Drone and Divers: 

Colony-level monitoring

Photo © Steve Schill, The Nature Conservancy

The Nature Conservancy's (TNC) scientists collect underwater videos and high-resolution imagery using drones to inform and validate satellite and airborne data-derived products. These field data are used to train machine-learning algorithms that classify habitat types and conditions.

Drones with RGB (natural color) cameras can be used to map and monitor smaller reef tracts (<5 km2) on a regular basis. Flying at 400 ft above the water, stereo photos are collected at 3-4 cm spatial resolution and used to create orthoimages and digital surface models of reef features. These data are helpful for detecting species at the colony level and assessing damage after a storm.

TNC scientists collect drone imagery and underwater videos in Old Harbour Bay, Jamaica in 2019.

In addition to aerial drone data, GPS-referenced underwater videos and bathymetric data are collected in the field to assist with benthic habitat type identification. These data document habitat condition and the information are used as training data when classifying satellite imagery. Our team uses a SeaView Sea-Drop 6000 HD underwater video camera with a 30 m cable. We typically collect 50-60 video transects per field day. Our underwater survey database contains thousands of video transects that have been collected at a variety of locations since 2010. These data provide an important baseline for evaluating and detecting future change. 

Examples of videos collected on behalf of the Climate Resilient Eastern Caribbean Marine Managed Areas Network (ECMMAN) can be viewed here. Another important field dataset collected simultaneously, are bathymetric field measurements acquired at 3 pts/sec interval using a Lowrance Elite7Ti ® system with a xSonic P319 (50/200kHz) transducer and 10Hz GPS receiver. The data provide ground-reference information for depth model comparisons and mapping reef structure and geomorphic zones. 


Structure-from-Motion (SfM) is a technique of creating precise and accurate 3D models by taking overlapping (stereo) digital photos which are processed into incredibly accurate and highly detailed 3D surface models and photo mosaics. Photos can be captured from a plane, drone, or diver to achieve different scales of measurements. These methods are increasingly being used for monitoring coral reefs at very precise scales. Photos taken 2-5 meters above the reef at different perspectives are stitched together based on key features matched between adjacent images using photogrammetry software. Using this method, we can detect changes in coral growth and loss at the millimeter scale based on differences in the three-dimensional structure (i.e., rugosity) between time periods. In addition to structure, we can also monitor changes in live coral, biodiversity, disease, and impacts from invasive species. 

For automated data collection, TNC has designed and tested a low-cost and transportable small Unmanned Surface Vehicle (sUSV) called the “Reef Rover.” The vehicle operates using Ardupilot open source software and can be used by marine managers to map and monitor marine environments in shallow areas (<10m depth). The imaging system uses two Sony a6300 mirrorless cameras to collect stereo photos that can be later processed into underwater high resolution orthophoto mosaics and digital surface models. The propulsion system consists of two small brushless motors powered by lithium batteries that follow pre-programmed survey transects and are operated by an RTK GPS-guided autopilot control board. Examples of some of the products created by the Reef Rover can be seen for a coral reef near Catalina Island in the Dominican Republic and a visualization of Devil’s Grotto in Grand Cayman. 

While SfM is a powerful method for monitoring coral reef changes, it has not been widely adopted by coral reef managers due to a capacity gap. TNC seeks to fill this gap by developing low-cost, more user-friendly methods and workflows for acquiring and processing SfM data. Surface camera platforms are being used by snorkelers to collect quick and efficient datasets on a regular basis for calculating quantitative and detailed structural change at coral reef monitoring sites.