3D Images of 20,000 Vertebrates Open Source with oVert Museum Specimen Initiative

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Lanthanotus borneensis [Image: Ed Stanley, Florida Museum of Natural History]

While 3D scanning has been used to solve a murder case and recreate a metal passenger aircraft, among other things, it’s really making a positive impact for museums. But I’m not just talking about recreating pieces of artwork: scientists and researchers all over the world are using CT scan 3D imaging to scan museum specimens to learn more about ancient species. Thanks to a $2.5 million grant from the National Science Foundation (NSF), a new initiative called oVert, short for openVertebrate, has launched, in order to get specimens off of museum shelves and onto the Internet – by CT scanning 20,000 vertebrates and making the 3D images available to students, researchers, educators, and the general public.

Smaug giganteus [Images: Ed Stanley and Andy Lievertz, Florida Museum of Natural History]

The project is almost like a digital encyclopedia, and complements other NSF-sponsored efforts to digitize museum collections, like iDigBio, by adding the new, critical component of specimens’ internal anatomy. Because users will have virtual access to all sorts of specimens – the project will include representative specimens from over 80% of existing vertebrate genera – young students can see what a copperhead snake last ate and veterinarians can pre-plan large animal surgeries, while researchers can get an up close look at the circulatory system of a passenger pigeon and undergraduate students can 3D print skulls from multiple frog species, then compare and contrast them.

“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,” said Chris Austin, the LSU Museum of Natural Sciences Curator of Amphibians & Reptiles and a principle grant investigator. “It will help us develop a fuller understanding of our natural world.”

CT scan of hognose snake [Image: Ed Stanley, Florida Museum of Natural History]

CT scanning is non-destructive – it hits a specimen with X-rays from every single available angle in order to create snapshots, which a computer then knits together to from a detailed 3D visual replica. These high-tech images allow specimens to be virtually dissected in order to show internal structures and cross-sections, giving scientists a way to see the internal anatomy of specimens, like its stomach content, muscles, and organs, without having to physically cut them open. Some of the specimens for the oVert project will also be scanned using contrast-enhancing stains, in order to characterize soft tissues.

“Our goal is to provide data that offer a foothold into vertebrate anatomy across the Tree of Life. 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,” explained David Blackburn, oVert’s lead principal investigator and the associate curator of amphibians and reptiles at the Florida Museum of Natural History at the University of Florida, the grant’s lead institution.

Including the LSU Museum of Natural Science and the University of Florida, other research institutions included in the grant are:

  • CT scans reveal details of internal anatomy without damaging specimens. [Image: Ed Stanley, Florida Museum of Natural History]

    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
  • University of California, Berkeley
  • University of Kansas
  • University of Michigan
  • University of Texas, Austin
  • University of Washington
  • The Virginia Institute of Marine Science and Yale University

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

The oVert project 3D images will be housed in the MorphoSource public database, which was created by Duke University so that anyone, be it student, teacher, scientist, or just a curious person, can view the 3D data of species they are interested in. While phenomics – the study of how genes interact with the environment to make physical traits – used to be number one in understanding animal species, advances in understanding the function, evolution, and structure of genes and genomes have overtaken this line of study. Blackburn says that oVert, with its “searchable digital encyclopedia of thousands of vertebrate phenotypes,” could be a very valuable resource.

Co-principal investigator Ed Stanley, right, and David Blackburn compare a CT scan of a frog with a 3-D printed replica. [Image: Kristen Grace, Florida Museum of Natural History]

oVert makes the 3D data open source, which makes it easier for researchers to access vertebrate diversity. In addition, the oVert team hopes that the anatomical images will also be used in academic institutions, to inspire the next generation of scientists. However, while CT scanning is helping the team learn a lot of valuable information about the specimens, it’s a time-consuming and expensive process, which Blackburn says is “limiting the number of specimens that can be scanned.”

In order to really optimize the usefulness of the oVert project, researchers will be scanning what’s known as “super specimens,” which are representative of a species, in good condition, and also have corresponding information in iDigBio, like genetic data and where and when they were collected. Discuss in the openVertebrate forum at 3DPB.com.

[Source: Louisiana State University]

 

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