No animals harmed as wildlife specimen collection goes digital in 3D

Imagine you’re leading an expedition in the depths of a forest. You discover a species of frog that piques your interest. Conventional rules of taxonomy dictate that you capture the animal, euthanize it, and take it back to a lab or museum. But what if it’s a rare or threatened species? What if the animal you’re holding is one of the few remaining on the planet?

Like scientists and researchers around the world, Scott Trageser faced this conundrum for years. The conservationist and photographer often found himself wondering: is it worth euthanizing the animal to take it back to a lab?

Around July 2020 — at the height of the COVID-19 pandemic, when most people with an office job were checking in virtually, their digital presence on Zoom making up for their physical absence — a realization dawned on him. “I thought the technology was finally there to really push for digital specimens,” Trageser, executive director of Arizona-based nonprofit The Biodiversity Group, told Mongabay in a video interview.

A digital specimen, in this sense, would be the animal’s digital avatar, a three-dimensional, high-resolution, true-to-life virtual model of the creature (but with the mic still muted).

Trageser got to work, collaborating with Japanese electronics powerhouse Sony. The result: a 3D scanning system that can capture digital samples of animals in the wild, releasing them unharmed at the end of the process. While the technology is still in the early stages, Trageser and his team have used it to create digital specimens of 12 species found in Panama and Ecuador, including frogs such as Nymphargus balionotus and Atelopus longirostris. The virtual 3D models can be viewed on smartphones or with virtual or augmented reality headsets.

Apart from being a noninvasive method to study animals, digital specimens, unlike physical ones, also have the advantage of not degrading over time. Trageser said he believes it will also enable scientists and researchers to gain new perspectives and insights. “When you euthanize something and put it in alcohol, some colors diminish, and the animal will be in a special position, like how we splay out all the fingers, and that doesn’t represent the animal in a natural way,” he said.

The specimens collected so far have been “deposited” in a freely available digital database called MorphoSource in the hopes they can contribute to educational purposes. “Instead of having them locked away in a siloed museum, we can have anybody access them equally,” Trageser said. “We can bring those animals in the most lifelike state. It’s not the same as holding a real animal, but it will hopefully get us over the hump of being able to convince people that these animals are worth saving.”

The 3D scanning system looks a lot like a photo studio that puts animals in the spotlight. It consists of an array of cameras, connected to one another through a control box, that are set up like an upside-down tripod. Once the team captures an animal, they place it in the middle of the system. The cameras, which are all synced to take photos at the same time, then get to work and click rapid bursts of photos, usually in less than 5 seconds.

“I manually rotate it around because we don’t want motors making any noise,” Trageser said. “We do the dorsal scan first and take about 100 photos, and then flip the animal over for another 100 photos of the ventral side.”

Earlier this year, Trageser did a trial expedition in Panama over a period of six weeks. After finalizing the strategy and methodology there, he then tried it out in the Rio Manduriacu Reserve in Ecuador.

Keeping the animals still, even for a few seconds, is one of the biggest challenges. A slight tremor or a quick blink are enough to ruin the photos, forcing the team to start scanning from scratch. However, over time, Trageser said he’s come to realize that each individual animal has quirks that can keep them still just long enough to get the needed scans.

For instance, in Rio Manduriacu, the team was having trouble getting a specimen of glass frog to stay still. Trageser then realized that if he placed a droplet of water on the frog’s eyeball, it would blink and then stay still for a few seconds. “It was like being a frog whisperer,” he said. “It’s definitely a zen practice. You’re sitting there, waiting until it stays still, and then take the scan real quick.”

In some ways, however, having a virtual specimen is no substitute for having a physical one. For one, it’s not possible to study an animal’s internal morphology. Nor can researchers take a scanning electron microscope to the animal’s skin or look into its retina.

Then there’s the high cost, both of the equipment and the technical knowledge associated with using the system. Currently, it costs $8,000 to purchase the parts and assemble the system. For most conservation nonprofits and research teams that are usually scrambling for funds, that amount might act as a deterrent. Moreover, setting it up and operating it isn’t easy either.

“What’s concerning is that I’m the only individual in the world who can operate this thing right now,” Trageser said. “It is not a brag, but the positive benefit from this is limited to my time and where I go.”

Trageser said he’s currently working to make a version of the technology that’s cheaper and easier to use. He’s also planning more expeditions in the months ahead to further perfect the methodology and experiment with new applications. Next September, he’s preparing to travel to Halmahera Island in Indonesia for an expedition. Further down the line, there are also plans to take the system underwater to be able to capture marine life.

“It will be neat to be able to scan animals like jellyfish, which if taken out of water becomes an amorphous blob,” he said. “I think there are a lot of applications outside of the terrestrial environment as well.”

Abhishyant Kidangoor is a staff writer at Mongabay. Find him on 𝕏 @AbhishyantPK.

Banner Image: A species of frog scanned in the Ecuador by Scott Trageser. Image courtesy of Scott Trageser.