Standard operating procedures for the use of large-area imaging in tropical shallow water coral reef monitoring, research and restoration: Applications for Mission: Iconic Reefs restoration in the Florida Keys National Marine Sanctuary

This is a standard operating procedure (SOP) for the implementation of large-area imaging (LAI) to support coral reef science. LAI refers to an approach that leverages structure-from-motion (SfM) photogrammetry to generate a variety of composite digital representations of sessile benthic communities. These digital reconstructions can be visualized as 3-dimensional (3D) models, 2- dimensional (2D) map views (e.g., orthoprojections) and a variety of other image-based products from which a variety of key ecological metrics can be extracted. The first section of this document covers the generation of 3D models and associated products using imagery collected in the field and processed with the photogrammetric software Agisoft Metashape (Agisoft LLC, St. Petersburg, Russia). Next, instructions are provided for the use of the custom software platform Viscore for the extraction of benthic percent cover data, coregistration of time series imagery, generation of 2D map views, and project management. The final section provides guidance on the extraction of coral demographic data using the artificial intelligence (AI)–based data extraction software TagLab.