Structure from Motion (SfM) Coral (Adult and Juvenile) Annotations derived from Stratified Random Site (StRS) Imagery across the US Pacific from 2019 to 2023 for methods comparison

Description

Coral adult and juvenile coral colony demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers, and is documented separately here: https://www.fisheries.noaa.gov/inport/item/63095. The data were collected as part of the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) led National Coral Reef Monitoring Program (NCRMP) missions around the US Pacific from 2019 for method comparison. Refer to Lineage and URLs for links to publication.

The SfM surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. Surveys were conducted at sites randomly stratified across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). These sites represent a broad range of depths (1-25 m), habitat types (aggregate reef, patch reef, pavement, rock and boulder and rubble), coral cover, and diving conditions. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site to site comparisons should be used with caution.

During each survey, an 18m transect line was deployed along the isobath and photographed using underwater cameras while swimming in a back and forth swim pattern for later processing using an SfM approach. At depths of 1-20 m, SfM surveys were conducted over a 3 x 20m area and at depths > 20m, a 3 x 13m area was surveyed, both with the transect running down the middle of the survey area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for juvenile and adult coral colony demographic metrics. Data was collected for each site within four 2.5m2 segments, each 1m wide, along the transect (at 0-2.5m, 5-7.5m, 10-12.5m, and 15-17.5m). At deeper sites where a 3 x 13m area was surveyed, only the first three segments were analyzed in ArcGIS. For each adult coral colony (> 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), and estimated percent old mortality were recorded. Bleaching extent (% of living tissue with reduced pigmentation) and severity were also recorded. Juvenile coral colonies (0.7 to 5cm maximum diameter) were recorded within the first 1 m2 of the first 3 segments. For juvenile colonies, only ID and maximum diameter were recorded.

Resources

Name Format Description Link
SfM_Adult_demographic_MHI_2019.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. Open resource
SfM_Juvenile_Demographic_MHI_2019.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. Open resource
SfM_Adult_demographic_MHI_2019.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. Open resource
SfM_Juvenile_Demographic_MHI_2019.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. Open resource
SfM_Adult_demographic_MARI_2022.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago beginning in 2022 during REA surveys. Open resource
REFERENCE_GENUS_SPCODE.csv Unknown Lookup table for species and taxon codes used by the NOAA Fisheries Ecosystem Sciences Division across the US Pacific. Note: 'AAAA' is used to denote no colonies observed. Genus is provided as analysis can be performed at that level. Open resource
REFERENCE_GENUS_SPCODE.csv Unknown Lookup table for species and taxon codes used by the NOAA Fisheries Ecosystem Sciences Division across the US Pacific. Note: 'AAAA' is used to denote no colonies observed. Genus is provided as analysis can be performed at that level. Open resource
SfM_Juvenile_demographic_MARI_2022.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago in 2022 during REA surveys. Open resource
SfM_Juvenile_demographic_MARI_2022.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago in 2022 during REA surveys. Open resource
SfM_Adult_demographic_MARI_2022.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago beginning in 2022 during REA surveys. Open resource
SfM_Juvenile_demographic_AS-PRIA_2023.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout American Samoa in 2023 during REA surveys. Open resource
SfM_Juvenile_demographic_AS-PRIA_2023.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout American Samoa in 2023 during REA surveys. Open resource
SfM_Adult_demographic_AS-PRIA_2023.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the American Samoa in 2023 during REA surveys. Open resource
SfM_Adult_demographic_AS-PRIA_2023.csv Unknown Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the American Samoa in 2023 during REA surveys. Open resource
2023 Methods Comparison Tech Memo Unknown Publication utilizing the data describes in this record Open resource
2023 Methods Comparison Tech Memo Unknown Publication utilizing the data describes in this record Open resource
GCMD Keyword Forum Page Unknown Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords Open resource
GCMD Keyword Forum Page Unknown Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords Open resource
National Coral Reef Monitoring Program Unknown NOAA National Coral Reef Monitoring Program (NCRMP) website. Open resource
National Coral Reef Monitoring Program Unknown NOAA National Coral Reef Monitoring Program (NCRMP) website. Open resource
Full Metadata Record Unknown View the complete metadata record on InPort for more information about this dataset. Open resource
Full Metadata Record Unknown View the complete metadata record on InPort for more information about this dataset. Open resource
NOAA Data Management Plan (DMP) PDF NOAA Data Management Plan for this record on InPort. Open resource
NOAA Data Management Plan (DMP) PDF NOAA Data Management Plan for this record on InPort. Open resource
Coral Reefs in the Pacific Unknown NOAA Fisheries Website Open resource
Coral Reefs in the Pacific Unknown NOAA Fisheries Website Open resource
NOAA Fisheries Pacific Islands Region - Science Overview Unknown NOAA Fisheries Website Open resource
NOAA Fisheries Pacific Islands Region - Science Overview Unknown NOAA Fisheries Website Open resource
Pacific Islands Fisheries Science Center Website Unknown Pacific Island Fisheries Science Center homepage Open resource
Pacific Islands Fisheries Science Center Website Unknown Pacific Island Fisheries Science Center homepage Open resource

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