Data Management Plan (Deprecated)

The data described here are Structure from Motion (SfM) benthic habitat imagery from benthic transect surveys conducted at stratified random sites by the Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD)--formerly the Coral Reef Ecosystem Division--as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The SfM surveys replicates the visual Rapid Ecological Assessment (REA) survey methodology for corals conducted during ESD-led NCRMP missions across the Pacific Ocean beginning in 2019.

A stratified random sampling (StRS) design was employed to survey the coral reef ecosystems across the U.S. Pacific Regions (Hawaiian Archipelago, Mariana Archipelago, American Samoa, and the Pacific Remote Island Areas). The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0-30 m depth range. The stratification scheme included island, sub-island sector, reef zone, and depth in all regions, as well as habitat structure type in the Main Hawaiian Islands. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance by sampling more sites with larger hardbottom area and variance. Therefore, site-level analyses should be employed with caution.

Sites were imaged using underwater cameras along 3x20m (3x13m for sites deeper than 18m) transects to extract data for two coral life stages (juveniles, adults) across the U.S. Pacific Island areas beginning in 2019. Adult colony surveys record taxon (genus or species), morphology, colony size, partial mortality in two categories - old dead and recent dead, cause of recent dead partial mortality, and non-lesion forming condition including bleaching and disease. These data are used to calculate density, size distributions, average partial mortality and prevalence and mean severity of coral health conditions. Juvenile colony surveys include taxon (genus or species), morphology and size, and are used to calculate juvenile density and size distributions by taxon.

Lineage Statement:
The benthic SfM survey methodology, employed by the NOAA Ecosystem Sciences Division (ESD) began in 2019. Benthic imagery is collected at stratified random sites. These photos are evaluated for quality prior to processing and analysis.

Process Steps:

• A stratified random sampling (StRS) design was employed to survey the coral reef ecosystems through the U.S. Pacific regions. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats. The stratification scheme included island, reef zone, and depth in all regions, as well as habitat structure type in the Main Hawaiian Islands. The habitat structure types included simple, complex, and coral-rich. Depth categories of shallow (0-6 m), mid (> 6-18m) and deep (>18-30 m) were also incorporated into the stratification scheme. Allocation of sampling effort was proportional to strata area and variance in coral density . Sites were randomly selected within each stratum. A geographic information system (GIS) and digital spatial databases of benthic habitats (NOAA National Centers for Coastal Ocean Science NCCOS), reef zones (IKONOS satellite imagery, NDGC 1998) bathymetry (NDGC 1998, CREP benthic mapping data), and marine reserve boundaries (NOAA) were used to facilitate spatial delineation of the sampling survey domain, strata, and sample units. Map resolution was such that the survey domain could be overlain by a grid using a GIS with individual cells of size 50 m by 50 m in area. A one-stage sampling scheme following Cochran (1977) was employed. Grid cells containing hard-bottom reef habitats were designated as primary sample units (referred to as sites). (Citation: Winston M, Couch C, Huntington B, Vargas-Ángel B. 2020. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2019 Update)
• SfM benthic surveys were conducted by both the fish and benthic teams to record the benthic community composition. A 3 x 20 m or 3 x 13 m plot was visually established centered on a transect line. 3-4 depth markers were placed within the plot for scale. White balance settings were adjusted in situ using an 18% gray card. JPEG images were collected using a Canon SL2 or SL3 digital camera in an underwater housing with a dome port. Images were collected at each site by swimming in a back-and-forth motion 1 m above the substrate capturing images continuously to achieve a 60-80% overlap across consecutive images. (Citation: Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47)
• Images for each site were evaluated to remove extraneous or erroneous photographs (e.g. fins, blue water, excessive blur, etc.) At some sites images were color corrected and exposure corrected using Adobe Lightroom because white balance was not achieved in situ or a substantial number of images were dark, respectively. Image adjustments were batch run per site for consistent correction. Images were processed in Agisoft Metashape to create 3-dimensional models as well as 2-dimensional "orthomosaics" for each site to be used for data extraction. Image data includes ~1500 benthic photographs per survey site. Included in the archive package is a list of survey sites, including region, island, site, date (day, month, year), latitude (dd), longitude (dd), depth marker numbers with corresponding depth values, marker length for scaling models, camera model and lens focal length, if the images for a site were color or exposure corrected, and a unique image name. The file naming convention for each photo/image is NCRMP_SFM_StRS_YEAR_MissionID_REGION_ISLAND-Site#_IMG_####.jpg (Citation: Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47)

Each image set was evaluated for image quality. Images deemed unsatisfactory were removed from the image set. To ensure consistency, images were color corrected using Adobe Lightroom if it appeared that the camera they were taken from was not properly white balanced in the field or imagery from a site was consistently too dark.

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.