New 3D scanning campaign will reveal 20,000 animals in stunning detail

Known as the "Fish Guy," Adam Summers earned his moniker for an odd hobby turned academic obsession: giving dead fish a computerized tomography, or CT, scan. The biomechanist at Friday Harbor Laboratories on San Juan Island, Washington, has been haphazardly scanning fluid-preserved collections of fish for 20 years—"I literally traded Snickers bars for CT scans when I started out," he says—to create detailed 3D representations of the animals and study the intricacies of their internal architecture. Whenever he posted the beautifully rendered skeletons online, fellow fish admirers would eagerly ask what was up next. Summers's half-joking reply: "Don't worry, they are all next. I am scanning all fishes."

An iodine-injected frog reveals muscles, glands, nervous system, eggs, parasites, and more.


Then last year David Blackburn, a herpetologist at the Florida Museum of Natural History in Gainesville, saw Summers's #scanAllFish hashtag on Twitter and light-heartedly countered that he would "scan all frogs." Blackburn had just chatted with museum curators about starting a new digitization effort, so he also called Summers. They decided to up the ante and seek money to "scan it all." Now they have $2.5 million in National Science Foundation funding in hand, and on 1 September they will launch their project: oVert, for "Open Exploration of Vertebrate Diversity in 3D." Many scientists simply know it as the "scan-all-vertebrates" project.

Over the next 4 years, Blackburn will lead an effort to CT scan more than 20,000 vertebrate specimens, representing 80% of all genera, from 16 museum and university collections across the United States. oVert will also pick about 1000 of them—representing most vertebrate families—to soak in an iodine dye, which enhances contrast in soft tissues, allowing researchers to see the muscles, circulatory system, brain, and more.

The resulting 3D renderings will be uploaded to an existing digital depository, MorphoSource, created by Doug Boyer, an evolutionary anthropologist at Duke University in Durham, North Carolina, where they will be freely available for research in fields such as comparative anatomy, evolution, developmental biology, and biomimetics. "The vision is to get specimens off a shelf, into as many hands as possible, and into the context of big-scale research questions," Blackburn says.

Researchers could soon "have all of vertebrate diversity at our fingertips. … This would be immediately useful," says Beth Brainerd, who studies vertebrate morphology at Brown University.

A CT scan of a Mexican beaded lizard (Heloderma horridum)


Summers's hobby turned serious when his lab finally got its own CT scanner in 2015. He also stumbled upon a simple method that accelerated his output. By individually wrapping fish in alcohol-soaked cheesecloth to prevent them from drying out, and then stacking them into what he calls "fish burritos," he could scan many specimens at once. So far, he's done more than 4500 specimens and 2400 different species.

Fish CT scans from Summers's lab are already aiding other research. To design an energy-efficient robot for underwater exploration, Cassandra Donatelli at Tufts University in Medford, Massachusetts is using the 3D models to mimic the joints and movements of long and slender fish. Neuroanatomist Michael Hofmann at the University of Bonn in Germany is beginning a comparative study of the inner ears of fish to understand their hearing and orientation. And in April, Kevin Conway, an oVert participant and curator of fishes at Texas A&M University in College Station, described a new species of clingfish based on a scan that revealed about 2000 tiny teeth resembling toothbrush bristles.

"I've been shocked that almost every time we scan a species, we learn something new," says Matthew Kolmann, a postdoctoral researcher in Summers's lab whose CT scans of piranhas revealed that the fish tend to leave nasty pinhole bite marks on each other's bones. Blackburn calls these discoveries the "natural history bycatch," serendipitous glimpses into animal lifestyles.

A CT scan of a pirañha (Serrasalmus medinai)


Scans are an especially powerful tool for studying the anatomical quirks of rare organisms with only one or two known specimens, Blackburn adds, because "no one in their right mind would take these things apart." (The scans can also reveal some of a creature's diet—Blackburn has found frogs with ants, crabs, and even another frog in their stomachs.)

For oVert, six universities that already have CT scanners will scan their own specimens and ones from the other 10 institutions. Four researchers are leading the hunt for appropriate bird and mammal specimens, a challenging task since these animals are typically mounted as dry taxidermy. oVert aims to find fluid-preserved specimens with innards intact, which is more common for reptiles, amphibians, and fish.

Conway will be in charge of scanning anything especially large, with a budget for about 500 specimens up to 2 meters in length and weighing 250 kilograms. Juvenile or fetal specimens will be used for oversized species. In the past, his group has scanned gars, an eel, a bowhead whale fetus, and even a 2.5-meter bigeye sand tiger shark (which didn't completely fit inside the scanner).

A CT scan of a bowhead whale (Balaena mysticetus)


Since all specimens, some very old, will come from museum collections, their external shape may be deformed. But the internal anatomy should be preserved, and the iodine dye will highlight it further in select specimens. Among other uses, oVert will "open new doors" for understanding brain evolution in hard-to-find species, predicts Kara Yopak of the University of North Carolina in Wilmington, the neuroanatomy adviser to the project.

Education and outreach is a major goal of oVert. Bruce McFadden, vertebrate paleontology curator at the Florida Museum of Natural History in Gainesville is eager to use the 3D models in K-12 education. Previously, he's worked with science and art teachers to help a group of middle school girls reconstruct a life-sized jaw from the prehistoric shark megaladon, based on CT scans of its teeth. "They were real jazzed up about this," he says.

Boyer is excited at the prospect of being able to explore vertebrate shape and anatomy across thousands of species. "Everything we thought we knew about anatomical evolution, throw it out the window," he says. "This will be at such a different scale, we will have to go into it with new eyes."