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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 (NCEI Accession 0283598)

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Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery collected at established fixed sites to assess bleaching recovery from 2019-2021 in the Main Hawaiian Islands. 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.

Benthic imagery collected at permanent sites was generated into 3D dense point clouds (DPCs) using Agisoft Metashape software. DPCs from the same site, but different collection dates were converted into 2D orthomosaics and scaled, oriented and aligned together. Orthomosaics were sub-sampled by randomly distributing quadrats throughout the orthomosaic. Quadrat location was conserved across all orthomosaics associated with the same permanent site. Target coral species were identified within each quadrat and their perimeters were annotated until a sufficient sample size of each species was recorded. 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.

Dataset Citation

Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2023). Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021 (NCEI Accession 0283598). https://www.ncei.noaa.gov/archive/accession/0283598. In Ecosystem Sciences Division, Pacific Islands Fisheries Science Center. Benthic cover and other related datasets derived from Structure-from-Motion (SfM) imagery of coral reef ecosystems in Pacific Islands Regions. [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/PIFSC-SfM-DerivedData. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0283598

Full Text · XML

Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
Distribution Formats	CSV
Ordering Instructions	Contact NCEI for other distribution options and instructions.
Distributor	NOAA National Centers for Environmental Information +1-301-713-3277 ncei.info@noaa.gov
Dataset Point of Contact	NOAA National Centers for Environmental Information ncei.info@noaa.gov

Time Period	2019-10-08 to 2021-07-20
Spatial Bounding Box Coordinates	West: -158.0667 East: -155.8488 South: 19.42335 North: 21.47959
Spatial Coverage Map

General Documentation

NCEI Dataset Landing Page
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Descriptive Information
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Associated Resources

Benthic cover and other related datasets derived from Structure-from-Motion (SfM) imagery of coral reef ecosystems in Pacific Islands Regions
- https://www.ncei.noaa.gov/archive/accession/PIFSC-SfM-DerivedData
  NCEI Collection
Pacific Islands Fisheries Science Center, 2023: Coral Bleaching and Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021
- https://www.fisheries.noaa.gov/inport/item/65764
  InPort Metadata Record
Suka, Rhonda; Asbury, Mollie; Gray, Andrew Elisha; Winston, Morgan; Oliver, Thomas; Couch, Courtney S. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. NOAA technical memorandum NMFS PIFSC; 93. 2019. https://doi.org/10.25923/h2q8-jv47
- https://doi.org/10.25923/h2q8-jv47
  NOAA Technical Memorandum containing the standard operating procedures for processing Structure-from-Motion photomosaic imagery
Rodriguez, Caroline; Amir, Corinne; Gray, Andrew; Asbury, Mollie; Suka, Rhonda; Lamirand, Mia; Couch, Courtney S.; Oliver, Thomas. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures; Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. NOAA technical memorandum NMFS PIFSC; 120. 2021. https://doi.org/10.25923/a9se-k649
- https://doi.org/10.25923/a9se-k649
  NOAA Technical Memorandum containing the standard operating procedures for measuring coral vital rates using Structure-from-Motion photogrammetry
Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2022). Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event (NCEI Accession 0244392). NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0244392.
- https://www.ncei.noaa.gov/archive/accession/0244392
  Associated NCEI accession

gov.noaa.nodc:PIFSC-SfM-DerivedData

Publication Dates	publication: 2023-10-13
Data Presentation Form	Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status	Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility
Data Update Frequency	As needed
Purpose	The Hawaii Coral Bleaching Collaborative (HCBC) planned and executed a field survey response in 2019 that applied a structured, hypothesis-driven approach to document the extent of coral bleaching in the Hawaiian Archipelago, and laid the groundwork for tracking coral response and recovery through time. Fixed sites were revisited in 2020 and 2021 to examine survivorship, recovery, and growth following the 2019 bleaching event. The purpose of the Structure from Motion (SfM) surveys throughout the Main Hawaiian Islands is to efficiently and effectively collect coral demographic data.
Use Limitations	accessLevel: Public Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.

Dataset Citation	Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2023). Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021 (NCEI Accession 0283598). https://www.ncei.noaa.gov/archive/accession/0283598. In Ecosystem Sciences Division, Pacific Islands Fisheries Science Center. Benthic cover and other related datasets derived from Structure-from-Motion (SfM) imagery of coral reef ecosystems in Pacific Islands Regions. [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/PIFSC-SfM-DerivedData. Accessed [date].
Cited Authors	Ecosystem Sciences Division, Pacific Islands Fisheries Science Center
Collaborators	US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program (CREP)
Contributors	US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Resource Providers	Lori Luers US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center (NMFS/PIFSC)
Points of Contact	Morgan Winston US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division Lori Luers US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding Agency: US DOC; NOAA; NOS; Coral Reef Conservation Program (Coral Reef Conservation Program - CRCP)

Theme keywords	NODC DATA TYPES THESAURUS CORAL CORAL - BLEACHING CORAL - COLONY SIZE CORAL - SPECIES IDENTIFICATION NODC OBSERVATION TYPES THESAURUS biological GIS product laboratory analyses survey - biological survey - coral reef WMO_CategoryCode oceanography CoRIS Discovery Thesaurus Numeric Data Sets > Benthic CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat EARTH SCIENCE > Biosphere > Zoology > Corals EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Damage Assessment > Visual EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > GIS EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological 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 EARTH SCIENCE > Oceans > Marine Biology > Coral Communities Global Change Master Directory (GCMD) Science Keywords EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF EARTH SCIENCE > OCEANS > COASTAL PROCESSES > CORAL REEFS > CORAL BLEACHING EARTH SCIENCE > SOLID EARTH > GEOMORPHIC LANDFORMS/PROCESSES > COASTAL LANDFORMS > CORAL REEFS Provider Keywords SfM Structure from Motion
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center Contributing Organizations CRED CREP Coral Reef Ecosystem Division Coral Reef Ecosystem Program DAR DLNR Division of Aquatic Resources ESD Ecosystem Sciences Division Hawai'i Department of Land and Natural Resources PIFSC Pacific Islands Fisheries Science Center Global Change Master Directory (GCMD) Data Center Keywords DOC/NOAA/NMFS > National Marine Fisheries Service, NOAA, U.S. Department of Commerce DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce
Platform keywords	Provider Platform Names Various Small Vessels
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS photograph visual observation Global Change Master Directory (GCMD) Instrument Keywords VISUAL OBSERVATIONS > VISUAL OBSERVATIONS Provider Instruments Agisoft Metashape software ArcGIS Computer
Place keywords	NODC SEA AREA NAMES THESAURUS Hawaiian Islands Humpback Whale National Marine Sanctuary North Pacific Ocean CoRIS Place Thesaurus 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 > 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 > Oahu Island > Oahu (21N157W0003) Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN
Project keywords	NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program (CRCP) CORAL REEF STUDIES CRCP Project 31283 31361 Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities Hawai'i coral bleaching assessment and analysis
Keywords	NCEI ACCESSION NUMBER 0283598
Keywords	Send2NCEI Submission Package ID KXC5TK

Use Constraints	Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2023). Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021 (NCEI Accession 0283598). https://www.ncei.noaa.gov/archive/accession/0283598. In Ecosystem Sciences Division, Pacific Islands Fisheries Science Center. Benthic cover and other related datasets derived from Structure-from-Motion (SfM) imagery of coral reef ecosystems in Pacific Islands Regions. [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/PIFSC-SfM-DerivedData. Accessed [date].
Access Constraints	Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
Fees	In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.

Lineage information for: dataset
Processing Steps	2023-10-13T13:42:44Z - NCEI Accession 0283598 v1.1 was published.
Output Datasets	NCEI Accession 0283598 v1.1 NCEI Accession 0283598 v1.1 (download) published 2023-10-13T13:42:44Z

Lineage information for: dataset
Processing Steps	Parameter or Variable: CORAL - COLONY SIZE (measured); Units: square meter; Observation Category: GIS product; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Each coral was annotated at the patch level, and patches composing individual colonies, or '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.; Data Quality Method: 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.. Parameter or Variable: CORAL - SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: laboratory analysis; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA).; Data Quality Method: 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.. Parameter or Variable: CORAL - BLEACHING (measured); Units: percent; Observation Category: laboratory analysis; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Bleaching extent and severity were analyzed, when applicable.; Data Quality Method: Extent of bleaching as expressed by percent of patch exhibiting paling from 0-100%. Blank values denote no bleaching observations were conducted (survey years 2020 and 2021). The severity of bleaching from 1 (being slightly pale) to 3 (stark white). Blank values signify no bleaching observations were conducted (survey years 2020 and 2021). Values of 0 mean that the bleaching extent was 0%..

Lineage information for: dataset

Processing Steps

Parameter or Variable: CORAL - COLONY SIZE (measured); Units: square meter; Observation Category: GIS product; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Each coral was annotated at the patch level, and patches composing individual colonies, or '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.; Data Quality Method: 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..
Parameter or Variable: CORAL - SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: laboratory analysis; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA).; Data Quality Method: 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..
Parameter or Variable: CORAL - BLEACHING (measured); Units: percent; Observation Category: laboratory analysis; Sampling Instrument: photograph; Sampling and Analyzing Method: Structure-from-motion 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. Bleaching extent and severity were analyzed, when applicable.; Data Quality Method: Extent of bleaching as expressed by percent of patch exhibiting paling from 0-100%. Blank values denote no bleaching observations were conducted (survey years 2020 and 2021). The severity of bleaching from 1 (being slightly pale) to 3 (stark white). Blank values signify no bleaching observations were conducted (survey years 2020 and 2021). Values of 0 mean that the bleaching extent was 0%..

Acquisition Information (collection)
Instrument	photograph visual observation

Last Modified: 2024-09-17T19:23:35Z
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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 (NCEI Accession 0283598)

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