Dataset Overview | National Centers for Environmental Information (NCEI)

Benthic cover from automated annotation of benthic images collected at coral reef sites in the Pacific Remote Island Areas and American Samoa from 2018-06-08 to 2018-08-11 (NCEI Accession 0204646)

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The coral reef benthic community data described here result from the automated annotation (classification) of benthic images collected during photoquadrat surveys conducted by the NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (ESD, formerly the Coral Reef Ecosystem Division) as part of NOAA's ongoing National Coral Reef Monitoring Program (NCRMP). SCUBA divers conducted benthic photoquadrat surveys in coral reef habitats according to protocols established by ESD and NCRMP during the ESD-led NCRMP mission to the islands and atolls of the Pacific Remote Island Areas (PRIA) and American Samoa from June 8 to August 11, 2018. Still photographs were collected with a high-resolution digital camera mounted on a pole to document the benthic community composition at predetermined points along transects at stratified random sites surveyed only once as part of Rapid Ecological Assessment (REA) surveys for corals and fish (Ayotte et al. 2015; Swanson et al. 2018) and permanent sites established by ESD and resurveyed every ~3 years for climate change monitoring. Overall, 30 photoquadrat images were collected at each survey site.

The benthic habitat images were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015; Williams et al. 2019). Ten points were randomly overlaid on each image and the machine-learning algorithm "robot" identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to functional group (Tier 1: hard coral, soft coral, sessile invertebrate, macroalgae, crustose coralline algae, and turf algae) for coral, algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). These benthic data can ultimately be used to produce estimates of community composition, relative abundance (percentage of benthic cover), and frequency of occurrence.

Dataset Citation

Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2019). Benthic cover from automated annotation of benthic images collected at coral reef sites in the Pacific Remote Island Areas and American Samoa from 2018-06-08 to 2018-08-11 (NCEI Accession 0204646). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204646. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0204646

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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	2018-06-08 to 2018-08-11
Spatial Bounding Box Coordinates	West: -176.626077 East: -159.971695 South: -14.558022 North: 6.451465
Spatial Coverage Map

General Documentation

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Descriptive Information
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Associated Resources

Pacific Islands Fisheries Science Center, 2019: Benthic Cover from Automated Annotation of Benthic Images Collected at Coral Reef Sites in the Pacific Remote Island Areas and American Samoa in 2018, https://www.fisheries.noaa.gov/inport/item/57610.
- https://www.fisheries.noaa.gov/inport/item/57610
  InPort Metadata Record
Leveraging Automated Image Analysis Tools to Transform Our Capacity to Assess Status and Trends of Coral Reefs
- Leveraging Automated Image Analysis Tools to Transform Our Capacity to Assess Status and Trends of Coral Reefs (download)
  Journal article
Analysis of Benthic Survey Images via CoralNet: A Summary of Standard Operating Procedures and Guidelines
- PIFSC Administrative Report H-17-02 (download)
  PIFSC Administrative Report
Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation
- Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation
  O. Beijbom, P. J. Edmunds, C. Roelfsema, J. Smith, D. I. Kline, B. Neal, M. J. Dunlap, V. Moriarty, T-Y. Fan, C-J. Tan, S. Chan, T. Treibitz, A. Gamst, B. G. Mitchell, D. Kriegman. "Towards automated annotation of benthic survey images: variability of human experts and operational modes of automation". PLOS One, July 2015.
Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys
- Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys (download)
  This SOP describes the method to collect benthic images during a rapid ecological assessment survey.
Coral Reef Conservation Program (2016). Documentation for NOAA's Coral Reef Conservation Program (CRCP) National Coral Reef Monitoring Program (NCRMP) data archived at NCEI (NCEI Accession 0157633). NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0157633.
- https://www.ncei.noaa.gov/archive/accession/0157633
  Coral Reef Ecosystem Program Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Fish Surveys

Publication Dates	publication: 2019-10-29
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 use of the CoralNet machine-learning, image annotation tool is essential to the timely and cost-effective analysis of benthic imagery collected Pacific-wide under the auspices of the NOAA National Coral Reef Monitoring Program (NCRMP). Timely analysis and reporting of cover estimates are fundamental to understanding status and change of coral reef benthic communities, particularly in a fast-changing climate. 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 NOAA Coral Reef Conservation 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. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at some ~40 priority coral reefs systems across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The Ecosystem Sciences Division at NOAA Fisheries is leading biological and climate monitoring in the U.S. Pacific Islands Region. The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). The climate component of NCRMP in the Pacific provides a comprehensive view of climate change impacts on coral reef ecosystems and helps identify areas of resilience and vulnerability. The key indicators used to identify and monitor climate-driven trends include 1) thermal stress caused by changes in sea temperature, 2) ocean acidification resulting from changes in carbonate chemistry, and 3) ecological impacts by collecting data on coral growth rates, erosion, and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem. Each year, ESD scientists work closely with CRCP and partners during Pacific RAMP missions to collect data using moored oceanographic (subsurface temperature recorders) and ecological (calcification accretion units [CAUs] and autonomous reef monitoring structures [ARMS]) instruments stationed at fixed sites in the Pacific Ocean, and water samples collected by divers. The in-situ data (along with satellite-based observations) are also used in modeling efforts. Innovative analysis techniques are used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time.
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 (2019). Benthic cover from automated annotation of benthic images collected at coral reef sites in the Pacific Remote Island Areas and American Samoa from 2018-06-08 to 2018-08-11 (NCEI Accession 0204646). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204646. Accessed [date].
Cited Authors	Ecosystem Sciences Division, Pacific Islands Fisheries Science Center
Principal Investigators	Bernardo Vargas-Ángel US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Collaborators	Kevin Trick US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Contributors	US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Resource Providers	US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding Agency: NOAA Coral Reef Conservation Program

Theme keywords	NODC DATA TYPES THESAURUS HABITAT - BENTHIC NODC OBSERVATION TYPES THESAURUS benthic biological WMO_CategoryCode oceanography CoRIS Discovery Thesaurus Numeric Data Sets > Benthic CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat EARTH SCIENCE > Biosphere > Microbiota > Blue-green Algae EARTH SCIENCE > Biosphere > Vegetation > Algae > Algal Cover EARTH SCIENCE > Biosphere > Vegetation > Algae > Crustose Coralline Algae EARTH SCIENCE > Biosphere > Vegetation > Algae > Encrusting Macroalgae EARTH SCIENCE > Biosphere > Vegetation > Algae > Turf Algae EARTH SCIENCE > Biosphere > Zoology > Corals EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Quadrat Monitoring > Photograph Analysis 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 > 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 > Benthic biology 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 EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates Global Change Master Directory (GCMD) Science Keywords EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC
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; Ecosystem Sciences Division Contributing Organizations CRED CREP Coral Reef Ecosystem Division Coral Reef Ecosystem Program ESD Ecosystem Sciences Division PIFSC Pacific Islands Fisheries Science Center Global Change Master Directory (GCMD) Data Center Keywords 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	NODC PLATFORM NAMES THESAURUS NOAA Ship Hi'ialakai Global Change Master Directory (GCMD) Platform Keywords Ships ICES/SeaDataNet Ship Codes Hi'ialakai (call sign: WTEY, ICES code: 33HL, 2004)
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS photograph
Place keywords	NODC SEA AREA NAMES THESAURUS National Marine Sanctuary of American Samoa North Pacific Ocean Rose Atoll Marine National Monument South Pacific Ocean CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000) 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 > Swains Atoll (11S171W0001) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016) 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) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001) OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000) OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001) 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 > Howland Island > Howland Island (00S176W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001) OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013) OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014) OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012) Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN OCEAN > PACIFIC OCEAN > SOUTH PACIFIC OCEAN
Project keywords	NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program (CRCP) CORAL REEF STUDIES National Coral Reef Monitoring Program (NCRMP) Pacific Reef and Assessment Monitoring Program (Pacific RAMP)
Keywords	NCEI ACCESSION NUMBER 0204646
Keywords	Provider Keywords StRS automated annotation image analysis stratified random
Keywords	Send2NCEI Submission Package ID GDG2XL

Use Constraints	Cite as: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2019). Benthic cover from automated annotation of benthic images collected at coral reef sites in the Pacific Remote Island Areas and American Samoa from 2018-06-08 to 2018-08-11 (NCEI Accession 0204646). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0204646. 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	2019-10-29T20:07:23Z - NCEI Accession 0204646 v1.1 was published.
Output Datasets	NCEI Accession 0204646 v1.1 NCEI Accession 0204646 v1.1 (download) published 2019-10-29T20:07:23Z

Lineage information for: dataset
Processing Steps	Parameter or Variable: BENTHIC SPECIES - TAXA IDENTITIES (measured); Units: unitless; Observation Category: other; Sampling Instrument: photograph; Sampling and Analyzing Method: Benthic habitat images collected during photoquadrat surveys at stratified random (Ayotte et al. 2015; Swanson et al. 2018) and permanent sites (30 images per site) were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015; Williams et al. 2019). Ten points were randomly overlaid on each image and the machine-learning algorithm "robot" identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to functional group (Tier 1: hard coral, soft coral, sessile invertebrate, macroalgae, crustose coralline algae, and turf algae) for coral, algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). The description of each functional group is included in the benthic image analysis classification scheme.; Data Quality Method: Data sets derived from the machine-learning, image annotation tool, CoralNet, are highly reliable within the stipulated taxonomic context (Tier 1). Human, expert-analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program (Pacific RAMP) is used to train the machine-learning image analysis tool, CoralNet (Beijbon et al 2015), to generate fully-automated Tier 1 benthic estimates of site-level coral cover that are highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less; Williams et al. 2019). CoralNet was generally effective at estimating coral cover (Pearson’s r > 0.92 and with bias of 2% or less in 6 of 7 cases), but performance was mixed for other groups including algal categories. Pre- and post-automated benthic image analysis quality control procedures include checks for: 1) image quality integrity (focus, white balance, distance from seafloor); 2) image inventory (all images acquired for each island are included in the analysis); 3) duplicate sites; 4) complete and coherent upload of imagery to CoralNet; and 5) integrity and completeness of robot-generated image annotations..

Lineage information for: dataset

Processing Steps

Parameter or Variable: BENTHIC SPECIES - TAXA IDENTITIES (measured); Units: unitless; Observation Category: other; Sampling Instrument: photograph; Sampling and Analyzing Method: Benthic habitat images collected during photoquadrat surveys at stratified random (Ayotte et al. 2015; Swanson et al. 2018) and permanent sites (30 images per site) were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015; Williams et al. 2019). Ten points were randomly overlaid on each image and the machine-learning algorithm "robot" identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to functional group (Tier 1: hard coral, soft coral, sessile invertebrate, macroalgae, crustose coralline algae, and turf algae) for coral, algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). The description of each functional group is included in the benthic image analysis classification scheme.; Data Quality Method: Data sets derived from the machine-learning, image annotation tool, CoralNet, are highly reliable within the stipulated taxonomic context (Tier 1). Human, expert-analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program (Pacific RAMP) is used to train the machine-learning image analysis tool, CoralNet (Beijbon et al 2015), to generate fully-automated Tier 1 benthic estimates of site-level coral cover that are highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less; Williams et al. 2019). CoralNet was generally effective at estimating coral cover (Pearson’s r > 0.92 and with bias of 2% or less in 6 of 7 cases), but performance was mixed for other groups including algal categories. Pre- and post-automated benthic image analysis quality control procedures include checks for: 1) image quality integrity (focus, white balance, distance from seafloor); 2) image inventory (all images acquired for each island are included in the analysis); 3) duplicate sites; 4) complete and coherent upload of imagery to CoralNet; and 5) integrity and completeness of robot-generated image annotations..

Acquisition Information (collection)
Instrument	photograph
Platform	NOAA Ship Hi'ialakai

Last Modified: 2024-09-18T12:56:10Z
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Benthic cover from automated annotation of benthic images collected at coral reef sites in the Pacific Remote Island Areas and American Samoa from 2018-06-08 to 2018-08-11 (NCEI Accession 0204646)

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