Peabody joins venture to create ‘digital encyclopedia’ of vertebrate scans

Collage of images of frog bones and muscles
An iodine-injected frog reveals muscles, glands, nervous system, eggs, parasites, and more. (Image: Edward L. Stanley, David C. Blackburn)

The Yale Peabody Museum of Natural History will participate in a venture to essentially create a digital encyclopedia providing free virtual access to detailed anatomical scans of vertebrate specimens from 16 U.S. museums and institutions, as well as the extensive data accompanying them.

Called oVert, short for “Open Exploration of Vertebrate Diversity in 3D,” the project will use non-invasive x-ray computed tomography (CT) scanning on over 20,000 vertebrate specimens to generate high-resolution digital anatomical data. The project is supported by a $2.5 million grant from the National Science Foundation.Gregory Watkins-Colwell, collections manager for herpetology and ichthyology in Peabody’s Department of Vertebrate Zoology, is the lead principal investigator (PI) for the Peabody portion of the grant. Working with Yale students, he will select and prepare representative specimens — ones with innards intact. That means soaking them in an iodine dye to enhance contrast in soft tissues.

The Peabody is strong in fluid mammals and fish,” said Watkins-Colwell referring to the vertebrate groups he is likely to draw from in the endeavor.

The Peabody will ship prepared specimens to Harvard University, one of the six regional scanning centers. The Florida Museum of Natural History at the University of Florida is the grant’s lead institution. Overall, representative specimens from more than 80% of existing vertebrate genera will be scanned. Some 1,000 of these, representing most vertebrate families, will receive the iodine bath to enhance contrast.

Scanned and digitized images will be uploaded to MorphoSource, an existing public database created by Duke University, where they will be freely available to scientists, educators, students, and the public. Images can be dissected, layer by layer, to expose cross sections and internal structures — muscles, circulatory system, brain, and more.

Unraveling the story of the history of life

Bhart-Anjan Bhullar, assistant professor and assistant curator in Yale’s Department of Geology & Geophysics and co-PI on the grant for the Peabody, said this information will advance vertebrate biology research.

Here at Yale, the paleontology, anatomy, and development groups are heavily invested in 3D imaging, which can help us see things we had never before been able to see, including tiny, delicate structures deep within the bodies of rare organisms. Traditional dissection and other physical methods would destroy the architecture and the context of these structures, which are often crucial for unraveling the story of major transitions in the history of life,” he explained.

The oVert grant, he added, “will provide an enormous, open-access database of biological structure across all of vertebrate diversity, driving research on the history and current state of the biosphere for decades to come.”

Educators in universities and K-12 classrooms will be able to use the images to inspire future scientists, engineers and mathematicians — a major goal of the oVert team. Students at all levels, from third graders to seniors in high school, will be able to mine the data to see what a boa constrictor last ate, print a 3D frog skull, or view the circulatory system of a baby blue whale.

David Skelly, Peabody director, said: “The resource that will be created by the work will transform what we understand about animals. The fact that it can be shared across the entire global community of researchers is truly exciting.”

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