For Ramon Nagesan, research laboratory specialist at the U-M Museum of Zoology (UMMZ), a day’s work involves getting an unmatched view into the inner workings of archived animals. Nagesan runs the day-to-day operations of the museum’s MicroCT Scanning Laboratory. There, he and his colleagues use a MicroCT scanner to create three-dimensional digital renderings of the specimens in UMMZ’s collections—fish, birds, mammals, reptiles, and amphibians. What he finds can surprise even the most experienced researchers.
“These specimens can be old—some were collected over a century ago, some much more recently—and sometimes the notes and data associated with them aren’t very extensive,” he explains. “Sometimes we know certain things about the animals and assume others. But sometimes we find surprises.”
In 2019, Nagesan and his team were scanning a snake specimen—a fully intact, preserved creature with skin, musculature, and a skeleton—when they saw something strange inside it. As the scan progressed, they discovered the strange thing they were seeing inside the snake was . . . a frog!
“Legs, head, arms, and all,” says Nagesan. “This snake has been archived at the museum since 2018 and no one knew what was inside. Now, we have a beautiful scan of a coiled snake—what most people would associate with an image of a snake—that has a big frog coiled right through its gut.”
The specimens have been collected for research projects or animal surveys and had typically been preserved in jars. When the CT scanner arrived in 2018, the museum started an initiative to digitize them.
The scanner is similar to what you’d find in a hospital, only smaller. It creates a data set of several thousand cross-section images that illuminate the specimens’ anatomy from different angles. Digitally reconfigured, these slices produce a three-dimensional, proportionally accurate representation of the original specimen. “We can look at just the bone if we want to. Or we can look at the whole soft tissue structure,” Nagesan explains. “These scans can be thought of as facsimiles of the actual specimens—they’re effectively a one-to-one.” Researchers can use free software to download the data set and do whatever studies they need. “We’re opening the doors to our collection virtually,” he says.
As with the frog inside the snake, digital scans can uncover connections between animals and their environment without damaging the specimens. Cody Thompson, assistant research scientist and mammal collections manager at UMMZ, oversees the research activities of the museum’s mammal collections. “We’ve found residual evidence of prey that we could not have previously known without doing a complete dissection,” he explains. “Instead, we can now digitize it and know exactly, or at least relatively close to exactly, what that animal ate, what parasites infected it, while still preserving the specimen.”
UMMZ’s digitization projects run as part of several grants, including the oVert Project, a national, inter-institutional effort dedicated to collecting digital images of vertebrates. “We want to get data to three groups: researchers in the United States or abroad, educators who could use the data for classroom activities, and the public,” Thompson explains. “We want people to see what museums can do.”
A similar mission has been underway at the Museum of Paleontology (UMMP) for years. The University of Michigan Online Repository for Fossils (UMORF), launched in 2014, is a public-facing website full of 3-D representations of the museum’s fossils, everything from massive mammoths to snails and plants. “Initially, we wanted to make it easier for people to access these really large bones,” says Adam Rountrey (Ph.D. ’09), collection manager and 3-D specialist at UMMP and one of the UMORF project leads.
The team uses a process called photogrammetry that takes hundreds of images and uses computer software to create 3-D models. “It’s a really flexible system. On tiny fossils we can get the camera close and move the fossil on a turntable. On really big things, like a mastodon skeleton, we set up the camera on a boom and use a remote control to move it and take pictures.”
Typically the public doesn’t have access to research museums, but digitization projects bring them into the public sphere. UMORF wants to make its collection available to everyone, even from mobile devices. UMMP has digitized the U-M Museum of Natural History (UMMNH) dioramas that were on display before its move in 2019. The digital “Life Through the Ages” collection shows different environments throughout Earth’s history, complete with 3-D representations of plants and animals from millions of years ago.
Another UMORF feature, MI Backyard Fossils, allows people to compare UMORF’s 3-D models and images to fossils they find in their backyard or at the beach. “Someone studying a mastodon at another university or in the field can use UMORF’s digital models as a reference,” Rountrey explains. “It’s useful for K-12 classrooms, too, and a great tool to teach skeletal anatomy.”
“A lot of people go to a museum and only see the 30 or 40 specimens on display,” Nagesan says, “but that’s just scratching the surface. There are several million specimens in our collections at UMMZ.
“As a research museum in a public institution, this work allows us to use our resources to teach people about the climate crisis and rapid loss of biodiversity around our planet,” he continues. “Our little process of using CT scans to highlight obscure specimens helps, even in a small way, to emphasize the biggest issues of our time.”
Technology might create vibrant and precise digital images of specimens and fossils, but the daily work itself is tactile, methodical, and delicate. Undergraduate researchers are often the ones digging in. “Over the entire history of the project, we’ve probably had 100 undergraduates involved,” says Rountrey.
Lian Anderson (B.S. ’22), who transferred to LSA as a sophomore to study paleontology in the Department of Earth and Environmental Sciences, has worked as a technician at UMMP since her first semester on campus. She interacts directly with fossils, photographing them for UMORF, creating 3-D models on the computer, and measuring specimens to make sure online models are to scale.
Anderson digitizes the invertebrate fossil collection. “Basically anything that doesn’t have bones,” she says. “I love starfish. Their anatomy is almost alien-like. You can track geological events through invertebrate fossils by running isotope analyses on them. The fossils can also tell us about how they’ve evolved and split into different species.”
For Anderson, working with fossils hands-on is a labor of joy and intellectual discovery. “Often in paleontology, fossils are reserved for graduate students or upper-level undergraduates. To handle such famous fossils that papers are written about and are cited as examples of their species has been amazing.” Because UMORF helps simulate a hands-on experience, more students can digitally access unique and fragile fossil specimens. “I’ve been exposed to so much more than I would have just being in a lecture,” Anderson adds.
Shion Otsuka (B.S. ’22) started working on UMMZ’s digitization projects because she wanted experience with a wide array of animals. Otsuka is on the pre-vet track at LSA, studying ecology and evolutionary biology with a minor in sustainability. She started volunteering at UMMZ during the summer after her first year and now works as a research assistant. “Shion is our go-to person for managing the day-to-day activities of the grants associated with the CT scanner,” says Thompson. “She’s become a key collaborator on our team.”
“I remove the specimens from their jars and pack them to make sure they’re steady during the scan,” Otsuka explains. “I upload the data into the software programs. Touching the specimens is really cool. I haven’t been grossed out yet,” she adds with a laugh.
Some student researchers, like Otsuka, use the technology and skills they’ve developed to conduct their own research, present at national conferences, and write honors theses. Otsuka, for example, has used UMMZ’s digital archives to research shrews. “I use the scans to compare morphologies and to look at their venom glands,” she explains.
These students play a fundamental role in this research, and their ability to continue their studies and do their work remotely aligns with the original mission of the projects. Digitizing fossils remotely during the pandemic opened Anderson’s eyes to accessibility within the field of paleontology and the need to make things more digital. “It’s such an old discipline, and the methods can often seem outdated,” she says. “We’re bringing paleontology into the digital world.”
For years students and researchers have collaborated at the museums, interacting up-close with fossils and decades-old specimens, setting up the scans with their own hands. For researchers at UMMZ and UMMP, the pandemic made their digitization projects more relevant and made the fragility of the archives they handle more concrete.
While scans and models are very useful, Rountrey explains, they’re not equivalent to physical objects, which contain far more information “in” them than scans do. “The physical objects are still vital,” he explains. “There are many types of studies, like those that use DNA or chemical composition, that require physical access to the specimen.”
Digitizing specimens at UMMZ also means future students will have research opportunities. “The work we’re doing to digitize and store data online will remain available to everyone for years,” Otsuka says.
Thompson agrees. “The collections at UMMZ can be used by anyone, but we want to ensure that they’re available for scientific investigation and education for the next 100 years. Producing digital derivatives is a way to do that.”
The question is not scan versus physical object, Rountrey says, but how they complement each other. “We will always try to preserve the original physical specimen for future researchers and students. Digitized information about specimens makes them more accessible and can help with conservation, but we’ll always have a need for the physical specimens.”
By digitizing these specimens and fossils, researchers bring relics from the past to the present and into the future. “Some specimens we’ve scanned and made available are now extinct,” Nagesan says. “We’re not just talking about dinosaur fossils, we’re talking about animals that have only gone extinct in the last century, animals people may still remember.
“There’s a species of frog that only lived at a waterfall in East Africa. That waterfall was dammed and the frog’s habitat ruined. That frog is now extinct, and specimens of the species only exist in museums,” he continues. This example is a cautionary tale that adds urgency to Nagesan and his fellow researchers’ work. Other specimens that are currently being digitized by UMMZ, he explains, could well be extinct in the next several decades. “Their only representatives will be what we hold in these collections and make available digitally. Museum collections are not static places. They’re active research resources and dynamic archives of our planet’s biodiversity.”
When LSA classes couldn’t hold in-person labs, they used 3-D models. Models also gave researchers around the world access to the museums’ holdings when travel was restricted. The models also helped the students who work at UMMZ and UMMP maintain connection. “As a museum we highly value physical objects,” says Thompson. “But having these specimens in a digital format allowed students to continue their research when we couldn’t be in the museum.”
This was the case for rising senior Rhea Rajani. In March 2020, she was a first-year student studying biology on a pre-vet track. When Rajani arrived at LSA, she knew she wanted to study animals, but digitization wasn’t on her radar. When campus shut down because of COVID, Rajani moved home to Holland, Michigan, to finish the term remotely. She’d been working on the digitization project at UMMZ through the Undergraduate Research Opportunity Program (UROP). “When I started UROP, I didn’t know what research I wanted to do. I never thought I would be able to pick up the digitization software so fast. Now I know I can combine something I already loved with something completely new. It’s helped me grow my confidence about the future.”
Rajani studies the skeletal structures of bat wings and has been able to continue her research when she could not be in the museum. “When I went remote, I uploaded CT scans that we already collected onto an external hard drive and took it with me,” she says. “That whole time, I turned those scans into 3-D models.”
After conducting her research from home, Rajani appreciates the role digital tools can play in keeping us grounded. “Kids couldn’t take field trips or do hands-on activities with specimens, but with digital models they could still look at the same thing virtually. It wasn’t exactly like being in-person, but it meant that everyone’s learning didn’t have to stop.”
Do you want to see a mastodon tusk or the full skeleton of an extinct bird in 3-D? Of course you do. Learn more about the digitization efforts at the U-M Museum of Paleontology, and view a fish skull that looks like Groot when you spin it around on your computer monitor.
In LSA, we’re preparing students to create bold and purposeful change, wherever their individual paths lead. After graduation, Emmanuel plans to put his multicultural perspective and international studies degree to work in refugee and immigration advocacy. An LSA internship scholarship enabled him to gain precious experience with a nonprofit organization for LGBTQ+ asylum seekers — so he can start making a positive difference now.