Pacific Ocean. Ocean Science, 15(1), 75–82. https://doi.org/10.5194/os-15-75-2019

Rankin, S., & Barlow, J. (2007). VOCALIZATIONS OF THE SEI WHALE BALAENOPTERA BOREALIS OFF THE HAWAIIAN ISLANDS. Bioacoustics, 16(2), 137–145. https://doi.org/10.1080/09524622.2007.9753572

Burnham, R. E., Duffus, D. A., & Mouy, X. (2019). The presence of large whale species in Clayoquot Sound and its offshore waters. Continental Shelf Research, 177, 15–23. https://doi.org/10.1016/j.csr.2019.03.004

That’s so Real: Adult Beginners, Serial Podcast(s), and a whole lotta of Baja Gray Whale Video Analysis.

Celest Sorrentino, Research Technician, Geospatial Ecology of Marine Megafauna Lab

Hello again GEMM Lab family. I write to you exactly a year after (okay maybe 361 days after but who’s counting…) from my previous blog post describing my 2022 summer working in the GEMM Lab as an NSF REU intern. Since then, so much has changed, and I can’t wait to fill you in on it.

In June I walked across the commencement stage at UC Santa Barbara, earning my BS in Ecology, Evolution, and Marine Biology and my minor in Italian language. A week later, I packed my bags and headed straight back to the lukewarm beaches of Newport, Oregon as a Research Technician in the GEMM Lab. I am incredibly fortunate to have been invited back to the OSU Marine Mammal Institute to lend a hand analyzing drone footage of gray whales collected back in March 2023 when Leigh and Clara went down to Baja California, as mentioned previously in Clara’s blog

Fig. 1. View from the top! (of the bridge at Yaquina Bay Bridge in Newport, OR)

During my first meeting with Clara at the beginning of the summer we discussed that a primary goal of my position was to process all the drone footage collected in Baja so that the generated video clips could be later used in other analytical software such as BORIS and SLEAP A.I. Given my previous internships and past summer project, this video processing is familiar to me. My initial thoughts were:

Sweet! Watch drone footage, pop in some podcasts, note down when I see whales, let’s do this!*

Like any overly eager 23-year-old, I might have mentally cracked open a Celsius and kicked my feet up too soon. We added another layer to the goal: develop an ethogram – which requires me to identify and define the behaviors that the gray whales appear to be demonstrating within the videos (more on ethogram development in Clara’s previous blog.) This made me nervous. 

I don’t have any experience with behavior. How do I tell what is a real behavior or if the whale is just existing? What if I’m wrong and ruin the project? What if I totally mess this up?

Naturally, as any sane person, to resolve these thoughts I took to the Reddit search bar: “How to do a job you’ve never done before.” No dice. 

I pushed these thoughts aside and decided to just start the video analysis process. Clara provided me with the ethogram she is developing during her PhD as a point of reference (based on the published gray whale ethogram in Torres et al. 2018), I was surrounded by an insanely supportive lab, and I could Google anything at my fingertips. Fast-forward 6 weeks later: I had analyzed 128 drone videos of adult gray whales as well as mother-calf pairs, and developed an ethogram describing, 26 behaviors**. I named one of my favorite behaviors  a “Twirl” to describe when a gray whale lifts their head out of the water and performs a 360 turn. Reminds me of times when as a kid, sometimes all you really needed is a good spin!

Now I was ready to start a productive, open conversation with Leigh and Clara about this ethogram and my work. However, even walking up to that last meeting, remnants of those daunting, doubtful early summer thoughts persisted. Even after I double checked all the definitions I wrote, rewatched all videos with said behaviors, and had something to show for my work. What gives Brain?

A few days ago, as I sat on my family’s living room couch with my two younger sisters, Baylie and Cassey, Baylie wanted to watch some TikToks with me. One video that came up was of a group of adults taking a beginner dance class, having so much fun and radiating joy. The caption read, Being a beginner as an adult is such a fun and wild thing. Baylie and I watched the video at least 10x, repeating to each other phrases like, “Wow!” and “They’re so cool.” That caption and video has been on my mind since: 

Being a beginner as an adult is such a fun and wild thing.

Being a beginner as an adult is also scary. 

Having just graduated, I can no longer say I am undergraduate student. Now, I am a young adult. This was my first research technician job, as an adult. Don’t adults usually have everything figured out? Can adults be beginners too?

Yes. In fact, we’re beginners more than we realize. 

  • I was a beginner cooking my mother’s turkey recipe 3 years ago for my housemates during the pandemic (Even after having her on Facetime, I still managed to broil it a little too long.) 
  • I was a beginner driver 5 years ago in a rickety Jeep driving myself to school (Now, since I’ve been back home, I’ve been driving my little sisters to school.)
  • I was a beginner NSF REU intern just a year ago. (This summer I was the alumni on the panel for the current NSF REU interns at Hatfield.)
  • I was a beginner science communicator presenting my NSF REU project at Hatfield last summer. (This summer, I presented my research at the Animal Behavior Society Conference.) 
Fig 2A. Group Pic with the LABIRINTO Lab and GEMM Lab at the ABS Portland Conference!
Fig 2B. Clara Bird (left), Dr. Leigh Torres (middle), and I (right) at the ABS Portland Conference. 

I now recognize that during my time identifying and defining behaviors of gray whales in videos made me take on the seat of a “beginner video and behavioral analyst”. I could not rely on the automated computer vision lens I gained from previous internships, which felt familiar and secure. 

 Instead, I had to allow myself to be creative. Dig into the unfamiliar in an effort to complete a task or job I had never done before. Allowing myself to be imperfect, make mistakes, meanwhile unconsciously building a new skill. 

This is what makes being a beginner as an adult such a fun thing. 

I don’t think being a beginner is a wild thing, although it can definitely make you feel a wild range of emotions. Being a beginner means you’re allowing yourself to try something new. Being a beginner means you’re allowing yourself the chance to learn.

Whether you’re an adult beginner as you enter your 30s, adult beginner as you enter parenthood, adult beginner grabbing a drink with friends after a long day in lab, adult beginner as a dancer, or like me, a beginner of leaving behind my college student persona and entering a new identity of adulthood, being a beginner as an adult is such a fun and normal thing.

I am not sure what will be next, but I hope to write to you all again from this blog a year from now, as an adult beginner as a grad student in the GEMM Lab. For anyone approaching the question of “What’s next”, I encourage you to read “Never a straight Path” by GEMM Lab MSc alum Florence Sullivan, a blog that has brought me such solace in my new adult journey and advice that never gets old.

Being a beginner—that, is so real. 

Fig 3A. Kayaking as an adult beginner of the Port Orford Field Team!
Fig 3B “See you soon:” Wolftree evenings with the lab.
Fig 3C. GEMM Lab first BeReal!

*I listened to way too many podcasts to list them all, but I will include two that have been a GEMM Lab “gem” —-thanks to Lisa and Clara for looping me in and now, looping you in!)

**(subject to change)


Torres LG, Nieukirk SL, Lemos L, Chandler TE (2018) Drone Up! Quantifying Whale Behavior From a New Perspective Improves Observational Capacity. Front Mar Sci 510.3389/fmars.2018.00319

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Embracing Failures for Personal and Professional Growth 

By Autumn Lee, Mount Holyoke College rising senior, GEMM Lab REU Intern 2023

Hello! My name is Autumn Lee, and I am a GEMM lab REU student this summer being mentored by Allison Dawn and Dr. Leigh Torres! I am a rising senior at Mount Holyoke College studying Neuroscience and Behavior, focusing on coastal and marine science. It has been a pleasure working with the GEMM Lab this summer, and I have enjoyed learning more about the field of research before I graduate. 

As part of the research experience for undergraduates (REU) program, I am doing an independent project this summer in addition to our intense fieldwork for the TOPAZ project. I am working with the CamDo underwater video data that the GEMM Lab has collected since 2020. You can read Allison’s recent blog post to learn more about our CamDo underwater housings. Over the previous seasons, scuba divers have deployed our CamDo’s in our two study sites near Port Orford Titchener Cove and Mill Rocks on a weekly schedule of collection and redeployment. My project focuses on developing a methodology for examining the interactions between zooplankton prey and marine predators, and to quantify zooplankton density from the swarms seen on camera. Even though I hope my project’s success will contribute to the field, embarking on new method protocols always carries a risk of failure. Science tends to focus on successes; only in the footnotes do we hear about failures, wrong turns, and forgotten ideas. However, failure is how research advances; and with scientists who are brave enough to take that first step and humble enough to accept and reflect on failure.

Figure 1: Team prepping CamDo setup for deployment 

In the past, I have learned to troubleshoot computer software and lab equipment. However, there were already protocols in place, and my research contributions were part of another student’s pre-defined project. Unlike my previous research experience, for my REU project, I had to learn how to use unfamiliar software, set achievable goals, overcome obstacles, and devise a plan to accomplish them without relying on a team of peers. This is a project Allison and I have been working on together outside of field work, but we have not been without support. Both Victoria Hermanson, a Biological Science Aid with the Antarctic Ecosystem Research Division, and Suzie Winquist, a graduate student at the Marine Mammal Institute, have inspired and guided us through using VIAME for our research questions.

Taking that leap into uncharted waters, we chose to work with two software programs that were new to me called VIAME (Video and Image Analytics for the Marine Environment) and ImageJ. Our goal was to utilize VIAME so that it could distinguish between zooplankton or predators in our CamDo videos (from the hundreds of unannotated frames) and then use ImageJ to quantify the density of zooplankton in those identified frames. Although it has been exciting to use this software that uses Artificial Intelligence (AI) to track and detect prey and predator interactions in video footage, we have encountered many challenges along the way. Within 10 weeks, we had to learn this new software, train it to identify zooplankton and predators, and calculate density using classified frames that we would train. When tackling such an ambitious project in a limited time frame, we expected some setbacks, and through the advice of experienced professionals and the support of Allison (as well as a healthy dose of self-determination), we were able to gain success by breaking down the project into smaller tasks and using trial and error to fix any issues that arose.

Figure 2: Photo of Allison and myself working together to problem solve a VIAME error 

Although we have had some failures along the way, we have accomplished a lot, and I am eager to share some results with you. First, we developed and fine-tuned a workflow in VIAME to use AI to identify zooplankton prey and predators in our CamDo videos.

Figure 3:  Screenshot of VIAME program that illustrates how we trained a model to identify zooplankton prey (yellow boxes) and fish predators (blue box) in the CamDo videos. 

 In addition, we implemented a workflow in ImageJ (another software program designed to process and analyze scientific images) to quantify zooplankton density from frames identified by VIAME with zooplankton. Even though it took a lot of trial and error, our primary objectives were met, and we learned a great deal for future GEMM projects.

Figure 4: An example processed output image depicting how ImageJ  recognized bodies of zooplankton (black outlines) and counted individual zooplankton ( red dots). 

While working on my independent project, I learned that an ability to troubleshoot software and data processing can apply to tricky field work situations as well. For instance, when we lost a weighted cage attachment that protects our RBR concerto sensor, we needed a temporary solution until the divers recovered  our lost gear. So our team discussed a few different DIY options. After a frantic afternoon of trial and error, we ultimately decided on using a milk jug as a temporary cage. While it wasn’t the most glamorous solution, the GEMM lab is known to think outside the box as a fundamental part of both the fieldwork and research process. 

Figure 5: Photo of Allison testing out our RBR milk jug temporary setup 

I have found through this experience that sometimes it is more valuable to struggle and learn skills than to immediately succeed. I am hopeful that this lesson has prepared me for my future, and I couldn’t be more grateful. It has been an interesting summer for me as far as adapting to failures and embracing them. It was a difficult transition leaving my new friends at Hatfield in Newport where I spent my first 4 weeks and embracing an entirely different living dynamic here in Port Orford. With the field season and my research approaching its end, I realize how much I appreciate all the new people I have met here. Before this summer, I had not had many opportunities to interact with similar and enthusiastic marine scientists. Now I live and work with marine science mentors and peers in the field every day, which has been an invaluable experience, and I am grateful for the opportunity to learn from and interact with these inspiring people. It has been a meaningful summer, and I look forward to continuing to build relationships and learn from my failures during this next phase of my life. 

    Figure 6: Photo of Zoop Troop, from left to right Natalee, Autumn, Allison, Jonah, Aly 

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Accurate and Precise: Learning how to track a focal species

By Jonah Lewis, rising junior at Pacific High School, GEMM Lab Intern 2023

Hello, I’m Jonah Lewis, the other high school intern for the TOPAZ/JASPER Project. I am a rising junior for Pacific High School in Port Orford. I am interested in many things, including computer sciences, electrical sciences, different types of engineering, and lately, marine biology. At the end of February, my biology teacher, Hilary Johnson, was looking for high schoolers to join this internship and I decided that it could be a great experience for me. I applied, and somewhere in March, before I knew it, I was being interviewed by Allison Dawn, our Zoop Troop Sergeant, and Leigh Torres, the head of the operation. I was so nervous for my interview, and tried my best to do well. Then on March 31st, I saw the job offer email, and my family and I were overjoyed. Now that we are in our fourth week, I can say the people and the experiences have been amazing, but my favorite part of all has been the cliff site and the adrenaline rush of tracking a whale moving across the ocean.

Figure 1: Jonah smiles after fixing a whale using the theodolite. 

Theodolite is an important aspect of this research project. This instrument was invented by Leonard Digges back in the 1550’s and is a highly accurate instrument for mapping, engineering, etc. Read here to learn more about the theodolite’s component parts, written by last year’s intern Nichola Gregory, a previous JASPER intern. In Port Orford, we use it for tracking where a gray whale blows and surfaces! Setting up the theodolite can be a challenge for newcomers, but as you repeatedly put this device together, and then take it down, you understand and can troubleshoot better and faster than the previous time. It took me and the team some practice to be able to get all three ways it needs to level just right, or else the instrument decides to throw a fit. For example, when the theodolite isn’t exactly leveled right, or maybe the batteries are low, or the cord just isn’t plugged in all the way, it will just beep at you, trying to say there is an error. After the theodolite is properly leveled, you connect it to the computer that runs our software program called Pythagoras.

Not only does the physical setup require care, but “fixing” a whale requires technique. Here, we are trained to be both accurate and precise when following our focal species. To be accurate, we would need to position the theodolite scope so that the whale is close to the crosshairs. To be precise, we need to fix the whale in the same location on the theodolite crosshairs consistently. Our team has learned how to be both accurate and precise.

Figure 2: Accurate and precise diagram using the crosshairs of a theodolite as reference, diagram by A. Dawn.

Being on cliff team can get tedious, even when you are not using the theodolite to fix a whale. Staring at the waves and the horizon can feel like an eternity, especially when gray whales aren’t active in our study area. Yet, during this time we have to be “on effort”. Being on effort is making sure you scan the horizon consistently, both you and a partner are constantly looking at our study sites. All this is best represented by our team manager Allison: On the cliff with her, she is always looking at the ocean, paying attention to both sites, and for at least the first hour or longer, she will not sit down. 

Figure 3: Kelp bed behind the jetty while a whale flukes in the background.

After we collect all of our data from kayak and cliff each day, we head down to the dry lab and get prepared to download and transfer our data to a hard drive known as “Tharp”. I learned that Marie Tharp was a woman in the 20th century, who mapped the ocean floors, which helps scientists even now. (The GEMM Lab names each hard drive after famous scientists; it helps to track the many hard drives.) When I use the hard drive, I think about her and about how I also helped collect data for mapping features in our marine study site. During the first week of data collection, Allison and I looked through the theodolite scope, found obvious kelp patches on the surface of the water, and fixed many times around the edges, making a complete polygon around the kelp beds. 

Figure 4: Team bonding at the Prehistoric Gardens in Port Orford

This internship for the past four weeks has been an amazing experience. In addition to our fieldwork, I’ve been able to participate and connect with many other interns and professionals here at the Field Station. I have also enjoyed connecting with visitors from all different areas who come by and ask what research we’re doing on the cliff.  At the field station I have fun hanging with the guys at the house as well, where we play sports in our downtime and cook together. I also learn about what projects they are doing, from urchin culling to sea otter research, it all fascinates me. I have helped POSS (Port Orford Sustainable Seafood) with bagging fish, washing dishes, and in return they provide samples of the amazing food they make. I am overjoyed about what I have learned and the people I have met during this experience, and am so thankful to be a part of the ninth year of this project.

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Diving into new experiences

By Natalee Webster, Oregon State University rising senior, GEMM Lab Intern 2023

When I was younger, I was terrified of the water, sobbing on a rock across the river, afraid to be immersed in the unknown. Flash-forward to the present and I have one more year left to finish my undergraduate degree in Biology at Oregon State University with a focus in Marine Biology. I was a little hesitant about choosing a more focused degree since I wasn’t sure what aspect of sciences piqued my interest more. However my curiosity for the ocean grew as I took the PADI Open Water scuba class through school. After earning my certification, I discovered I loved being in the water, and seeing the habitats I read about firsthand. I quickly took my Advanced Scuba and worked my way up to Divemaster, and ultimately AAUS Scientific diving. This new certification provided me with skills for a career in marine biology, performing tasks and taking surveys underwater. Through the diving community at OSU, I met Allison Dawn, our graduate student leader of the TOPAZ/JASPER project studying gray whale foraging ecology. Through meeting her I was informed about this project and decided to apply. Now, as I write, we are working on week three of this project, and I could not be happier with my decision. This internship has already taught me so much about the hard work and logistics that goes into studying the behaviors of large marine mammals in the field, as well as what it is like to closely work with a team to accomplish our goals.

Figure 1. Port of Port Orford at dawn.

Each morning we wake up before the sun with a new set of goals, with a variety of tasks ahead that certainly keeps you on your toes. Long-time readers will know of our kayak and cliff methods, but another aspect of this project is our CamDo underwater cameras. These are cameras that we place in Mill Rocks and Tichenor Cove, our two sampling sites, for a week at a time for longer term footage. In order to deploy these cameras we utilize scuba equipment to properly place them in a location. When the week is up, we go to recover the cameras to gather the data, replace SD card and batteries, and reset them for another week of underwater video footage. 

Although CamDo deployment is not a required part of this internship, I have been able to use my scientific diving certification to assist this project on the dives. I appreciate the opportunity to take apply skills to assist the project from a different perspective. Before my first week here I had never dove off the Oregon coast from a boat, so this task was daunting, as I was still getting to know everyone around the field station, and get a sense of my environment.

Figure 2. Photo of Natalee geared up for a dive in Mill Rocks. 

Our very first dive at Mill Rocks was intimidating but exciting. Allison and I got up before dawn to prepare the cameras and get to the dive boat the Black Pearl. Allison is our dive tender, handling equipment and logistics, and we worked alongside two other divers — Caroline Rice, an intern with ORKA here at the Port Orford field station, and Kevin Buch, our dive leader and the dive safety officer and scientific diving professor at OSU. Once we rolled off the boat and started our descent I began to feel more in my element as the green waters surrounded us. As we continued further and further to the ocean floor, I realized that visibility was turning from a green you could see rays of sunlight through, into a dark black — barely visible further than five inches from my face. We were able to position the camera lander as needed, but we could not secure the camera because of those black-out conditions. While I waited in the waters for direction on the dive, I put my face as close to the rock as the tides would let me and I saw a purple urchin underwater for the first time, and let me tell you, in the dark waters it was eerie. We finally surfaced and got on the boat to venture off to Tichenor Cove in an attempt to deploy the other CAMDO. Here, I realized that despite the best preparation, scientists need to remain adaptable and determined in the face of challenging ocean conditions.  

Figure 3. A screenshot of CAMDO footage showing fish swimming in the water column.

As we prepared for the next dive and began our descent, I silently wondered what I had gotten myself into. I hoped that not all dives off the Oregon Coast were as dark. While slowly descending into Tichenor Cove, I was pleasantly surprised to see that the waters were beautiful in contrast to the darkness of Mill Rocks. Tichenor seemed to be a safe haven in comparison to Mill Rocks; rather than the strong current pushing me along the rocks and urchins, I was able to calmly swim through the rocks and look at the many sea stars, nudibranch, anemones, and different hues of purple urchins living along them. 

Figure 4. Photos taken from GoPro of Tichenor Cove environment, showing rockfish, urchins, and an anemone. 

More recently, we recovered the camera for data processing. While comparing the footage between the two locations, I have learned the ocean is incredibly variable. From clear blue waters where you can clearly see juvenile and adult fish swimming in the water column, compared to nothing but murky brown and black waters. This variability inspired me to think more deeply about what the gray whales see while they forage for food. Dr. Leigh Torres visited our team and I was able to discuss our dives and inquire about the methods these whales use in order to eat. My basic knowledge of whale anatomy tells me that they have eyes; however, I was curious if they used eyesight to locate zooplankton and other food. Leigh informed me that these whales have whiskers! This was an exciting discovery for me, I googled it later and found that gray whales and many other baleen whales have hair follicles, called vibrissae (watch this NOAA video to learn more!), around their rostrum and mouth they use as tactile sensors. Leigh Torres has hypothesized a “sense-of-scale” that illustrates an interchange of sensory modalities such as vision, audition, chemoreception, magnetoreception and somatosensory perception that allows whales to track and capture of prey (Torres 2017). Research in this sensory field continues to grow to better understand how marine mammals  capture and track prey at various scales.

Figure 5. Image of a gray whale, the spot markings along its jaw and rostrum are hair follicles known as vibrissae. (2016)

Seeing these small segments of their habitat myself while underwater has given me much more respect for how these gray whales are able to forage in such a challenging and changing environment. My teammate Autumn is currently working on quantifying the zooplankton abundance recorded in the footage taken through CAMDO, so stay tuned on the Port Orford blogs to hear more about their project!

Figure 6. Photo of Aly, Natalee, and Autumn before kayak training. Honorable mention to the bucket hats. 

The opportunity to participate in this year’s Gray Whale Foraging Ecology project is something I will not take for granted and will appreciate greatly for years. It has given me the opportunity to grow my knowledge about the marine environment that I have been fascinated with, as well as given me skills and training in methods of field research. I  even got to apply my hard-earned underwater skills and conduct my first official scientific dives! I have been able to interact with the long-time locals of Port Orford, whether it be a fisherman sharing their orca encounter tales to retired photographers that chase the whales along the shore. The field station houses many projects focusing on different aspects of the Oregon coast from sea urchins and kelp to river otters along the shores and to outreach programs within the community. When everyone is settling back into the field station after their long day of work, it is great to be gathered in the kitchen and hear about the progress we’ve made and the experiences we’ve had. I look forward to the remaining three weeks I have in Port Orford with this community and my team! Wish us luck as we prepare to deploy the next round of CamDo cameras next week.

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Torres, L.G. (2017), A sense of scale: Foraging cetaceans’ use of scale-dependent multimodal sensory systems. Mar Mam Sci, 33: 1170-1193. https://doi.org/10.1111/mms.12426

What pushes whales north in the Baja. (2016). iTravel Cabo. Retrieved August 7, 2023, fromhttp://www.itravel-cabo.com/news/cabo-news/what-pushes-whales-north-in-the-baja.

How to be a Zooper Trooper: Getting Comfy with the Uncomfortable

By Aly Covey, Marshfield High School student, GEMM Lab Intern 2023

Hello, everyone! My name is Aly Covey and I am a rising senior, one of two high school interns part of the  TOPAZ/JASPER project this summer. I have the pleasure of introducing the team name for this year. We came up with our name not too long after meeting each other last week, when our team member Autumn started calling the zooplankton samples we collected  “zoop soup”, which then led us to call our team the “zoop troop” (because it rhymes!). We had some other contenders for names, but none of them felt just right. I think this is because Zoop Troop has begun to mean more to us than just the convenient rhyme. We’ve all heard the phrase “being a trooper”, which describes someone who overcomes their struggles and we certainly have embodied that in each task, where we have demonstrated resilience in the face of specific challenges and pushing forward despite discomfort both mentally and physically.

Figure 1: Logo for this year’s team name, created by Autumn Lee.

As a team, we have bonded over this quality of resiliency, and quickly became close during our first week. We go on routine sunset beach walks where we look at interesting sand fleas, baby shrimp, and bring back pocket-fulls of shells and beach glass. As well as our group meals that always lead to fun conversation and a warm, family, feel. Personally, I have enjoyed getting to know everyone on the team and seeing their unique skills. Since the first day, Jonah has constantly been trying to help cook and clean for Zoop Troop whenever he can. Natalee and I have bonded over our daily need to find time for a quick cat nap. We usually find Autumn working on her individual research project in the kitchen. And of course, Allison has earned the name of “Whale Mom” because of her dedication to taking care of the team’s needs outside of the daily training and being the best mentor to all of us. 

Over the last two weeks of training, I learned all the new technology and protocols the team needs to successfully use the gear for our research. Allison has been such a huge help teaching us the in’s and out’s of everything while still letting us make mistakes and allowing us to learn from them. So far, I feel confident in all the things I have learned. That said, I still wonder what it will feel like out in the field without a supervisor helping when something goes wrong. Allison has given us a few “non-data collecting” days to feel out the scene without her there and so far I, and whoever I’m working with that day, seem to be feeling fairly satisfied in our skill level, and it has been a nice opportunity to help each other when needed. 

Figure 2: Team prepping CamDo for deployment underwater

For me, it has been uncomfortable allowing myself to fail at certain tasks and having to restart from the beginning to get it right the next time. Patience is such an important skill needed for the work we do everyday. It’s very exciting to feel myself slowly start enjoying the idea of “trial and error” as I lean into all the new information we have absorbed these past few weeks. 

Although it is frustrating at times, I believe the team does a great job of creating a fun environment for each other while still being able to slow down and take in all the small details needed for each new task Allison teaches us. This experience has shown me that in order to persevere, you need to get comfortable with the uncomfortable.

Figure 3: Aly and Natalee learning kayak sampling skills

While completing tasks on my own, I am vigilant to catch errors and run over each protocol in my head multiple times before going out into the field. For example, our theodolite is a very important but delicate piece of equipment we use on the cliff to track and fix on the whales we see out in the water. It is incredibly tedious to set up Theota (our nickname for the theodolite) in a sufficient amount of time without messing up the leveling, cords, or measuring needed to properly run the program. During training, we get up to the cliff around 8am and are able to take as much time as we need to correctly level, connect the telescope to the computer, and reach each fix point without feeling rushed. However, during a “real” workday, we are up on the cliff as early as 6am, held to a standard of having all our gear fully charged and ready to go for the day, as well as being able to efficiently set everything up and ready to watch the whales and be the safety watch for kayak team. The first few times I put up Theota, I got very annoyed with having trouble leveling out everything, but after my 4th or 5th set up, I was feeling very confident in my ability and also being able to quickly move from one place to another to fix on something out in the water. 

Figure 3:  Aly fixing on a whale through the theodolite  

Like cliff site tasks, on-the-water protocols call for adaptability when things get rough; and the kayak is, in my opinion, more rigorous in protocol requirements, with much more room for error than the cliff work. This is likely because of the many types of gear we use while sampling from the kayak: we conduct visibility measurements, RBR Concerto and GoPro deployments, zooplankton net sampling — all while navigating in tricky ocean conditions. During our training, Allison took us out in the morning and taught us each how to properly navigate with the GPS and use all the sampling equipment like a pro. While it was a nice opportunity to double check everything with her, I knew going out without her wouldn’t be so easy. My first morning without Allison’s support, I had to redo multiple stations but was able to correct myself and learn from my mistakes. 

It is incredibly tiresome, but so rewarding to go out in the field early in the morning and come back to the lab in the afternoon with a tote full of new zooplankton samples or pictures of high-quality whale flukes to show everyone. The protocols in the lab are extensive, but the team has done a great job of taking tasks into their own hands and finishing processing data on their own accord.

Figure 4:  Zoop Troop on a beach walk 

So far, this internship has been an incredible opportunity for me, not just in my career but also in my personal life. I have learned so much from my team, everyone staying in the field station, and all the amazing people that I’ve had the pleasure to meet in the community. It has been so intriguing to learn about another small town in my home state of Oregon and compare all the similarities and differences from my home, Coos Bay. I’m so excited for what is to come in these next 4 weeks of research and for the team to keep you all informed. Having another summer to learn about the Pacific Ocean and solidify my love for marine life is such an endearing opportunity and I’m very grateful. I’m most excited for the first day I am able to complete all 12 sampling stations with ease. I believe my skills will continue to improve and I don’t expect any day to be dull working on this project. 

Zoop Troop team member, Aly, signing off!

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Updates from the 2023 Port Orford Gray Whale Foraging Ecology Project (team name TBD!)

Allison Dawn, Master’s student, OSU Department of Fisheries, Wildlife and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Greetings from the South Coast Outpost, aka the Port Orford Field Station! Long-time GEMM lab blog readers will know that by this time of the year, our TOPAZ and JASPER projects are fully underway. We have officially entered our 9th consecutive year of these two integrated projects, which provides experiential learning internships to high school and undergraduate students while conducting long-term monitoring of gray whale foraging ecology in our small study region.

Much like last year, the Port Orford Field Station is at full capacity, with our team of five plus six other NSF REU, MSI, and Sea Grant interns. The research efforts here span a wide-range of subjects, including the long-standing ORKA kelp-urchin monitoring projects, river otter predation, science communication initiatives with the Redfish Rocks Marine Reserve, and more. This diversity in subject matter makes for excellent discussion during our communal dinners, and keeps the field station’s labs bustling with a variety of samples, gear, and equipment being transported in-and-out on a daily basis. Needless to say, it is a thriving environment for young scientists who are passionate about the community and ecosystems of the southern Oregon Coast. 

This is my third year participating in the project, and my second time as the solo graduate team leader. After having defended my master’s thesis this past June, I have been so excited to return to this incredible study site and share what I have learned about the system here with a new group of interns. I will write about my thesis work in a separate blog soon, but for now, I’d like to introduce you to the excellent group of motivated students that are on the team this year!

Figure 1: Autumn draws a pyramid while learning the equation for estimating zooplankton patch density, as provided in Hermanson, 2019.

First up, we have Autumn Lee.  Autumn is one of the GEMM Lab’s three REU students and together we are diligently working to automate the detection of zooplankton and predator occurrence from our in situ underwater cameras using the program VIAME. We hope to describe the predator-prey dynamics in Port Orford and a new, calculated metric for zooplankton patch density. Autumn moved to Mount Holyoke College, MA after celebrating their high school graduation with a drive-through commencement in Spring 2020. Despite the challenging start to undergrad due to COVID, Autumn is now a rising senior with a major in Neuroscience and Behavior with a certificate in Coastal Marine Sciences. Initially Autumn wanted to be a neurosurgeon or do veterinary medicine, but has always loved the ocean. After taking a few marine science classes back home, they decided to apply for our REU project in hopes of gaining their first marine science fieldwork experience. Autumn is excited to connect with like-minded students, the community, and volunteer with Port Orford Sustainable Seafood with the goal of consuming as much fresh, local seafood as possible in these six weeks.

Figure 2: Natalee beams after having captured two separate whales on camera for the first time.

Next on our team is Natalee Webster! Natalee is originally from St. Helens, OR and has her associates degree from Portland Community College. Natalee was on a nursing track but slowly accumulated environmental and marine biology classes that led her to obtain her first SCUBA diving certification. After this, she was hooked and decided to major in biology with a focus in marine biology. Now, Natalee has earned both her dive master and AAUS scientific dive certifications, and has already helped us deploy our underwater in situ cameras. Like Autumn, Natalee is excited to get involved with the community, meet other interns, and get her first scientific fieldwork experience. In addition to her water sport skills, she is already quite a natural at taking photos from the cliff site.

Figure 3: Aly enjoying a sunny morning on the cliff site with our high-powered binoculars.

Aly is a rising senior at Marshfield High School in Coos Bay, Oregon where her favorite subject is science. In particular, her favorite class is AP environmental where she first learned how to read dissolved oxygen graphs and was fascinated by how this metric can describe water quality for public health considerations. As of now, Aly is considering several colleges, including Oregon State University, with aspirations to major in marine science. Interestingly enough, she used to be afraid of the water. Despite this fear, and being the intrepid person she is, Aly taught herself how to surf during COVID and has since found a new-found respect for the ocean — so much so that she is now ready to make marine conservation her career. Aly is excited for our kayak training session next week and is ready to get in the water to start collecting zooplankton samples. Aly has had a consistently positive attitude during training week, even when learning the most tedious tasks, and can always make our team laugh. 

Figure 4: Jonah poses near Port Orford Sustainable Seafood while listening to the Junket audio tour of the town. 

Jonah is a junior at Pacific High School here in Port Orford where his favorite classes are math and woodshop, and he also loves to get involved in sports such as track and field, soccer, and basketball. As a freshman, Jonah took a 3-D printing class which affirmed his desire to learn more engineering techniques. While considering a summer job, Jonah was excited to watch our recruitment presentation and learn that he could use specialized equipment for marine science applications. He is now considering Oregon State University and Oregon Institute of Technology for his undergraduate career. Jonah has been a quick learner with excellent attention to detail, and is also an excellent cook — which myself and the others are grateful for. He is excited to spend more time on the cliff and wants to perfect his theodolite techniques to track whale movements.

Figure 5: First team photo! We were all very excited and grateful to have been greeted by two whales on our first day together.

In just this first week, we have deployed underwater cameras, tracked multiple whales in one day from the cliff, obtained Basic Life Safety/CPR certifications, and practiced kayak sampling methods from the dock. Next week, we have our kayak safety training, and will have many more days of practicing the cliff and kayak methods before we jump into official data sampling days. I know the team is just as excited as I am for the rest of the season, especially because of this increase in whale activity. It is heartening to see so many whales after our low occurrence year in 2021. Stay tuned for more updates, including what we decide for this year’s team name!

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Whale Filled Summer in the GEMM Lab

By Cristy Milliken, Thomas More University, GEMM Lab REU Intern

It’s summertime in the GEMM Lab, meaning many visiting students, interns, and technicians working in the lab (12 additional people to be precise!). This influx of new faces in the lab means blog posts by some new people, including me, Cristy Milliken, as I am an NSF REU intern. I am a rising junior at Thomas More University where I am majoring in Biology along with obtaining a double minor in marine biology and environmental science. Prior to this internship I knew little about humpback whales aside from them being baleen whales and large mammals. Safe to say, I know much more about humpbacks after researching them for the SLATE project. SLATE stands for Scar-based Long-term Assessment of Trends in whale Entanglements. The project utilizes photos of humpback whales that have been collected from 2005 to 2023 to develop and refine methods of analyzing scaring rates. These methods of scar analysis will be used to determine the effectiveness of fishing regulations in Oregon. The SLATE project started recently (February 2023) and thus the current stage of the project is focused on analyzing many individual photographs of humpback whales captured in Oregon waters to determine the presence or absence of an entanglement scar.

Finding evidence of a scar on a whale is tricky, and we have encountered a few issues while developing our methodology.  There is no universal method to analyze the scarring rate in whales, yet we are building off the methods created and utilized by Annabelle Wall and Jooke Robbins (Wall et al., 2019; Robbins., 2012). Robbins first developed the method of scar analysis using images of humpback whales in the Gulf of Maine. Wall refined the methods by creating set categories that classified every sighting of each  individual to determine the likelihood of being entangled in the past. The image scoring methods have some flaws, and the descriptions can be vague, leaving more questions than answers. One specific issue we faced was how best to define when an image is of the dorsal or perpendicular side of a whale’s tailstock because there were photos that were a mix of both body parts as seen in Figure 1. In the end, we chose to classify photos that did not show a clear view of both insertion points of the fluke into the tailstock as a perpendicular tailstock. It is important to make this distinction because the view of a whale’s body part can show very different markings that could change our perspective of the whale’s possible entanglement history. We also have to assess the quality of each image because the quality can hide or show details that could influence our ability to access the whale’s history. The quality of the photos range from being very good to being illegible, which can make scoring a bit difficult. Aside from these issues, I have been making progress and I have been enjoying the work that I am doing knowing could help researchers in the future. This area of research is something that I could possibly pursue in the future because I enjoy working in an area helping with conservation efforts.

Figure 1: Perpendicular tail fluke of a humpback whale. Photo taken by Jenn Tackaberry; Copyright Cascadia Research Collective.

In addition to my research project, I am also expanding my personal connections and boundaries.  I have started to feel more comfortable here in Newport, although I do miss my family. Everyone in the GEMM lab, as well as in the MMI in general, was very welcoming and kind so that made things easier to settle in. I have also been learning about other projects occurring since everyone has been showing off all the amazing videos and data being collected.  

It’s hard to believe that it’s already been four weeks since I’ve arrived in Oregon. Had anyone told me that after my freshman year of college I would spend an entire summer in Oregon studying humpback whales scarring I would have never believed them and called them crazy. I’ve spent the majority of my life in Ohio thinking that it’d be impossible to study marine biology. But yet I was offered the opportunity to work in the GEMM lab and I will always be thankful for the opportunity.

Confidence has always been a struggle for me, but I wanted to challenge my insecurities, so I put myself out there in my application. Doing so opened up this opportunity and it makes me glad that I took the chance. Internships are a great way to build up confidence while gaining research experience, especially this one. I have met many amazing and kind people here and it has created an amazing atmosphere here at the Hatfield Marine Science Center. So, this is my message to everyone: take the chance and reach out because the opportunity could be an arm’s length away.


  1. Robbins, J. (2012). Scar-based Inference Into Gulf of Maine Humpback Whale Entanglement: 2010.
  2. Wall, A. (2019). Temporal and spatial patterns of scarred humpback whales (Megaptera novaeangliae) off the U.S. West Coast. Master thesis, Macquarie University, Sydney, Australia.