Coral Reef Structural Complexity derived from Structure-from-Motion (SfM) imagery collected at Stratified-Random Sites (StRS) across the U.S. Pacific since 2019

Description

The data described here are structural complexity estimates derived from Structure-from-Motion (SfM) benthic habitat imagery from diver transect surveys conducted at stratified-random sites (StRS) by the Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD) as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The coral reef photos, collected by scuba divers, are used to generate 3-dimensional models, digital elevation models (DEMs) and orthomosaics using Agisoft Metashape photogrammetric software. The digital elevation models were analyzed in R studio to derive estimates of habitat structural complexity, using metrics such as: rugosity, fractal dimension, and height range, among others. The source imagery is archived and described separately at https://www.fisheries.noaa.gov/inport/item/63095.
The SfM surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. Sites were imaged using underwater cameras along 3x20m (3x13m for sites deeper than 18m) transects across the U.S. Pacific Island areas beginning in 2019. Please refer to the Lineage section for SOPs -- 2019 and 2022 have slightly different processing steps. Complexity metrics were estimated for each site within five or six 4m2 DEM sampling plots, which can then be averaged for the site. Rugosity is measured as the ratio between surface area and planar area within a sampling plot, Fractal dimension is measured using the variation or standard deviation method (see Lineage section below), and height range is measured as the difference between the deepest and shallowest point within a sampling plot.
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. Allocation of sampling effort was proportional to the strata hardbottom area. The StRS design effectively reduces estimated variance by sampling more sites with larger hardbottom area and variance.

Resources

Name Format Description Link
ESD_SfM_StructuralComplexity_Pacific_2022.csv Unknown Coral reef structural complexity dataset generated by extracting metrics from digital elevation models developed from imagery collected during the National Coral Reef Monitoring Program surveys across the U.S. Pacific Islands regions. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site-level information. This data file will be updated as more data is collected and derived for different Pacific Islands regions. Currently data includes: stratified random sites across Guam and CNMI during the 2022 NCRMP mission, as well as in 2019 in the Hawaiian archipelago. Currently data includes: stratified random sites surveyed as part of NCRMP across Guam and CNMI in 2022, as well as the Hawaiian archipelago in 2019. Open resource
ESD_SfM_StructuralComplexity_Pacific_2022.csv Unknown Coral reef structural complexity dataset generated by extracting metrics from digital elevation models developed from imagery collected during the National Coral Reef Monitoring Program surveys across the U.S. Pacific Islands regions. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site-level information. This data file will be updated as more data is collected and derived for different Pacific Islands regions. Currently data includes: stratified random sites across Guam and CNMI during the 2022 NCRMP mission, as well as in 2019 in the Hawaiian archipelago. Currently data includes: stratified random sites surveyed as part of NCRMP across Guam and CNMI in 2022, as well as the Hawaiian archipelago in 2019. Open resource
ESD_SfM_StructuralComplex_MHI_2019.csv Unknown DEPRECATED- data is now under a singular Pacific-wide file as described. Structural complexity dataset generated by extracting data from digital elevation models developed from 1imagery collected at StRS across the Main Hawaiian Islands during the 2019 NCRMP mission. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site information. Open resource
ESD_SfM_StructuralComplex_MHI_2019.csv Unknown DEPRECATED- data is now under a singular Pacific-wide file as described. Structural complexity dataset generated by extracting data from digital elevation models developed from 1imagery collected at StRS across the Main Hawaiian Islands during the 2019 NCRMP mission. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site information. Open resource
A geometric basis for surface habitat complexity and biodiversity Unknown This study presents a geometric basis for surface habitats that unifies ecosystems and spatial scales. Open resource
A geometric basis for surface habitat complexity and biodiversity Unknown This study presents a geometric basis for surface habitats that unifies ecosystems and spatial scales. Open resource
habtools: An R package to calculate 3D metrics for surfaces and objects Unknown habtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow. Open resource
habtools: An R package to calculate 3D metrics for surfaces and objects Unknown habtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow. Open resource
Geological age and environments shape reef habitat structure Unknown Published 2022 results using structural complexity dataset from the Hawaiian islands. Open resource
Geological age and environments shape reef habitat structure Unknown Published 2022 results using structural complexity dataset from the Hawaiian islands. 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
GitHub Repository for R Scripts used in Structural Complexity Analysis Unknown 'GEOLOGICAL AND ENVIRONMENTAL FACTORS SHAPE REEF HABITAT STRUCTURE IN THE MAIN HAWAIIAN ISLANDS' Open resource
GitHub Repository for R Scripts used in Structural Complexity Analysis Unknown 'GEOLOGICAL AND ENVIRONMENTAL FACTORS SHAPE REEF HABITAT STRUCTURE IN THE MAIN HAWAIIAN ISLANDS' Open resource
Processing Coral Reef Imagery Using Structure-from-Motion Photogrammetry: Standard Operating Procedures (2023 Update) Unknown Published 2023 Standard Operating Procedures to collect and reconstruct Digital Elevation models and orthomosaics from coral reef photos using Structure from Motion photogrammetry methods. Open resource
Processing Coral Reef Imagery Using Structure-from-Motion Photogrammetry: Standard Operating Procedures (2023 Update) Unknown Published 2023 Standard Operating Procedures to collect and reconstruct Digital Elevation models and orthomosaics from coral reef photos using Structure from Motion photogrammetry methods. Open resource
Linking fish biomass and coral reefs structural complexity across the Mariana Archipelago Unknown Published technical memorandum using the 2022 structural complexity dataset from the Mariana Archipelago. Open resource
Linking fish biomass and coral reefs structural complexity across the Mariana Archipelago Unknown Published technical memorandum using the 2022 structural complexity dataset from the Mariana Archipelago. 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 Webiste Open resource
Coral Reefs in the Pacific Unknown NOAA Fisheries Webiste Open resource
NOAA Fisheries Pacific Islands Region - Science Overview Unknown Online Resource Open resource
NOAA Fisheries Pacific Islands Region - Science Overview Unknown Online Resource 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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