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Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021

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: September 14, 2023 at 12:00 AM
Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. This data includes coral species identification, bleaching extent and severity, colony diameter, perimeter, and planar size. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers and is documented and described separately. The data was collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands, and in subsequent years (2020, 2021) to assess recovery. The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. Two datasets are provided: an annotations file which provides coral demographic information of 6 target species at 12 fixed sites across 3 years, as well as a site metadata file which describes the site and surveys which were used to generate models for which annotation data was derived. Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA). Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred. Note an update in methodology: The data was collected in two stages. During the first stage of data collection that was completed in 2021, for each coral patch, (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded. In 2023 the methodology was updated for the second stage of data collection; the updated dataset includes measures of planar area and a "genet" (colony) identification column. The 2023 dataset was also collected following an update to the model process methodology (see Lineage). Users should refer to the most updated dataset published in 2023.

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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 > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF EARTH SCIENCE > OCEANS > COASTAL PROCESSES > CORAL REEFS > CORAL BLEACHING OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > HAWAII ISLAND OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > LANAI OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > OAHU

Complete Metadata
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accessLevel non-public
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describedByType application/octet-steam
description Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. This data includes coral species identification, bleaching extent and severity, colony diameter, perimeter, and planar size. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers and is documented and described separately. The data was collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands, and in subsequent years (2020, 2021) to assess recovery. The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. Two datasets are provided: an annotations file which provides coral demographic information of 6 target species at 12 fixed sites across 3 years, as well as a site metadata file which describes the site and surveys which were used to generate models for which annotation data was derived. Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA). Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred. Note an update in methodology: The data was collected in two stages. During the first stage of data collection that was completed in 2021, for each coral patch, (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded. In 2023 the methodology was updated for the second stage of data collection; the updated dataset includes measures of planar area and a "genet" (colony) identification column. The 2023 dataset was also collected following an update to the model process methodology (see Lineage). Users should refer to the most updated dataset published in 2023.
distribution 
                                            [
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    "@type": "dcat:Distribution",
    "title": "2019_SfMSiteMetadata.csv",
    "accessURL": "https://accession.nodc.noaa.gov/0244392",
    "mediaType": "text/html",
    "description": "Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch level information.",
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  },
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    "title": "HCBC_2019_TaxaList.csv",
    "accessURL": "https://accession.nodc.noaa.gov/0209239",
    "mediaType": "text/html",
    "description": "Reference table of full taxa names per taxa code.",
    "describedByType": "application/octet-stream"
  },
  {
    "@type": "dcat:Distribution",
    "title": "BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021",
    "accessURL": "https://accession.nodc.noaa.gov/0283598",
    "mediaType": "text/html",
    "description": "Annotations of 3D coral models generated from patch level analysis in 2022 using imagery from follow-up surveys in 2021 and 2020 (Oahu only) to revisit fixed sites established in 2019 for bleaching assessment. A subset of metrics from 2019 was collected again, using an updated methodology described in the Lineage section.",
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  {
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    "title": "GCMD Keyword Forum Page",
    "accessURL": "https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords",
    "mediaType": "text/html",
    "description": "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",
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identifier https://data.noaa.gov/waf/NOAA/nmfs/pifsc/iso/xml/65764.xml
issued 2021-11-01T00:00:00.000+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 > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC",
  "EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF",
  "EARTH SCIENCE > OCEANS > COASTAL PROCESSES > CORAL REEFS > CORAL BLEACHING",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > HAWAII ISLAND",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > LANAI",
  "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > OAHU",
  "Computer > Computer",
  "31283",
  "31361",
  "Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities",
  "Hawai'i coral bleaching assessment and analysis",
  "Numeric Data Sets > Benthic",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching",
  "EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)",
  "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs",
  "EARTH SCIENCE > Oceans > Marine Biology > Coral",
  "EARTH SCIENCE > Oceans > Marine Biology > Coral Communities",
  "NEARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis",
  "CORAL",
  "CORAL - COLONY SIZE",
  "CORAL - SPECIES IDENTIFICATION",
  "GIS product",
  "derived products",
  "in situ",
  "survey - coral reef",
  "CORAL REEF STUDIES",
  "National Coral Reef Monitoring Program",
  "Ocean Acidification Program",
  "US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division",
  "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 > Honolulu > Oahu (21N157W0003)",
  "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)",
  "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 > 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 > Oahu Island > Oahu (21N157W0003)",
  "Coastal Waters of Hawaii",
  "Central Pacific Ocean",
  "North Pacific Ocean",
  "photograph",
  "scale",
  "VARIOUS SMALL VESSELS",
  "CRED",
  "CREP",
  "Coral Reef Ecosystem Division",
  "Coral Reef Ecosystem Program",
  "DAR",
  "DLNR",
  "Department of Land and Natural Resources",
  "Division of Aquatic Resources",
  "ESD",
  "Ecosystem Sciences Division",
  "PIFSC",
  "Pacific Islands Fisheries Science Center",
  "SfM",
  "Structure from Motion",
  "coral demography",
  "DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce",
  "Ocean and Climate Change"
]
landingPage https://www.fisheries.noaa.gov/inport/item/65764
language 
                                            []
license https://creativecommons.org/publicdomain/zero/1.0/
modified 2023-09-14T00:00:00.000+00:00
publisher 
                                            {
  "name": "Pacific Islands Fisheries Science Center",
  "@type": "org:Organization"
}
rights otherRestrictions, unclassified
spatial -155.830367,19.42335,-158.0667,21.47959
temporal 2019-10-08T00:00:00+00:00/2021-07-20T00:00:00+00:00
title Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021

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