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USGS team invented a new camera system to create highly detailed 3-dimensional models of the seafloor that are proving to be invaluable for coastal hazards research and habitat restoration efforts.

Scientific equipment mounted on two yellow pontoons sitting on the deck of a research vessel
The SQUID-5 is specifically designed to allow the construction of high resolution (sub-centimeter) 3D models of the seafloor using SfM techniques.

It is challenging to track changes in complex habitats, especially when they’re underwater. Several techniques have been developed to map terrestrial (on land) ecosystem structure such as beaches, sand dunes, forests, and mountains by using aircraft equipped with lasers (a technique called lidar) or cameras to stitch together 3-dimensional models of the landscape (a method called “structure-from-motion”). But mapping small-scale details on the seafloor using data collected from an aircraft is more difficult. Using recent advances in technology and newly developed equipment and software, the USGS invented a way to collect high-resolution underwater images and convert them into highly accurate 3-dimensional models of the seafloor. In fact, these data are incredibly valuable to both scientists and resource managers and are being used for several different research and restoration efforts.

To produce accurate models of underwater habitats, the USGS created the SQUID-5, or Structure-from-motion (SfM) Quantitative Underwater Imaging Device with 5 cameras. SQUID-5 is towed behind a boat to capture overlapping high-resolution images of the seafloor with accurate GPS locations which are converted into high-resolution, 3-dimensional models of seafloor structures. “With this technology, USGS scientists can detect changes in seafloor elevation and structure of coastal and marine habitats as small as a few millimeters. The quality and detail of these data are very useful for accurately measuring and tracking changes in seafloor structure, elevation, and habitats,” says Gerry Hatcher, the lead engineer of the SQUID-5 development team.

A man sits at a computer inside the cabin of a boat with water visible through the window in the background.
Gerry Hatcher controls SQUID-5 image acquisition over Looe Key Sanctuary Preservation Area (SPA). (Credit: Dave Zawada, USGS. Public domain.)

Currently, the 3D models resulting from this work are being used to support ongoing USGS research on seafloor elevation change to better predict coastal hazards for oceanfront communities. The shallow coastal seafloor and structures like coral reefs are natural barriers that help protect coastlines by breaking up storm waves before they reach land. As sea level continues to rise and nearshore habitats such as coral reefs simultaneously erode and degrade from climate change, ocean acidification and other processes, these effects combine to accelerate increasing water depth. These deeper water depths near the shoreline allow larger waves to reach further onshore when there’s no shallow structure to break them up before hitting the coast. Therefore, increased erosion of the seafloor can potentially threaten lives and infrastructure in our coastal zones. 

“These data are extremely useful. We can use these images to create models that help us predict which areas of the coastline are at risk from the combined effects of these hazards,” says Dr. Kim Yates, the lead investigator on the seafloor elevation-change project. “With protective reefs eroding away and sea-levels rising at the same time, we’re finding that more homes, buildings, and coastal communities as a whole are at greater risk of flooding, especially when a big storm hits.”

two people on the back deck of a boat wearing life vests operating scientific equipment hanging over the side of the boat
Dave Zawada (left) and Gerry Hatcher prepare to deploy the SQUID-5 off the R/V Sallenger over Looe Key, FL.

USGS also converts this information into stakeholder tools that can help conservation partners identify and characterize areas of interest for coral reef restoration efforts, measure baseline and changing seafloor conditions, and monitor restoration progress. For example, these data help identify areas along the Florida Reef Tract where the seafloor is stable or unstable due to elevation-change, which helps focus resources where habitat restoration efforts will be most effective. The SQUID-5 images help identify what is causing these changes on the seafloor and which habitats are most affected.

Due to devastating losses in corals over the past few decades, large-scale coral reef restoration initiatives are underway throughout the Florida Keys. Several government agencies and conservation groups are working to plant nursery-grown corals on the Florida Keys Reef Tract to help boost reef growth and aid in natural coral reproduction – another area where USGS is providing important scientific information. However, if the corals are not planted in suitable locations, it could decrease the effectiveness of this effort. The data collected by USGS and their new SQUID-5 technology can be used by these organizations for characterizing baseline seafloor conditions to help guide their restoration efforts. These techniques can also be used to track the long-term progress of reef recovery, especially given that the resolution of SQUID-5 data allows scientists to detect changes smaller than half an inch—including the size of individual corals.

The National Oceanic and Atmospheric Administration (NOAA) Florida Keys National Marine Sanctuary (FKNMS) is particularly interested in this USGS work due to its applicability to the new Mission: Iconic Reefs—one of the world’s largest coral reef restoration projects, certainly the largest in the US. The 3-dimensional maps created by the USGS team will be critical to this restoration effort. The Sanctuary plans to plant corals across more than 800,000 m2 of reef habitat across seven “iconic reefs”–sites that represent the iconic diversity and productivity of Florida Keys coral reefs. Mission: Iconic Reefs is an approximately 100 million dollar effort expected to take place over the next 20 years. This project is not fully funded, and resourcing this effort will take a broad range of partnerships and fundraising efforts over time.

Map of Florida Keys with stars marking seven different reefs.
Iconic Reefs sites of interest for Mission: Iconic Reefs. USGS has conducted SQUID-5 mapping operations at Eastern Dry Rocks and Looe Key Reef as of August 2021.

Mission: Iconic Reefs is an ambitious undertaking to restore the coral reef habitats of the Florida Keys National Marine Sanctuary. We hope that this restoration effort will eventually stimulate natural reproduction, and help protect our ecosystem and our local economy that depends on a healthy ecosystem,” says Sarah Fangman, Superintendent Florida Keys National Marine Sanctuary. “USGS expertise in mapping these areas, provides critical baseline imagery that allows NOAA and our partners to develop a more comprehensive understanding of the restoration efforts and eventual natural recovery.

NOAA has been extremely helpful throughout this project,” says Dr. Yates. “They have provided space in their Key West office to use as an equipment staging area, provided their research vessel for the first SQUID-5 mapping application, and temporarily removed mooring buoys within survey zones to minimize gaps in USGS data collection. This is no small task, as many dive and snorkeling operations use these buoys to tie up their boats when taking visitors out to the reef. This kind of support from NOAA and understanding from the community really shows how important this work is for helping to restore the coral reefs that support the local economy.”

So far, the USGS team has mapped more than 130,000 m2 at Eastern Dry Rocks Sanctuary Preservation Area (SPA) and 170,000 m2 at Looe Key SPA and nearby areas, a combined area larger than 55 football fields. A total of 356,267 images, more than 4 terabytes of data, were collected from both locations.

USGS is recognized leader in ocean mapping and continues to improve upon the methods for collecting data to create seafloor maps that can be used to inform and guide habitat restoration planning, implementation, monitoring, and outcomes.

A transect image and 3D model of a coral reef, and a graph displaying reef elevation across the transect
Example of data collected by SQUID-5 at Cheeca Rocks in the Florida Keys during a SQUID-5 system test conducted prior to acquisition activities at Looe Key and Eastern Dry Rocks. A. Color-enhanced orthomosaic imagery (many photos stitched together) with two example transects for measuring elevation. B. Bathymetry (water depth) data collected by SQUID-5 in the same two survey passes. C. Elevation profiles along the two transects shown in A & B. From


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