Coral reef ecosystems are rapidly changing, and a persistent problem with monitoring changes in reef habitat complexity rests in the spatial resolution and repeatability of measurement techniques. We developed a new approach for high spatial resolution (<1 m) mapping of nearshore bathymetry and three-dimensional habitat complexity (rugosity) using airborne high-fidelity imaging spectroscopy. Using this new method, we mapped coral reef habitat throughout two bays to a maximum depth of 25 m and compared the results to the laser-based SHOALS bathymetry standard. We also compared the results derived from imaging spectroscopy to a more conventional 4-band multispectral dataset. The spectroscopic approach yielded consistent results on repeat flights, despite variability in viewing and solar geometries and sea state conditions. We found that the spectroscopy-based results were comparable to those derived from SHOALS, and they were a major improvement over the multispectral approach. Yet, spectroscopy provided much finer spatial information than that which is available with SHOALS, which is valuable for analyzing changes in benthic composition at the scale of individual coral colonies. Monitoring temporal changes in reef 3D complexity at high spatial resolution will provide an improved means to assess the impacts of climate change and coastal processes that affect reef complexity.
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