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From Smallest Mammal to Oldest Dinosaur: Unique DigiMorph Web site reveals 3-D interior of natural objects

For 35 years, the largest egg in the world has sat in the collection at the National Geographic Society’s Explorers Hall in Washington, D.C. Discovered in Madagascar, this egg of the extinct elephant bird presented scientists with a familiar conundrum: How to study a precious object without destroying it?

Dr. Timothy Rowe with the elephant bird egg inside the CT scanner
Dr. Timothy Rowe poses inside the CT scanner with the elephant bird egg, the largest egg in the world.

If the egg contained a preserved embryo, it might help scientists understand how these giant birds—which could reach 11 feet in height—developed. But there was no way to find out without opening up the egg. A visit to the High Resolution X-ray Computed Tomography Facility at The University of Texas at Austin in 1999 changed that.

The UTCT scanning facility in the Jackson School of Geosciences houses the first scanner of its kind in the world used in a scientific academic setting. Employing the same technology found in the medical CT scan, the scanner allows scientists to observe the interior of opaque, solid objects without altering the objects in any way. The DigiMorph Web site then makes three-dimensional views of those interiors available to anyone with access to the World Wide Web.

“Those of us who study objects really share similar problems,” says Dr. Timothy Rowe, who co-directs the UTCT scanning facility with Dr. William Carlson and Dr. John Kappelman. “How do you see inside the object? How do you measure it? Even if you can hold the object in your hand, you can’t squeeze the information it preserves out of it.”

The CT scanner gets at that information by making X-ray slices through an object. These slices display differences in X-ray absorption arising mainly through differences in density within an object. When the slices are put back together, scientists are able literally to see the object inside and out, in three dimensions. The object itself is untouched.

The X-ray CT was originally developed in Great Britain in 1971 as a medical diagnostic tool. Its inventors earned the Nobel Prize for Medicine in 1979. While the medical CT uses a relatively low level X-ray to examine the human body, industrial CTs were developed to penetrate denser objects.

Skeleton of the hog-nosed bat
The skeleton of the hog-nosed bat, the world’s smallest mammal, was nearly impossible to study before it was scanned. Read more about bats and the DigiMorph Web site.

The University of Texas at Austin became home to the first industrial-grade scanner dedicated to academic research in 1997. Rowe explains that Carlson was really the mastermind behind the project.

“He was interested in problems behind the crystallization of garnets in minerals,” he says. “He and his colleagues would grind up rocks to measure how many garnets were inside, but after a lifetime, you still might not have a statistically significant sample. So he was looking at tools that might automate our ability to look inside rocks, or look inside bones to see their internal structure, the things we’d been thinking about but had never been able to get to before.”

Industrial-grade scanners, which have significantly more power than their medical counterparts, proved the ideal tool. Carlson, Rowe and Kappelman began scanning objects on scanners available at a local scanning firm. The results were so astounding they eventually secured funding from the National Science Foundation (NSF), the W. M. Keck Foundation and The University of Texas at Austin to bring a scanner to the university. The scanner was designed specifically to meet the needs of the lab in scanning objects of varying sizes and shapes.

It has been in constant use since. Scientists the world over have used the UTCT scanning facility, and specimens they have brought to the lab carry an impressive list of superlatives: the world’s oldest dinosaurs, smallest bat, oldest bird and largest egg, as well as a number of species for which only one known specimen exists. Rowe admits that it’s the kind of thing he never dreamed of when imagining his career as a paleontologist.

“Some of the specimens were really famous, and you can almost see the grime on them from Charles Darwin’s hands and all the famous people who have handled these things,” he says. “It’s an exciting thing to be able to take an object like that and see a whole bunch of new things and to look at it in a completely different way.”

Texas horned lizard and the thorny devil, of Australia
Three-dimensional images allow for comparisons between species, like this comparison of the Texas horned lizard and the thorny devil, of Australia.

The scanner was even used to debunk a claim that a fossil had been discovered that provided an important link between birds and dinosaurs. The fossil, dubbed “Archaeoraptor liaoningensis,” became a subject of controversy after its photograph appeared in the November 1999 issue of National Geographic Magazine. Scanning and analysis at the UTCT scanning facility revealed that the specimen was actually a mosaic of several other fossils and not one specimen. In other words, it was a fraud.

More than 50 museums worldwide have used the UTCT scanning facility, from the Royal Botanic Gardens, Kew, in England to the Carnegie Museum of Natural History in Pittsburgh, to gather information never before available.

Now much of that information is available through the DigiMorph site. DigiMorph is the first large three-dimensional site on the Web, and it’s a natural extension of the work being done at the UTCT scanning facility.

Each image created by the scanner is a digital image. As such, the images can be manipulated, allowing scientists to compute and measure, enlarge and shrink, isolate individual elements and take things apart.

For example, when looking at a scan of the thorny devil, a horned lizard native to Australia, digital imaging enables the user to look at the specimen with and without skin, to measure the distance between the eyes, to see if the lizard’s horn is composed of bone or soft material, to enlarge the skull and view it from any angle. The user can also make comparisons between the lizard and other horned lizards that have been scanned.

Realizing that these data could have immeasurable benefit for researchers, Rowe wrote a grant to the NSF Digital Libraries Program, which funded the creation of the DigiMorph. Word of its value is spreading quickly, and this March alone, the site received visits from about 20,000 users viewing 50,000 pages. Close to 200 specimens, ranging from rare seeds to fossils to tadpoles to hummingbirds, are available, with more being added every week.

DigiMorph offers far more than a simple visual of the object. The user can view each image in three dimensions, rotate it, watch animations from the scan itself, slice it open and look at it from the inside out, and otherwise manipulate the data to gather information.

For scientists and lay users, this allows access to specimens often impossible to encounter in person. And for professors and teachers, it provides a powerful teaching tool. Rowe, for example, uses DigiMorph images in his freshman-level class on dinosaurs.

This palm fruit nut, less than 4 cm long, was scanned for the Royal Botanic Gardens, Kew, in England A CT slice of the palm fruit nut
This palm fruit nut, less than 4 cm long, was scanned for the Royal Botanic Gardens, Kew, as part of a study investigating long-term seed storage of endangered palms. The image on the right shows a CT slice of the nut, revealing its many layers. Viewers can watch an animation of the 513 slices made during the scan.

“We’ve scanned the world’s oldest dinosaurs, brought them here from Argentina,” he says. “It’s one thing to stand in front of a class and say ‘Herrerasaurus is the world’s oldest dinosaur.’ Instead I bring up this head. I can show them the teeth, the eyes, the dimensions of the skull. Then I can say, ‘By the way, this is Herrerasaurus, should you care to remember the name.’

“It’s just a much more compelling and informative way of getting across what these guys really are,” he says.

The DigiMorph site also makes printing of physical models possible, using a three-dimensional rapid prototyper. The printer sprays wax on a metal plate, layer by layer, until an exact three-dimensional replica is created. It’s possible to create life-size models, or to make an enlargement, or to replicate just one element of an object—a bone or skull, for example. Ultimately, though, the prints allow people to hold in their hands exact copies of precious fossils and specimens.

And what about the elephant bird egg? The scan of the egg revealed there was, indeed, an embryo remaining inside in a loose accumulation of bones. Digital imaging allowed researchers to slice the egg open and print it out at life size. The tip of the embryo’s beak, one of its feet and parts of its vertebrae can be clearly distinguished.

Graduate student Amy Balanoff is working with the elephant bird egg data to isolate each remaining bone, render it in three dimensions and print it out. She will ultimately be able to reconstruct the skull of the embryo of a bird that’s been extinct for 400 years. For the first time, scientists may have the information they need to understand how the elephant bird grew to its enormous size.

The egg itself rests safely in Washington, where it can be viewed, whole and intact, for generations to come.

Vivé Griffith

Photo of Tim Rowe: Joseph Jaworski

Images courtesy Digital Morphology

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  Updated 2014 October 13
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