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The SeaBED autonomous underwater vehicle (AUV) is a new imaging platform designed for high resolution optical and acoustic sensing. This low cost vehicle has been specifically designed for use in waters up to 2000 m to carry out video transects, bathymetric and side-scan sonar surveys. In this paper we detail the systems issues associated with navigation, control, and imaging that led us to our particular hardware and software design choices so as to allow us to operate in shallow, shelf and ocean basin environments. We illustrate the strengths of our design with data obtained during two research cruises associated with mapping coral reefs off Puerto Rico and Bermuda. In both these cases, SeaBED was deployed in extremely challenging terrain associated off the shelf edge and was successful in returning high quality color imagery of deep coral habitats.