3D Reconstruction

We create high-resolution 3D models of coral reef habitats using Structure-from-Motion photogrammetry tools. These models are used to map coral disease and investigate how changes in reef architecture affect ecological processes.


Molecular Profiling

Multi-omic and 3D cartographic platforms are utilized to characterize the molecular underpinnings of healthy and diseased coral tissue. This approach collates an array of molecular data from individual corals to determine how the colony microbiome influences physiology.


Quantitative Ecology

Coral reefs are complex systems and require robust statistical tools to decipher drivers of coral health and community structure. We utilize an array of multivariate approaches to analyze ecological data to understand how environmental change affects reef systems. 



Epizootiology is the science dealing with the character, ecology, and causes of diseases in animals. Studying the epizootiology of coral diseases helps us accurately describe conditions and determine ecological and biological drivers of coral health. 




We created the Coral Health Atlas as a portal to share research data and interactive products with the public. If you would like to learn more about our research and take interactive tours of our sites, then please visit the Coral Health Atlas.



Burns JHR, Fukunaga A, Pascoe KH, Runyan A, Craig BK, Talbot J, Pugh A, Kosaki RK (2019) 3D Habitat Complexity of Coral Reefs in the Northwestern Hawaiian Islands is Driven by Coral Assemblage Structure. Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLII-2/W10, 61-67, 2019. DOI:10.5194/isprs-archives-XLII-2-W10-61-2019

Magel JMT, Burns JHR, Gates RD, Baum JK (2019) Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance. Scientific Reports. 9(1) 2512: DOI: 10.1038/s41598-018-37713-1

Adolf JE, Burns JHR, Walker JK, Gamiao S (2019) Near shore distributions of phytoplankton and bacteria in relation to submarine groundwater discharge-fed fishponds, Kona coast, Hawai‘i, USA. Estuarine, Coastal and Shelf Science. Volume 219: Pages 341-353

Fukunaga A, Burns JHR, Craig BK, Kosaki R (2019) Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs. Journal of Marine Science and Engineering. 7, 27; doi:10.3390/jmse7020027

Burns JHR, Johnson-Sapp K, Bahr KD, Fukunaga A, Swatland D, Kosaki R (2018) Innovative 3D imaging tools for assessing damages to coral reef habitats caused by grounding events. Marine Sanctuaries Conservation Series ONMS-18-03; 18 pp.

Couch CS, Burns JHR, Liu G, Steward K, Gutlay TN, Kenyon J, et al. (2017) Mass coral bleaching due to unprecedented marine heatwave in Papahānaumokuākea Marine National Monument (Northwestern Hawaiian Islands). PLoS ONE12(9): e0185121

Burns JHR, Delparte D (2017) Comparison of commercial structure-from-motion photogrammetry software used for underwater three-dimensional modeling of coral reef environments. ISPRS/CIPA Archives, Underwater 3D Recording and Modeling, Commission II, Volume XLII-2/W3

Price M, Raupp JT, Keogh K, Burns JHR (2016) Managing a sigh of relief: The wreck of USNS Mission San Miguel. Journal of the Australasian Institute for Maritime Archaeology. 40: 17

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M (2016) Data for spatial analysis of growth anomaly lesions on Montipora capitata corals using 3D reconstruction techniques. Data in Brief. 9: 460-462

Burns JHR, Alexandrov T, Ovchinnikova E, Gates RD, Takabayashi M (2016) Investigating the spatial distribution of Growth Anomalies affecting Montipora capitata corals in a 3-dimensional framework. Journal of Invertebrate Pathology. 140: 51-57

Caldwell JM, Burns JHR, Couch C, Ross M, Runyon C, Takabayashi M, Vargas-Ángel B, Walsh W, Walton M, White D, and Williams G (2016) Hawaiʻi Coral Disease database (HICORDIS): species-specific coral health data from across the Hawaiian archipelago. Data in Brief. 8: 1054-1058.

Burns JHR, Delparte D, Kapono L, Belt M, Gates RD, Takabayashi M (2016) Assessing the impact of acute disturbances on the structure and composition of a coral community using innovative 3D reconstruction techniques. Methods in Oceanography. 15-16: 49-59

Gregg TM, Mead L, Burns JHR, Takabayashi M (2015) Puka Mai He Ko ‘a: The Significance of Coral in Hawaiian Culture. In Ethnobiology of Corals and Coral Reefs (pp. 103-115). Springer International Publishing.

Burns JHR, Delparte D, Gates RD, Takabayashi M. (2015) Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077

Burns JHR, Delparte D, Gates RD, Takabayashi M (2015) Utilizing underwater three-dimensional modeling to enhance ecological and biological studies of coral reefs. ISPRS/CIPA Archives, Underwater 3D Recording and Modeling, Commission V, Volume XL-5/W5

Burns JHR, Gregg TM, Takabayashi M (2013) Does coral disease affect symbiodinium? Investigating the impacts of growth anomaly on symbiont photophysiology. PLoS ONE 8(8): e72466

Burns JHR, Takabayashi M (2011) Histopathology of Growth Anomaly Affecting the Coral, Montipora capitata: Implications on Biological Functions and Population Viability. PLoS ONE 6(12): e28854

Burns JHR, Rozet NK, Takabayashi M (2011) Morphology, severity, and distribution of growth anomalies in the coral, Montipora capitata, at Wai‘ōpae, Hawai‘i. Coral Reefs 30: 819-826

Takabayashi M, Gregg TM, Farah E, Burns JHR, Teves K, Cody NH (2010) The prevalence of skeletal growth anomaly and other afflictions in scleractinian coral at Wai‘ōpae, Hawai‘i. Proc 11th Int Coral Reef Symp 18: 820-824