Scientists have scanned thousands of animals in 3D, which is accessible to everyone

The openVertebrate project has made 3D CT scans of thousands of museum specimens freely available to the public

A total of 18 science museums collaborated on the openVertebrate (oVert) project, a five-year project to create 3D reconstructions of vertebrate specimens and make them freely available on the Internet.

The researchers have published a summary of the project in the journal BioScience, reviewing the samples scanned so far and providing insights into how the data could be used to raise new questions and advance the development of innovative technologies.

“When these specimens were first collected, there was no idea what the future would hold,” said Edward Stanley, co-principal investigator of the oVert project and associate scientist at the Florida Museum of Natural History.

Natural history museums emerged in the 16th century as cabinets of curiosities in which some wealthy individuals collected rare and exotic specimens, most of which they kept for themselves. Since then, museums have become a focal point for the public, with exhibitions showcasing biological diversity to anyone who is interested.

open vertebrate

Collections are no longer kept behind closed doors

However, most museum collections remain behind closed doors and are only accessible to scholars who must travel to view them or have a small number of loaned specimens mailed to them. The oVert research team wants to change this situation.

“It’s prohibitive in many ways to ask someone to get on a plane and travel to you to collaborate,” says David Blackburn, principal investigator of the oVert project and curator of herpetology at the Florida Museum. “We now have scientists, teachers, students and artists from all over the world using this data remotely.”

Between 2017 and 2023, members of the oVert project conducted CT scans of more than 13,000 specimens, representing species representative of the entire vertebrate tree of life. These include more than half of all genera of all amphibians, reptiles, fish and mammals. CT scanners use high-energy X-rays to look beyond the outside of an organism and see the dense bone structure beneath. Therefore, skeletons represent the majority of oVert reconstructions. A small number of samples were also stained with a temporary solution, which increases contrast and allows researchers to visualize soft tissues such as skin, muscles and other organs.

The models provide a detailed insight into the internal parts of a sample, which previously could only be observed through destructive dissection and tissue removal.

“Museums are constantly at a crossroads,” Blackburn says. “They want to protect the specimens, but also want people to be able to use them.” “oVert is a way to reduce exhibition loss while improving access, and is the next logical step in the mission of museum collections.”

Turtles, amphibians and even whales

The oVert project was initially funded with $2.5 million from the National Science Foundation, along with eight additional partner grants totaling $1.1 million that were used to expand the scope of the project. The original goal was to scan only specimens preserved in ethyl alcohol, which make up the majority of fish, reptile and amphibian collections. Samples that are too large to be stored in liquids also won’t fit in a CT scanner, but researchers were reluctant to leave them out.

A grant to the Idaho Museum of Natural History was used to create a digital model of a humpback whale. The entire specimen was too large to be scanned with sufficient resolution. So the researchers carefully dissected the skeleton, created 3D models of each bone, and then reassembled the physical and digital specimen.

Even medium-sized specimens sometimes required a little ingenuity, as was the case with a number of iconic turtles from the California Academy of Sciences.

“They have the largest collection of Galapagos tortoises in the world. These are not things that are packed in boxes and rented out,” explains Blackburn.

Using funding from another grant, the curators had to find a way to photograph each turtle in a 360-degree rotation. Photographing their underparts was problematic because their curved shells made it impossible to keep them upright. After several trial-and-error tests, they decided to place the samples on inflatable tubes to float.

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Scientists have already used the project’s data to gain surprising insights into nature.

Amazing discoveries in the scanner

In 2023, Edward Stanley performed routine CT scans of spiny mice and was surprised to find that their tails were covered with an inner lining of bone plates called osteoderms. Before this discovery, armadillos were thought to be the only living mammals with these structures.

“When you scan, all sorts of things jump out at you,” Stanley said. “I study osteoderms and as fate would have it, I had to scan these specific specimens that day and noticed something strange about their tails on the X-ray. That always happens. “We found all sorts of strange and unexpected things.”

oVert’s CT scans were also used to determine what killed a rock snake, considered the rarest snake species in North America. Another study showed that a group of frogs called pumpkin toads had become so small that the fluid-filled canals in their ears that give them balance no longer worked properly, causing them to fall while jumping. An extensive study of more than 500 oVert specimens found that frogs lost and regained teeth more than 20 times throughout their evolutionary history. Another study concluded that Spinosaurus, a giant dinosaur larger than Tyrannosaurus Rex and thought to have lived in water, was not a good swimmer and therefore likely stayed on land.

And the list goes on, full of ideas that would have been impossible or impractical before the project began. “Because we have been working on this for so long, we have a comprehensive framework that allows us to take a more comprehensive look at evolutionary questions,” says Stanley.

The value of oVert goes beyond scientific research. Artists have used 3D models to create realistic replicas of animals, photos of oVert specimens have been displayed in museums, and specimens have been integrated into virtual reality headsets, allowing users to interact with and manipulate them.

Unlimited possibilities

oVert models are also used by educators. From the beginning of the project, Blackburn and her colleagues made it a priority to reach children and adults. They organized workshops where teachers could learn how to use data in their classrooms.

“It completely changed my evolutionary unit,” says Jennifer Broo, a high school teacher in Cincinnati. “I teach freshmen and sophomores and I love them, but they can be a difficult audience. They know when something is wrong and are therefore less involved. oVert models allow you to convey concepts at an appropriate level while maintaining the authenticity of the science. My teaching has improved greatly because I have had the opportunity to work with real data and present it to my students.

The possible uses of oVert are practically unlimited. The biggest challenge will be developing tools that are sophisticated enough to analyze the data. Never before have so many three-dimensional specimens of natural history been publicly available and instantly accessible, and realizing their full potential will require new advances in machine learning and supercomputing.

“Generating the data is just the beginning,” says Jaimi Gray, a postdoctoral fellow at the Florida Museum working on NoCTURN (Non-Clinical Tomography Users Research Network), a project developed toward the end of oVert to make the best use of the data . CT scans. “The goal of oVert has always been to facilitate research into vertebrate diversity. “We will continue to research, but the goal of NoCTURN is to give people the tools to use data, whether for research, education or industry.”


Increasing the impact of scientific vertebrate collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network

Photo: OpenVertebrate

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