Data Management Plan

The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 years apart. In situ surveys, post-processing, and analysis were funded by NOAA Coral Reef Conservation Program (CRCP) and Ocean Acidification Program (OAP). Data collection was conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD).

Survey sites consisted of sites previously established by collaborators from Scripps Institution of Oceanography, starting as far back as 2014, and new sites established in 2019 by NOAA ESD. During each survey, physical markings which identify each permanent survey site were either established or found using GPS coordinates previously collected. During image collection, the diver swam at a constant distance from the bottom of the reef while continuously capturing overlapping photographs, capturing approximately 100 m2 of reef habitat. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time.

Due to the labor-intensive and time-consuming nature of coral annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. Each site was sub-sampled by randomly distributing a minimum of 10 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated (n >/=30 for each target coral species). The target taxa species consisted of two genera - Pocillopora and Porites.

In total, this dataset currently includes planar area and associated vital rates measurements for 5 coral species in 2 genera (Pocillopora and Porites) at 14 sites throughout the Hawaiian Archipelago and 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago.

Lineage Statement:
Benthic imagery was collected at permanent sites and generated into 3D dense point clouds (DPCs) using Agisoft Metashape software. DPCs from the same site, but different collection dates were converted into 2D orthoprojections and scaled, oriented and aligned together. Next, the orthoprojections were exported for annotation. Orthoprojections were sub-sampled by randomly distributing quadrats throughout the orthoprojection. Quadrat location was conserved across all orthoprojections associated with the same permanent site. Target coral species were identified within each quadrat and their perimeters were annotated until a sufficient sample size of each species was recorded. The changes in coral planar area of each coral colony was tracked by linking annotations of the same live coral across each time point. All statistics and figures were performed in R.

Process Steps:

• Prior to image collection, each site was set up by placing at least two scale bars of known length, with ground control points (GCPs) at the end of each bar, 2-3 m away from the center of the survey area. At many sites, rebar caps with GCPs were also placed on the reference pins (36 in tall stainless steel rods used to mark the site). During plot set up, one diver drew a diagram of the plot, marking the location of each scale bar, reference pin, and distinctive benthic features. The depth and identification numbers of each scale bar were recorded in the diagram as well. Divers swam ~1m off the seafloor, collecting enough photographs to produce 60%-80% image overlap and complete two full passes of the site. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649)
• Images for each site were evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. Following image quality control, each set of raw images were imported, aligned separately in Agisoft Metashape and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019). For the Hawaiian Archipelago dataset, DPCs were then imported into Viscore, a custom visualization software (Petrovic et al., 2014), where all DPCs from the same site, but from different time points, were scaled, oriented and aligned together using the GCP information. Each DPC was converted into a 2D orthorectified image (orthoprojection) and an identical top-down view of all othoprojections of the same site but different time points were exported from Viscore. For the Mariana Archipelago dataset, all scaling, orienting, alignment and 2D model creations were completed using Agisoft Metashape. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649)
• Due to the labor-intensive and time-consuming nature of annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. To sub-sample each site, we selected the region where there was the most spatial overlap across all orthoprojections of the same site. Next, 10-30 0.5m2 quadrats were generated at random throughout the selected area and each labelled in numerical order. Within the first 10 quadrats, all coral species on the target coral species list were annotated if their centroid fell within the quadrat. Corals were annotated by tracing the full perimeter of live coral tissue patches. During annotation, the original JPEG imagery was viewed alongside the orthoprojection to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection (e.g. under ledges). If one or several coral species on the target list did not reach n = 30 live patches within the first 10 quadrats. These species were identified and annotated in additional quadrats, and sometimes outside the quadrats, until a higher sample size could be reached. Unique identifying numbers were assigned to each patch of live coral tissue link coral patches across time and to track fission/fusion events. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649)
• Annotations were exported and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing coral unique identifier, data in incorrect columns). Before analysis, all corals patches < 19 cm2 and corals that were not present in both the initial and final time point were removed from the dataset. For the Hawaiian archipelago dataset, absolute change in coral patch area (cm2) was calculated in R. (Citation: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649)

During coral annotation, the original JPEG imagery was viewed alongside the orthoprojection using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection. Annotations were quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing or duplicated coral colony ID, data in incorrect columns).

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

NOAA IRC and NOAA Fisheries ITS resources and assets.