Open-source workflow from Perry Institute for Marine Science researchers enables automated data processing, arming reef managers worldwide with rapid, easy-to-use solutions for large area imaging.

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Written by Lily Haines | PIMS | WhatsApp +1 (613) 791-6045 | lhaines@perryinstitute.org

June 17, 2025—NASSAU | Coral reefs cover less than one percent of the ocean floor yet anchor a quarter of all marine life. Protecting them has been the Perry Institute for Marine Science’s (PIMS) mission for more than 50 years—work that spans cutting-edge coral restoration, fisheries research and the Caribbean-wide Reef Rescue Network of coral nurseries.

Now PIMS scientists, working with Arizona State University, have unveiled ReefShape, an automated photogrammetry pipeline that converts thousands of underwater photographs into millimeter-accurate, 3-D and 2-D reef maps in hours instead of days. Their method, published this week in the Journal of Visualized Experiments (JoVE), gives managers from Abaco to Zanzibar a practical and streamlined way to track bleaching, storm damage and restoration success at the millimeter scale.

“We needed a method that’s easy to teach, automatic, and lets us focus on actually saving coral reefs rather than just making maps of them,” said lead author Will Greene, photogrammetry specialist and research scientist at PIMS.

The reef-mapping bottleneck

Photogrammetry—the digital alchemy that converts overlapping photos into lifelike 3D models—has transformed archaeology, forestry and even Hollywood. Yet under water it has remained a specialist’s sport: equipment can top US $20,000, and the software pipeline still relies on hours of manual clicks. In the meantime reefs around the world bleach, crumble or succumb to disease weeks before new data reach managers’ desks.

Headquartered in the United States, PIMS is a non-profit research organisation dedicated to ocean conservation and community engagement around the world. Through its flagship Reef Rescue Network—the region’s largest coalition of coral nurseries—PIMS has already planted tens of thousands of elkhorn, staghorn and fused staghorn corals throughout the Caribbean, restored critical reef habitat, and trained hundreds of local divers, students and tourism operators in reef-monitoring techniques. PIMS also leads research on sustainable fisheries, mangrove and seagrass restoration, and partners with governments to translate science into policy that safeguards coastal livelihoods.

Three simple upgrades

Turning big-picture conservation goals into on-the-ground action—and doing it fast enough to matter—meant re-engineering reef mapping for the realities of a dive boat. Instead of inventing another costly gadget, Greene’s team asked what the absolute essentials were and how to make each one fool-proof. The answer distilled into three simple upgrades that, together, turn a labour-intensive workflow into a backpack-friendly kit:

1. Permanent corner markers. Four dinner-plate-sized markers drilled into the reef plot corners act as digital anchor points. Software recognises them automatically, snapping every future survey into perfect alignment.
2. Phone-based GPS logging. A free Survey123 form guides divers to collect surface positions and depth readings of the markers, then formats the data for the processing script—no spreadsheets, transcribing coordinates, or typos.

A fully scripted pipeline. Custom Python code drives Agisoft Metashape processing through a graphic interface, whizzing through image alignment, mesh generation, orthomosaic building, data export and even structural-complexity metrics with no keyboard input beyond run.

From dive to desktop in 1 hour 58 minutes

Using the fully automated ReefShape script, a 200 square meter, 1,300-image reef plot can be processed in under 2 hours on a modern laptop—roughly 400 percent faster than the same dataset handled with earlier, semi-manual workflows. Even on 2018-era hardware, the scripted pipeline still shaved hours off turnaround because most of the speed-up comes from automation and careful workflow optimization, not brute processor power.

Stress-tested during a record heatwave                                                                                                                                                        ReefShape’s coming-of-age moment arrived during the record marine heatwave that washed over The Bahamas in August 2023. Having surveyed Simms Point Reef seven months earlier, the team returned with a camera and retraced their path above the permanent markers. Hours later, side-by-side mosaics revealed that over 90 percent of corals in several species had bleached completely, while a handful of colonies clung to colour.

“That immediate feedback lets us prioritise restoration sites and share data with partners before the next storm hits,” says Dr. Craig Dahlgren, PIMS executive director and co-author on the new paper. “It’s like switching from film to livestream.”

Democratizing a critical tool

Everything needed to utilize the workflow—recommended camera system, field equipment, a suitable computer and software—comes in around US $5,000 ($8,000 without educational software discounts). The scripts and step-by-step manual live for free on GitHub, and the authors encourage anyone mapping coral, seagrass, mangroves or shipwrecks to fork and improve the code.

The design is deliberately tolerant: while the protocol gives specific instructions for researchers wanting a cookbook-style approach, it works for plots from 25 m² to > 1,000 m², depths down to 30 m, any camera system and swim pattern with sufficient overlap, and on any recent computer. The ReefShape software includes adjustable controls to suit different data collection strategies and researcher needs while remaining streamlined and easy to use, automatically exporting data pre-formatted for analysis in free software packages like QGIS or TagLab.

Why it matters

Coral reefs occupy less than one per cent of the ocean floor yet shelter a quarter of marine speciesand buffer tropical coastlines from storms.

With mass-bleaching events now recurring every few years, conservationists need diagnostics that are fast, cheap and repeatable—tools that turn snapshots into time-lapse. ReefShape, its creators argue, is a step toward that future.                                                                                                                  “Our goal wasn’t another complex method,” says Greene, now completing a PhD at Arizona State University on GIS-driven 3-D reef mapping. “It was to hand every reef manager a simple, comprehensive monitoring tool, then get out of the way so they can use it.”

ReefShape was developed by Will Greene, Sam Marshall, Dr. Jiwei Li and Dr. Craig Dahlgren, with funding from the Disney Conservation Fund and the U.S. National Science Foundation. Fieldwork was conducted under permits from the Bahamas Department of Environmental Planning & Protection. Full documentation and code: https://github.com/Perry-Institute/ReefShape.

PHOTO CAPTION:

1st insert: Time-series aligned imagery of Simm’s Point Reef in New Providence before (left) and during (right) the 2023 mass bleaching event. The data were processed automatically in ReefShape, allowing researchers to rapidly analyze the extent and severity of the bleaching event (bottom panel), uncovering different patterns among the various coral species present.

3rd insert: The ReefShape field kit—ready for a single-tank survey. (A) Mirrorless camera with wide-angle rectilinear lens; (B) matching underwater housing and dome port; (C) Bluetooth-enabled “kickboard” GPS for surface positioning; (D) reusable coded corner markers that lock each plot to precise coordinates; and (E) coded scale bars that set the model’s exact dimensions.

Video caption:

Fly-through of a ReefShape 3D model of a coral reef: a centimetre-scale, colour-true reconstruction that lets scientists measure coral growth, bleaching and erosion without getting wet.