Tools for integrating inertial sensor data with video bio-loggers, including estimation of animal orientation, motion, and position
Open accessAbstract
Bio-logging devices equipped with inertial measurement units—particularly accelerometers, magnetometers, and pressure sensors—have revolutionized our ability to study animals as necessary electronics have gotten smaller and more affordable over the last two decades. These animal-attached tags allow for fine scale determination of behavior in the absence of direct observation, particularly useful in the marine realm, where direct observation is often impossible, and recent devices can integrate more power hungry and sensitive instruments, such as hydrophones, cameras, and physiological sensors. To convert the raw voltages recorded by bio-logging sensors into biologically meaningful metrics of orientation (e.g., pitch, roll and heading), motion (e.g., speed, specific acceleration) and position (e.g., depth and spatial coordinates), we developed a series of MATLAB tools and online instructional tutorials. Our tools are adaptable for a variety of devices, though we focus specifically on the integration of video, audio, 3-axis accelerometers, 3-axis magnetometers, 3-axis gyroscopes, pressure, temperature, light and GPS data that are the standard outputs from Customized Animal Tracking Solutions (CATS) video tags. Our tools were developed and tested on cetacean data but are designed to be modular and adaptable for a variety of marine and terrestrial species. In this text, we describe how to use these tools, the theories and ideas behind their development, and ideas and additional tools for applying the outputs of the process to biological research. We additionally explore and address common errors that can occur during processing and discuss future applications. All code is provided open source and is designed to be useful to both novice and experienced programmers.
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With these tools, researchers can reconstruct sensorimotor loops in free-ranging animals, revealing how vocalizations line up with movement, habitat use, and even social interactions.
“With these tools, we can reconstruct sensorimotor loops in free-ranging animals, revealing how vocalizations line up with movement, habitat use, and even social interactions (Cade et al. 2021).”
From Listening forward: emerging roles of bioacoustics in ecology, evolution, and conservation (2026) · cites this paper as Cade et al. 2021
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Deployment of biologging tags on free swimming large whales using uncrewed aerial systems
Wiley, D. N., Zadra, C. J., Friedlaender, A. S., Parks, S. E., Pensarosa, A., Rogan, A., Shorter, K. A., Jorge Urbán, R., & Kerr, I. (2023) · Royal Society Open Science · doi:10.1098/rsos.221376 · Cited by 35 · see citing works
Self-citationScaling of maneuvering performance in baleen whales: larger whales outperform expectations
Segre, P., Gough, W., Roualdes, E. A., Cade, D., Czapanskiy, M., Fahlbusch, J., Kahane-Rapport, S., Oestreich, W. K., Bejder, L., Bierlich, K. C., et al. (2022) · Journal of Experimental Biology · doi:10.1242/jeb.243224 · Cited by 22 · see citing works
Self-citationBlue whales increase feeding rates at fine-scale ocean features
Fahlbusch, J. A., Czapanskiy, M. F., Calambokidis, J., Cade, D. E., Abrahms, B. L., Hazen, E. L., & Goldbogen, J. A. (2022) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2022.1180 · Cited by 29 · see citing works
Self-citationKleivane, L., Kvadsheim, P. H., Bocconcelli, A., Øien, N. I., & Miller, P. J. O. (2022) · Animal Biotelemetry · doi:10.1186/s40317-022-00303-0 · Cited by 28 · see citing works
Evidence for Size-Selective Predation by Antarctic Humpback Whales
Cade, D. E., Kahane‐Rapport, S. R., Wallis, B., Goldbogen, J. A., & Friedlaender, A. S. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.747788 · Cited by 28 · see citing works
Self-citationWaller, M. J., Queiroz, N. C., da Costa, I., Cidade, T., Loureiro, B., Womersley, F. C., Fontes, J., Afonso, P., Macena, B. C. L., Loveridge, A., et al. (2023) · Journal of Fish Biology · doi:10.1111/jfb.15475 · Cited by 26 · see citing works
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Self-citationFast and Furious: Energetic Tradeoffs and Scaling of High-Speed Foraging in Rorqual Whales
Gough, W. T., Cade, D. E., Czapanskiy, M. F., Potvin, J., Fish, F. E., Kahane‐Rapport, S. R., Savoca, M. S., Bierlich, K. C., Johnston, D. W., Friedlaender, A. S., et al. (2022) · Integrative Organismal Biology · doi:10.1093/iob/obac038 · Cited by 22 · see citing works
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Self-citationAcoustic signalling and behaviour of Antarctic minke whales ( Balaenoptera bonaerensis )
Casey, C. B., Weindorf, S., Levy, E., Linsky, J. M. J., Cade, D. E., Goldbogen, J. A., Nowacek, D. P., & Friedlaender, A. S. (2022) · Royal Society Open Science · doi:10.1098/rsos.211557 · Cited by 15 · see citing works
Self-citationHigh‐speed chases along the seafloor put Bryde's whales at risk of entanglement
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Self-citationBehavioral response of megafauna to boat collision measured via animal-borne camera and IMU
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Self-citationKendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Animal Biotelemetry · doi:10.1186/s40317-022-00287-x · Cited by 13 · see citing works
Using accelerometry tags to quantify gray whale foraging behavior
Colson, K. M., Pirotta, E., New, L., Cade, D. E., Calambokidis, J., Bierlich, K. C., Bird, C. N., Ajó, A. F., Hildebrand, L., Trites, A. W., et al. (2024) · Marine Mammal Science · doi:10.1111/mms.13210 · Cited by 11 · see citing works
Self-citationPygmy Blue Whale Diving Behaviour Reflects Song Structure
Davenport, A. M., Erbe, C., Jenner, M., Jenner, K. C. S., Saunders, B. J., & McCauley, R. D. (2022) · Journal of Marine Science and Engineering · doi:10.3390/jmse10091227 · Cited by 10 · see citing works
Exfoliating Whales–Sandy Bottom Contact Behaviour of Humpback Whales
Meynecke, J., Gustafon, J., & Cade, D. E. (2023) · Journal of Marine Science and Engineering · doi:10.3390/jmse11030600 · Cited by 10 · see citing works
Self-citationPose-gait analysis for cetacean biologging tag data
Zhang, D., Goodbar, K., West, N., Lesage, V. S., Parks, S. E., Wiley, D. N., Barton, K. L., & Shorter, K. A. (2022) · PLoS ONE · doi:10.1371/journal.pone.0261800 · Cited by 9 · see citing works
Life in the slowest lane: Feeding allometry lowers metabolic rate scaling in the largest whales
Blawas, A. M., Videsen, S. K. A., Cade, D. E., Calambokidis, J., Friedlaender, A. S., Johnston, D. W., Madsen, P. T., & Goldbogen, J. A. (2025) · Science Advances · doi:10.1126/sciadv.adw2232 · Cited by 9 · see citing works
Self-citationAcoustic behavior of gray whales tagged with biologging devices on foraging grounds
Clayton, H., Cade, D. E., Burnham, R. E., Calambokidis, J., & Goldbogen, J. A. (2023) · Frontiers in Marine Science · doi:10.3389/fmars.2023.1111666 · Cited by 9 · see citing works
Self-citationHazel dormouse in managed woodland select for young, dense, and species-rich tree stands
Mortensen, R. M., Fuller, M. F., Dalby, L., Berg, T. B., & Sunde, P. (2022) · Forest Ecology and Management · doi:10.1016/j.foreco.2022.120348 · Cited by 9 · see citing works
Manning, J. C., Rosengarten, S., Hooper, C., & Fuentes, M. M. P. B. (2025) · Animal Biotelemetry · doi:10.1186/s40317-025-00406-4 · Cited by 8 · see citing works
MetaWild: A Multimodal Dataset for Animal Re-Identification with Environmental Metadata
Li, Y., Zhao, D., Qiao, T., Wu, Y., Pang, B., & Koh, Y. S. (2025) · ACM International Conference on Multimedia (ACM MM) · doi:10.1145/3746027.3758249 · Cited by 7 · see citing works
Daily energetic expenditure and energy consumption of short-finned pilot whales
Gough, W. T., Madrigal, B. C., Hollers, A., Currie, J. J., Baird, R. W., West, K. L., Fahlman, A., Fish, F. E., Evans, L., van Aswegen, M., et al. (2025) · Journal of Experimental Biology · doi:10.1242/jeb.249821 · Cited by 7 · see citing works
Self-citationHumpback whale suckling behavior: an insight into the mother-offspring strategy in mysticetes
Ratsimbazafindranahaka, M. N., Huetz, C., Reidenberg, J. S., Saloma, A., Andrianarimisa, A., Charrier, I., & Adam, O. (2023) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-023-03369-9 · Cited by 7 · see citing works
Time synchronisation for millisecond-precision on bio-loggers
Wild, T. A., Wilbs, G., Dechmann, D. K. N., Kohles, J. E., Linek, N., Mattingly, S., Richter, N., Sfenthourakis, S., Nicolaou, H., Erotokritou, E., et al. (2024) · Movement Ecology · doi:10.1186/s40462-024-00512-7 · Cited by 6 · see citing works
New urban habitat for endangered humpback whales: San Francisco Bay
Markowitz, T. M., Keener, W., Webber, M. A., Payne, A. R., Lane, R. S., Fahlbusch, J. A., & Calambokidis, J. (2024) · Aquatic Conservation Marine and Freshwater Ecosystems · doi:10.1002/aqc.4107 · Cited by 7 · see citing works
Self-citationSimmonds, S., Cheng, L. K., Ruha, W., Taberner, A. J., Du, P., & Angeli, T. R. (2023) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2023.3332852 · Cited by 5 · see citing works
Chimienti, M., Kato, A., Seydi, V., Schoombie, S., Hinke, J. T., Joy, R., Lidgard, D. C., Oosthuizen, W. C., Papastamatiou, Y. P., Ropert‐Coudert, Y., et al. (2025) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70063 · Cited by 4 · see citing works
Six decades of animal accelerometry: trends, applications, and future directions
Rudd, J. L., Collins, M. A., Righton, D. A., White, H. L., Witt, M. J., Wright, S. R., & Hawkes, L. A. (2026) · Movement Ecology · doi:10.1186/s40462-026-00641-1 · Cited by 4 · see citing works
Lam, C. H., Tam, C., & Lutcavage, M. E. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.879503 · Cited by 3 · see citing works
Evidence of sociality and group foraging in Antarctic minke whales (Balaenoptera bonaerensis)
Allen, J., Cade, D. E., Casey, C. B., Weindorf, S., Johnston, D. W., Linsky, J. M. J., Goldbogen, J. A., Nowacek, D. P., & Friedlaender, A. S. (2024) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-024-03481-4 · Cited by 3 · see citing works
Self-citationHampton, C. M., DeGroot, B. C., Brewster, L. R., Bassos‐Hull, K., Metzger, B. A., Mooney, T. A., & Ajemian, M. J. (2025) · Animal Biotelemetry · doi:10.1186/s40317-025-00416-2 · Cited by 2 · see citing works
Invited Review: Precision livestock farming technologies in swine intensive production
Buonaiuto, G., Nannoni, E., Sardi, L., Belperio, S., Sanzò, C., & Martelli, G. (2026) · Applied Animal Science · doi:10.15232/aas.2025-02699 · Cited by 2 · see citing works
Hollers, A., Gough, W. T., van Aswegen, M., Szabo, A. R., Evans, L., Currie, J. J., Blawas, A. M., Fahlman, A., Goldbogen, J. A., & Bejder, L. (2026) · Conservation Physiology · doi:10.1093/conphys/coag041 · Cited by 2 · see citing works
Self-citationKrylova, A., Blawas, A. M., Fahlbusch, J. A., Calambokidis, J., Clayton, H. M., Friedlaender, A. S., Stimpert, A. K., Goldbogen, J. A., & Cade, D. E. (2026) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2025.0344 · Cited by 2 · see citing works
Self-citationVariance-Reduced Stochastic Optimization for Efficient Inference of Hidden Markov Models
Sidrow, E., Heckman, N., Bouchard‐Côté, A., Fortune, S. M. E., Trites, A. W., & Auger‐Méthé, M. (2024) · Journal of Computational and Graphical Statistics · doi:10.1080/10618600.2024.2350476 · Cited by 2 · see citing works
Ayoub, A., Caruso, F., Segre, P. S., Hickmott, L. S., Warren, J. D., Chiang, G., Bahamonde, P., & Bocconcelli, A. (2024) · Ethology Ecology & Evolution · doi:10.1080/03949370.2024.2419125 · Cited by 2 · see citing works
Sidrow, E., Heckman, N., McRae, T. M., Volpov, B. L., Trites, A. W., Fortune, S. M. E., & Auger‐Méthé, M. (2025) · PLoS ONE · doi:10.1371/journal.pone.0325321 · Cited by 2 · see citing works
Movement and sound production in yearling humpback whales: age-class comparisons
Zeh, J. M., Lammers, M. O., Pack, A. A., & Parks, S. E. (2025) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-025-03575-7 · Cited by 1 · see citing works
Acoustic behaviour of endangered Hawaiian false killer whales
Madrigal, B. C., Gough, W. T., Currie, J. J., Bejder, L., Hollers, A., Baird, R. W., Mooney, T. A., & Pacini, A. F. (2026) · Royal Society Open Science · doi:10.1098/rsos.250918 · Cited by 1 · see citing works
Self-citationHumpback whales match song production to dive patterns
Zeh, J. M., Lammers, M. O., Kügler, A., Pack, A. A., Pérez-Marrufo, V., Schonwald, M., & Parks, S. E. (2026) · Current Biology · doi:10.1016/j.cub.2026.07.014 · Cited by 1 · see citing works
Clayton, H. M., Cade, D. E., Fahlbusch, J. A., Kendall-Bar, J. M., Calambokidis, J., Pyenson, N. D., & Goldbogen, J. A. (2026) · Journal of Experimental Biology · doi:10.1242/jeb.252034 · Cited by 1 · see citing works
Self-citationHigh-precision localized feeding by blue whales
Ryan, J. P., Ledesma, A. I. V., Oestreich, W. K., Benoit‐Bird, K. J., Goldbogen, J. A., Calambokidis, J., & Fahlbusch, J. A. (2026) · Current Biology · doi:10.1016/j.cub.2026.08.010 · Cited by 1 · see citing works
Self-citationSchoombie, S., de Wet, T., Britz, S., Lowther, A., & Oosthuizen, W. C. (2025) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.70026 · Cited by 1 · see citing works
“Why keep your mouth shut?” Inshore South African Bryde’s whales abort lunges within feeding dives
Clemente, J. D., Briefer, E. F., Nabe‐Nielsen, J., Segre, P. S., Penry, G. S., & Garagouni, M. (2025) · Ethology Ecology & Evolution · doi:10.1080/03949370.2025.2482528 · Cited by 1 · see citing works
Pose-gait analysis for cetaceans with biologging tagsPreprint
Zhang, D., Goodbar, K., West, N., Lesage, V. S., Parks, S. E., Wiley, D. N., Barton, K. L., & Shorter, K. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.13.472407 · Cited by 1 · see citing works
Listening forward: emerging roles of bioacoustics in ecology, evolution, and conservation
Zsebők, S. (2026) · Biologia Futura · doi:10.1007/s42977-026-00322-5
Zang, E. J., Lammers, M. O., Pack, A. A., & Hatch, L. T. (2023) · Marine Mammal Science · doi:10.1111/mms.13085
How deep is their lunch: Inshore South African Bryde’s whales shift attack mode at different depths
Clemente, J. D., Segre, P. S., Garagouni, M., Wiśniewska, D. M., Kahane‐Rapport, S. R., Gough, W. T., Wahlberg, M., Goldbogen, J. A., Penry, G. S., Nabe‐Nielsen, J., et al. (2025) · Marine Ecology Progress Series · doi:10.3354/meps14845
Self-citationBlawas, A. M., Shearer, J. M., Fahlman, A., Read, A. J., & Nowacek, D. P. (2025) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.00145.2025
Kendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19845634
Kendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19845643
Kendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19845637
Kendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19845631
Kendall-Bar, J. M., Mukherji, R., Nichols, J., Lopez, C., Lozano, D. A., Pitman, J. K., Holser, R. R., Beltran, R. S., Schalles, M. D., Field, C. L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.19845628
Passive three-dimensional precision method for locating vocalizing animals and other sound sources
Grande, K. C., Schneider, F. K., & Schneider, B. (2026) · Research on Biomedical Engineering · doi:10.1007/s42600-025-00444-0
A Behavioral Response Study with an Operational Marine Vibrator and Very Low Frequency Whales
Southall, B. L., Fahlbusch, J. A., Casey, C. B., Fregosi, S., Clayton, H., Barkowski, J., Jones, R. A., & Calambokidis, J. (2026) · Springer eBooks · doi:10.1007/978-3-031-94229-7_131-1
Self-citationHumpback whale mother-calf interactions : investigating nursing, swimming, and vocal behaviors
Ratsimbazafindranahaka, M. N. (2023) · doi:10.70675/31a05faaz7056z4724z8526zee648f150adc
DeepWave TurbNet: a Hybrid CNN-LSTM Framework for Ocean Turbulence Prediction
Mishra, J. P., Singh, K., Chaudhary, H., & Sharda, S. (2026) · Izvestiya Atmospheric and Oceanic Physics · doi:10.1134/s0001433826700131
Energetic scaling of propulsive costs across body sizes in humpback whales
Nemeth, C., Gough, W. T., van Aswegen, M., Hollers, A., Evans, L., Szabo, A., & Bejder, L. (2026) · Marine Ecology Progress Series · doi:10.3354/meps15212
Self-citationWiley, D. N., Cade, D. E., Friedlaender, A. S., Goldbogen, J. A., Kendall-Bar, J. M., Parks, S. E., Thompson, M. A., Weinrich, M. T., & Silva, T. L. (2026) · Behavioral Ecology and Sociobiology · doi:10.1007/s00265-026-03770-0
Self-citationSprint-like cardiac dynamics support repeated acrobatic lunges in foraging rorqual whales
Blawas, A. M., Fahlbusch, J. A., Barkowski, J., Cade, D. E., Calambokidis, J., Friedlaender, A. S., Southall, B. L., Ponganis, P. J., & Goldbogen, J. A. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2613082123
Self-citationTo flee or not to flee: anti-predator response of humpback whales on their breeding ground
Pichot, L., Ratsimbazafindranahaka, M. N., Martin-Marin, S., Huetz, C., Adam, O., Charrier, I., & Curé, C. (2026) · iScience · doi:10.1016/j.isci.2026.116953
3D tracking of marine megafauna to advance movement ecology
D’Antonio, B., Hays, G. C., Calich, H. J., da Costa, D. P., Favilla, A. B., Giuggioli, L., Harcourt, R. G., Evans, K., Meekan, M. G., Marley, S. A., et al. (2026) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2026.08.003
Fish locomotor dynamics quantified using multiple inertial measurement units
White, C. F., Castro‐Santos, T., Goerig, E., & LAUDER, G. V. (2026) · Royal Society Open Science · doi:10.1098/rsos.251863
A Behavioral Response Study with an Operational Marine Vibrator and Very Low Frequency Whales
Southall, B. L., Fahlbusch, J. A., Casey, C. B., Fregosi, S., Clayton, H. M., Barkowski, J., Jones, R., & Calambokidis, J. (2026) · Springer eBooks · doi:10.1007/978-3-032-05843-0_131
Self-citation
- Authors
- Cade, D. E., Gough, W. T., Czapanskiy, M. F., Fahlbusch, J. A., Kahane-Rapport, S. R., Linsky, J. M. J., Nichols, R. C., Oestreich, W. K., Wisniewska, D. M., Friedlaender, A. S., & Goldbogen, J. A.
- Affiliations
- University of California, Santa Cruz (US)
- Hopkins Marine Station (US)
- Cascadia Research Collective (US)
- The University of Queensland (AU)
- Corresponding author
- Cade, David E.
- ORCID
- Venue
- Animal Biotelemetry
- Published
- 2021-08-26
- Volume
- 9
- Issue
- 1
- ISSN
- 2050-3385 (ISSN-L)
- OpenAlex
- W3195109539
- Cited by
- 78
- References
- 85
- Citations by year
- 2026: 20 · 2025: 12 · 2024: 7 · 2023: 12 · 2022: 26 · 2021: 1
- FWCI
- 6.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Animal Biotelemetry (publishedVersion, cc-by)
- University of Southern Denmark Research Portal (University of Southern Denmark) (acceptedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- world wildlife fund
- National Science Foundation (IOS-1656691, OPP-1643877)
- Office of Naval Research (YIP #N000141612477)
- Stanford University (Terman Fellowship, Anne T. and Robert M. Bass Fellowship)
- Topics
- Physical Sciences › Environmental Science › Ecology › Marine animal studies overview
- Physical Sciences › Engineering › Ocean Engineering › Underwater Vehicles and Communication Systems
- Physical Sciences › Engineering › Aerospace Engineering › Inertial Sensor and Navigation
- Keywords
- inertial measurement unit, accelerometer, magnetometer, gyroscope, pressure sensors, GPS, cetaceans, marine animal behavior, data processing software, MATLAB software
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