Virtual Reefs – recreating Sodwana Bay’s coral reefs in 3D

by Samantha Hofmeyr and Dr Dave Pearton

Off the coast of northern KwaZulu-Natal in the clear, blue, warm waters of the iSimangaliso Wetland Park World Heritage Site, lie the vibrant, highly diverse coral reefs of Sodwana Bay. These reefs are a hotspot for diving and other recreational activities, and they support the livelihoods of many people. Globally, coral reefs support more than a quarter of all marine organisms and they are essential for the livelihoods of around 275 million people. One of the first things you notice when diving on a reef is its incredible diversity and complexity, it has a multitude of little nooks and crannies, crammed with all sorts of life. This forms network of complex, three-dimensional ecosystems created, in part, by the varying structures of the corals themselves. Importantly, more complex topography (physical structure), means more habitat area, breeding, feeding and nursery spaces for reef organisms, contributing to the great diversity and productivity found on coral reefs. Many local and global threats to these ecosystems are increasing in intensity and frequency as the human population grows. These disturbances (including overfishing, pollution, and climate-change driven coral bleaching) are causing large scale loss of live coral cover and thereby reducing topographic complexity and the corresponding services.

The association between the complexity of the reef and fish abundance and diversity.

Reef health is generally documented by monitoring programs using two-dimensional (2D) photographs to measure the abundance and cover of corals over time. Technology and computing power has advanced so rapidly in recent years that we can now create three-dimensional (3D) models of an area using basic action cameras such as a GoPro. In years past this would have required a room-sized mainframe to do this, but now it can be done with a reasonably powerful desktop computer. We are using these models to monitor the coral reef ecosystems of Sodwana Bay in 3D space. This will allow us to better assess reef health, by including measurements of 3D structure and topographic complexity.

We are creating 3D models of the Sodwana Bay reefs using Structure-from-Motion photogrammetry, which uses images taken from video footage of the coral reef. The software identifies a specific point from multiple angles in several images at a time, to identify where the point lies in 3D space. The software identifies thousands of points in this manner and creates what is called a sparse point cloud, followed by a dense point cloud, and then a triangulated mesh is textured to create the model.

The process of creating a model using Structure-from-Motion software.

We tested the utility of these models through a series of analyses that determine how accurately and efficiently it can measure basic characteristics of the reef community such as coral cover. We further evaluated how photogrammetry may contribute to monitoring through 3D topographic metrics such as rugosity. Rugosity is the ratio between the 2D and 3D surface area of the reef and tells us how complex the structure in that area is. We used the digital elevation models derived from the 3D models, which gives us depth information, to measure the 2D and 3D area of the reefs and calculate rugosity.

The digital elevation model that shows depth information. 
The side view of a reef, indicating the difference in 2D and 3D surface area.









Creating these 3D models allows us to monitor large areas of reef and provide measurements of ecologically important parameters like topographic complexity. It can be used to further study the relationship between the structure of corals and the topographic complexity of the reef to aid in habitat mapping and analysis and monitoring recovery after disturbances. We hope to use these models as a visual tool for education for anyone who can’t experience these amazing ecosystems first hand by using virtual swim-throughs over the reef in 3D space or virtual reality dives (see the swim through video below). Additionally, the collection of video footage is a simple task that provides an opportunity for citizen science and public involvement in the monitoring of these productive and biodiversity rich ecosystems.