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

Published by Pacific Islands Fisheries Science Center | National Oceanic and Atmospheric Administration, Department of Commerce | Catalog Last Checked: May 10, 2026 at 06:02 AM | Dataset Last Updated: January 01, 2025 at 12:00 AM
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.

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DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce EARTH SCIENCE EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > UNITED STATES MINOR OUTLYING ISLANDS OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > GUAM OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > NORTHERN MARIANA ISLANDS

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accessLevel non-public
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describedByType application/octet-steam
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.
distribution 
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  {
    "@type": "dcat:Distribution",
    "title": "ESD_SfM_StructuralComplex_MHI_2019.csv",
    "accessURL": "https://accession.nodc.noaa.gov/0268310",
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    "description": "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.",
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identifier https://data.noaa.gov/waf/NOAA/nmfs/pifsc/iso/xml/67851.xml
issued 2022-11-01T00:00:00.000+00:00
keyword 
                                            [
  "DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce",
  "EARTH SCIENCE",
  "EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > UNITED STATES MINOR OUTLYING ISLANDS",
  "OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > GUAM",
  "OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > NORTHERN MARIANA ISLANDS",
  "31360",
  "31525",
  "743",
  "NOAA Coral Reef Conservation Program",
  "Pacific National Coral Reef Monitoring Program",
  "Geographic Information > Digital Elevation Model",
  "Map Images > Coral Mapping",
  "Map Images > Topography",
  "Numeric Data Sets > Benthic",
  "EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis",
  "EARTH SCIENCE > Oceans > Bathymetry/Seafloor Topography > Rugosity",
  "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs",
  "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Rugosity",
  "EARTH SCIENCE > Oceans > Marine Biology > Coral",
  "CORAL - CENSUS",
  "photograph",
  "computer",
  "derived products",
  "CORAL REEF STUDIES",
  "Coral Reef Conservation Program",
  "National Coral Reef Monitoring Program",
  "US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Aguihan > Aguihan Island (Aguijan) (14N145E0006)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Northern Mariana Islands > Northern Mariana Islands ( CNMI ) (18N146E0000)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Rota > Rota Island ( Luta ) (14N145E0007)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Sarigan Island > Sarigan Island (16N145E0003)",
  "COUNTRY/TERRITORY > Northern Mariana Islands > Tinian > Tinian Island (14N145E0005)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Swains Atoll (11S171W0001)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012)",
  "COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016)",
  "COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii (21N160W0000)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Kauai Island (22N159W0001",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Molokai Island (21N157W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > French Frigate Shoals (24N166W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Lisianski Island (25N173W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Northwestern Hawaiian Islands (28N178W0000)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Pearl and Hermes Reef (27N176W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Kalawao > Kahoolawe Island (20N156W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Kauai > Niihau Island (21N160W0001)",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Lanai Island (20N156W0002",
  "COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Maui Island (20N156W0004",
  "COUNTRY/TERRITORY > United States of America > Hawaiian Islands (21N157W0027)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Baker Island (00N176W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Howland Island (00S176W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Johnston Atoll (16N169W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001)",
  "COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001)",
  "OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000)",
  "OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001)",
  "OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001)",
  "OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Baker Island > Baker Island (00N176W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands (21N157W0027)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii > Hawaii (21N160W0000",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii Island > Hawaii Island (19N155W0003",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kahoolawe Island > Kahoolawe Island (20N156W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kauai Island > Kauai Island (22N159W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Lanai Island > Lanai Island (20N156W0002)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Maui Island > Maui Island (20N156W0004)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Molokai Island > Molokai Island (21N157W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Niihau Island > Niihau Island (21N160W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Howland Island > Howland Island (00S176W0001",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Johnston Atoll > Johnston Atoll (16N169W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands (28N178W0000)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > French Frigate Shoals (24N166W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Lisianski Island (25N173W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001)",
  "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001)",
  "OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013)",
  "OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014)",
  "OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Aguihan Island Reefs > Aguihan Island (Aguijan) (14N145E0006)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Mariana Archipelago > Northern Mariana Islands ( CNMI ) (18N146E0000)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Maug Island > Maug Island (20N145E0001)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Pagan Island > Pagan Island (18N145E0001)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Rota Island > Rota Island ( Luta ) (14N145E0007)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Saipan Island > Saipan Island (15N145E0002)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Sarigan Island > Sarigan Island (16N145E0003)",
  "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Tinian Island Reefs > Tinian Island (14N145E0005)",
  "Coastal Waters of Hawaii",
  "Central Pacific Ocean",
  "North Pacific Ocean",
  "OSCAR ELTON SETTE",
  "Agisoft",
  "American Samoa",
  "CNMI",
  "CRED",
  "CREP",
  "Complexity metrics",
  "Coral Reef Ecosystem Division",
  "Coral Reef Ecosystem Program",
  "ESD",
  "Ecosystem Sciences Division",
  "Fractal dimension",
  "Guam",
  "Height range",
  "Mariana Archipelago",
  "PIFSC",
  "Pacific Islands Fisheries Science Center",
  "Pacific Remote Island Areas",
  "Reef Assessment and Monitoring Program",
  "Reef habitat complexity",
  "Rugosity",
  "SfM",
  "Structure from Motion",
  "digital elevation model",
  "DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce",
  "Structure From Motion"
]
landingPage https://www.fisheries.noaa.gov/inport/item/67851
language 
                                            []
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2025-01-01T00:00:00.000+00:00
publisher 
                                            {
  "name": "Pacific Islands Fisheries Science Center",
  "@type": "org:Organization"
}
rights otherRestrictions, unclassified
spatial -154.8042,19.07632,-160.2518,22.20357
temporal 2019-04-21T00:00:00+00:00/2019-08-06T00:00:00+00:00
title Coral Reef Structural Complexity derived from Structure-from-Motion (SfM) imagery collected at Stratified-Random Sites (StRS) across the U.S. Pacific since 2019

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