Thousands of Natural History Specimens CT-Scanned by Scientists, Accessible for Free

Natural history museums have entered a new stage of discovery and accessibility — one where scientists around the globe and curious folks at home can access valuable museum specimens to study, learn or just be amazed. This new era follows the completion of openVertebrate, or oVert, a five-year collaborative project among 18 institutions to create 3D reconstructions of vertebrate specimens and make them freely available online.

The team behind this endeavor, which includes scientists at the University of Washington and its Burke Museum of Natural History & Culture, published a summary of the project March 6 in the journal BioScience, offering a glimpse of how the data can be used to ask new questions and spur the development of innovative technology.

Natural history museums have become valuable resources for the public, with exhibits highlighting biodiversity, evolution and conservation. But most museum collections remain behind closed doors, accessible only to scientists who must either travel to see them or ask that a small number of specimens be transported on loan. The oVert team wanted to change that.

“If you require someone to get on a plane and travel to you to collaborate, that’s prohibitive in a lot of ways,” said David Blackburn, head of the oVert project and curator of herpetology at the Florida Museum of Natural History. “Now we have scientists, teachers, students and artists around the world using these data remotely.”

Between 2017 and 2023, oVert project members took CT scans of more than 13,000 vertebrate specimens. For the project, a team at the UW’s Friday Harbor Laboratories scanned more than 7,200 specimens — mostly fish, but also reptiles, amphibians and mammals — using the facility’s micro-CT scanner. Many of the specimens scanned at Friday Harbor came from the Burke Museum’s permanent collection. The UW team also trained more than 150 researchers, students and educators from around the world on how to CT scan specimens and analyze them for study purposes.

Since CT scanners use high-energy X-rays to peer past an organism’s exterior and view the dense bone structure beneath, most oVert reconstructions are skeletons. But, for some specimens, researchers took extra steps to visualize soft tissues, such as skin, muscle and other organs. The models give an intimate look at internal portions of a specimen that could previously only be observed through destructive dissection and tissue sampling.

“oVert is a way of reducing the wear and tear on samples while also increasing access, and it’s the next logical step in the mission of museum collections,” said Blackburn.

The project initially sought to scan only specimens preserved in ethyl alcohol, which represent the bulk of fish, reptile and amphibian collections. But researchers were reluctant to leave out larger specimens and came up with creative solutions. Project members at the Idaho Museum of Natural History, for example, painstakingly took apart a humpback whale skeleton to produce 3D models of each individual bone and digitally reassemble the whole skeleton. To scan mummified tortoises from the California Academy of Sciences’ collection, researchers had to pose them on top of inflatable swimming tubes.

Scientists have already used data from the project to gain new insights. One study of more than 500 oVert specimens, for example, revealed that frogs have lost and regained teeth more than 20 times throughout their evolutionary history. A separate study concluded that Spinosaurus, a massive dinosaur that was larger than Tyrannosaurus rex and thought to be aquatic, would have actually been a poor swimmer, and thus likely stayed on land. UW’s contributions to oVert have to date resulted in more than 40 peer-reviewed publications.

“It is so exciting to deposit the skeletal data for a new species in a repository where any scientist can access it,” said oVert team member Adam Summers, a UW professor of biology and of aquatic and fishery sciences, who is based at Friday Harbor Labs.

Artists have used the 3D models to create realistic animal replicas, and photographs of oVert specimens have been displayed in museums, including the Burke. Specimens have been incorporated into virtual reality headsets that give users the chance to interact with and manipulate them.

oVert models have also been used by educators in both K-12 and university settings, including in UW courses taken by hundreds of students.

“Digital 3D models of fish skeletons were incredibly useful during the COVID-19 pandemic, when remote labs meant UW students couldn’t access physical specimens,” said oVert team member Luke Tornabene, a UW associate professor of aquatic and fishery sciences and curator of fishes at the Burke Museum. “And now, we continue to use them as invaluable educational tools even though we’re back in the lab in person.”

The biggest challenge will be creating tools that are sophisticated enough to analyze the data, researchers say. This is the largest number of 3D natural history specimens released for public use, and it will take further developments in machine learning and supercomputing to use them to their full potential.

“In fact, the UW has a collaborative NSF grant to do just that — develop free, open-source software to look at all these new data and quantify their shapes,” said Summers.

Katherine Maslenikov, collections manager of fishes at the Burke, is also a member of the oVert team and a co-author on the new paper. oVert was funded by the National Science Foundation.