3D scans of bat skulls help natural history museums open up dark corners of their collections

Picture a natural history museum. What comes to mind? Childhood memories of dinosaur skeletons and dioramas? Or maybe you still visit to see planetarium shows or an IMAX feature? You may be surprised to hear that behind these public-facing exhibits lies a priceless treasure trove that most visitors will never see: a museum’s collections.

Far from being forgotten, dusty tombs, as is sometimes the perception, these collections host the very cutting edge of research on life on this planet. The sheer scale of some of the largest collections can be staggering. The Smithsonian National Museum of Natural History, for instance, houses over 150 million specimens. Even a smaller academic institution, like the Research Museums Center of the University of Michigan, houses a labyrinth of specimen vaults, preserving millions of skeletons, fossils, dried plant material and jarred organisms.

Most importantly, poring over this wealth of knowledge at any given time are active researchers, working to unravel the intricacies of Earth’s biodiversity. At the University of Michigan, where I received my Ph.D. in ecology and evolutionary biology, I worked nestled among these skeletons, fossils and other natural treasures. These specimens were critical to my research, as primary records for the natural history of the world.

Yet despite the incalculable value of these collections, I often wondered about how to make them more accessible. A project to digitally scan hundreds of bat skulls was one way to bring specimens that would look at home in an antique Victorian collection straight to the forefront of 21st-century museum practices.

In most museums, specimens – like these bats in the Research Museums Complex at the University of Michigan’s Museum of Zoology – are carefully protected in drawers and cabinets, with meticulous metadata that record where and when they were collected. Dale Austin, Department of Ecology and Evolution, University of Michigan, CC BY-ND

A valuable resource, largely hidden from view

By researching variation among and within collection specimens, biologists have uncovered many ecological and evolutionary mysteries of the natural world. For instance, a recent study on bird specimens traced the increasing concentration of atmospheric black carbon and its role in climate change over more than a century. Scientists can collect ancient DNA from specimens and gather information about historical population levels and healthy genetic diversity for organisms that are now threatened and endangered.

My own research on global bat diversity used hundreds of museum specimens to conclude that tropical bats coexist more readily than many biologists expect. This finding fits with an overall pattern across much of the tree of life where tropical species outnumber their temperate cousins. It may also help explain why in many parts of Central and South America, bats are among the most abundant and diverse mammals, period.

However, research on these specimens often requires direct access, which can come at a steep price. Researchers must either travel to museums, or museums must ship their specimens en masse to researchers – both logistical and financial challenges. Museums are understandably wary of shipping many specimens that are truly irreplaceable – the last evidence that some organisms ever existed in our world. A museum’s budget and carbon footprint can quickly balloon with loans. And as physical specimens cannot be in more than one location at once, researchers may have to wait an indefinite amount of time while their materials are loaned to someone else.

A different way to access biological specimens, using micro-CT scans. Shi et al, PLoS ONE 13(9): e0203022,, CC BY-ND

CT scanning bat skulls

I have tried to tackle these issues of access with my collaborators Daniel Rabosky and Erin Westeen using micro-CT technology. Just like with medical CT scanning, micro-CT uses X-rays to digitize objects without damaging them – in our case, these scans occur at the fine scale of millionths of meters (micrometers). This means micro-CT scans are incredibly accurate at high resolutions. Even very tiny specimens and parts are preserved in vivid detail.

For my Ph.D. research, we used micro-CT scanning to digitize nearly 700 individual bat skulls from our museum’s collection. With estimates of about 1,300 described species, bats represent about 25 to 30 percent of modern mammal species, second only to rodents. However, one of the reasons researchers have long been fascinated by bats is their immense diversity of behavior and function in nature. Much of this ecological diversity is encoded in their skulls, which vary broadly in shape and size.