Bioinspiration Lab OverviewTeamPublicationsLatest NewsTechnologiesData The bioinspiration lab develops instruments and techniques to explore mysteries of the deep sea for bioinspired design. With a focus on imaging, our technologies reveal novel views of marine organisms not otherwise possible, which we use to study the amazing adaptations animals have developed for life in a deep, cold, and dark environment.We bring the laboratory into the ocean by developing minimally invasive techniques to understand physical-biological interaction using fine-scale measurements of organismal behavior in their natural environment. This instrumentation includes DeepPIV, a laser-based 2D imaging system that can be used to look through transparent tissues, and EyeRIS, a plenoptic camera system capable of imaging particle fields and tissue surface movement in 3D. In addition to these systems developed for deployment up to 4000 meter deep using remotely operated vehicles, we’re developing similar instrumentation for autonomous underwater vehicles to increase the spatial and temporal scale of our observations. Furthering the usefulness of these integrations, we’ve worked on enabling and integrating machine learning approaches to processing visual data through projects such as FathomNet and ML-tracking.We also bring the ocean into the laboratory by using both novel and commonly used diagnostic engineering techniques to study biological and physical processes in more detail in a controlled environment, including shore-based and shipboard labs. This includes setups that use lasers or other advanced light sources to study morphology, locomotion, and fluid interactions in detail using highspeed cameras.The lessons we learn during in-situ and laboratory studies can be used to improve ocean technology that advances exploration and discovery of our vastly underexplored ocean. Bringing the Laboratory into the ocean To bring the laboratory into the ocean, we develop less-invasive techniques to understand biological-physical interactions by furthering fine-scale measurements of organismal behavior and their physical and chemical environments. DeepPIV is an instrument that allows for high temporal and spatial resolution measurements of fluid motion that serves as a proxy for energetics, forces generated, transport, and performance (with Alana Sherman and Bruce Robison, MBARI). Deep particle Image Velocimetry (DeepPIV) has been used in novel ways to reconstruct 3D gelatinous structures using structured light.Additional instrumentation developments in the short- and long-term involve coupling behavioral and environmental sensors (e.g., accelerometers, magnetometers, temperature, depth, salinity, light, dissolved oxygen) on minimally invasive platforms [ITAG: tagging package, collaboration with Aran Mooney (Woods Hole Oceanographic Institution) and Alex Shorter (University of Michigan), funded by The National Science Foundation Instrument Development for Biological Research program NSF-IDBR]Mesobot: stereo tracking underwater vehicle, collaboration with Dana Yoerger (Woods Hole Oceanographic Institution) and Steve Rock (Stanford University), funded by The National Science Institute Ocean Technology and Interdisciplinary Coordination Program NSF-OTIC to allow for quantification of organismal behaviors (e.g., swimming, feeding, reproduction) in response to the environment (e.g., thermoclines, oxygen minimum zones) to understand when organismal behaviors are selected in specific environmental conditions, and to predict organismal response to a changing ocean. Bringing the ocean into the laboratory To bring the ocean into the laboratory, we employ both cutting edge and commonly used diagnostic techniques in engineering to study biological and physical processes in more detail. We collect organisms using SCUBA and ROVs and transport them into the laboratory to further investigate features that cannot be adequately understood using in situ methods. This is an active area of research with collaborative efforts on understandingGiant larvacean ecology (with Bruce Robison, MBARI),Tomopterid fluid interactions to enable agile swimming and maneuvering (with Karen Osborn, Smithsonian),Mechanisms behind swimming by prayiid siphonophores (with Jack Costello and Sean Colin), arguably the largest organisms on our planet, andFluid interactions with benthic filter feeders (with James Barry, MBARI).In addition, using small-scale robotics, rapid prototyping, and advanced, optically clear and soft materials, we can design and build mechanical mimics to investigate how marine systems function in detail, and evaluate optimization and performance. Not only do these mechanical mimics contribute to the understanding of systems being studied, they will also streamline the technological pipeline to apply these lessons learned more rapidly to underwater technology. Team Directory Kakani Katija Principal Engineer Joost Daniels Research Engineer Paul Roberts Electrical Engineer Giovanna Sainz Research Assistant Eric Orenstein Research Engineer Kevin Barnard Software Engineer Jon Erickson Senior Mechanical Engineer Alana Sherman Electrical Engineering Group Lead Denis Klimov Electrical Engineer Lilli Carlsen Ocean Vision AI Engagement Coordinator Projects All Projects Deep-Sea Coral and Sponge Community Studies Project Deep-Sea Coral and Sponge Community Studies Studies of deep-sea coral and sponge ecosystems at Sur Ridge and Davidson Seamount focus on oceanographic and biological factors influencing their diversity and abundance. The Octopus Garden Project The Octopus Garden Octopus (Muusoctopus robustus) breeding at deep-sea hydrothermal springs at the base of Davidson Seamount are a current focus of ecological research. Publications All Publications Katija, Kakani, E. Orenstein, B. Schlining, L. Lundsten, K. Barnard, G. Sainz, O. Boulais, M. Cromwell, E. Butler, B. Woodward, and K.L.C. Bell. 2022. FathomNet: A global image database for enabling artificial intelligence in the ocean. Scientific Reports, 12(15914): 1–14. https://doi.org/10.1038/s41598-022-19939-2 Masmitja, I., M. Martin, K. Katija, S. Gomariz, and J. Navarro. 2022. A reinforcement learning path planning approach for range-only underwater target localization with autonomous vehicles. In 2022 IEEE 18th International Conference on Automation Science and Engineering (CASE), Mexico City, Mexico, August 2022, 675–682. IEEE. https://doi.org/10.1109/CASE49997.2022.9926499 Cones, S.F., D. Zhang, K.A. Shorter, K. Katija, D.A. Mann, F.H. Jensen, J. Fontes, P. Afonso, and T.A. Mooney. 2022. Swimming behaviors during diel vertical migration in veined squid Loligo forbesii. Marine Ecology Progress Series, 691: 83–96. https://doi.org/10.3354/meps14056 Katija, K., E. Orenstein, B. Schlining, L. Lundsten, K. Barnard, G. Sainz, O. Boulais, B. Woodward, and K.C. Bell. 2021. FathomNet: A global underwater image training set for enabling artificial intelligence in the ocean. arXiv: 2109.14646. https://doi.org/10.48550/arXiv.2109.14646 Daniels, J., N. Aoki, J. Havassy, K. Katija, and K.J. Osborn. 2021. Metachronal swimming with flexible legs: A kinematics analysis of the midwater Polychaete Tomopteris. Integrative and Comparative Biology, 61: 1658–1673. https://doi.org/10.1093/icb/icab059 Latest News All News News MBARI and Monterey Bay Aquarium bring the deep sea to land with new exhibition News 04.12.22 News Effective and elegant: New research reveals swimming mechanics of the gossamer worm News 09.28.21 News New laser system provides 3D reconstructions of living deep-sea animals and their mucous filters News 06.03.20 Technologies All Technologies Instrument EyeRIS Technology EyeRIS An instrument that captures 3D video with a single camera using lightfield imaging. Vehicle, Remotely Operated Vehicle (ROV) ROV Ventana Technology ROV Ventana A remotely operated vehicle equipped with a Sea-Bird 19plus V2 CTD package including a dissolved oxygen sensor, transmissometer, and spatial lasers mounted on the main camera. Instrument Wave Glider-Based Communications Hotspot Technology Wave Glider-Based Communications Hotspot An integrated system that enables autonomous devices to talk back. Software Video Annotation and Reference System (VARS) Technology Video Annotation and Reference System (VARS) A software interface and database system that provides tools for describing, cataloging, retrieving, and viewing the data associated with deep-sea video archives. Vehicle, Autonomous Surface Vehicle (ASV) Wave Glider Technology Wave Glider An autonomous surface vehicle built by Liquid Robotics, purchased and outfitted with sensors and communications gear by MBARI engineering. Vehicle, Autonomous Underwater Vehicle (AUV), Tethys Class Long Range AUV (LRAUV) Technology Long Range AUV (LRAUV) The long-range AUV (LRAUV) greatly expands the types of observations and experiments possible with autonomous platforms. Vehicle, Remotely Operated Vehicle (ROV) MiniROV Technology MiniROV The MiniROV is used to conduct shallow water transects and make in situ observations. Vehicle, Remotely Operated Vehicle (ROV) ROV Doc Ricketts Technology ROV Doc Ricketts An integrated unmanned submersible research platform with features providing efficient, reliable, and precise sampling and data collection. Instrument Deep Particle Image Velocimetry (DeepPIV) Technology Deep Particle Image Velocimetry (DeepPIV) The DeepPIV consists of a laser and optics that illuminate a quantifiable sheet of fluid. Data All Data Data Bioinspiration Lab Data Data FathomNet FathomNet is a publicly available database that makes use of existing (and future), expertly curated data from several sources Sketchfab – DeepPIV
Deep-Sea Coral and Sponge Community Studies Project Deep-Sea Coral and Sponge Community Studies Studies of deep-sea coral and sponge ecosystems at Sur Ridge and Davidson Seamount focus on oceanographic and biological factors influencing their diversity and abundance.
The Octopus Garden Project The Octopus Garden Octopus (Muusoctopus robustus) breeding at deep-sea hydrothermal springs at the base of Davidson Seamount are a current focus of ecological research.
Katija, Kakani, E. Orenstein, B. Schlining, L. Lundsten, K. Barnard, G. Sainz, O. Boulais, M. Cromwell, E. Butler, B. Woodward, and K.L.C. Bell. 2022. FathomNet: A global image database for enabling artificial intelligence in the ocean. Scientific Reports, 12(15914): 1–14. https://doi.org/10.1038/s41598-022-19939-2
Masmitja, I., M. Martin, K. Katija, S. Gomariz, and J. Navarro. 2022. A reinforcement learning path planning approach for range-only underwater target localization with autonomous vehicles. In 2022 IEEE 18th International Conference on Automation Science and Engineering (CASE), Mexico City, Mexico, August 2022, 675–682. IEEE. https://doi.org/10.1109/CASE49997.2022.9926499
Cones, S.F., D. Zhang, K.A. Shorter, K. Katija, D.A. Mann, F.H. Jensen, J. Fontes, P. Afonso, and T.A. Mooney. 2022. Swimming behaviors during diel vertical migration in veined squid Loligo forbesii. Marine Ecology Progress Series, 691: 83–96. https://doi.org/10.3354/meps14056
Katija, K., E. Orenstein, B. Schlining, L. Lundsten, K. Barnard, G. Sainz, O. Boulais, B. Woodward, and K.C. Bell. 2021. FathomNet: A global underwater image training set for enabling artificial intelligence in the ocean. arXiv: 2109.14646. https://doi.org/10.48550/arXiv.2109.14646
Daniels, J., N. Aoki, J. Havassy, K. Katija, and K.J. Osborn. 2021. Metachronal swimming with flexible legs: A kinematics analysis of the midwater Polychaete Tomopteris. Integrative and Comparative Biology, 61: 1658–1673. https://doi.org/10.1093/icb/icab059
News Effective and elegant: New research reveals swimming mechanics of the gossamer worm News 09.28.21
News New laser system provides 3D reconstructions of living deep-sea animals and their mucous filters News 06.03.20
Instrument EyeRIS Technology EyeRIS An instrument that captures 3D video with a single camera using lightfield imaging.
Vehicle, Remotely Operated Vehicle (ROV) ROV Ventana Technology ROV Ventana A remotely operated vehicle equipped with a Sea-Bird 19plus V2 CTD package including a dissolved oxygen sensor, transmissometer, and spatial lasers mounted on the main camera.
Instrument Wave Glider-Based Communications Hotspot Technology Wave Glider-Based Communications Hotspot An integrated system that enables autonomous devices to talk back.
Software Video Annotation and Reference System (VARS) Technology Video Annotation and Reference System (VARS) A software interface and database system that provides tools for describing, cataloging, retrieving, and viewing the data associated with deep-sea video archives.
Vehicle, Autonomous Surface Vehicle (ASV) Wave Glider Technology Wave Glider An autonomous surface vehicle built by Liquid Robotics, purchased and outfitted with sensors and communications gear by MBARI engineering.
Vehicle, Autonomous Underwater Vehicle (AUV), Tethys Class Long Range AUV (LRAUV) Technology Long Range AUV (LRAUV) The long-range AUV (LRAUV) greatly expands the types of observations and experiments possible with autonomous platforms.
Vehicle, Remotely Operated Vehicle (ROV) MiniROV Technology MiniROV The MiniROV is used to conduct shallow water transects and make in situ observations.
Vehicle, Remotely Operated Vehicle (ROV) ROV Doc Ricketts Technology ROV Doc Ricketts An integrated unmanned submersible research platform with features providing efficient, reliable, and precise sampling and data collection.
Instrument Deep Particle Image Velocimetry (DeepPIV) Technology Deep Particle Image Velocimetry (DeepPIV) The DeepPIV consists of a laser and optics that illuminate a quantifiable sheet of fluid.
Data FathomNet FathomNet is a publicly available database that makes use of existing (and future), expertly curated data from several sources