UH Hilo marine scientist uses 3D modeling to monitor Pacific coral reef structures

John H. R. Burns is converting past data and 2D images of reefs into 3D reconstructions. The 3D imagery gives scientists and the public more information than previously available through traditional mapping methods. 

By Leah Sherwood.

Pocillopora meandrina colony
Click on image above to explore 3D interactive model of Pocillopora meandrina colony from Wai‘opae, Hawai‘i Island (outside link). Model created by John Burns.

John H. R. Burns, an assistant professor of marine science at the University of Hawai‘i at Hilo, has developed a research program that enhances coral reef research by converting 2D images and other data from coral surveys into 3D reconstructions of the reef habitats, using a technique called structure-from-motion photogrammetry.

John Burn on boat.
John Burns

Burns and Brianna Craig, a Hollings Scholar with the National Oceanic and Atmospheric Administration and undergraduate in the marine science department at UH Hilo, discuss this 3D imaging in a research article published this year in the Journal of Marine Science and Engineering. Their article, “Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs,” demonstrates the effectiveness of incorporating 3D reconstructions of the benthic (sea floor) habitat into the ecological monitoring of coral reefs.

For decades, marine scientists have been conducting survey dives to monitor the health of coral reefs. Information gathered during these surveys is vital for documenting coral community characteristics and for monitoring phenomena such as bleaching events that occur when the ocean water warms up.

“Since scientists started studying and monitoring coral reefs many decades ago, a lot has revolved around simple metrics of coral cover,” says Burns. “So you take a 2D image with measurements, and calculate this year’s coral cover and diversity. But that information only provides a limited analysis and cannot detect changes in the structural complexity of the reef habitat. To get the bigger picture, you need to look at the 3D structure of the reef. This is something that everybody understands because this 3D structure, with its crazy Dr. Seuss shapes and colors, is the most captivating part of the reef.”

Montipora capitata and Pocillopora meandrina colonies.
Click on image above to explore 3D model of Montipora capitata and Pocillopora meandrina colonies at Wai‘opae, Hawai‘i Island (outside link). Model created by John Burns.

Traditional methods for surveying coral reef structures and habitats are labor and time intensive. Scientists use SCUBA and explore underwater habitats with heavy equipment while taking measurements of coral structures in situ. Burns decided to apply structure-from-motion photogrammetry as a way to leverage these existing labor-intensive surveying methods to extract even more information from them.

Burns’s 3D reconstructions also provide a better way to track changes occurring over time because they are not static like traditional pencil-and-paper data collection.

“2D measurement allows you to characterize coral reefs, but what it doesn’t tell you is how the ecosystem is shifting in terms of its functionality based on changes occurring to the physical structure of the habitat,” says Burns. “That’s because corals are ecosystem engineers, like trees. The 3D architecture provided by the living corals creates dynamic habitat that supports incredibly high levels of abundance and diversity of associated reef organisms. By their very existence they create a metropolis for organisms.”

Burns received his master of science in tropical conservation biology and environmental science from UH Hilo and his doctor of philosophy in zoology from UH Mānoa. He did his doctoral work at Mānoa under the guidance of the late coral reef expert Ruth Gates who encouraged him to develop his idea of converting past data and 2D images into 3D reconstructions of reefs.

“When I first started experimenting with 3D modeling of reef structures there were plenty of naysayers, but Ruth always thought it was possible and believed in the idea,” says Burns.

Coral reef plot.
Click on image aboe to explore 3D reconstruction of coral reef plot at Wai‘opae, East Hawai‘i Island (outside link). Model created by John Burns, March 2017.

Burns coauthored another study published in February in Scientific Reports, “Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance,” where the authors used structure-from-motion photogrammetry to create 3D reconstructions of long-term coral reef monitoring sites in Kiritimati. That paper addresses how the structural complexity of the reef changed after the mass bleaching that occurred during the 2015-2016 El Nino event.

Reef structure complexity is important because it brings benefits such as resilience in the face of environmental stresses and high fish abundance and diversity.

“In today’s environmental situation we are facing an increase in the intensity and frequency of disturbance whether it is from storms and stronger weather events like El Nino, pollution, or large-scale factors such as climate change,” says Burns. “We are finding that these disturbance events have disproportionate impacts on the health and mortality of certain species, and we need to understand this better in order to predict how changing environmental conditions will alter coral reefs in the future.”

The MEGA Lab

When he joined the faculty at UH Hilo in 2018, Burns created the Multiscale Environmental Graphical Analysis (MEGA) Lab, which is dedicated to understanding the state of corals found all over the Hawaiian Archipelago and in other locations in the Pacific Ocean. In the MEGA lab, UH Hilo graduate and undergraduate students representing art, marine science, and the computer science and engineering departments use advanced technologies to create high-resolution 3D reconstructions of underwater habitats. This work supports any array of projects from tracking coral health to mapping newly discovered archeological sites.

Since its inception, the MEGA lab has received several large research grants to conduct underwater 3D mapping throughout the Pacific Ocean. For one project, Burns and Briana Noll, a computer science major in her senior year at UH Hilo, are designing a “virtual museum” that allows users to experience coral reefs without ever donning a swimsuit. Participants can explore the various reefs around the Hawaiian Archipelago and Pacific Ocean, including those found in the Northwestern Hawaiian Islands and Kapoho Bay, the area covered by the lava flow following the eruption of the Kilauea volcano last summer. Noll is using the Epic Unreal Engine platform and Unreal 4 software to create an interactive user experience based on data and visualizations provided by Burns.

“My hope is that this will be used for education on the health and protection of coral, not just here in Hawaiʻi but globally,” says Noll.

Selected projects at the MEGA Lab

  • “Co-Knowledge Production of Historic Property and Habitat Assessments on Navy Coastal Submerged Lands for the Island of Guam,” funded by the Department of Defense Naval Facilities Engineering Command.
  • “Peleliu’s Forgotten WWII Battlefield,” funded by NOAA Ocean Exploration and Research.
  • “Ike Wai: Securing Hawaiʻi’s Water Future. A cross disciplinary project that aims to increase understanding of Hawaiian island hydrology to provide improved data for decision-making tools,” funded by the National Science Foundation’s Established Program to Stimulate Competitive Research (EPSCoR).
  • “Understanding Biotic Response to Environmental Change in Tropical Ecosystems Through a Place-Based Context,” funded by the NSF Centers for Research Excellence in Science and Technology (CREST).


About the author of this story: Leah Sherwood is a graduate student in the tropical conservation biology and environmental science program at UH Hilo. She received her bachelor of science in biology and bachelor of arts in English from Boise State University. 

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