Around the Pier: Scripps Collection to Participate in Project to Create 3-D Digital Archive of Every Vertebrate Genus


A new initiative funded by the National Science Foundation will yield 3-D images of the external and internal anatomy of 20,000 specimens representing nearly every genus of vertebrate, including fishes, amphibians, reptiles, birds, and mammals. The computer tomography (CT) scans will be made available online to researchers, educators, students, and the public.

The project, called oVert, short for openVertebrate, complements other NSF-sponsored museum digitization efforts, such as iDigBio and the Digital Fish Library, by adding a crucial component that has been difficult to capture — the intact skeleton and other internal features of a vast array of specimens. The Marine Vertebrate Collection of Scripps Institution of Oceanography at the University of California San Diego — which houses more than two million fish specimens, representing over 90 percent of the world’s fish families and nearly 6,000 species from around the globe — will provide samples for scanning as part of the project. The Florida Museum of Natural History at the University of Florida (UF) leads the effort, with 16 research institutions participating.

“Our collection is especially strong in pelagic and deep-sea fishes from around the world and in coastal fishes from the eastern Pacific Ocean, and we have already begun acquiring CT scans of specimens from the collection in conjunction with ongoing studies on the evolution of blenniiform fishes,” said Phil Hastings, a professor of marine biology and curator of marine vertebrates at Scripps Oceanography, and a co-principal investigator on the oVert grant.

CT scanning is a non-destructive technology that bombards a specimen with X-rays from every angle, creating thousands of snapshots that a computer stitches together into a detailed 3-D visual replica that can be virtually dissected, layer by layer, to expose cross-sections and internal structures. The scans allow scientists to view a specimen inside and out — its skeleton, muscles, internal organs, parasites, even its stomach contents — without touching a scalpel.

With virtual access to specimens, researchers could peel away the skin of a passenger pigeon to glimpse its circulatory system, a class of third graders could determine a shark’s last meal, undergraduate students could 3-D print and compare fins and skulls across a range of fish species, and a veterinarian could plan a surgery on a giraffe at a zoo. Individual internal organs can even be isolated and manipulated, making even more advanced research possible.

“Using a computer we can ‘dissect’ out individual structures to study and compare them in greater detail," Hastings said.

The project will encompass representative specimens from more than 80 percent of existing vertebrate genera, and a selection of these will also be scanned with contrast-enhancing stains to characterize soft tissues.

“Our goal is to provide data that offer a foothold into vertebrate anatomy across the Tree of Life,” said David Blackburn, oVert’s lead principal investigator and associate curator of amphibians and reptiles at the Florida Museum of Natural History.. “This is a unique opportunity for museums to have a pretty big reach in terms of the audience that interacts with their collections. We believe oVert will be a transformative project for research and education related to vertebrate biology.”

As part of oVert, these images will be housed in MorphoSource, a public database created by Duke University that scientists, educators, students, or the curious can search for 3-D data on their species of interest.

CT scanning offers a wealth of data about specimens, but it’s an expensive and time-intensive process, limiting the number of specimens that can be scanned, Blackburn said. To maximize the usefulness of oVert, researchers will select and scan “super specimens,” those that are representative of a species, are in good condition, and have corresponding data in iDigBio — information such as where, when and by whom they were collected. Ideally, the specimen would also have genetic data.

One of the key features of oVert is making these data freely available, Blackburn said.

“The realm of questions that can be asked in biology is often constrained by what is accessible. This lowers the barrier for people to work on a broader diversity of vertebrate life,” said Blackburn.

"Natural history collections such as the Scripps Marine Vertebrate Collection are irreplaceable resources that document the earth’s diversity,” said Hastings, “and are key to understanding the history of the earth as well as changes related to human activities including global climate change.”

In addition to easing researchers’ access to vertebrate diversity, the oVert team also envisions the anatomical images being used in universities and schools, inspiring the next generation of scientists, engineers, and mathematicians. The Florida Museum will partner with UF’s Center for Precollegiate Education and Training to develop and run yearly workshops with high school science teachers to create lesson plans based on digital and 3-D printed specimens.

"This is an excellent example illustrating the value of natural history collections” Hastings said. “This project would have been inconceivable only a few years ago, but technological advances, including computing and data storage capacity, have opened a new opportunity to survey the diversity of vertebrates using specimens already present in these collections."

The project, which kicked off Sept. 1, will require several crucial steps before virtual access is possible. Specimens must be hand-selected, shipped, tracked, scanned, uploaded to MorphoSource, and integrated with corresponding data in iDigBio. Multiply this process by 20,000 across 16 museum collections, and the workflow can quickly become daunting.

“We regularly send fish specimens to researchers around the world, so selecting ideal specimens for this project will be a fun challenge,” said Scripps collection manager Ben Frable.

In addition to Scripps Oceanography and the Florida Museum at UF participating research institutions include the Academy of Natural Sciences of Drexel University, the California Academy of Sciences, Cornell University, Duke University, the Field Museum of Natural History, Harvard University, Louisiana State University, Texas A&M University, the University of California, Berkeley, the University of Chicago, the University of Kansas, the University of Michigan, the University of Texas, Austin, the University of Washington, the Virginia Institute of Marine Science, and Yale University.

  – Mallory Pickett (adapted from a University of Florida news release)








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