INNOVATIVE 3D IMAGING TOOLS FOR 

ASSESSING DAMAGES TO CORAL REEF 

HABITATS CAUSED BY GROUNDING 

EVENTS

November 2018 | sanctuaries.noaa.gov

NATIONAL MARINE SANCTUARIES CONSERVATION SERIES ONMS-18-03
U. S. Department of Commerce

Wilbur Ross, Secretary

National Oceanic and Atmospheric Administration

RADM Timothy Gallaudet, Administrator (Acting)

National Ocean Service

Nicole LeBoeuf, Assistant Administrator (Acting)

Office of National Marine Sanctuaries

Dr. Rebecca Holyoke, Director (Acting)

Report Authors:

John Burns1,2,3, Kelsey Johnson-Sapp4

, Keisha Bahr3, 

Atsuko

Fukunaga1,2, David Swatland1, and Randy Kosaki1

1 Papahānaumokuākea Marine National Monument, NOS, 

 NOAA

 2 Joint Institute for Marine and Atmospheric Research 3 University of Hawaiʻi 4 Duke University

Suggested Citation:

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. U.S. Department of 

Commerce, National Oceanic and Atmospheric 

Administration, Office of National Marine Sanctuaries, 

Silver Spring, MD. 18 pp. 

Cover Photo:

Recovery of the stranded buoy at Lisianski. Photo: 

Swatland
About the National Marine Sanctuaries

Conservation Series

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Administration, serves as the trustee for a system of underwater parks encompassing more than 

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their waters, giant humpback whales breed and calve their young, coral colonies flourish, and 

shipwrecks tell stories of our maritime history. Habitats include beautiful coral reefs, lush kelp 

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are home to valuable commercial industries.

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Disclaimer

Report content does not necessarily reflect the views and policies of the Office of National Marine 

Sanctuaries or the National Oceanic and Atmospheric Administration, nor does the mention of trade 

names or commercial products constitute endorsement or recommendation for use.

Report Availability

Electronic copies of this report may be downloaded from the Office of National Marine Sanctuaries 

website at http://sanctuaries.noaa.gov. 

Contact

Dr. John Burns

University of Hawaiʻi at Hilo

Marine Science Department

200 W Kawili Street., Hilo HI 96720

johnhr@hawaii.edu
Table of Contents

Abstract iv

Key Words iv

Introduction 1

Methods and Results 4

Conclusion 8

Literature Cited 10

Acknowledgements 11
Abstract

On November 6, 2015, a National Oceanic and Atmospheric Administration (NOAA) National 

Data Buoy Center (NDBC) weather buoy was reported to be stranded on Neva Shoal, southeast 

of Kapou (Lisianski) Island in the Northwestern Hawaiian Islands (NWHI). The buoy mooring 

consisted of 13.72 m of 2.54 cm chain, 365.76 m of 2.54 cm wire, and nearly 2,438.40 m of 2.54 

cm nylon mooring line. The buoy broke free from its assigned station 394.29 km northeast of 

Honolulu on March 10, 2013. The buoy continued to transmit information and drifted northeast 

before reversing course and drifting into Papahānaumokuākea Marine National Monument 

(PMNM) where it ran aground on the Neva Shoal in about 12.19 m of water in an area of high 

coral cover. Following the initial stranding in November 2015, the buoy moved more than 1.93 

km in a southwesterly direction, most likely caused by larger swell events. The intermittent 

movement was due to a portion of the mooring being still attached to the buoy and dragging 

along the benthic substrate. The total damage caused by the dragging chain was significant and 

spread over a large spatial area. The buoy was recovered by the F/V Lady Alice on May 26, 

2016. Researchers on the NOAA Rapid Assessment and Monitoring Program expedition 

surveyed the reef locations where the buoy was stranded after the removal of the buoy. 

Researchers were able to visit the last two recorded locations at which the buoy was stranded on 

May 7 and 8, 2016. Overlapping imagery was collected from the areas exhibiting damage from 

the buoy mooring. The images were processed using Structure-from-Motion photogrammetry to 

create 3D reconstructions of the affected coral reef habitats. The resulting 3D models and 

orthophotomosaics were analyzed with geospatial software to accurately quantify the impacts 

from the buoy stranding at these two locations. Utilizing this innovative methodology provides a 

useful visual and quantitative method for assessing the impacts and damage associated with 

grounding damage on coral reef habitats. 

Key Words

Weather buoy, grounding, coral reef, reef damage, damage assessment, 3D reconstruction, 

structure-from-motion, 3D mapping, Northwestern Hawaiian Islands, Papahānaumokuākea 

Marine National Monument, Hawaiʻi
Introduction

On November 6, 2015, the National Data Buoy Center (NDBC) in Mississippi notified the 

NOAA Office of National Marine Sanctuaries (ONMS) for Papahānaumokuākea Marine 

National Monument (PMNM) in Honolulu, Hawaiʻi that one of its weather buoys appeared to be 

stranded on Neva Shoal, southeast of Lisianski Island in the Northwestern Hawaiian Islands 

(NWHI). NDBC is part of the National Weather Service (NWS) and is responsible for the 

deployment, operation, tracking, and recovery of NOAA weather buoys. 

The buoy is 3.05 m wide, extends 2.44 m below and 5.49 m above the waterline, weighs 

1360.777 kg, and is made of closed cell foam. The buoy mooring consisted of 13.72 m of 2.54 

cm chain, 365.76 m of 2.54 cm wire, and nearly 2,438.40 m of 2.54 cm nylon mooring line 

(Figure 1). The buoy went adrift from its assigned station 394.29 km northeast of Honolulu on 

March 10, 2013. The buoy continued broadcasting position and weather info from the time it 

broke loose until it was retrieved. According to NDBC plots, the buoy drifted northeast towards 

the west coast of North America, then reversed course and drifted into the monument where it 

eventually became stranded on Neva Shoal in about 12.19 m of water on coral-dominated reef 

habitat. 

PMNM immediately began looking at options to retrieve the buoy. NOAA did not have a ship 

available until May, and the United States Coast Guard was unable to retrieve the buoy until 

September 2016. Winter weather in the NWHI produces sea and wind conditions that are not 

conducive to having a large ship work near a shallow reef with divers in the water, and the buoy 

grounding occurred at the start of the winter season. NDBC elected to contract a vessel and 

divers to conduct a retrieval operation, with a target date of mid to late April. During January and 

February, PMNM staff worked closely with NDBC to provide information for, and review of, 

the Statement of Work, and then to review and provide feedback on the proposals. In March, 

after NDBC selected a contractor, monument staff completed the National Environmental Policy 

Act (NEPA) and Endangered Species Act (ESA) documentation for the buoy recovery operation. 

In accordance with the 2006 Presidential Proclamation, activities in the monument must be 

issued a multi-agency permit. The buoy retrieval operation was permitted under the annual CoTrustee’s Conservation & Management permit, which allows the seven co-managing agencies or 

their representatives to conduct activities that further the conservation and management goals of 

the monument. Despite having a contract completion date of April 30, the contractor delayed the 

recovery vessel’s departure and negotiated a revised contract completion date of June 5. The F/V 

Lady Alice recovered the buoy on May 26, 2016.

Since the initial stranding in November 2015, the buoy moved more than 1.931 km in a 

southwesterly direction, which was most likely driven by the frequent large swell events. The 

movement of the buoy after the initial stranding was intermittent, indicating that a majority of the 

attached mooring was dragging along the bottom causing the buoy to remain stationary until 

wave energy moved it into a new location. 
Figure 1. Schematic diagram of the stranded buoy. The diagram provides technical information for all 

components of the mooring as well as its deployed location and date of mooring failure. (Image: NOAA)
PMNM research cruise that departed in May reallocated ship days to conduct surveys of the 

buoy stranding sites. The buoy was stranded at several locations for multiple days, and moved 

west from one location to another until it was retrieved (figures 2 and 3). The last three sites the 

buoy was stranded at for over 10 days are called Site A and Site B, and the site from which the 

buoy was retrieved is called Site C (figures 2 and 3). Due to time limitations, the benthic 

research team was only able to survey Site B and Site C to assess for damage from the stranding. 

The benthic researchers had previously used 3D Structure-from-Motion photogrammetry 

techniques to survey coral health at long-term monitoring sites throughout PMNM. The same 3D 

reconstruction techniques were used to map the observed reef damage at both sites in order to 

provide a quantitative assessment of the buoy grounding impact on the coral reef habitat.

Figure 2. Map showing the buoy stranding locations from November 2015 to May 2016. The buoy was 

stranded a substantial amount of time at Site ASite B, and was recovered from Site C. Divers were able 

to conduct damage assessment surveys at Site B and Site C after the buoy was retrieved. (Image: 

NOAA
Methods and Results

Divers visually surveyed the coral reef habitat at the coordinates for Site B and Site C (figures 2 

and 3). Once damage was visually confirmed at the coordinates, the divers surveyed as much 

surrounding reef areas as possible for damages caused by the buoy mooring. Damage was 

classified in three categories: abrasion, breakage, and death. Abrasion was identified as scarring 

to the live coral tissue caused by the mooring chain dragging along the benthic substrate. 

Breakage was identified as any pieces of coral broken and scattered on the benthos caused by 

dragging of the mooring chain. Death was any pieces or area of coral tissue that exhibited 

complete tissue mortality. Since the buoy and chain had been removed prior to the surveys, the 

divers were unable to collect any photos of the active damage occurring from the mooring chain. 

Images of the survey area were collected from planar and oblique angles with 70 to 80 percent 

overlap using methods developed for 3D reconstruction of underwater habitats (Burns et al. 

2015, Burns et al. 2016). Ground control points (GCPs) were placed throughout the surveyed 

Figure 3. Map showing the number of days the buoy was stranded at each location from November 

2015 to May 2016. (Image: NOAA)
plots to enable accurate geo-referencing and spatial scaling. All photos were taken with a Canon 

5D Mark III digital SLR camera with a 24 to 70 mm lens in an Ikelite housing with a 20.32 cm 

hemispheric dome port. 

Three-dimensional reconstructions and orthophotomosaics of the coral reef plots were rendered 

using Agisoft PhotoScan modeling software (Agisoft LLC., St. Petersburg, Russia). Images were 

uploaded into the PhotoScan software and camera calibration was performed internally using 

Brown’s distortion model. The overlapping images were aligned using scale-invariant feature 

transform algorithms to detect key points and match the overlapping image sequences. The 

invariant features were then used to create geometrical projective matrices and determine the 

exact position and orientation of the camera for each sequential image (Verhoeven et al., 2012; 

Westoby et al., 2012). 3D geometry was constructed on the 2D image plane using extrinsic 

parameters to link the pixel coordinates of an image point with the corresponding coordinates in 

the camera reference frame (Stal et al., 2012). Iterative bundle adjustments enable refinement of 

3D coordinates and reduced reprojection error in order to create a sparse 3D point cloud that 

accurately represents the structure of the photographed coral reef plots. Markers were digitally 

annotated onto each of the GCPs and the reference x,y,z values of the GCPs were used to 

optimize the alignment of the photos and to create spatially accurate 3D point clouds. After the 

initial point cloud was optimized, a dense point cloud was generated and used to construct a 

continuous mesh surface that was then triangulated and rendered with the sequential images to 

create textured 3D digital surface models.

Digital elevation models (DEM) and orthophotomosaics from each reef plot were created in 

Agisoft and exported to ArcMap geospatial software. 3D topographic features of the coral plots 

are quantified from the DEM by calculating the surface properties of cells in three by three 

windows (Burns et al. 2016, Couch et al. 2017). The DEM resolution was set to one centimeter 

and polygons were annotated onto the data layers using the ArcMap editor tools. Annotations for 

the damage included “abrasion,” “breakage,” and “death” (Figure 4). Polygons were manually 

annotated over all areas of the survey plots exhibiting any of the three conditions of coral 

damage. Annotating the data layers allowed for extracting 2D and 3D habitat data for the various 

types of observed coral damage. The data associated with each annotation were used to quantify 

the precise surface area of each type of damage (abrasion, breakage, and death) caused by the 

buoy stranding in both surveyed reef plots (figures 5 and 6).
The Site B survey area was 878.80 m2 and the Site C survey area was 356.90 m2

. The surface 

area for each observed type of coral damage as well as proportional values of the total surveyed 

areas for Site B and Site C is presented in Table 1. At Site B, 24.31 m2 of the surveyed coral reef 

showed signs of abrasion, 23.53 m2 of the surveyed coral reef had experienced breakage from the 

buoy mooring, and 15.56 m2 of the surveyed coral suffered mortality from the buoy damage 

(Figure 5). At Site C, 69.64 m2 of the surveyed coral reef showed signs of abrasion, 10.14 m2 of 

the surveyed coral reef had experienced breakage from the buoy mooring, and 120.83 m2 of the 

surveyed coral suffered mortality from the buoy damage (Figure 6). 

Figure 4. Images showing the three forms of recorded damage abrasion, breakage, and death. All forms 

of damage are evident in each image, and the arrows highlight specific examples. (Images:John 

Burns/NOAA)
Figure 5. Site B orthophotomosaic (top) and annotated orthophotomosaic (bottom).

The annotated image and legend show the total area analyzed and each observed 

type of damage. (Images: John Burns/NOAA)

Figure 6. Site C orthophotomosaic (top) and annotated orthophotomosaic (bottom).

The annotated image and legend show the total area analyzed and each observed

type of damage. (Images: John Burns/NOAA)
Site name 

and survey 

area

 (m2)

Coral Abrasion Coral Breakage Coral Death

Area

 (m2)

Percentage 

of total 

survey area

Area

 (m2)

Percentage 

of total 

survey 

area

Area

 (m2)

Percentage 

of total 

survey area

Site B

24.31 2.77% 23.53 2.68% 15.56 1.77% 878.8

Site C 

69.64 19.51% 10.14 2.84% 120.83 33.85% 356.9

Conclusion

Due to the short time-frame (two days) for investigating the damage, only two survey plots (Site 

B and Site C) could be completed to assess impacts caused by the stranded buoy. Visually 

identifying areas that were affected was initially difficult because of high turbidity and current at 

both sites. However, once the areas affected by damage were identified, the impacts were evident 

at both locations. Coral abrasion, breakage, and mortality were distinctly evident along paths 

where the mooring chain had been dragged across the benthos. 

Site C exhibited an overall larger spatial area of coral abrasion, coral breakage, and coral 

mortality, with a combined total of 200.6 m2

. Site B had an overall spatial area of 63.4 m2 that 

was affected by buoy damage. These numbers only reflect the damage that was digitally 

annotated within the imagery collected during the two completed surveys. Considering the 

expansive area over which the buoy drifted while stranded at Neva Shoal, the actual overall 

damage to coral reef habitats at this atoll is likely to be substantially larger than reported here for 

these two specific locations. 

Mapping the spatial scope of the buoy-grounding damage is an important step toward assessing 

potential ecological impacts to the affected coral reef communities. The damages to these coral 

communities can have serious implications for the management and conservation of coral reefs 

in PMNM. Coral mortality is often associated with invasion of the dead coral skeletons by algae 

(Done 1992). Mortality occurring at a large spatial scale can result in algal overgrowth (Couch et 

al. 2017) and possible phase-shifts to an algal dominated reef system (Done 1992). 

 Table 1. Total spatial area of each observed form of coral damage caused by the buoy stranding at both sites. 
Physical injury to corals can also cause substantial increases in disease susceptibility. Previous 

research has found corals with physical injury to be four times more susceptible to tissue loss 

diseases (Lamb et al. 2014). Physical injuries, such as abrasion and breakage, can reduce 

immune function associated with regeneration of coral tissue, which results in an increases 

susceptibility to disease (Mydlarz et al. 2006). 

The observed buoy damage is concerning because it caused both coral mortality as well as 

physical damage in the form of abrasion and breakage to live coral tissue. These impacts should 

be monitored and tracked over time to determine if the affected corals become susceptible to 

algal overgrowth or disease. It is important to monitor and observe the impacts of this 

disturbance event as loss of live coral can result in degradation of 3D habitat complexity (Burns 

et al. 2016, Couch et al. 2017). Loss of habitat complexity provided by live corals can reduce the 

diversity and abundance of associated reef organisms because complex habitat provides more 

refuge space, decreases the encounter rate between competitors, and promotes niche 

specialization (Komyakova et al., 2013). This buoy-stranding event provides a unique 

opportunity to monitor the reef habitat post-disturbance and quantify potential long-term 

ecological impacts associated with the physical damage to coral communities.

The 3D mapping analysis indicates that both locations exhibited several forms of physical 

damage caused by the buoy stranding. Considering the large-spatial areas affected at each site 

63.4 m2 at Site B and 200.60 m2 at Site C this stranding event warrants further monitoring to 

assess the long-term ecological implications. Monitoring the fate of the affected coral 

communities can provide useful information for managers to predict potential impacts from 

future groundings occurring on coral reef ecosystems. Developing a better understanding of how 

stranding events can affect coral health and ecosystem function may lead to improved tracking 

technology and rapid response plans to retrieve buoys that have detached from their mooring 

systems. The 3D methods described in this study provide a powerful tool for precisely 

quantifying the impacts of disturbance to coral reef habitat. Future assessments of groundings 

and physical disturbances to reef habitats could use a similar approach to ensure a visual baseline 

and thorough quantification of damage is conducted. 
Literature Cited

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, 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

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 ONE 12(9): e0185121

Done TJ (1992) Phase shifts in coral reef communities and their ecological significance. 

Hydrobiologia. Nov 1;247(1-3):121-32.

Komyakova, V., Munday, P.L., Jones, G.P., 2013. Relative importance of coral cover, habitat 

complexity and diversity in determining the structure of reef fish communities. PLoS One 8 (12), 

e83178.

Lamb JB, True JD, Piromvaragorn S, Willis BL (2014) Scuba diving damage and intensity of 

tourist activities increases coral disease prevalence. Biological Conservation. Oct 1;178:88-96.

Mydlarz LD, Jones LE, Harvell CD (2006) Innate immunity, environmental drivers and disease 

ecology of marine and freshwater invertebrates. Evol. Syste., 37:251-288

Stal C, Bourgeois J, De Maeyer P, De Mulder G, De Wulf A, Goossens R, Hendrickx M, Nuttens 

T, Stichelbaut B. 2012. Test case on the quality analysis of structure from motion in airborne 

applications. In: Proceedings of the 32nd EARSeL symposium: ‘advances in geosciences’ 

Mykonos, Greece. p. 11

Verhoeven G (2012) Getting computer vision airborne: using structure from motion for accurate 

orthophoto production. In: RSPSoc archaeology special interest group meeting spring 2012. 4-6

Westoby MJ, Brasington J, Glasser NF, Hambrey MJ, Reynolds JM (2012) ‘Structure-fromMotion’ photogrammetry: a low-cost, effective tool for geoscience applications. Geomorphology 

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Acknowledgements

This material is based upon work supported by the National Science Foundation under the 

CREST-PRF Award #1720706 and EPSCoR Program Award OIA

#1557349. Any opinions, findings, and conclusions or recommendations expressed in this 

material are those of the author(s) and do not necessarily reflect the views of the National 

Science Foundation. The authors would like to thank the NWS, ONMS, and PMNM staff 

involved in organizing the removal of the stranded buoy. We also thank the crew of the NOAA 

Ship Hiʻialakai (R334) for their support with conducting dive operations and facilitating surveys 

at the buoy stranding locations. Lastly, we thank the three anonymous peer reviewers.