For seven years, a CT scanner has been whirring away nearly around the clock, tucked inside of a lab at the University of Michigan Research Museums Center.

Inside the machine, scientists scan animal specimens: snakes, lizards, frogs, bats, rodents, wasps, fish, a whole red fox, an armadillo. The scanner, a microCT scanner, aims concentrated X-rays at the specimens, which are fixed to a metal plate. The metal plate rotates throughout the scan, and the X-rays bounce off the specimen, caught by a detector, which translates the light waves into anatomical slices of the specimen.

Lab technician Haley Martens, having tuned a computer program that controls how fine-grained the images will be, reassembles the anatomical slices into 3D images of the animal’s nervous system, skeleton, circulatory system, or whatever element of the specimen researchers want to examine. The machine has the capability of imaging the most minute part of an animal without causing any damage to the specimen itself.

Now, the U-M MicroCT Scanning Laboratory has recently completed its 10,000th scan: a 3D scan of a wolverine skull, collected in British Columbia in 1948. The skull is part of the U-M Museum of Zoology’s specimen collection, housed at the Research Museums Center, a U-M building off campus that holds more than 20 million specimens across four museums.

“In the world of museums, one of the core missions is the preservation of these specimens for long-term care, long-term research in perpetuity for uses that we can’t necessarily predict,” said lab manager Ramon Nagesan. “The MicroCT Lab has really been an excellent tool for us to delve deep into these specimens without damaging or destroying them.

“We can essentially generate a whole view of the anatomy of the organisms we scan, everything from skeletal structures to nervous tissue, and, critically, we can do this without damaging or destroying the specimens. This 10,000th scan is important for us because it represents reaching a huge milestone in terms of the data we’ve generated.”

Just as critically, much of this data is available for researchers outside of the U-M community to use, Nagesan said. Each scan that is made is uploaded to the lab’s online catalogue, from which researchers can request CT scans or even STL files to create 3D printed versions of the specimens.

Fine-grained data

Like a CT scanner at a hospital, the microCT scanner uses X-rays to take images of bone, muscle and other soft tissues. But the microCT scanner can take much more fine-grained images. “Micro” refers to the resolution of the scans: a microCT is any scan between about one micron (a strand of spider’s silk is about three to eight microns) to about 150 microns, according to Nagesan. A typical medical CT scanner operates at about 650 microns. The lower the number, the higher the resolution, he said.

During the scan of the wolverine skull or for other skeletal scans, the microCT scanner will take 1,600 images of the skull. Other scans that require higher resolution, such as scanning fluid specimens that are stained to see the soft tissue, high density scans such as fossils, or low density specimens such as plants, will take more images and spend more time in the scanning machine, Martens said.

Depending on the resolution and how the specimen is prepared, the scanner can make anatomical images of the specimen’s skeleton or exoskeleton, muscle, nervous system, circulatory system, or even the contents of its stomach, no matter the age of the specimen.

“Working in the CT lab is an incredible learning experience, as I am constantly gaining knowledge on the species I am scanning, as well as the technology I am working with. Every week poses new and exciting challenges, from scanning cordyceps fungus in insects to large reticulated pythons, Roman glass vessels, and even living leaves,” Martens said. “As CT scanning is becoming increasingly more popular and important in our field, I am lucky to be part of thrilling new research, such as finding diet items in snakes and seeing into the brains of wasps.”

While this 10,000th scan represents just a tiny fraction of the 22 million items held at the Research Museums Center, that number includes at least one representative of every vertebrate genus held in an initiative called the Open Vertebrate Thematic Collections Network, or oVert, according to Nagesan. The initiative, funded by the National Science Foundation, aimed to produce CT scans of about 20,000 fluid-preserved specimens from U.S. museum collections. With that project completed in 2022, the lab workers now scan based on projects submitted to the lab.

Imaging the past for the future

As the wolverine skull was being scanned, two undergraduate students pushed carts of garter snakes toward the Museum of Zoology’s collections to be catalogued, donated by a U-M alum whose career centered around the animal. While the oldest specimen in the Museum of Zoology has been in the collection for about two centuries, specimens continue to flow into the collections, either through donation or through original research, according to Hernán López-Fernández, director of the Museum of Zoology.

“We are trying to grow because fundamentally, our ability to learn from the past and how we are changing biodiversity into the future absolutely requires that we keep recording what biodiversity looks like today,” he said. “It’s really critical that our collections continue to grow, and we do that very judiciously, very carefully and very thoughtfully.”

Each specimen can tell a wealth of information about how the animal lived, López-Fernández said. With new technologies such as the microCT scanning and genomic-level sequencing of specimens, researchers can look at a 150-year-old sample and look at not only its skeleton, but what it ate, how it grew and where it lived.

“A fish or a snake that was collected in a place that no longer exists because now there’s a parking lot or an apartment building or a mall, we can go back and understand their biology,” López-Fernández said.

“Having this historical collection is revealing itself as increasingly fundamental to understanding how the planet is changing—with environmental changes of all kinds: global warming, as well as the transformation of ecosystems into urban or semi-urban areas. Often the only record we have of what a certain part of the planet looked like is what’s sitting in our collections.”