The visual documentation of seafloor habitats is playing an increasing important role in understanding habitats like coral reefs. Our new collaboration with the Sandin Lab at the Scripps Institution of Oceanography is focusing on developing a pipeline to automate the data collection and annotation of large swaths of coral reefs. Our invited paper at this years International Conference on Underwater Networks and Systemsdiscusses the issues related to collecting this data, the challenges with processing the data, and the potential to automate the process through computer vision and robotic systems.