• MMRP

3D-laser scanning is helping us to better understand the health status of marine mammals

Blog written by Lars Bejder, Fabien Vivier and Kristi West


Isn’t technology amazing?! There are now so many innovative technologies available for use in the field of marine science. Cutting-edge technology in marine mammal research includes, but is not limited to, unoccupied aerial systems (UAS; drones), tri-accelerometer archival tags, multi-sensor high-resolution acoustic recording tags, satellite telemetry and sophisticated passive acoustic monitoring techniques. Moreover, laboratory techniques in the fields of metabolomics and endocrinology are also providing exciting new avenues to study marine mammals. As such, technological advances are allowing us to better understand the behavior, ecology, physiology and biomechanics of marine mammals which, in turn, is providing critical information toward their conservation. It sure is an exciting time to be a marine mammal biologist!


Over the past several years the Marine Mammal Research Program at the Hawaii Institute of Marine Biology has been developing capabilities in 3D-laser scanning and imaging of marine mammals in Hawaii. In some cases, we have been able to obtain scans of live animals in collaboration with Dolphin Quest Oahu. However, in the majority of cases, scans are conducted on deceased animals. The three-dimensional scans provide a plethora of information, including precise morphometric and volume measurements and information on scarring rates and severity. We are also using the 3D scans to calibrate and ground-truth the precision of body volume measurements of whales and dolphins obtained via unoccupied aerial system (UAS; drones) photogrammetry. Coupled with auxiliary data available through post-mortem investigations, the scans become even more valuable. Three-dimensional scans are also great for outreach and educational purposes to raise awareness about marine mammals and their conservation threats. Below are a couple of examples of how we have used 3D scans to measure the size, length and volume of a false killer whale and several other smaller dolphins.


PhD candidate Fabien Vivier 3D laser-scanning a deceased dolphin. NMFS Permit #18786.


False killer whale 3D-laser scan coupled with necropsy investigations


False killer whales (Pseudorca crassidens) are of particular conservation interest as this species is known to interact with longline fisheries in Hawaii. A Take Reduction Team (consisting of fishermen, researchers, NGOs as well as state and federal agencies) has been working for over a decade to find ways to minimize potential False killer whales bycatch.


In December 2019 the UH Health and Stranding Lab (UHHSL), led by Dr Kristi West, was notified by NOAA fisheries observers of a false killer whale mortality that had occurred outside of the Hawaii EEZ. The carcass was stored in the onboard freezer until returning to shore in Honolulu. In almost all stranding cases, fresh dead carcasses are necropsied immediately to ensure that histopathology findings are not compromised by freezing and thawing of the carcass. Being that this accidentally by-caught false killer whale had already been frozen by the fishing vessel in order to be able to transport it to shore, a necropsy was scheduled for a couple of months later. This allowed time for planning and coordination in order to obtain additional data from this specimen that has not previously been possible during past strandings of Hawaiian false killer whales.



The frozen carcass of the sub-adult male was scanned prior to thawing and produced wonderful results (see video above). The total body volume measurement of the animal was calculated to be 0.229 cubic meters and provides the first total body volume measurement from a false killer whale where accompanying weight and length data are available. The total body length of this animal was 277cm and it weighed 221kg.


A 3D scan of a false killer whale.


Several opportunities have already arisen to utilize the false killer whale body scan data, including a NOAA-led project to build a life-size false killer whale model that will be used for a hook sinking experiment. Data obtained from the scan are also being used to better understand the volume of individual cetacean extremities to compare body volume measurements obtained by unmanned aerial vehicles and traditional water displacements. Lastly, the 3D scan is being shared with Cascadia Research Collective for outreach and educational purposes. For further information on Cascadia’s research on false killer whales in Hawaii, see: https://www.cascadiaresearch.org/hawaiian-cetacean-studies/false-killer-whales-hawaii


Bottlenose dolphin scans in collaboration with Dolphin Quest:


PhD candidate Fabien Vivier has been working on developing scans on a variety of dolphin species in Hawaii. In collaboration with the UHHSL, Fabien created 3D-scans of stranded dolphins including striped dolphins (Stenella coeruleoalba, n = 3), a Fraser’s dolphin (Lagenodelphis hosei, n=1), and pygmy killer whales (Feresa attenuata, n=5). Moreover, Fabien has been fine-tuning the technique in collaboration with Dolphin Quest Oahu. Specifically, he has developed the technique by scanning live bottlenose dolphins housed at Dolphin Quest, Oahu. The process of scanning and post-processing takes some practice, but fortunately Fabien is on top of it now!


An example of the different layers created during post-processing of a 3D-scan of a bottlenose dolphin housed at Dolphin Quest, Oahu.


Once the scans are collected, they need to be ‘cleaned’, and processed, with the different layers / files to be assembled, to obtain the final 3D-object, which are then used for measurements. Once the final 3D image is created, morphometric measurements such as total length, girth at certain positions, and volume can be obtained. In the third row of images in the above figure, we have cross-sectioned the dolphin to estimate the body girth, and body volume of the different sections. Once combined with physical measurements (girth, length, body width / body height) and UAS-derived measurements, we will be able to refine the ways of assessing the health of free-ranging individuals using UASs.



The MMRP is looking forward to further developing this technology in partnership with collaborators, and stakeholders. We are grateful to Dr Josh Madin who has kindly lent us his 3D laser scanner – which has allowed this work to proceed. Thank you, Josh!

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