Building virtual reefs for science

A researcher swims up and down the coral reef with a camera, taking thousands of pictures. These will be stitched together to create a 3D photomosaic to help analyse the reef
© Scripps Institution of Oceanography at UC San Diego

The traditional way for marine biologists to study coral reefs is to scuba dive for an hour or so and note down what they see on waterproof slates. Now, during a single dive, scientists can take photographs that can be stitched together into an intricate, three-dimensional view.

“It’s underwater virtual reality,” says Prof Stuart Sandin, a marine biologist at Scripps Institution of Oceanography, UC San Diego. “It makes you feel like you’re immersed.”

Using a system with two cameras rigged at different angles, a diver swims up and down a reef as if they are ‘mowing the lawn’. Around 3,000 images taken from a standard 10 x 10m plot are then analysed by computer using a technique known as ‘structure from motion’.

A researcher swims up and down the coral reef with a camera, taking thousands of pictures. These will be stitched together to create a 3D photomosaic to help analyse the reef © Scripps Institution of Oceanography at UC San Diego
A researcher swims up and down the coral reef with a camera, taking thousands of pictures. These will be stitched together to create a 3D photomosaic to help analyse the reef
© Scripps Institution of Oceanography at UC San Diego

The technique, which took Sandin years to develop by collaborating with teams of computer scientists and engineers, is now being rolled out around the world.

So far, 30 hectares of reef have been mapped. Besides producing stunning underwater vistas, all sorts of valuable information can be extracted from these e-reefs.

A photomosaic of a coral reef in the Palmyra Atoll, which was created from 2,700 images
© Scripps Institution of Oceanography at UC San Diego

At Boston University, undergraduate student researcher Coretta Granberry meticulously traces on a digital tablet the outlines of individual corals, so she can calculate their areas and make comparisons over time. “You get a very detailed, intimate image of the reef and how everything is connected,” she says.

The corals she studies are growing thousands of miles away, in the Phoenix Islands in the middle of the Pacific. Her professor, Dr Randi Rotjan, leads expeditions every three to five years to these extremely remote reefs. “Out there, the closest people to you are on the International Space Station,” says Rotjan.

The SSV Robert C. Seamans alongside Nikumaroro island
Image: Jan Witting

These isolated, protected islands are helping to show how reefs respond to rising sea temperatures. “If you leave reefs alone locally, what are they going to look like when global change is the only stressor?” says Rotjan.

Armed with images taken from the same plots in 2012 and 2015, Granberry and her colleagues will track how the individual corals in the Phoenix Islands change, to see if they shrink, grow or get overgrown by something else.

Surveying the reef with the photography rig
Image: Craig Cook

As time capsules, e-reefs will allow scientists in the future to wind back the clock and answer new questions that nobody can anticipate. “You’re in essence exploring in four dimensions,” says Sandin.

E-reefs are also a powerful tool for showing what the reefs are like right now. You watch everyone’s eyes glow, from the most seasoned scientists, to a politician, to a community leader, to a child

Dr Randi Rotjan

This is especially important in the Phoenix Islands Protected Area, where local people of Kiribati who drove the conservation efforts live too far away to visit the reefs across the enormous archipelago. “E-reefs become the mechanism to show people in country what they’re protecting, and why,” Rotjan says.

Map detailing the seamounts and submerged reefs located within the Phoenix Islands Protected Area
Image: Kerry Lagueux / Anderson Cabot Center for Ocean Life

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