Experience a 4-D Whale Necropsy, From the Comfort of Your Computer

Share this posting on social media!

By Ellen Chenoweth

Chenoweth is a University of Alaska Southeast (UAS) affiliate professor, as well as a Research Advising and Mentoring Professional (RAMP), with the University of Alaska Fairbanks (UAF) Biomedical Learning and Student Training (BLaST) program.

Dead whale washed up on the beach
PHOTO Credit: Screenshot of 3D scans provided by Josh Houston

SITKA, Alaska—Most whale biologists spend their careers in boats getting a glimpse at whales only when they come up to the surface to breathe or occasionally to feed. Being able to walk right up to a whale, and even look inside its body, offers scientists and stranding network volunteers a rare and meaningful opportunity to learn from whales at close range. Necropsies are like autopsies for wild animals, which consist of close examination of the tissues after death. Through the use of 3-D scanning technology over time (hence 4-D), the University of Alaska Southeast (UAS) Whalelab has developed a free virtual portal that allows broader access to this experience.  

If You Can Scan a House, Why Not a Whale?

The idea for a virtual whale necropsy was inspired by 3-D scans of buildings and mountains created by Josh Houston, a Sitka-based drone pilot and digital 3-D modeler. These scans appear as stunning high-resolution photographs that the user can spin around and zoom in and out to view the subject from different angles. By applying this new technology to a whale, Chenoweth and her team hoped to give students an active-learning experience they would be unlikely to have any other way. UAS Professor of Marine Biology, Jan Straley, and Chenoweth requested a grant from the University of Alaska Biomedical Learning and Student Training (BLaST) program to fund the project. However, even with funding in hand, the project wouldn’t be able to begin unless a dead whale was discovered, something that hasn’t occurred in Sitka Sound in nearly 5 years.  

The Whale Shows Up

On Sunday, March 14, 2021, the U.S. Coast Guard flight crew reported a dead whale on a popular, remote surf beach near Sitka, Alaska. That same day, Houston visited the whale site with Dennis Rogers on the M/V Northern Song, an 84-foot expedition yacht, to 3-D scan the whale by drone.

The whale was found belly-up, bloated, but still in decent shape on the wide flat beach, so it was suitable for the necropsy. The necropsy occurred later that week on a beautiful sunny day following a stormy night. Incredibly, the whale had turned over in the surf and was now in a prone position, which allowed the team to scan its dorsal side as well. Led by UAS Assistant Professor of Fisheries Technology Lauren Wild, a team of trained volunteers collected measurements and photographs. The team peeled back the layers of skin and blubber and gathered tissue samples from the internal organs. Houston used his iPad and Polycam software to combine Lidar and visible light spectrum imaging to scan different cavities of the whale as the team exposed them. In the following months, Houston returned to the whale three more times to document the results of wave action, decomposition and scavenging on the carcass, until only human and animal tracks remained to mark the site.

Gone But Not Forgotten

During the following months, the team enlisted Kathy Burek-Huntington, D.V.M., to provide her expert analysis of the scans as a veterinary pathologist. Using the platform Sketchfab, she provided feedback and resources as Chenoweth inserted annotations, references, and photographs to provide more information. The scans are linked chronologically so anyone can follow their curiosity and explore the whale themselves. The open access format allows it to be used broadly by high school classrooms, college courses, researchers, or by other curious people.

The necropsy will also be formally incorporated into distance-delivered University of Alaska Southeast courses beginning with Biology 175, Current Topics in Marine Research, this fall and a new one-credit course, One Health Perspectives: Marine Mammals of Alaska, beginning in March 2022. 

Access the 4-D virtual necropsy and watch the Whales in the Wild video about boat-based whale surveys at the University of Alaska Whale Lab.

Close-up of whale necropsy
PHOTO Credit: Screenshot of 3D scans provided by Josh Houston


The necropsy team was led by Lauren Wild, Ph.D., a research biologist and professor of fisheries technology at the University of Alaska Southeast (UAS-Sitka) and former BLaST Graduate Research Mentoring Assistant, under the authorization of NOAA Fisheries. She was assisted by Ellen Chenoweth, Ph.D. (UAS-Sitka), Leigh Engel (Sitka Tribe of Alaska), Molly Grear (Pacific Northwest National Laboratories), Ted Hasty (NOAA Fisheries Law Enforcement), Josh Houston (Jfactory), Stacy Golden (Sitka School District), Paul Norwood, Brooke Schafer, and Pat Swedeen (City of Sitka). Learn more at the NOAA Fisheries website about stranded animal response and what to do if you find a dead or stranded marine mammal. The U.S. Coast Guard (USCG) originally sighted and reported the whale on Kruzof Island near Sitka and provided transportation to and from the site. Dennis Rogers (M/V Northern Song), and Mike Litman (M/V The Royal Baby) also provided boat transportation out to the whale.

Drew Stafford at the USCG District 17 office was integral in scheduling the effort through the Sitka Air Station. Pilots Erik Oredson and Treston Taylor and their crew Amanda Perham, David Braaten and William Flowers were on the first flight to the whale. The second flight was piloted by Mike Seavey and Michael Carrol and crewed by Desean Brown and Raul Perezrosario. 

This virtual workshop was assembled and annotated by Ellen Chenoweth, and Kathy Burek Huntington, D.V.M., and funded by UAF BLaST. The scan and technical expertise were provided by Jfactory. Jan Straley (UAS-Sitka), Taylor Stumpf (Metlakatla Indian Association), Lauren Wild, Matt Goff (Sitka Nature), Sadie Wright (NOAA Fisheries), Maggie Castellini (University of Alaska Fairbanks), Steve Lewis and Emma Park (UAS-Sitka), Mandy Keogh (NOAA Fisheries), Brooke Schafer, Paul Norwood, Paul Kraft (UAS-Sitka) and Ashely Szoke (UAS-Sitka) provided valuable feedback.

The Diversity Program Consortium Coordination and Evaluation Center at UCLA is supported by Office of the Director of the National Institutes of Health / National Institutes of General Medical Sciences under award number U54GM119024.
Need Assistance? Please contact our support team: info@diversityprogramconsortium.org .