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Biology participates in creating digital encyclopedia

Tuesday, September 5, 2017 - 10:45

A $2.5 million National Science Foundation grant will daylight thousands of specimens from their museum shelves by CT scanning 20,000 vertebrates and making these data-rich, 3-D images available online to researchers, educators, students and the public.

The project 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.

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 in a zoo.

More than one quarter of the world’s vertebrate species will be scanned and digitized through this project, and researchers will aim to include specimens from more than 80 percent of existing vertebrate genera. A selection of these will also be scanned with contrast-enhancing stains to characterize soft tissues. There are almost 70,000 vertebrate species described today, and more than half of those are fishes.

The UW has already made a dent in scanning and digitizing many of the fish species included in this project through the #ScanAllFishes effort, led by Adam Summers, a UW professor of aquatic and fishery sciences and of biology. For the past two years, Summers and colleagues have used a small CT scanner at Friday Harbor Laboratories to produce scores of fish scans from specimens gathered around the world.

A CT scan of the spotfin hatchetfish.


A CT scan of the spotfin hatchetfish.Adam Summers/University of Washington

In contrast, micro-CT scanners like the one at Friday Harbor Labs can pick up incredible detail of small vertebrates that are difficult to study at life size, he explained. UW scientists have scanned some of the smallest fish in the world and can zoom in to the digital file to examine anatomy not visible with the naked eye. They can also 3-D print specimens larger than life.

“We are going to be exploring the capabilities of understanding vertebrate anatomy at the finest scales,” Tornabene said.

The UW’s three CT scanners will focus mainly on digitizing key species in the Burke Museum’s collection of 12 million fish specimens, as well as the museum’s large bat collection. In addition to Tornabene and Summers, Katherine Maslenikov, Burke Museum fish collections manager, and Sharlene Santana, curator of mammals at the museum and assistant professor of biology, will lead the effort at the UW.


Read the full article in UW Today

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