Structure from Motion (SfM) Photogrammetry Survey
Pilot Project for Kahalu'u Bay

Seven Sisters 3D Kahaluu Mapping Banner.jpg


As part of the Coral Lovers mission, Silver Spiral Seas commissioned a pilot project using Structure from Motion (SfM) technology to determine whether or not the methodology could be adopted by the Kahaluʻu Bay Education Center (KBEC) to prospectively monitor coral cover in Kahaluʻu Bay.

SfM is a photogrammetric range imaging technique for estimating three-dimensional structures from two-dimensional image sequences (see more detailed explanation here). We chose to map two of our favorite spots in the bay, nicknamed "Seven Sisters (Plot 1)" and "The Old Cleaner Wrasse Station" (Plot 2).

Green Sea Turtle Swimming Over the Seven Sisters and Yellow Tangs at the Old Cleaner Wrasse Station

Green Sea Turtle Swimming Over the Seven Sisters and Yellow Tangs at the Old Cleaner Wrasse Station

Plot 1 was selected for its resiliency to many extreme stressors affecting it simultaneously. It's located in a spot in the bay that bears heavy traffic from snorkelers, in part because it's easy for novices to access. As such, it is exposed to increased levels of chemical sunscreens and other contaminants from swimmers.  In addition, the coral heads are adjacent to an extensive lava rock shelf which heats a large volume of shallow water that collects on it during high tide and then empties here as the tide ebbs.

Plot 2 was chosen based upon perceived changes to the topography, which seemed to have escalated within just the past 24 months. We call it "The Old Cleaner Wrasse Station” because for decades it was the home to a large cleaner wrasse station that serviced hundreds of fish a day— many of which were large specimens that came in from the deeper sea for the grooming that these beautiful endemic wrasses provided. Sadly, we haven’t observed any Hawaiian cleaner wrasses in this structure for at least two years, and the large and unusual fish that previously frequented this location are no longer present. In addition, the center area of the site seems to be disappearing, though the cause of this isn’t entirely known. It’s possible that the coral heads are declining and dying, resulting in the central structure being reduced to rubble during high surf conditions. It’s also possible that humans may be purposefully or accidentally contributing to the "shrinking" of this section of the reef, evidenced by the watermelon-sized piece of lobe coral that was discovered broken off and upside-down on the remaining coral head one morning last November. Unfortunately, by the time that the KBEC staff and Silver Spiral Seas arrived to place it back where it belonged, it had mysteriously disappeared.

Broken Lobe Coral on Old Cleaner Wrasse Station, November 2018


Bryant Grady, one of the most versatile and talented students we've encountered, masterminded the project. Bryant is a senior at the University of Hawaii at Hilo researching habitat complexity and the morphological and physical characteristics of coral reefs around Hawaii using 3D modeling and geographic imaging software to assess benthic surfaces and reef health.

Together, with Kathleen Clark from KBEC, we snorkeled out into the bay with our gear during a tide with sufficient water depth to capture the images on November 11th, 2018. We placed Ground Control Points (GCPs) and reflective articulated triangulators on the outside corners of each 10m x 10m survey plot in order to designate the boundaries of the survey area. In addition, we videotaped the plots and took GPS coordinates for later comparison.

Collage 3D Kahaluu Mapping.jpg


Once the GCPs and the reflective articulated triangulators were in place, SfM photogrammetry surveys were used to calculate percent coral coverage, surface area, and coral community composition at each of the two pilot test survey sites. Bryant (the SfM surveyor) swam in a boustrophedonic pattern over the survey area while taking thousands of continuous photos ensuring 60-80% overlap of the images (Burns et al. 2015). Images were taken with a Canon 5D Mark IV using a 16-35 mm lens (Canon U.S.A., Inc Melville, New York, USA) with an Ikelite housing that has an 8 inch hemispheric dome port (Ikelite Underwater Systems, Indianapolis, Indiana, USA), reducing refraction and ensuring high quality images.

When the survey was completed, Bryant uploaded the images into PhotoScan modeling software (v1.4.4, Agisoft LLC., St. Petersburg, Russia). 3-dimensional (3D) model generation was conducted using the methods in Burns et al. (2015). Digital Elevation Models (DEM) and orthomosaics were built and exported out of Agisoft to be used for data extraction on ArcMap. The Add Surface Information tool was used to calculate 3D/2D surface area of each plot. Cropped survey area orthomosaics were analyzed using CoralNet (UC San Diego, California, USA), an online annotation tool for classifying percent coral coverage by species, as well as percent algal, macro-fauna, and abiotic benthos coverage. Each survey plot orthomosaic had 300 points randomly generated onto the image. Benthic structure under each point was classified, and species noted if benthos was identified as coral. Each 10m x 10m plot was subdivided into sixteen 2.5m x 2.5m plots that were used to analyze percent coverage.

Kahalu'u Mapping Pilot Methodology Figure 1.jpg


And now for the cool stuff— check this out!

Survey Plot 1 - Seven Sisters Benthic Cover Orthomosaic

Survey Plot 1 - Seven Sisters Benthic Cover Orthomosaic

Survey Plot 2 - Old Cleaner Wrasse Station Benthic Cover Orthomosaic

Survey Plot 2 - Old Cleaner Wrasse Station Benthic Cover Orthomosaic

and now for the seriously cool stuff…

Seven Sisters - Plot 1 Structure from Motion (SfM) Photogrammetry Survey Pilot Project for Kahalu'u Bay

Old Cleaner Wrasse Station - Plot 2 Structure from Motion (SfM) Photogrammetry Survey Pilot Project for Kahalu'u Bay


Silver Spiral Seas has been thrilled to play a part in this prospective SfM study of coral cover in Kahaluʻu Bay. It is our sincere hope that these pilot test data can be used to generate support for 3D mapping of the entire bay so that the results can be integrated into the multidisciplinary marine conservation effort lead by Cindi Punihaole of KBEC. Under Cindi's impetus, multiple groups from diverse disciplines are collecting data on a wide variety of factors influencing coral reef health. These projects include the Submarine Groundwater Discharge Drone Study, chemical analysis of contaminants such as chemicals in sunscreen, the Coral Lovers pilot project for crowdsourcing a decentralized depository of video footage, examination of the effects of nitrogen on corals, and a pilot sewage system project to transfer waste from septic tanks and cesspits to a self-contained system.

Very few marine habitats, especially those subjected to extreme anthropogenic stressors, have been longitudinally examined by so many scientific fields simultaneously. In this, Kahaluʻu Bay provides a unique opportunity to serve as a model for guiding resource management and policy.

In collaboration with:

Bryant Grady
University of Hawaii at Hilo

Cindi Punihaole Kennedy
Director, Kahalu'u Bay Education Center
Program of The Kohala Center

Kathleen Clark
Marine Stewardship and Education Specialist
Kahalu'u Bay Education Center

I ka lokahi ko kākou ka ola ai
— The wellbeing of all of us is in our unity