The Small Details are a Big Deal: How 3D Modeling Advances Our Knowledge of Coral Reefs

Written by Abigail Engleman, Florida State University

Structural complexity plays an important role in shaping marine communities. In tropical marine systems, coral is a dominant ‘ecosystem engineer’, creating habitat for a variety of reef species. Different corals create reefs with distinctive large- and small-scale structural characteristics. A reef’s shape, size, vertical relief, and spatial distribution influence the diversity of organisms that call it home. Understanding the connection between structures, and the reefs’ ability to maintain biodiversity and ecosystem services (such as food, pharmaceuticals, coastal protection, recreation, etc.) is essential to coral reef conservation.

Knowing this, researchers typically include measures of structural complexity in their reef assessments. Traditional quantification methods lack detailed information on reef characteristics, leaving knowledge gaps that limit our understanding of coral reef ecology. Applying 3D modeling technologies in marine research helps to fill those gaps, deepening our understanding of marine ecosystems.


Fig. 1 Coral reefs created from different coral species, showing drastically different large- and small-scale structural complexity. These variations influence the diversity of organisms that inhabit the reef structures.

Traditional Measurement Methods

Rugosity Index

Getting accurate, comparable complexity measurements is a rather, well, complex task…  or at least it was using traditional techniques. One common approach is to measure the Reef Rugosity Index, which is a ratio of a known transect length to the length of a chain draped across the reef structure. This measure serves as a loose rating of reef structure but fails to inform researchers on structural details.

Fig. 2 One traditional approach to measuring structural complexity on coral reefs: the chain and transect Reef Rugosity measure (Illustration by Abigail Engleman)

Visual Assessments

Another traditional approach involves rating or categorizing the reef structure through visual observations. Researchers using this technique create structural complexity scales or categories, then group the reef based on the most common structural features found at the site. As with the Rugosity Index, this measure misses important details about reef structure and shape—meaning data interpretation is based on vague structural features.

Surface Area and Volume Estimates

Smaller-scale estimates of coral surface area or volume require researchers to hand-measure sections of coral, then extrapolate their estimates to account for the coral cover at a site. Though more specific than the previous two techniques, this method relies on over-generalized surface area and volume calculations, which can easily be misinterpreted. Not to mention, hand measuring coral colonies is a timely endeavor…

New Approach to Measuring Structural Complexity

With recent advancements in technology, researchers can now create 3D reef models that include detailed calculations of structural complexity. Scientists use 3D scanners, CT scanners, photogrammetry, and video digitization* to create high-resolution models from both natural reefs and dry species samples.

* Check out these articles for more information on each technique: 3D scanners (e.g. Reichert et al., 2016), CT scanners (e.g. Gutierrez-Heredia et al., 2015), photogrammetry (e.g. Ferrari et al., 2016), and video digitization (e.g. Gutierrez-Heredia et al., 2016)


Fig. 3 3D models showing structural complexity at a reef-scale [(a); Ferrari et al., 2016)] and colony scale [(b); House et al., 2018]

Expanding Our Understanding of Coral Reef Ecosystems

3D models offer researchers the ability to measure structural complexity in ways that are directly relevant to their ecological questions. For example, the González-Rivero et al. (2017) study on damselfish predation used 3D modeling to measure structural complexity in terms of damselfish’s exposure to a predator’s field of view, and the amount of hiding spaces to escape to. This unique approach showcases the broad scope of ecological questions that can now be answered when using 3D models for structural complexity measures.

Future Applications

Climate Change and Human Impacts

3D modeling not only expands the number of studies we can conduct now, but it also creates virtually endless opportunities for studies in the future. Generating 3D reef models will be important for tracking the influence of ocean acidification, and other components of climate change, which may degrade reef structure.

Monitoring and Conservation

3D modeling provides accurate baselines to compare future reefs with, simplifying monitoring efforts. Conservationists can compare reef models between years, and easily identify any changes in structure over time. 3D models are also vital to creating reef restoration techniques that can sustainably repair damaged environments.

Advantages of 3D Modelling Methods

  • Do not require physical interaction with reef environments, meaning they are less invasive than traditional measuring techniques
  • Allow researchers to easily calculate measures of structural complexity
  • Visuals can be digitally sent for education and outreach purposes
  • Assess structural complexity on multiple size and spatial scales
  • Expand our understanding of the roles structures play in reef ecosystems
  • High-resolution measurements of reef characteristics
  • Can be scaled up (g. reef-wide research) or scaled down (e.g. microscopic coral shape) using different modeling equipment for applicability across numerous studies
  • Easier and more accurate replicability than traditional methods
  • Results can easily be compared between studies
  • Can be low-cost
  • Some 3D scanning methods assess external and internal structures, unlike traditional methods (see figure, below)


Fig. 4 Coral species’ differ in both their overall shape and small-scale structure. Corals secrete calcium carbonate on the outer layer of their skeleton, building intricate reefs as they grow. Because species differ in shape and growth form, their internal structures consequently differ as well. Some 3D modeling methods (e.g. CT scans) can model the internal complexity, in addition to outer shape.

Take a look at the referenced articles, below, for more information.The advantages of 3D modeling in marine research are seemingly endless. These technologies are quickly revamping the way we test coral reef ecosystems and showing that the small details do, in fact, have a big impact on coral reef diversity.


Ferrari R, McKinnon D, He H, et al (2016) Quantifying multiscale habitat structural complexity: A cost-effective framework for underwater 3D modelling. Remote Sens. doi: 10.3390/rs8020113

Ferrari R, Marzinelli EM, Rezende Ayroza C, et al (2018) Large-scale assessment of benthic communities across multiple marine protected areas using an autonomous underwater vehicle. 1–20. doi: 10.1371/journal.pone.0193711

González-Rivero M, Harborne AR, Herrera-Reveles A, et al (2017) Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology. Sci Rep 7:1–15. doi: 10.1038/s41598-017-14272-5

Gutiérrez-Heredia L, D’Helft C, Reynaud EG (2015) Simple methods for interactive 3D modeling, measurements, and digital databases of coral skeletons. Limnol Oceanogr Methods 13:178–193. doi: 10.1002/lom3.10017

Gutierrez-Heredia L, Benzoni F, Murphy E, Reynaud EG (2016) End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites. PLoS One. doi: 10.1371/journal.pone.0149641

House JE, Brambilla V, Bidaut LM, et al (2018) Moving to 3D: relationships between coral planar area, surface area and volume. PeerJ 6:e4280. doi: 10.7717/peerj.4280

Reichert J, Schellenberg J, Schubert P, Wilke T (2016) 3D scanning as a highly precise, reproducible, and minimally invasive method for surface area and volume measurements of scleractinian corals. Limnol Oceanogr Methods 14:518–526. doi: 10.1002/lom3.10109

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