National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected during Stratified Random Surveys (StRS) across the Hawaiian Archipelago f...

The coral reef benthic community data described here result from the 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 during ESD-led NCRMP missions to the islands and atolls of the Hawaiian Archipelago in 2013, 2016, and 2019 according to protocols established by ESD and NCRMP. 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 and Winston et al. 2020, respectively), with 30 photoquadrat images collected at each survey site. A stratified random sampling (StRS) design was employed to survey these coral reef ecosystems. 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.

The benthic habitat images were quantitatively analyzed using the Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software from 2010-2014 and using the web-based image annotation tool, CoralNet (Beijbom et al. 2015) from 2015 to present. Ten points were randomly overlaid on each image and analysts identified the organism or type of substrate beneath, with 300 annotations (points) generated per site following Lozada-Misa et al. (2017). Images are analyzed to produce three functional group levels of benthic cover: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae), Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda), and Tier 3 (e.g., Hard Coral = Astreopora sp, Favia sp, Pocillopora; Macroalgae = Caulerpa sp, Dictyosphaeria sp, Padina sp).

The benthic data resulting from the collection and annotation of benthic imagery can ultimately be used to produce estimates of benthic community taxonomic composition, relative abundance (percentage of benthic cover), and frequency of occurrence, which are fundamental to understanding the status and change of coral reef benthic communities.

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 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 (ESD) at NOAA Fisheries is leading biological 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). Innovative analysis techniques are then 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.

Raw survey data includes metadata for each survey (where, when, who, area); site characteristics (depth, reef type, habitat); unique image name and individual point observations identified 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.).

While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.

Hawaiian Archipelago including the main and Northwestern Hawaiian Islands.

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NOAA Coral Reef Ecosystem Program (CREP) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

CREP welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. CREP has a very diverse set of field activities that generates large volumes of data using an array of data collection protocols.

The following recommendations are for your consideration as you use this data:

1) Data analyses should take all field exigencies into account. The most effective way to do this would be active collaboration with CREP principal investigators.

2) In all presentations, product releases, or publications using data generated by CREP, proper acknowledgement of both CREP and the individuals responsible for data collection is expected. Citing the DOI (if available) is preferred, a non-DOI example is listed below.

3) If you collect or generate data for the same study areas, CREP requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the CREP Data Management Team of any errors and discrepancies that are discovered during the course of using these data. They are further urged to bring to the attention of the Team all problems and difficulties encountered in using these data. This information is necessary in order to improve the collections and to facilitate more efficient and economical data processing and retrieval. The users are asked to supply copies of any missing data that may be located, and to provide information as to significant subsets and special aggregations of data that are developed in using the material provided.

Example citation:

"This publication makes use of data products provided by the Ecosystem Sciences Division (ESD), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Coral Reef Conservation Program (CRCP). The analysis and interpretations presented here are solely that of the current authors.”

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

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Please cite NOAA Fisheries, Ecosystem Sciences Division (ESD) when using the data.

Example:

Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, 2020: National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected during Stratified Random Surveys (StRS) across the Hawaiian Archipelago from 2013 to 2019, https://www.fisheries.noaa.gov/inport/item/36155.

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PIFSC Oracle database view: MV_BIA_CNET_ANALYSIS_NCEI_DATA (CoralNet) / MV_BIA_PERC_COVER_PHOTO_STR_RW (CPCe)

Data sets derived from image analysis are highly reliable within the stipulated taxonomic context. Each time a production run is performed for a region a calibration exercise is conducted by all staff that will participate in that round of image analysis classification. Usually 100-150 photos are selected from the photos being processed as part of the production run series, or other region-relevant photo streams. Then, CPCE or CoralNet assigns 10 random points per photo. Each photo analyst is asked to classify the same set of points in each of the photos used as part of the calibration exercise. The goal of the calibration exercise is to assess inter-observer variability. Inter-observer variability rates are available upon request for each production run.

Handheld GPS units were used to locate random sites and mark site locations.

Data sets derived from image analysis include ~30 benthic photographs per survey site from both the fish and benthic team surveys. The fish team conducts the photoquadrat surveys along one 30-m transect, as does the benthic team since 2018. Prior to 2018, the benthic team conducted surveys along 2 independent 18-m transects. Therefore, the site level image data prior to 2018 contains one transect (A) for fish team surveys and two transects (A and B) for benthic team surveys. Appropriate site level benthic cover estimates are generated from all 30 images.

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, percent cover estimates for some sites may derive from differing number of points between sites. Although the analysis process is statistically robust to allow for differing n (points) between sites the users should be aware of this limitation.

For REA survey imagery analyzed or collected since 2013, classification is completed to the functional group/genus level (Tier 3).

Only shallow water (0 to 30 meter depth range) hard-bottom habitats are surveyed. The survey sites were randomly selected using a systematic process based on available habitat and bathymetric data. Although efforts are made to include broad spatial coverage of surveys at each island, weather conditions and other environmental constraints may have prevented the team from surveying exposed reef areas.

There are several missions in which the benthic images collected by the program are in the process of or have not yet been analyzed. In some cases, the benthic imagery sets are not planned to be analyzed due to funding and resource constraints. Contact the NOAA Fisheries, Ecosystem Sciences Division at nmfs.pic.credinfo@noaa.gov for more information.

The same method of image analysis was used at each surveyed site.

Quality control is enforced by means of point-to-point, inter-observer calibration exercises that are conducted before each image analysis production series. Training modules and standard operating procedures have also been developed and documented to ensure improved performance and consistent imagery analysis results produced by multiple analysts.

NOAA IRC and NOAA Fisheries ITS resources and assets.

The stratified random sampling (StRS) design and benthic photoquadrat survey methodology, employed by the NOAA Fisheries, Ecosystem Sciences Division (ESD) since 2013. Benthic imagery is collected at stratified random sites. The imagery is analyzed using Coral Point Count with Excel Extentions (CPCe) or CoralNet to derive benthic cover values.