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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title: 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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abstract: 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.
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.
credit: Related Funding Agency: US DOC; NOAA; NOS; Coral Reef Conservation Program (Coral Reef Conservation Program - CRCP)
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otherConstraints: 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). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0283598. Accessed [date].
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title: Benthic cover and other related datasets derived from Structure-from-Motion (SfM) imagery of coral reef ecosystems in Pacific Islands Regions
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title: 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
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title: 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
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title: 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
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title: 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.
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beginPosition: 2019-10-08
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supplementalInformation: Submission Package ID: KXC5TK
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description: 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..
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description: 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..
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description: 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%..
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acquisitionInformation: (MI_AcquisitionInformation)
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description: still images used as the basis for making parameter determinations
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