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Diving In! Coral Reef Modeling in 3D

Diving In! Coral Reef Modeling in 3D

Diving into 3D Coral Reef Modeling

Nina Chung

Thomas Jefferson High School for Science and Technology

This article was originally included in the 2018 print publication of Teknos Science Journal.

A thumbs-down is signaled— the scuba signal for “descend.” Elevating my deflator hose, fighting all my instincts, I remind myself to breathe normally as the water engulfs me. When the mask crosses the threshold into the transparent aquamarine water, I plunge into another universe. A universe where schools of yellow-striped snappers dart around the reef, swimming close enough to touch. Where flamingo-tongue snails, banded coral shrimp, christmas tree worms, spiny lobsters, black groupers, angelfish, and butterflyfish thrive. Where everything falls silent, save for the soft sounds of the Cuban coral reefs.

Coral reefs are tropical environments that house a wide variety of marine life. Coral, the foundation species of reefs, are slow-growing, highly sensitive animals that provide a structurally complex substrate and healthy environment which allows other organisms in the ecosystem  to thrive. However, reefs are acutely susceptible to human activity, such as nutrient pollution and overfishing. Overfishing of herbivores has resulted in a phenomenon called phase shift, when coral reefs become dominated by algae. The loss of structural complexity of the reef and a subsequent loss of biodiversity accompanies phase shift. One of the impacted herbivores, Diadema antillarum or the Caribbean Long-Spined Black Sea Urchin, is a keystone species in Caribbean reefs that experienced a mysterious die-off in 1983-1984. By restoring D. antillarum populations, phase shift and loss of biodiversity on these reefs can be prevented.

Diving in the Cuban coral reefs inspired me to do my senior research project on this incredible ecosystem. Last July, on a research expedition to Cuba with fellow students at Thomas Jefferson’s Oceanography Lab, we learned a simple method of reef modeling which uses only a GoPro camera and some computer programs using SfM, or Structure-from-Motion algorithms (Young, Dey, Rogers, & Exton, 2017). We learned that structural complexity, or surface roughness, strongly influences biodiversity and ecosystem productivity on the reef (González-Rivero et al., 2017).

Structural complexity of reefs can be measured in several different ways. The old chain-and-tape method, which involves laying a chain atop a reef and measuring the length of the chain used over the horizontal distance, damaged the reef, and is neither time nor cost effective (Leon, Roelfsema, Saunders, & Phinn, 2015). Now, around the world, 3D photogrammetry advancements are being made to effectively model and quantify structural complexity of reefs and understand how they correlate with biodiversity. In other words, 3D modeling technology has enabled the rendering of increasingly accurate coral reef models from video data.

Scientists around the world have created costly underwater cameras and imaging systems to calculate structural complexity (Chennu, Färber, De’ath, de Beer, & Fabricius, 2017). In fact, coral reefs have been in the news recently, highlighting the incredible technological advancements that allow divers to collect video data and create models efficiently, but with expensive underwater video equipment (Olsen, 2018). However, the method I was taught is very low-cost and widely available. Rugosity is a widely accepted measure of coral reef structural complexity, and the method I am using calculates linear rugosity in addition to two other complexity values known as fractal dimension and vector dispersion (Young et al., 2017). Scientists have since been brainstorming more intricate measures of complexity such as number of crevices, food availability, and the extent of field of view (González-Rivero et al., 2017).

These increasingly comprehensive and detailed evaluations of reef terrain roughness help evaluate overall health of coral reefs, in addition to measuring how close some reefs are to undergoing phase shift from coral-dominated to algae-dominated reefs. Phase shift is when rapid transitions from coral- to macroalgae-domination occur. This has occurred on tropical reefs worldwide, but it is most prevalent in the Caribbean (Holbrook, Schmitt, Adam, Brooks, 2016). My research fights phase shift by evaluating structural complexity as part of the effort to re-establish algae-eating Diadema antillarum urchin populations on reefs.  Through video data collected by myself and the research team in Cuba, I model small sections of reef, four square meters at a time, and calculate the structural complexity therein.

Reef modeling is highly useful in building an understanding of both the small-scale habitat and the large-scale coastal protections that reefs provide. My research focuses more on the former, as only four square meters of reef are modeled at a time. A more spatially complex habitat provides more habitat space per square meter of the reef. For example, small fish prefer complex branching corals over round, stony corals. On reefs that have undergone phase shift, soft turf algae reduce spatial complexity even further. On the other hand, modeling of larger-scale reef features, such as reef slope, help determine the degree of coastal protection that reefs provide. Reefs form out from shores, so these aspects of reef shape help mitigate impact when waves reach shore. If sea level rises and the slow-growing reefs do not fully grow, then there will be much more impact onshore. (A. Chennu, personal communication, Feb. 6, 2018).

In addition to shoreline protection, reefs provide a wide array of other ecosystem services to humanity, including environmental, recreational, and commercial benefits. Without them, many species would go extinct, a key food source would disappear, and tropical tourism industries would suffer. Preventing phase shift would preserve all these services. At this rate, decades from now, during a descent onto a coral reef, there will be reefs covered in gray-green algae, hardly any fish in sight, and bleached, colorless corals—a universe undesirable for descent. With my research aiding the effort to restore urchins, I take pride in helping restore the incredible biodiversity of Caribbean coral reefs and improving global environmental health.


Chennu, A., Färber, P., De'ath, G., de Beer, D., & Fabricius, K. E. (2017). A diver-operated hyperspectral imaging and topographic surveying system for automated mapping of benthic habitats. Scientific Reports, 7. https://doi.org/10.1038/s41598-017-07337-y

González-Rivero, M., Harborne, A. R., Herrera-Reveles, A., Bozec, Y.-M., Rogers, A., Friedman, A., . . . Hoegh-Guldberg, O. (2017). Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology. Scientific Reports, 7. https://doi.org/10.1038/s41598-017-14272-5

Holbrook, S. J., Schmitt, R. J., Adam, T. C., & Brooks, A. J. (2016). Coral reef resilience, tipping points and the strength of herbivory. Scientific Reports, 6. https://doi.org/10.1038/srep35817

Leon, J. X., Roelfsema, C. M., Saunders, M. I., & Phinn, S. R. (2015). Measuring coral reef terrain roughness using ‘Structure-from-Motion’ close-range photogrammetry. Geomorphology, 242, 21-28. https://doi.org/10.1016/j.geomorph.2015.01.030

Olsen, E. (2018, January 16). Despite global warming, some reefs are flourishing, and you can see it in 3D. Retrieved from QUARTZ website: https://qz.com/1180919/coral-reefs-thrive-despite-global-warming-say-scientists- with-3d-images-from-scripps-institution-of-oceanography/

Young, G. C., Dey, S., Rogers, A. D., & Exton, D. (2017). Cost and time-effective method for multi-scale measures of rugosity, fractal dimension, and vector dispersion from coral reef 3D models. PLoS ONE. https://doi.org/10.1371/journal.pone.0175341

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