Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014
The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 years apart. In situ surveys, post-processing, and analysis were funded by NOAA Coral Reef Conservation Program (CRCP) and Ocean Acidification Program (OAP). Data collection was conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD).
Survey sites consisted of sites previously established by collaborators from Scripps Institution of Oceanography, starting as far back as 2014, and new sites established in 2019 by NOAA ESD. During each survey, physical markings which identify each permanent survey site were either established or found using GPS coordinates previously collected. During image collection, the diver swam at a constant distance from the bottom of the reef while continuously capturing overlapping photographs, capturing approximately 100 m2 of reef habitat. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time.
Due to the labor-intensive and time-consuming nature of coral annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. Each site was sub-sampled by randomly distributing a minimum of 10 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated (n >/= 30 for each target coral species). The target taxa species vary by region and include Acropora, Montipora, Pocillopora, Porites.
In total, this dataset includes planar area and associated vital rates measurements for 5 coral species in 2 genera (Pocillopora and Porites) at 14 sites throughout the Hawaiian Archipelago, 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago and 4 genera (Pocillopora, Porites, Acropora and Montipora) at 11 sites across American Samoa and Pacific Remote Islands and Atolls (PRIAs).
Resources
7 resources available
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SfM_VitalRates_MHI_NWHI.csv
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SfM_VitalRates_MARIAN_2022.csv
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Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion SOP
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Measuring Coral Vital Rates Using TagLab SOP
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SFM_VitalRates_AMSM_PRIA_2023.csv
TEXT/HTML -
GCMD Keyword Forum Page
TEXT/HTML -
Full Metadata Record
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| @type | dcat:Dataset |
|---|---|
| accessLevel | non-public |
| contactPoint |
{ "fn": "Not provided - Contact data.gov", "hasEmail": "mailto:datagovsupport@gsa.gov" } |
| describedByType | application/octet-steam |
| description | The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 years apart. In situ surveys, post-processing, and analysis were funded by NOAA Coral Reef Conservation Program (CRCP) and Ocean Acidification Program (OAP). Data collection was conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD). Survey sites consisted of sites previously established by collaborators from Scripps Institution of Oceanography, starting as far back as 2014, and new sites established in 2019 by NOAA ESD. During each survey, physical markings which identify each permanent survey site were either established or found using GPS coordinates previously collected. During image collection, the diver swam at a constant distance from the bottom of the reef while continuously capturing overlapping photographs, capturing approximately 100 m2 of reef habitat. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time. Due to the labor-intensive and time-consuming nature of coral annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. Each site was sub-sampled by randomly distributing a minimum of 10 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated (n >/= 30 for each target coral species). The target taxa species vary by region and include Acropora, Montipora, Pocillopora, Porites. In total, this dataset includes planar area and associated vital rates measurements for 5 coral species in 2 genera (Pocillopora and Porites) at 14 sites throughout the Hawaiian Archipelago, 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago and 4 genera (Pocillopora, Porites, Acropora and Montipora) at 11 sites across American Samoa and Pacific Remote Islands and Atolls (PRIAs). |
| distribution |
[ { "@type": "dcat:Distribution", "title": "SfM_VitalRates_MHI_NWHI.csv", "accessURL": "https://accession.nodc.noaa.gov/0257945", "mediaType": "text/html", "description": "Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), and adult coral colony observations identified to the lowest taxonomic level possible (usually species) including initial and final size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Main Hawaiian Islands from 2014-2019. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "SfM_VitalRates_MARIAN_2022.csv", "accessURL": "https://accession.nodc.noaa.gov/0282457", "mediaType": "text/html", "description": "Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Mariana Archipelago from 2014-2022. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion SOP", "accessURL": "https://repository.library.noaa.gov/view/noaa/32739", "mediaType": "text/html", "description": "Vital Rates Technical Memorandum", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "Measuring Coral Vital Rates Using TagLab SOP", "accessURL": "https://www.fisheries.noaa.gov/resource/document/measuring-coral-vital-rates-using-taglab-semi-automatic-coral-annotation-and", "mediaType": "text/html", "description": "This standard operating procedure (SOP) provides a time savings comparison between manual annotation using the previous Vital Rates workflow (Rodriguez et al. 2021) and our TagLab-assisted Vital Rates workflow. We posit that, although TagLab remains an ongoing project of the Visual Computing lab and requires additional testing, it reduces personnel hours by 40%, making it a worthwhile approach to quantifying coral vital rates. Pacific Islands Fisheries Science Center technical memoranda are issued to promptly disseminate scientific and technical information to marine resource managers, scientists, and the general public. Their contents cover a range of topics, including biological and economic research, stock assessment, trends in fisheries, and other subjects. Administrative reports typically have not been reviewed outside the Center; therefore, they are considered informal publications. The material presented in administrative reports may later be published in the formal scientific literature after more rigorous verification, editing, and peer review.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "SFM_VitalRates_AMSM_PRIA_2023.csv", "accessURL": "https://accession.nodc.noaa.gov/0307802", "mediaType": "text/html", "description": "Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout American Samoa and Pacific Remote Islands and Atolls (PRIAs) from 2014-2023. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division.", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "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). 2026. GCMD Keywords, Version 24. 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", "describedByType": "application/octet-stream" }, { "@type": "dcat:Distribution", "title": "Full Metadata Record", "accessURL": "https://www.fisheries.noaa.gov/inport/item/63093", "mediaType": "text/html", "description": "View the complete metadata record on InPort for more information about this dataset.", "describedByType": "application/octet-stream" } ] |
| identifier | https://data.noaa.gov/waf/NOAA/nmfs/pifsc/iso/xml/63093.xml |
| issued | 2022-07-26T00:00:00.000+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 > BENTHIC", "EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF", "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA", "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > BAKER ISLAND", "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS", "OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HOWLAND ISLAND", "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", "NOAA Coral Reef Conservation Program", "Numeric Data Sets > Benthic", "EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat", "EARTH SCIENCE > Biosphere > Zoology > Corals", "EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Growth", "EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis", "EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)", "EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs", "EARTH SCIENCE > Oceans > Marine Biology > Coral Communities", "CORAL", "CORAL - COLONY SIZE", "CORAL - SPECIES IDENTIFICATION", "derived products", "CORAL REEF STUDIES", "Coral Reef Conservation Program", "Ocean Acidification Program", "US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division", "(14S170W0042) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000)", "COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001)", "COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001)", "COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001)", "COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002)", "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 > Tutuila Island (14S170W0016)", "COUNTRY/TERRITORY > United States of America > American Samoa > Ofu Island > Ofu (14S169W0002)", "COUNTRY/TERRITORY > United States of America > American Samoa > Olosega Island > Olosega (14S169W0016)", "COUNTRY/TERRITORY > United States of America > American Samoa > Ta'u Island > Ta'u (14S169W0015)", "COUNTRY/TERRITORY > United States of America > American Samoa > Tutuila Island > Fagasa Bay (14S170W0014)", "COUNTRY/TERRITORY > United States of America > American Samoa > Tutuila Island > Fagatele Bay (14S170W0002)", "COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000)", "COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003)", "COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001)", "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 > 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)", "Coastal Waters of Hawaii", "OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000)", "OCEAN BASIN > Pacific Ocean > American Samoa > Manu'a Islands (14S170W0038)", "OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001)", "OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016)", "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 > Maui Island > Maui Island (20N156W0004)", "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 > Northwestern Hawaiian Islands (28N178W0000)", "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001)", "OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001)", "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001)", "OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Guam > Guam (13N144E0000)", "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 > Saipan Island > Saipan Island (15N145E0002)", "Central Pacific Ocean", "Equatorial Pacific Ocean", "North Pacific Ocean", "Pacific Remote Islands Marine National Monument", "Papahanaumokuakea Marine National Monument", "Rose Atoll Marine National Monument", "South Pacific Ocean", "NW Pacific", "Agisoft Metashape", "ArcGIS", "TagLab", "Viscore", "photograph", "scale", "HI'IALAKAI", "OSCAR ELTON SETTE", "RAINIER", "CNMI", "CRED", "CREP", "Commonwealth of the Northern Marianas Islands", "Coral Reef Ecosystem Division", "Coral Reef Ecosystem Program", "ESD", "Ecosystem Sciences Division", "NCRMP", "PIFSC", "Pacific Islands Fisheries Science Center", "RAMP", "Reef Assessment and Monitoring Program", "Scripps Institution of Oceanography", "SfM", "Structure from Motion", "MHI", "Main Hawaiian Islands", "Marianas", "NWHI", "Northwestern Hawaiian Islands", "PMNM", "PRIA", "PRIMNM", "Pacific Remote Island Area", "Pacific Remote Islands Marine National Monument", "PapahÄnaumokuÄkea Marine National Monument", "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/63093 |
| language |
[]
|
| license | https://creativecommons.org/publicdomain/zero/1.0/ |
| modified | 2025-09-01T00:00:00.000+00:00 |
| publisher |
{ "name": "Pacific Islands Fisheries Science Center", "@type": "org:Organization" } |
| rights | otherRestrictions, unclassified |
| spatial | -154.806789,-14.373615,144.618287,28.455623 |
| temporal | 2014-01-27T00:00:00+00:00/2014-01-27T00:00:00+00:00 |
| title | Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014 |
