3D Bat Skull Scans Help Natural History Museums Open Dark Corners In Their Collections


Imagine a natural history museum. What comes to my mind? Childhood memories of dinosaur skeletons and dioramas? Or maybe you’re still visiting to see planetarium shows or an IMAX feature? You might be surprised to learn that behind these public exhibits hides an invaluable treasure that most visitors will never see: a museum’s collections.

Far from being forgotten, dusty tombs, as is sometimes believed, these collections house the cutting edge of research on life on this planet. The magnitude of some of the larger collections can be staggering. The Smithsonian National Museum of Natural History, for example, houses over 150 million specimens. Even a smaller academic institution, like the Research Museums Center at the University of Michigan, is home to a maze of specimen vaults, preserving millions of skeletons, fossils, dried plant material, and potted organisms.

More importantly, active researchers are constantly examining this wealth of knowledge, as they strive to unravel the intricacies of Earth’s biodiversity. At the University of Michigan, where I obtained my doctorate. in ecology and evolutionary biology, I worked nestled among these skeletons, fossils and other natural treasures. These specimens were essential to my research, as the primary documents of the natural history of the world.

Yet despite the incalculable value of these collections, I have often wondered how to make them more accessible. A project to digitally digitize hundreds of bat skulls was a way to bring specimens that would look like they were right at home in an ancient Victorian collection directly to the forefront of 21st century museum practices .

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

A precious resource, largely hidden from view

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

My own research into global bat diversity has used hundreds of museum specimens to conclude that tropical bats coexist more easily than many biologists realize. This finding fits a general trend in 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 be expensive. Researchers either have to go to museums or museums have to send their specimens en masse to researchers – both logistical and financial challenges. Museums are naturally wary of shipping many truly irreplaceable specimens – the last proof that some organisms have ever existed in our world. A museum’s budget and carbon footprint can quickly increase with loans. And because physical specimens can’t be in more than one location at a time, researchers may have to wait indefinitely while their materials are on loan to someone else.

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

CT scan bat skulls

I tried to address these access issues with my collaborators Daniel Rabosky and Erin Westeen using micro-CT technology. Much like medical computed tomography, micro-CT uses X-rays to scan objects without damaging them – in our case, these scans occur at the fine scale of one millionth of a meter (micrometers). This means that micro-CT scans are incredibly accurate at high resolution. Even very tiny specimens and parts are preserved in great detail.

For my research doctorate, we used micro-CT scanning to digitize nearly 700 bat skulls from our museum’s collection. With estimates of around 1,300 described species, bats make up about 25 to 30 percent of modern mammal species, just behind rodents. However, one of the reasons researchers have long been fascinated by bats is their immense diversity of behaviors and functions in nature. Much of this ecological diversity is encoded in their skulls, which vary widely in shape and size.

At the Michigan School of Dentistry’s micro-CT facility, we scanned each bat skull at high resolution. Each scan produced hundreds of thousands of images per specimen – each image a tiny cross-section of an original skull. With these “stacks” of sections, we then reconstructed surfaces and volumes in 3D. Basically, we recreated a 3D “digital specimen” from each of the 700 or so originals.

Users can manipulate 3D cranial model created from micro-scanners of a woman Desmodus rotundus, the common vampire bat.

Digital specimens open doors

In partnership with MorphoSource at Duke University, we have since published our digital specimens in an open access repository for researchers, educators and students. Each digital specimen is associated with the same identifying data as its original, allowing search without travel or shipping. Best of all, many delicate parts can be digitally dissected without fear of irreparable damage. Digital specimens can even be 3D printed at different scales for use in educational settings and museum exhibits.

My colleagues Dan and Erin have continued to expand these efforts to other vertebrates in our museum. Our hope is that the wider scientific community will embrace open access digital specimen data in the same way that publicly available digital genetic data has been adopted throughout biology. Digitization can extend the reach of every museum, especially as the prices of digitization fall and open-access micro-CT software becomes more convenient.

This digital revolution comes at a time when many natural history museums are in danger. Museums around the world are crippled by budget cuts and decades of neglect, with devastating consequences.

One way to revitalize museums is to embrace digital missions that preserve invaluable data and foster global collaboration. Far from rendering physical collections obsolete, digitization can modernize natural history museums, as it has done with libraries and other museums of art, history and culture. The originals will always be there for those looking to delve deep into natural history. Rather, the digital wing can invite curiosity and questions about sources that most museums could never dream of reaching otherwise.

When I started out as a biologist, I was plagued by the common concerns of researchers. What was going to happen to all of my data? Who else would ever see him? Scientists never know what new life can be breathed into our basic research after years, decades, centuries. I think of the hundreds of former scientists who have subconsciously contributed data to my own research, spanning nearly 130 years and six continents of expeditions.

By digitizing their previous efforts, my colleagues and I made sure that they can reach a large audience, far beyond what they had possibly imagined. The potential impact of a specimen should no longer be limited by the walls and constraints of a museum. Instead, museums can open their doors to a digital future, inviting anyone into the endless wonders of the natural world.


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