Reconstructing restoration: how coral photogrammetry happens

“Ten by five metres doesn't sound like a lot, but it’s quite a large area when you're swimming back and forth, up and down and then crossways,” explains Kate Craggs. But why on earth was she swimming a checkerboard in the first place? The one-word answer would be ‘photogrammetry’, but if you’ve been following the story of our partnership with Coral Spawning International and Nature Seychelles, you’ll know that the real answer is far more absorbing.

Don’t be put off by the name – because photogrammetry is absolutely fascinating and even more so when it’s applied to the coral reefs of Seychelles. “It involves taking lots and lots of photographs, then blending those photographs together using image-processing software,” simplifies Dr Jamie Craggs. “The software overlaps your images, so you can combine all these two-dimensional images into a three-dimensional view.”

This brief explanation alone means you can probably already see why it’s such a useful tool for Dr Craggs and his fellow marine scientists, as it means they can bring their undersea work above land to examine, assess and, most importantly, measure every aspect of the reefs they are working to restore. Over time they can also clearly see the impact of their work beyond the beauty of growing corals. In practice, however, photogrammetry sits right at the end of the process and, as Kate said, it can be challenging.

“We selected six sites to study on Cousin Island Special Reserve. At three, we placed a piece of tarpaulin over the reef and then pumped new coral larvae underneath it to encourage settlement in that area,” explains Dr Craggs. Kate and the team from Nature Seychelles then meticulously measured out each of the plots, using rope to create transect lines and positioned scale markers, so that there are reference points for measurement. “Each marker has a unique coded pattern, allowing the photogrammetry software to recognise and accurately scale the 3D model later on,” adds Dr Craggs. When the measuring dives are complete, the photography dive begins.

Every inch of the area needs to be captured on camera and that’s not as straightforward as it might sound. “It’s challenging in as much as you can't predict the current and swells,” explains Kate. “So, trying to maintain a consistent speed and height over the reef was tricky. When you have corals of differing heights, that means you have to constantly correct your depth as you’re swimming over with the camera.” Accuracy here is important, so having the right tools makes all the difference.

She uses a wide-angled lens on a Canon EOS R5 Mark II in a waterproof housing and, as you might expect, the images it takes – a shot every second – are crisp, colour accurate and precise. “It gives us exquisite detail,” adds Dr Craggs. “And this is really exciting.” But this isn’t just about them being lovely to look at. The fine detail also provides distinctive features, improving the accuracy of the reconstruction. “The first thing you have to do is stitch them together and make something called a ‘sparse point cloud’,” he explains. This is kind of like a rough draft of dots, each one representing a feature in the reef that appears in multiple overlapping images, allowing the software to calculate the basic shape of the space. There’s little detail at this point, hence ‘sparse’.

“Then we do some filtering, to create the ‘dense point cloud’, which creates many – often millions – more points and fills in much more information. Finally, we create the ‘mesh’, which fills in groups of dots and gives the overall 3D model its surface texture.” To reach this takes some very heavy computational lifting but, zooming in, you can see the coral in remarkable detail. “We can go right the way down to a couple of millimetres across, so we're getting incredible resolution. The quality is so good, the edges are clearly defined, and this is going to improve the accuracy of our measuring methods”.

If you’re thinking that measuring the growth of coral is a ‘yes it’s grown/no it hasn’t’ kind of activity, you couldn’t be further from the reality. Photogrammetry is an important tool in the monitoring of each of the six sites, helping Dr Craggs and the marine scientists of Nature Seychelles to track and understand what is happening – whether the coral has ‘taken’ to its new environment, survival rates and the growing shape, size and structure of the reef. It’s used alongside other measurements, such as water quality and temperature or light penetration, to paint a picture of reef health over time.

Photogrammetry also creates another important way to make comparisons over time. The 3D renderings can be ‘flattened’ and turned into what is called an ‘orthomosaic’. This is where the coded scale markers, which Kate and her fellow divers positioned across each plot, come into their own. “They make sure that everything aligns correctly to create a two-dimensional image from hundreds of photographs,” explains Dr Craggs. The measured plots are a permanent fixture in the reef, as they allow the team to capture periodic replicas of the ‘flat map’. “Then we can overlay them and directly measure how much a patch of coral has grown over six months, a year, or more.”

Kate and the team from Nature Seychelles will repeat the exercise regularly, swimming up and down, left and right, methodically photographing the six plots of coral – half which have had extra larvae introduced and half without. “Then we’ll be able to zoom in and see where our baby corals are and begin the process of measuring,” says Dr Craggs. “Ultimately, the whole point is to pull out the data, analyse it and modify our approach as necessary. It’s trial, test, modify, improve – a constant journey.”

Follow the progress of our work with Nature Seychelles and Coral Spawning International here. And find out more about Canon photogrammetry solutions.