3D Coral Imaging: Using a GoPro to Visualize Coral Reefs

By Alex Reulbach

Photo by Holobionics. [CC-BY-SA 4,0]

Habitats across the world are quickly disappearing due to damaging human activities, and coral reefs are no exception. With coral reef disappearance accelerating at an alarming rate, scientists are working rapidly to understand the reasons these habitats are dying before it is too late. One method for studying coral reefs, used by UNC-Chapel Hill marine ecologist Esteban Agudo and his team, has allowed scientists to quickly study coral reef ecosystems at a previously inconceivable level of detail. The method-structure from motion photogrammetryhas allowed Agudo and his team to further our understanding of coral reef habitats by making 3-dimensional (3D)

Ph.D. student Esteban Agudo reconstructions of coral reefs and analyzing these structures for ecological trends. Esteban Agudo, a marine ecologist and PhD student in the Department of Biology, lived in Venezuela before joining the Bruno Lab at UNC in 2019. Agudo’s research with his team in Venezuela focused on exploring the fish communities found within coral reefs in Archipelago de Los Roques National Park. During Agudo’s time working with his research team and his colleague Dr. Jose Cappelletto in Venezuela that he stumbled upon the process of 3D reconstruction that his current research relies upon. Being avid divers, Agudo and Cappelletto would frequently record their dives with a GoPro camera. On one of these trips, Agudo realized the potential his GoPro videos could have in studying the structure of coral reefs. As Agudo recalls, “At first we just started playing, just using a GoPro to take videos and finding the right software to use for 3-dimensional reconstruction. In that way we came up with pretty decent reconstructions of coral reef structure.”¹ As soon as they realized that this method of coral reef restoration was successful, they believed it could be utilized to solve problems in marine ecology. To see if their method of 3D reconstruction could effectively be used to answer ecological questions, Aldo Croquer, Agudo’s former advisor and one of the team members, suggested that they start out on a small scale. They wanted to know “how much coral reef fish are related to the structural complexity of a coral colony.”¹ Agudo relates structural complexity in coral reefs to the 3D framework that plants and trees create in a forest. In more structurally complex forests, different plants and trees create many nooks and crannies have many nooks and crannies that give refuge to the animals that inhabit the forest. The idea is very similar in coral reef habitats. “Coral reef fish are totally dependent on the refuge that they can find between the corals, rocks, and sponges you can find in a coral reef,” says Agudo.¹ More structurally complex corals have a greater number of holes, overhangs, and nooks that many reef fish depend on for shelter from predation. Agudo and his team hypothesized that as the structural complexity of a coral colony increased, the reef fish abundance and biodiversity would increase as well.

Figure 1. A. cervicornis colony (a) and 3D reconstruction created from the image (b, c) To research this hypothesis, Agudo and his team headed north to Archipelago de Los Roques National, 100 miles off the coast of Venezuela Park. Once there, they used their GoPros to record 20 different coral colonies of the keystone coral species Acropora cervicornis and then created 3D reconstructions that modeled the coral colonies’ structural complexity.² Acropora cervicornis is a keystone species because it is essential to building the structural complexity of the coral reef that the other reef species rely upon. By comparing the structural complexity of the individual coral colonies to data collected about the fish communities via visual census, Agudo and his team were able to conclude that increased structural complexity of the coral colonies did indeed lead to higher fish abundance and biodiversity. The successful application of their method in an ecological experiment, while small in scale, demonstrated the effectiveness of using the GoPro to produce accurate 3D reconstructions.

“When coral dies, the structure of the reef starts falling apart. This is something that is called coral reef flattening. If coral reefs become flat, fish lose their refuge and are more likely to disappear.” With their method scientifically verified, Agudo and his team returned to Los Roques National Park to implement their method on a much larger scale. Agudo and his team wanted to know if the relationship between structural complexity and fish communities they saw on the scale of individual coral colonies would be similar on a much larger, reef-wide scale. They repeated the same methods they had used in the small scale study, but recorded 50 meter transects of coral reef instead of just one small coral colony.³ What they discovered was that “structural complexity and the number of holes and the sizes of the holes in the reef actually explain fish abundance and fish biodiversity.”¹ Their important discovery demonstrated that their method of 3D reconstruction could be implemented to successfully recreate 3D structures of large swaths of coral reefs and in enough detail to answer important ecological questions. Agudo and his team’s successful application of structure from motion photogrammetry to perform ecological experiments is just one way that this method can be used. “One of the most important applications is coral reef monitoring. With this method of 3D reconstruction, you can have a more accurate picture of what is happening to coral reefs,” Agudo explained. ¹ With the health of coral reefs across the globe at an all-time low, coral reef monitoring is essential to understanding how coral reefs will respond to the ever-increasing threat of climate change. Agudo and his team believe that one of the main problems concerning coral reefs in the face of climate change is coral reef flattening. Agudo explains, “When coral dies, the structure

Figure 2. Esteban collecting data on fish communities via

visual census of the reef starts falling apart. The phenomenon is called coral reef flattening. If coral reefs become flat, fish lose their refuge and are more likely to disappear.”¹ Monitoring the structural complexity of coral reefs over time using Agudo’s 3D reconstruction method could help scientists determine if a coral reef is healthy or not. While Agudo and his team have already discovered much about the relationship between structural coral reef complexity and fish communities, there is still more to explore. Agudo and his team’s next step is to see if the relationship they found between structural coral reef complexity and fish communities is consistent among different types of marine ecosystems. Agudo remarks, “It can be interesting to compare how much structural complexity different habitats have, and try to see how these relate to fish communities.”¹ Without a doubt, the answer to this question will be invaluable to our understanding of the relationship between habitats and fish community composition. Agudo and his team hope that their method of 3D reconstruction will be able to answer this question and many more in the coming years.

References

1. Interview with Esteban Agudo, Ph.D. student 10/16/20 2. E. Agudo-Adriani; J. Cappelletto; F. Cavada-Blanco; A. Croquer. PeerJ 2016, 4, eCollection 3. E. Agudo-Adriani; J. Cappelletto; F. Cavada-Blanco; A. Croquer. Frontiers in Marine Sciences 2019, 6, eCollection