Short Citation:
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.

Item Identification

Title: 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
Short Name: NCRMP: Benthic Cover Climate PRIAs
Status: On Going
Creation Date: 2016-12
Revision Date: 2019-09-16
Publication Date: 2019
Abstract:

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). The photoquadrat surveys were conducted at coral reef sites according to protocols established by ESD and NCRMP during ESD-led NCRMP missions to the islands and atolls of the Pacific Remote Island Areas (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.

The benthic habitat images were quantitatively analyzed using Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software from 2010-2014 and the web-based annotation tool, CoralNet (Beijbom et al. 2015), from 2015 to present. 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.

DOI (Digital Object Identifier): https://doi.org/10.7289/v54m92v0
DOI Registration Authority: NOAA

Keywords

Theme Keywords

Thesaurus Keyword
CoRIS Discovery Thesaurus Numeric Data Sets > Benthic
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Microbiota > Blue-green Algae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Crustose Coralline Algae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Encrusting Macroalgae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Turf Algae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Benthic biology
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral Communities
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Ocean Chemistry > Climate Change
CRCP Project 743
CRCP Project National Coral Reef Monitoring Program
ISO 19115 Topic Category 002
ISO 19115 Topic Category biota
NODC DATA TYPES THESAURUS BENTHIC COMMUNITIES
NODC DATA TYPES THESAURUS BENTHIC SPECIES
NODC DATA TYPES THESAURUS BENTHIC SPECIES - TAXA IDENTITIES
NODC INSTRUMENT TYPES THESAURUS photograph
NODC OBSERVATION TYPES THESAURUS benthic
NODC OBSERVATION TYPES THESAURUS other
NODC PLATFORM NAMES THESAURUS HI'IALAKAI
NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS National Coral Reef Monitoring Program
NODC PROJECT NAMES THESAURUS Pacific Reef and Assessment Monitoring Program
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None Ecosystem Sciences Division
None ESD
None Pacific Islands Fisheries Science Center
None PIFSC
None RAMP
None Reef Assessment and Monitoring Program

Spatial Keywords

Thesaurus Keyword
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Baker Island (00N176W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Howland Island (00S176W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Johnston Atoll (16N169W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Baker Island > Baker Island (00N176W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Howland Island > Howland Island (00S176W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Johnston Atoll > Johnston Atoll (16N169W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001)
NODC Sea Area Names Thesaurus Equatorial Pacific Ocean
NODC Sea Area Names Thesaurus Pacific Remote Islands Marine National Monument
None Pacific Remote Island Areas
None PRIA
None PRIMNM

Physical Location

Organization: Pacific Islands Fisheries Science Center
City: Honolulu
State/Province: HI
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: CSV Files
Maintenance Frequency: As Needed
Maintenance Note:

Updated September 2019 to add benthic data generated from images collected in 2017.

Data Presentation Form: Table (digital)
Entity Attribute Overview:

Raw survey data includes metadata for each survey (where, when, who); site characteristics (depth, reef zone); unique image name, and individual point observations of benthic elements identified at 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).

Entity Attribute Detail URL: https://www.fisheries.noaa.gov/inport/item/36151
Distribution Liability:

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.

Data Set Credit: PIFSC Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program

Support Roles

Data Set Credit

CC ID: 873623
Date Effective From: 2014
Date Effective To:
Contact (Organization): NOAA Coral Reef Conservation Program (CRCP) (CRCP)
Address: 1305 East West Highway 10th Floor
Silver Spring, MD 20910-3281
Phone: (301) 713-3155
URL: http://coralreef.noaa.gov

Data Steward

CC ID: 873624
Date Effective From: 2014
Date Effective To:
Contact (Person): Vargas-Angel, Bernardo
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: bernardo.vargasangel@noaa.gov
Phone: (808)725-5423

Distributor

CC ID: 873625
Date Effective From: 2016
Date Effective To:
Contact (Organization): National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD)
Address: NOAA/NESDIS E/OC SSMC3, 4th Floor, 1351 East-West Highway
Silver Spring, MD 20910-3282
Phone: (301) 713-3277

Distributor

CC ID: 873626
Date Effective From: 2014
Date Effective To: 2016
Contact (Person): Kanemura, Troy T
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: troy.kanemura@noaa.gov
Phone: (808)725-5422

Metadata Contact

CC ID: 873627
Date Effective From: 2014
Date Effective To:
Contact (Person): DesRochers, Annette M
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: annette.desrochers@noaa.gov
Phone: (808)725-5461
Business Hours: 8 am - 5 pm

Originator

CC ID: 873628
Date Effective From: 2014
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 873629
Date Effective From: 2014
Date Effective To:
Contact (Person): Vargas-Angel, Bernardo
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: bernardo.vargasangel@noaa.gov
Phone: (808)725-5423

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Pacific Remote Island Areas (PRIA) including Baker, Howland, Jarvis, and Wake islands, Kingman Reef, and Johnston and Palmyra atolls.

Extent Group 1 / Geographic Area 1

CC ID: 369549
W° Bound: -176.62393
E° Bound: -159.97881
N° Bound: 16.76343
S° Bound: -0.38234
Description

Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra), and Johnston Atoll. These six of the seven PRIA are routinely surveyed as part of the American Samoa RAMP (ASRAMP) missions (Johnston, Baker and Howland during the first leg of ASRAMP, and Jarvis, Kingman, and Palmyra during the last leg of ASRAMP).

Extent Group 1 / Geographic Area 2

CC ID: 369550
W° Bound: 166.59824
E° Bound: 166.65115
N° Bound: 19.31654
S° Bound: 19.27116
Description

Wake Island, one of the seven PRIA, is routinely surveyed as part of the Mariana Archipelago RAMP (MARAMP) missions.

Extent Group 1 / Time Frame 1

CC ID: 369551
Time Frame Type: Range
Start: 2014-03-16
End: 2014-03-19
Alternate Start As Of Info: HA1401
Description:

MARAMP 2014

Extent Group 1 / Time Frame 2

CC ID: 369552
Time Frame Type: Range
Start: 2015-01-26
End: 2015-04-27
Alternate Start As Of Info: HA1501
Description:

ASRAMP 2015

Extent Group 1 / Time Frame 3

CC ID: 873630
Time Frame Type: Range
Start: 2017-04-19
End: 2017-04-20
Alternate Start As Of Info: HA1701
Description:

Time frame of benthic images collected at Wake during MARAMP 2017 that were analyzed for benthic community data.

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

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 Access Procedure:

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

Data Access Constraints:

None

Data Use Constraints:

Please cite PIFSC Ecosystem Sciences Division (ESD) when using the data.

Example:

Ecosystem Sciences Division; Pacific Islands Fisheries Science Center, 2019: 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.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 369404
Download URL: http://accession.nodc.noaa.gov/0159145
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MV_BIA_PERC_COVER_PHOTO_CLI_RW PRIAs 2014.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across Wake Island in 2014 by the NOAA Coral Reef Ecosystem Program (CREP)

File Date/Time: 2016-12-20 00:00:00
File Type: csv (comma-separated values)

Distribution 2

CC ID: 369401
Download URL: http://accession.nodc.noaa.gov/0159152
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MV_BIA_CNET_ANALYSIS_DATA PRIAs 2015.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across the Pacific Remote Island Areas in 2015 by the NOAA Coral Reef Ecosystem Program (CREP)

File Date/Time: 2016-12-24 00:00:00
File Type: csv (comma-separated values)

Distribution 3

CC ID: 873631
Download URL: http://accession.nodc.noaa.gov/0202300
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MV_BIA_CNET_ANALYSIS_DATA_CLIMATE_Wake_2017.csv
Description:

Benthic community data from annotated benthic images collected during photoquadrat surveys at permanent sites and climate stations at Wake Atoll of the Pacific Remote Island Areas in 2017 by the PIFSC Ecosystem Sciences Division (ESD).

File Date/Time: 2019-08-30 00:00:00
File Type: csv (comma-separated values)

Distribution 4

CC ID: 873632
Download URL: https://accession.nodc.noaa.gov/0157633
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: PIFSC_H-17-02_2017_SOP_ImageAnalysis_CN.pdf
Description:

PIFSC Administrative Report, January 2017: Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines

File Date/Time: 2017-01-31 00:00:00
File Type: PDF

URLs

URL 1

CC ID: 369394
URL: http://coralnet.ucsd.edu/
Name: CoralNet
URL Type:
Online Resource
File Resource Format: HTML
Description:

CoralNet Home Page

URL 2

CC ID: 369395
URL: http://cnso.nova.edu/cpce/
Name: Coral Point Count with Excel Extensions
URL Type:
Online Resource
File Resource Format: HTML
Description:

Coral Point Count with Excel Extensions (CPCe) Home Page

URL 3

CC ID: 369397
URL: http://www.coris.noaa.gov/monitoring/
Name: NOAA National Coral Reef Monitoring Program
URL Type:
Online Resource
File Resource Format: PHP
Description:

NOAA National Coral Reef Monitoring Program (NCRMP) website.

URL 4

CC ID: 873633
URL: https://origin-apps-pifsc.fisheries.noaa.gov/ecosystem_sciences/
Name: Ecosystem Sciences Division
URL Type:
Online Resource
Description:

NOAA Fisheries, Pacific Islands Fisheries Science Center website

Technical Environment

Description:

PIFSC Oracle database views:

CoralNet: MV_BIA_CNET_ANALYSIS_DATA

CPCe: MV_BIA_PERC_COVER_PHOTO_CLI_RW

Data Quality

Accuracy:

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 and mark site locations.

Comparability:

Survey transects were marked to allow direct, site-level temporal comparisons.

Completeness Measure:

The data set derived from the annotated images is as good as the images themselves; poor images with low contrast, inappropriate white balance, or out of focus may have been discarded. Therefore, total annotations for some sites may have differing number of points between sites (300 annotations are expected per site if there were 30 photographs and 10 point analyzed per photograph). Although the analysis process is statistically robust to allow for differing n (points) between sites, users should be aware of this limitation.

Completeness Report:

Only shallow water (0 to 30 meter depth range) hard-bottom habitats are surveyed.

Classification is completed to the functional group/genus level (Tier 3).

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 ESD at nmfs.pic.credinfo@noaa.gov for more information.

Conceptual Consistency:

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

Quality Control Procedures Employed:

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

Data Management

Have Resources for Management of these Data Been Identified?: Yes
Approximate Percentage of Budget for these Data Devoted to Data Management: Unknown
Do these Data Comply with the Data Access Directive?: Yes
Is Access to the Data Limited Based on an Approved Waiver?: No
Approximate Delay Between Data Collection and Dissemination: Unknown
Actual or Planned Long-Term Data Archive Location: NCEI-MD
Approximate Delay Between Data Collection and Archiving: Unknown
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

The image analysis data is captured in two different locations: exported files from CPCe or CoralNet that reside on a file server, which are ingested into a table in the PIFSC Oracle database. Both the file server and PIFSC Oracle database are maintained and regularly backed up by PIFSC ITS.

Lineage

Lineage Statement:

Benthic photographs were collected during photoquadrat surveys conducted at permanent sites and climate stations in coral reef habitats by the PIFSC Ecosystem Sciences Division. The imagery was later analyzed using Coral Point Count with Excel Extentions (CPCe; 2014 and prior) or CoralNet (starting in 2015) to generate benthic community data.

Sources

Beijbom, Oscar, Peter J. Edmunds, Chris Roelfsema, Jennifer Smith, David I. Kline, Benjamin P. Neal, Matthew J. Dunlap, et al. 2015. “Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.” Edited by Chaolun Allen Chen. PLOS ONE 10 (7): e0130312.

CC ID: 873635
Contact Role Type: Publisher
Contact Type: Organization
Contact Name: PLOS ONE
Publish Date: 2015-07-08
Citation URL: https://doi.org/10.1371/journal.pone.0130312
Citation URL Name: PLOS ONE
Source Contribution:

Research article, RE: CoralNet

Kohler, Kevin E., and Shaun M. Gill. 2006. “Coral Point Count with Excel Extensions (CPCe): A Visual Basic Program for the Determination of Coral and Substrate Coverage Using Random Point Count Methodology.” Computers & Geosciences 32 (9): 1259–69.

CC ID: 873750
Contact Role Type: Publisher
Contact Type: Organization
Contact Name: ScienceDirect Computers & Geosciences
Publish Date: 2006-11-01
Citation URL: https://doi.org/10.1016/j.cageo.2005.11.009
Citation URL Name: ScienceDirect
Source Contribution:

Research article, RE: CPCe

Lozada-Misa P, Schumacher BD, Vargas-Angel B. 2017. Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines. Pacific Islands Fisheries Science Center, PIFSC Administrative Report, H-17-02, 169 p.

CC ID: 873634
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center, PIFSC
Publish Date: 2017-01-31
Citation URL: https://doi.org/10.7289/V5/AR-PIFSC-H-17-02
Citation URL Name: NOAA Institutional Repository
Source Contribution:

The published benthic image analysis SOP using CoralNet.

Process Steps

Process Step 1

CC ID: 873751
Description:

SCUBA divers conduct benthic photoquadrat surveys at permanent sites established in hard-bottom habitat at ~15-m depths. A subset of the permanent sites (climate stations) were established at north, south, east, and west points around the island/atoll. The divers estimate and delineate 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 mark every meter of the L-shaped 15-m transect used for photoquadrat documentation. Divers photograph the reef at 1-m intervals on both sides of the 15-m tape, generating 30 photographs per survey site.

Photoquadrat images are organized by site, color-corrected (if necessary), and quality controlled to remove non-photoquadrat/poor quality images. An optical validation script is used to re-name photos and enforce several validation checks.

Process Contact: Barkley, Hannah C
Email Address: hannah.barkley@noaa.gov

Process Step 2

CC ID: 873752
Description:

Benthic habitat images collected during photoquadrat surveys at permanent sites and climate stations (30 images per site) were quantitatively analyzed using Coral Point Count with Excel extensions (CPCe; Kohler and Gill 2006) software through 2014 or by using the web-based annotation tool CoralNet (Beijbom et al. 2015) from 2015 to present. Ten points were randomly overlaid on each image by CPCe or CoralNet 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). 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).

The detailed list of each functional group level or tier is included in the benthic image analysis classification scheme.

Process Contact: Vargas-Angel, Bernardo
Phone (Voice): (808)725-5423
Email Address: bernardo.vargasangel@noaa.gov
Source: Lozada-Misa P, Schumacher BD, Vargas-Angel B. 2017. Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines. Pacific Islands Fisheries Science Center, PIFSC Administrative Report, H-17-02, 169 p.

Process Step 3

CC ID: 873776
Description:

Raw survey data includes unique image name, individual point observations identified at three levels, and the corresponding physical data that reflect the description of the site. The physical data includes: region, island, site, date, latitude, longitude, reef zone, and depth.

Process Contact: Vargas-Angel, Bernardo
Phone (Voice): (808)725-5423
Email Address: bernardo.vargasangel@noaa.gov

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity (ENT) Benthic Image analysis classification scheme
Entity (ENT) Entities: MV_BIA_CNET_ANALYSIS_DATA CLIMATE

Catalog Details

Catalog Item ID: 36148
Metadata Record Created By: Troy T Kanemura
Metadata Record Created: 2016-12-30 15:16+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2020-08-03 16:13+0000
Metadata Record Published: 2017-01-23
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2018-01-24