National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across the Pacific Remote Island Areas from 2018-06-08 to 2018-08-10 (NCEI Accession 0239474)
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title: National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across the Pacific Remote Island Areas from 2018-06-08 to 2018-08-10 (NCEI Accession 0239474)
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abstract: The coral reef benthic community data described here result from the annotation (classification) of benthic images collected during photoquadrat surveys at permanent sites in the islands and atolls of the Pacific-Remote Island Areas (PRIA) in 2018. These surveys are 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) according to protocols established by ESD and NCRMP during ESD-led NCRMP missions to PRIA from 2014 to 2018. SCUBA divers conducted benthic photoquadrat surveys at permanent sites established in coral reef habitats by ESD. A select number of these sites were chosen in hard-bottom habitat at ~15-m depths, and a subset of the permanent sites (climate stations) were established at north, south, east, and west points around each of the islands and atolls. The divers estimated and delineated each site’s rectangular perimeter by temporarily placing measuring tapes with 1-m markers starting from a permanently installed reference stake on the reef. Along the nearshore 10-m side of the survey site and the downslope 5-m side, the measuring tapes marked every meter of the L-shaped 15-m transect used for photoquadrat documentation. The divers photographed the reef at 1-m intervals on both sides of the 15-m tape, generating 30 photographs per survey site. Benthic habitat images were quantitatively analyzed using the web-based annotation tool, CoralNet (Beijbom et al. 2015). Ten points were randomly overlaid on each image and human analysts identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to genus/morphology for hard corals, and to genus/functional group for algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). In general, the analysis resulted in three levels of benthic community data, including taxa group (Tier 1: hard coral, soft coral, macroalgae, turf algae, etc.), morphology (Tier 2: massive, branching, upright macroalgae, etc.), and genus (Tier 3). These benthic data can ultimately be used to produce estimates of relative abundance (percentage of benthic cover), frequency of occurrence, benthic community taxonomic composition, and relative generic richness.
purpose: The NOAA 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 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 10 priority coral reefs 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 climate monitoring in the U.S. Pacific Islands Region. 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.
credit: Related Funding Agency: NOAA Coral Reef Conservation Program
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title: Pacific Islands Fisheries Science Center, 2021: National Coral Reef Monitoring Program: Benthic Cover from Annotated Benthic Images Collected During Photoquadrat Surveys at Climate Stations across the Pacific Remote Island Areas since 2014, https://www.fisheries.noaa.gov/inport/item/36148.
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title: Beijbom, O., Edmunds, P. J., Roelfsema, C., Smith, J., Kline, D. I., Neal, B. P., Dunlap, M. J., Moriarty, V., Fan, T.-Y., Tan, C.-J., Chan, S., Treibitz, T., Gamst, A., Mitchell, B. G., & Kriegman, D. (2015). Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation. PLOS ONE, 10(7), e0130312. https://doi.org/10.1371/journal.pone.0130312
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title: Lozada-Misa, P., Schumacher, B., & Vargas-Ángel, Bernardo, 1965-. (20 C.E.). Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Pacific Islands Fisheries Science Center. https://doi.org/10.7289/v5/ar-pifsc-h-17-02
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description: Parameter or Variable: BENTHIC COMMUNITIES (measured); Units: unitless; Observation Category: visual estimate; Sampling Instrument: photograph; Sampling and Analyzing Method: Benthic habitat images collected during photoquadrat surveys are quantitatively analyzed visually with the assistance of a web-based, machine-learning, image annotation tool, CoralNet. The robot tool annotates ten random points on each image for a total of 300 points per site, which are then reviewed by human analysts. The human annotations are then used to train the robot. This data is the final form of the robot-assisted human annotations. Taxa identification occurs at three functional group levels of benthic cover. Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Astreopora sp, Favia sp, Pocillopora, etc.; Macroalgae = Caulerpa sp, Dictyosphaeria sp, Padina sp, etc.); Data Quality Method: ACCURACY: 1) Each analyst is required to complete training and a calibration exercise prior to image analysis (classification/annotation), and follows the Benthic Image Analysis Standard Operating Procedure (Lozada-Misa et al. 2017). For a calibration exercise, a subset of photos (~100-150) are selected from the production series and CoralNet assigns 10 random fixed points per photo. Each analyst classifies the same set of points for each of the photos used in the calibration exercise. The goal of the calibration exercise is to assess inter-observer variability. 2) Handheld GPS units were used to locate random sites and mark site locations. COMPLETENESS REPORT: The data set derived from the image analysis is as good as the images themselves; poor images with low contrast, inappropriate white balance, or out of focus may have to be discarded. Therefore, benthic estimates for some sites may derive from differing numbers of points between sites. Although the analysis process is statistically robust to allow for differing n (points) between sites, users should be aware of this limitation..
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