Biotech & Health

Universities and museums join in effort to ‘scan all vertebrates’


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It seems that even scientific endeavors fall victim to feature creep — or in the case of an effort to scan all fishes that has expanded to include all vertebrates, creature creep. More than a dozen learning institutions are pooling their resources to create detailed 3D scans, inside and out, of more than 20,000 animals.

The undertaking could be said to have started more than 20 years ago, when Adam Summers, a dedicated biologist at the University of Washington, began his quest to scan every fish in the sea. What may have been considered eccentric then can only be called essential now: new ways of digitizing and sharing scientific data are sprouting up everywhere, and Summers’ prescient work has spurred other experts to attempt the same.

David Blackburn at the Florida Museum of Natural History decided he’d attempt to scan all frogs (his own specialty) to complement Summers’ collection. But after it became clear others wanted to contribute in kind, they decided to seek real funding and just scan everything. Every vertebrate, anyway — if you wanted to scan every arthopod, jelly, and so on, the task grows by an order of magnitude (or two).

Blackburn (left) and co-principal investigator Ed Stanley scan a frog.

The resulting project, backed by a $2.5 million National Science Foundation grant, is called openVertebrate, or oVert for short. It will take advantage of modern scanning, distribution and reproduction techniques to make this information as comprehensive and accessible as possible. Herpetologist who wants to check for evidence of microfractures in snake ribs? Get in there. Ten-year-old who wants to 3D-print a lizard skull at dinosaur size? Go for it.

The goal is to get 20,000 scans, which is only a fraction of all the vertebrates out there, but they’ll have been carefully selected to represent 80 percent of all genera — so you probably won’t get multiple robins, for instance, but you will get multiple songbirds.

The team, or rather science alliance (I’ve coined a term), is using a variety of tools to scan specimens stored at their various archives, but mostly CT machines, which use x-rays to produce detailed internal imagery. It’s what Summers has been using, but different machines have different applications.

One, at Texas A&M, is big enough that it can scan things up to six feet long, while the micro-CT scanner Summers uses can capture the details of tiny specimens. In the shot below, for instance, you can see that a frog the size of your thumb has eaten a single ant.

And just because these pictures are incredibly cool, check out this one — a gluttonous hog-nosed snake that has eaten a salamander (mid-digestion) and a frog (mid-swallow).

A few lucky species will get a special treatment to bring out the contrasts of their soft tissues, allowing for organ structures, blood vessels and other systems that you’d have to open the sucker up to see. You can see the results of that process below.

A scan of this frog reveals its skeleton, muscle structure, even some parasites lurking in there.

These aren’t just static pictures, either. They’re detailed 3D models that can be manipulated, downloaded and separated (in case you wanted to figure out what kind of frog the snake ate).

They’ll be uploaded to MorphoSource, a repository for 3D data hosted by Duke University. The models will be free to access, though you need an account. Here’s a huge collection of frogs (if this post seems a little amphibian-heavy, complain to Blackburn.)

The data, once properly tagged and cleaned up, could be invaluable for teachers and students, or just for curious people who’ve always wanted to look inside a bowhead whale but have never had the opportunity.

“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,” Blackburn told the University of Washington.

No word when the project will be completed — it only officially starts on September 1, after all. But with the NSF funding everyone should be chugging away knowing their work is supported at the federal level — and maybe more money is forthcoming if the project pans out.

Lastly, here’s the full list of partners, if you’d like to contact one for more info:

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, Louisiana State 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.

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