Structure from Motion (SfM) Photogrammetry Survey
Pilot Project for Kahalu'u Bay
OVERVIEW
This content was contributed by Silver Spiral Seas LLC, who 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). Two spots in the bay were chosen, 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
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 was 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. You can find out more about Plot 1 in the “Features” section for the Seven Sisters.
Plot 2 was chosen based upon perceived changes to the topography, which seemed to have escalated in the 24 months prior to this project. It was nicknamed "The Old Cleaner Wrasse Station” by one of the team members 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 deeper waters for the grooming that these beautiful endemic wrasses provided. Although the cleaner wrasses were not observed for many years prior to this study, we’ve recently heard reports that they’ve taken up residence again! Unfortunately, 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 colony one morning in 2018 and disappeared within a couple hours after. You can find out more about Plot 2 in the “Features” section for the Old Cleaner Wrasse Station.
Broken Lobe Coral on Old Cleaner Wrasse Station, November 2018
THE TEAM
Bryant Grady masterminded the project. At the time, Bryant was a senior at the University of Hawaiʻi at Hilo researching habitat complexity and the morphological and physical characteristics of coral reefs around Hawaiʻi using 3D modeling and geographic imaging software to assess benthic surfaces and reef health. Christine Zalewski, then managing director of Silver Spiral Seas, had snorkeled the bay for 30 years and had specific coral colonies in mind for the project. Together, with Kathleen Clark from KBEC, they snorkeled out into the bay with their gear during a tide with sufficient water depth to capture the images on November 11th, 2018. They 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, they videotaped the plots and took GPS coordinates for later comparison.
METHODOLOGY
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.
RESULTS
And now for the cool stuff— check this out!
Survey Plot 1 - Seven Sisters 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
THE FUTURE
Dear Ocean is thrilled that Silver Spiral Seas has shared this SfM study of coral cover in Kahaluʻu Bay with the Digital Coral Ark. It is our sincere hope that archiving these pilot test data will lead to their integration into longitudinal multidisciplinary marine conservation efforts. Very few marine habitats, especially those subjected to extreme anthropogenic stressors, have been longitudinally examined by so multiple scientific fields simultaneously. In this, Kahaluʻu Bay provides a unique opportunity to serve as a model for guiding resource management and policy.
“I ka lokahi ko kākou ka ola ai”
— The wellbeing of all of us is in our unity