3D ‘encyclopedia’ to show vertebrates inside and out

CT scan shows salamander and toad were hognose snake's last meal. (Credit: Ed Stanley/Florida Museum of Natural History)

A new initiative will take specimens from museum shelves to the internet by CT scanning 20,000 vertebrates and making the 3D images available to researchers, educators, students, and you.

The oVert project, short for openVertebrate, will complement other museum digitization efforts, by adding a crucial component that has been difficult to capture—specimens’ internal anatomy.

With this kind of virtual access, researchers could peel away the skin of a passenger pigeon to glimpse its circulatory system, a class of third-graders could figure out a copperhead’s last meal, undergraduate students can 3D-print and compare skulls across a range of frog species, and a veterinarian could prepare for a surgery on a giraffe at a zoo.

“In a time when museums and schools are losing natural history collections and giving up due to costs, we are recognizing the information held in these specimens is only getting more valuable,” says project co-principal investigator Luke Tornabene, assistant professor of aquatic and fishery sciences at the University of Washington. “I think this project is going to help create a renaissance of the importance of natural history collections.”

The project will include representative specimens from more than 80 percent of existing vertebrate genera. Some 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,” says David Blackburn, the project’s lead principal investigator and associate curator of amphibians and reptiles at the Florida Museum of Natural History at the University of Florida.

“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.”

CT scanning is a nondestructive technology that bombards a specimen with X-rays from every angle, creating thousands of snapshots that a computer stitches together into a detailed 3D visual replica.

The image 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.

Images scanned for the project will be housed in MorphoSource, a public database created by Duke University that scientists, educators, students, and the simply curious can mine for 3D data on their species of interest.

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“It’s exciting to glimpse the inside of rare and precious specimens, but that is just the beginning,” Blackburn says. “This opens up is a whole world of vertebrate biology research.”

Advances in understanding the structure, function, and evolution of genes and genomes have outpaced phenomics—the study of how genes interact with the environment to produce physical traits, or phenotypes. By providing a searchable digital encyclopedia of thousands of vertebrate phenotypes, oVert could be a valuable resource in narrowing the gap, Blackburn says.

“This is moving phenomes into big data science. Even though traits have been the interface between development, paleontology, evolution and systematics since Aristotle, the big data we tend to think about are genomics and species distributions.”

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

One of the key features of the initiative is making these data freely available, Blackburn says.

“We’re not going to hoard the data. 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.”

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The project, which officially begins September 1, and will be complete in about four years, is not without its challenges: Providing virtual access to specimens still requires boots-on-the-ground work. 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, Blackburn says.

“It’s not going to be without some growing pains.”

The National Science Foundation grant will allow researchers about four years to complete the work. Other research institutions involved in the work include Cornell University; Texas A&M University; the University of California, Berkeley; the University of Kansas, the University of Michigan, the University of Texas, Austin; Yale University; the Academy of Natural Sciences of Drexel University, the California Academy of Sciences, the Field Museum of Natural History, Harvard University, Louisiana State University, the Scripps Institution of Oceanography at the University of California, San Diego, and the Virginia Institute of Marine Science.

Duke University and the University of Chicago are also partners in the oVert project.

Source: University of Florida