New Digital Encyclopedia of 3-D Vertebrate Specimens Offers Open Source Data and Images


CT image of a hognose snake, Heterodon platyrhinos, showing its last two meals: a salamander and a toad.

Photo Credit: Ed Stanley, Florida Museum of Natural History

BATON ROUGE – A $2.5 million National Science Foundation grant will launch oVert, a new initiative to “teleport” museum specimens from their shelves to the Internet by CT scanning 20,000 vertebrates and making these data-rich, 3-D images available to researchers, educators, students and the public.

oVert, short for openVertebrate, complements other NSF-sponsored museum digitization efforts, such as iDigBio, by adding a crucial component that has been difficult to capture — the internal anatomy of specimens.

“As we’re seeing in various fields, 3-D imaging technology is the future. CT scan 3-D imaging is also the future of rapid biodiversity discovery and description. It will help us develop a fuller understanding of our natural world,” said LSU Museum of Natural Sciences Curator of Amphibians & Reptiles Chris Austin, who is a principle investigator on this grant.

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 copperhead’s last meal, undergraduate students could 3-D print and compare skulls across a range of frog species and a veterinarian could plan a surgery on a giraffe at a zoo.

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 at the University of Florida, the grant’s lead institution. “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 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.

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 mine for 3-D data on their species of interest.

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 said.

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. In addition to easing researchers’ access to vertebrate diversity, the oVert team also envisions the anatomical images being used in university and schools, inspiring the next generation of scientists, engineers and mathematicians.

Sixteen research institutions are included in the grant: LSU Museum of Natural Science;  the University of Florida; the Academy of Natural Sciences of Drexel University; the California Academy of Sciences; Cornell University; the Field Museum of Natural History; Harvard University; the Scripps Institution of Oceanography at the University of California, San Diego; Texas A&M University; the University of California, Berkeley; 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.

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


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Natalie van Hoose
Florida Museum of Natural History