Image capture for 3D photogrammetry of stony corals V.2 v1

This is a protocol for generating images for underwater coral colony-level photogrammetry. In this protocol, we utilize Olympus Tough cameras and custom-made, adjustable PVC arrays that incorporate unique Agisoft Metashape markers for automatic scaling during the model building process and bleaching color cards. Instructions for creating your own Scaling and Color Object for Underwater Photogrammetry References (SCOUPRs) are included here, along with our Underwater Image Capture Pipeline that includes tips to collect photographs to improve model building, and Pre-Processing instructions. Updates from V1: V2 SCOUPR builds that allow for autoscaling in Metashape and other minor improvements In-depth workflow and additional imaging guidance Changes to in water methodologies that allow for the removal image pre-processing steps, thus streamlining the overall pipeline Though this protocol is primarily used by the Kenkel lab for 3D model generation of Acropora cervicornis colonies, these methods can be applied to corals of all morphologies (or any object, really). Our photosets are later batched processed and autoscaled using Agisoft Metashape command-line scripts integrated with USC's high-performance computing system. Additional resources: V2 scripts for batch processing and autoscaling models can be found here: https: //github. com/mayagomez/metashapebatchₚrocess and DOI: 10. 5281/zenodo. 17136227 Additional guidance for using Metashape on the command line and V1 scripts can be found here: https: //github. com/wyattmillion/Coral3DPhotogram. Our lab's protocol for deriving coral morphological and growth data from 3D models can be found here: Phenotyping in MeshLab.