Abstract

Coral reefs underpin many Caribbean fisheries, and the health of their benthic communities is a critically important indicator of habitat quality. Using underwater photogrammetry or large area imaging (LAI) technology to map and monitor sections of reef is becoming a widely used tool for conservation practitioners. A variety of approaches have been used, but a systematic approach to data collection and processing remains a need for many researchers looking to utilize the technology. We present a straightforward and comprehensive workflow to generate high-resolution digital reef models in both 2D and 3D formats. Our techniques allow for the mapping of large (up to ~1000m2) areas of reef with less than 60 minutes of in-situ work and can yield sub-mm model resolution at any depth and for many types of reef structures. The process involves real-world georeferencing using automatically-detectable permanent ground control markers that allow for the integration of the resulting data into geographic information systems (GIS) programs for analysis, and the alignment of subsequent datasets at millimeter accuracy. We have developed a suite of publicly-available processing scripts to automate the data processing workflow, streamlining and dramatically simplifying the normally time-consuming and complex process. The resulting data can be analyzed in a variety of programs to conduct terrain analysis and rugosity characterization, coral and benthic community statistics, 3D coral colony measurements, and change over time from time-series imagery. The data acquisition techniques presented here are designed to be future-proof, allowing for a wide range of novel processing workflows and analyses to be implemented as technology improves.