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National Coral Reef Monitoring Program: Structure-from-Motion Coral Demography derived from Stratified Random Site Imagery collected across the Mariana Archipelago from 2022-05-10 to 2022-06-01 (NCEI Accession 0280938)

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Coral adult and juvenile coral colony demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery collected across the Mariana Archipelago in 2022. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Data was collected during the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD) led National Coral Reef Monitoring Program (NCRMP) mission across the Mariana Archipelago from 2022-05-10 to 2022-06-01.

The SfM surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. Surveys were conducted at sites randomly stratified across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). These sites represent a broad range of depths (1-25 m), habitat types (aggregate reef, patch reef, pavement, rock and boulder and rubble), coral cover, and diving conditions. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site to site comparisons should be used with caution.

During each survey, an 18m transect line was deployed along the isobath and photographed using underwater cameras while swimming in a back and forth swim pattern for later processing using an SfM approach. At depths of 1-20 m, SfM surveys were conducted over a 3 x 20m area and at depths > 20m, a 3 x 13m area was surveyed, both with the transect running down the middle of the survey area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for juvenile and adult coral colony demographic metrics. Data was collected for each site within four 2.5m2 segments, each 1m wide, along the transect (at 0-2.5m, 5-7.5m, 10-12.5m, and 15-17.5m). At deeper sites where a 3 x 13m area was surveyed, only the first three segments were analyzed in ArcGIS. For each adult coral colony (> 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), and estimated percent old mortality were recorded. Bleaching extent (% of living tissue with reduced pigmentation) and severity were also recorded. Juvenile coral colonies (0.7 to 5cm maximum diameter) were recorded within the first 1 m2 of the first 3 segments. For juvenile colonies, only ID and maximum diameter were recorded.
  • Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2023). National Coral Reef Monitoring Program: Structure-from-Motion Coral Demography derived from Stratified Random Site Imagery collected across the Mariana Archipelago from 2022-05-10 to 2022-06-01 (NCEI Accession 0280938). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0280938. Accessed [date].
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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 2022-05-10 to 2022-06-01
Spatial Bounding Box Coordinates
West: 144.634585
East: 145.811663
South: 13.241626
North: 20.037076
Spatial Coverage Map
General Documentation
Associated Resources
  • Winston, Morgan; Couch, Courtney S.; Ferguson, Marie; Huntington, Brittany; Swanson, Dione W.; Vargas-Ángel, Bernardo. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA technical memorandum NMFS-PIFSC; 92. 2019. https://doi.org/10.25923/w1k2-0y84
  • 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
  • Couch, C. S., Oliver, T. A., Suka, R., Lamirand, M., Asbury, M., Amir, C., Vargas-Ángel, B., Winston, M., Huntington, B., Lichowski, F., Halperin, A., Gray, A., Garriques, J., & Samson, J. (2021). Comparing Coral Colony Surveys From In-Water Observations and Structure-From-Motion Imagery Shows Low Methodological Bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943
  • Pacific Islands Fisheries Science Center, 2023: National Coral Reef Monitoring Program: Structure from Motion (SfM) Coral (Adult and Juvenile) Annotations derived from Stratified Random Site (StRS) Imagery across the US Pacific since 2019.
Publication Dates
  • publication: 2023-08-04
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
Supplemental Information
Submission Package ID: 2N4AXY
Purpose The data were collected as part of the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD) led National Coral Reef Monitoring Program (NCRMP) missions around the US Pacific from 2019. The National Coral Reef Monitoring Program (NCRMP) details a long-term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various Coral Reef Conservation Coral Reef Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. The purpose of the Structure from Motion (SfM) surveys throughout the US Pacific is to efficiently and effectively collect coral demographic data. SfM-derived data collection occurred along the same transects as in situ diver coral demographic surveys as a means to compare the use of SfM as a tool for quantifying coral demographic metrics in comparison to traditional visual in situ assessments.
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). National Coral Reef Monitoring Program: Structure-from-Motion Coral Demography derived from Stratified Random Site Imagery collected across the Mariana Archipelago from 2022-05-10 to 2022-06-01 (NCEI Accession 0280938). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0280938. Accessed [date].
Cited Authors
Principal Investigators
Contributors
Resource Providers
Points of Contact
Publishers
Acknowledgments
  • Related Funding Agency: US DOC; NOAA; NOS; Coral Reef Conservation Program
Theme keywords NODC DATA TYPES THESAURUS NODC OBSERVATION TYPES THESAURUS WMO_CategoryCode
  • oceanography
CoRIS Discovery Thesaurus
  • Numeric Data Sets > Benthic
CoRIS Theme Thesaurus
  • EARTH SCIENCE > Biosphere > Ecological Dynamics > Species Richness
  • 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 > Coral Colony Size and Condition
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Rapid assessment studies
  • EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > BioDiversity
  • EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral reef ecology > Coral cover
  • EARTH SCIENCE > Oceans > Marine Biology > Coral
  • EARTH SCIENCE > Oceans > Marine Biology > Coral Communities
Global Change Master Directory (GCMD) Science Keywords Provider Keywords
  • SfM
  • Structure from Motion
Data Center keywords NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords Submitter Data Center Keywords
  • CRED
  • CREP
  • Coral Demography
  • Coral Reef Ecosystem Division
  • Coral Reef Ecosystem Program
  • ESD
  • Ecosystem Sciences Division
  • PIFSC
  • Pacific Islands Fisheries Science Center
Platform keywords NODC PLATFORM NAMES THESAURUS Global Change Master Directory (GCMD) Platform Keywords ICES/SeaDataNet Ship Codes
Instrument keywords NODC INSTRUMENT TYPES THESAURUS Global Change Master Directory (GCMD) Instrument Keywords Provider Instruments
  • GIS
Place keywords NODC SEA AREA NAMES THESAURUS CoRIS Place Thesaurus
  • 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 > Tinian > Tinian Island (14N145E0005)
  • COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000)
  • 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 > 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 > Tinian Island Reefs > Tinian Island (14N145E0005)
Global Change Master Directory (GCMD) Location Keywords
Project keywords NODC PROJECT NAMES THESAURUS CRCP Project
  • 743
  • National Coral Reef Monitoring Program
Provider Project Names
  • RAMP
  • Reef Assessment and Monitoring Program
Keywords NCEI ACCESSION NUMBER
Use Constraints
  • Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2023). National Coral Reef Monitoring Program: Structure-from-Motion Coral Demography derived from Stratified Random Site Imagery collected across the Mariana Archipelago from 2022-05-10 to 2022-06-01 (NCEI Accession 0280938). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0280938. 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
  • 2023-08-04T13:24:18Z - NCEI Accession 0280938 v1.1 was published.
Output Datasets
Lineage information for: dataset
Processing Steps
  • Parameter or Variable: CORAL - COLONY SIZE (measured); Units: square meter; Observation Category: GIS product; Sampling Instrument: GIS; Sampling and Analyzing Method: In ArcGIS, each site was set up for annotation by manually digitizing the transect and segments as a shapefile using the same sampling design as the PIFSC ESD-led in situ coral demography surveys, and setting up the attribute table in a geodatabase to mirror the in situ visual survey database (Swanson et al. 2018; Winston et al. 2019). To record and extract data from the orthomosaic, each coral colony was annotated following the in situ visual survey methods. Each colony was measured by digitizing a line across the maximum diameter of the colony. During annotation, the original JPEG imagery was viewed alongside the orthomosaic with the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges).; Data Quality Method: Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data were summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors..
  • Parameter or Variable: CORAL - SPECIES IDENTIFICATION (measured); Units: unitless; Observation Category: laboratory analysis; Sampling Instrument: visual observation; Sampling and Analyzing Method: In ArcGIS, each site was set up for annotation by manually digitizing the transect and segments as a shapefile using the same sampling design as the PIFSC ESD-led in situ coral demography surveys, and setting up the attribute table in a geodatabase to mirror the in situ visual survey database (Swanson et al. 2018; Winston et al. 2019). To record and extract data from the orthomosaic, each coral colony was annotated following the in situ visual survey methods. Each colony was taxonomically identified (to the lowest level possible), estimated percent old mortality, and bleaching extent and severity were recorded. During annotation, the original JPEG imagery was viewed alongside the orthomosaic with the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges).; Data Quality Method: Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data were summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors..
Acquisition Information (collection)
Instrument
  • swimmer/diver
  • visual observation
Platform
  • NOAA Ship Rainier
Last Modified: 2023-08-04T20:00:48Z
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