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Short Citation:
Pacific Islands Fisheries Science Center, 2022: National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across the Hawaiian Archipelago since 2013, https://www.fisheries.noaa.gov/inport/item/36146.

Item Identification

Title: National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across the Hawaiian Archipelago since 2013
Short Name: NCRMP: Benthic Cover at Climate Stations (Image Analysis) Hawaiian Archipelago
Status: On Going
Revision Date: 2021
Publication Date: 2016
Abstract:

The data described here result from benthic photo-quadrat surveys conducted along transects at climate stations and permanent sites identified by the Ocean and Climate Change team across the Hawaiian archipelago since 2013 . Benthic habitat imagery were quantitatively analyzed using Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software from 2010-2014 and a web-based annotation tool called CoralNet (Beijbom et al. 2016) from 2015 to present. In general, images are analyzed to produce 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.).

Climate stations are 3-4 sites per island that were selected in a stratified random fashion to be roughly equally spaced around the island, along the 15 m contour, on hard bottom, and at least 1 km away from a river mouth or embayment. Once selected we assess multiple features of the coral reef environment including in-situ temperature (STR), seawater carbonate, net carbonate accretion (CAU), and bioerosion (BMU). In 2013 and 2016, cryptobiota diversity (ARMS) was also assessed.

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

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 is intended to coordinate 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 will be 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.

Notes:

StRS and Climate cover data should be packaged to archive simultaneously.

Supplemental Information:

The National Coral Reef Monitoring Program (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 will consolidate 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 Coral Reef Ecosystem Program (CREP), now know as 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). Each year, CREP [ESD] scientists work closely with CRCP and local partners to collect biological data on fish populations and coral reef communities from strategically selected sites during Reef Assessment and Monitoring Program (RAMP) missions. 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.

DOI (Digital Object Identifier): https://doi.org/10.7289/v5f47mff
DOI Registration Authority: NOAA

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
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 > Algal Cover
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 > Baseline studies
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 > Benthos Analysis > Quadrat Monitoring > Photograph Analysis
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Transect Monitoring
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Transect Monitoring > Belt Transect
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Transect Monitoring > Point Counts
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Rapid Assessment Studies
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Mollusks > Tridacna
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Sponges
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 > Coastal Processes > Coral Reefs > Coral Reef Ecology > Coral Cover
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Hard Coral Cover
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Hard Coral Cover Live percentage
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Octocoral Cover
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 > Marine Biology > Marine Plants > Seagrass
CRCP Project 743
CRCP Project National Coral Reef Monitoring Program
ISO 19115 Topic Category 002
ISO 19115 Topic Category biota
NODC DATA TYPES THESAURUS REEF AND/OR BOTTOM REGIME - PERCENT COVER
NODC PLATFORM NAMES THESAURUS HI'IALAKAI
NODC PLATFORM NAMES THESAURUS OSCAR ELTON SETTE
NODC PLATFORM NAMES THESAURUS RAINIER
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 SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program
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

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii (21N160W0000)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Kauai Island (22N159W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Molokai Island (21N157W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > French Frigate Shoals (24N166W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Lisianski Island (25N173W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Northwestern Hawaiian Islands (28N178W0000)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Pearl and Hermes Reef (27N176W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Kauai > Niihau Island (21N160W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Lanai Island (20N156W0002)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Maui Island (20N156W0004)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaiian Islands (21N157W0027)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands (21N157W0027)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii > Hawaii (21N160W0000)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii Island > Hawaii Island (19N155W0003)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kauai Island > Kauai Island (22N159W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Lanai Island > Lanai Island (20N156W0002)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Maui Island > Maui Island (20N156W0004)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Molokai Island > Molokai Island (21N157W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Niihau Island > Niihau Island (21N160W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands (28N178W0000)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > French Frigate Shoals (24N166W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Lisianski Island (25N173W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001)
NODC Sea Area Names Thesaurus North Pacific Ocean
NODC Sea Area Names Thesaurus Papahanaumokuakea Marine National Monument
None Main Hawaiian Islands
None MHI
None Northwestern Hawaiian Islands
None NWHI

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
Data Presentation Form: Table (digital)
Entity Attribute Detail URL: https://www.fisheries.noaa.gov/inport/item/36149
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 Coral Reef Ecosystem Program and funded by the NOAA Coral Reef Conservation Program

Support Roles

Data Steward

CC ID: 369053
Date Effective From: 2013
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: 369059
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

Metadata Contact

CC ID: 1072058
Date Effective From: 2020
Date Effective To:
Contact (Person): Olenski, Brooke
Email Address: brooke.olenski@noaa.gov

Originator

CC ID: 369058
Date Effective From: 2013
Date Effective To:
Contact (Organization): NOAA Coral Reef Conservation Program (CRCP)
Address: 1305 East West Highway 10th Floor
Silver Spring, MD 20910-3281
Phone: (301) 713-3155
URL: https://coralreef.noaa.gov

Originator

CC ID: 369056
Date Effective From: 2013
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 369057
Date Effective From: 2013
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
View Historical Support Roles

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Hawaiian Archipelago including the main and Northwestern Hawaiian Islands.

Extent Group 1 / Geographic Area 1

CC ID: 369511
W° Bound: -178.383718
E° Bound: -166.11682
N° Bound: 28.459215
S° Bound: 23.627917
Description

Northwestern Hawaiian Islands (NWHI), including French Frigate, Kure, Lisianski, and Pearl & Hermes.

Extent Group 1 / Geographic Area 2

CC ID: 369512
W° Bound: -160.23392
E° Bound: -154.8176
N° Bound: 22.168448
S° Bound: 18.968567
Description

Main Hawaiian Islands (MHI), including Hawaii, Kauai, Maui, Oahu, Molokai, Niihau, and Lanai.

Extent Group 1 / Time Frame 1

CC ID: 369514
Time Frame Type: Discrete
Start: 2013-09-18
Alternate Start As Of Info: HA1305
Description:

NWHI RAMP 2013

Extent Group 1 / Time Frame 2

CC ID: 369515
Time Frame Type: Range
Start: 2013-10-22
End: 2013-10-30
Alternate Start As Of Info: SB1320
Description:

Shore-based surveys of Oahu

Extent Group 1 / Time Frame 3

CC ID: 369516
Time Frame Type: Range
Start: 2013-07-12
End: 2013-07-14
Alternate Start As Of Info: SE1305
Description:

Northwestern Hawaiian Islands mission (Kure)

Extent Group 1 / Time Frame 4

CC ID: 369517
Time Frame Type: Range
Start: 2013-09-05
End: 2013-09-13
Alternate Start As Of Info: HA1305
Description:

NWHI RAMP 2013

Extent Group 1 / Time Frame 5

CC ID: 369513
Time Frame Type: Range
Start: 2013-08-03
End: 2013-08-23
Alternate Start As Of Info: HA1304
Description:

MHI RAMP 2013

Extent Group 1 / Time Frame 6

CC ID: 573532
Time Frame Type: Range
Start: 2016-07-17
End: 2017-08-23
Alternate Start As Of Info: HA1606
Description:

MHI RAMP 2016

Extent Group 1 / Time Frame 7

CC ID: 573534
Time Frame Type: Discrete
Start: 2016-09-21
Alternate Start As Of Info: HA1606
Description:

NWHI RAMP 2016

Extent Group 1 / Time Frame 8

CC ID: 1071811
Time Frame Type: Range
Start: 2019-04-26
End: 2019-08-05
Alternate Start As Of Info: SE1902
Description:

MHI RAMP 2019

Extent Group 1 / Time Frame 9

CC ID: 1071812
Time Frame Type: Range
Start: 2019-08-27
End: 2019-09-04
Alternate Start As Of Info: RA1903
Description:

NWHI RAMP 2019

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

NOAA Ecosystem Science Division (ESD) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

ESD welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. ESD 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 ESD principal investigators.

2) In all presentations, product releases, or publications using data generated by ESD, proper acknowledgement of both ESD 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, ESD requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the ESD 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 Science 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 Ocean Acidification Program (OAP). 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 NOAA Fisheries Ecosystem Sciences Division (ESD) when using the data.

Example:

Ecosystem Sciences Division; Pacific Islands Fisheries Science Center (2021). National Coral Reef Monitoring Program: Benthic Percent Cover Derived from Analysis of Benthic Images Collected for Climate Stations across the Hawaiian Archipelago since 2013. NOAA's National Center for Environmental Information, https://www.fisheries.noaa.gov/inport/item/36146.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 369091
Download URL: https://accession.nodc.noaa.gov/0157720
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MV_BIA_CNET_ANALYSIS_DATA HAWAII 2013.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across the Hawaiian archipelago in 2013 by the NOAA Coral Reef Ecosystem Program (CREP), now know as the Ecosystem Sciences Division (ESD).

File Type: csv (comma-separated values)

Distribution 2

CC ID: 573537
Download URL: https://accession.nodc.noaa.gov/0164294
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MV_BIA_CNET_ANALYSIS_DATA HAWAII 2016.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across the Hawaiian archipelago in 2016 by the NOAA Coral Reef Ecosystem Program (CREP), now know as the Ecosystem Sciences Division (ESD).

File Type: csv (comma-separated values)

Distribution 3

CC ID: 1076652
Download URL: https://accession.nodc.noaa.gov/0240338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: MHI_2019_CLIMATE_BENTHIC_COVER.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across the Main Hawaiian Islands in 2019 by the NOAA Ecosystem Sciences Division (ESD)

File Date/Time: 2021-07-29 00:00:00
File Type: csv (comma-separated values)

Distribution 4

CC ID: 1076698
Download URL: https://accession.nodc.noaa.gov/0240338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2016 - Present)
File Name: NWHI_2019_CLIMATE_BENTHIC_COVER.csv
Description:

Image analysis data derived from photoquadrat benthic images at NCRMP climate stations and permanent sites across the Northwest Hawaiian Islands in 2019 by the NOAA Ecosystem Sciences Division (ESD)

File Date/Time: 2021-07-29 00:00:00
File Type: csv (comma-separated values)

URLs

URL 1

CC ID: 369080
URL: https://coralnet.ucsd.edu/
Name: CoralNet
URL Type:
Online Resource
File Resource Format: HTML
Description:

CoralNet Home Page

URL 2

CC ID: 369081
URL: https://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: 369082
URL: https://www.pifsc.noaa.gov/cred/corals.php
Name: NOAA Fisheries: Coral Reefs in the Pacific
URL Type:
Online Resource
File Resource Format: PHP
Description:

NOAA Fisheries: Coral Reefs in the Pacific website.

URL 4

CC ID: 369083
URL: https://www.coris.noaa.gov/monitoring/
Name: Coral Reef Information System: NOAA National Coral Reef Monitoring Program
URL Type:
Online Resource
File Resource Format: PHP
Description:

NOAA National Coral Reef Monitoring Program (NCRMP) website.

Technical Environment

Description:

PIFSC Oracle database view: MV_BIA_CNET_ANALYSIS_DATA (CoralNet) / MV_BIA_PERC_COVER_PHOTO_CLI_RW (CPCe)

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 appropriately marked to allow direct, site-level temporal comparisons.

Completeness Measure:

Complete; photoquads were taken at all sites surveyed. 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).

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.

Conceptual Consistency:

Training modules and standard operating procedures have been developed and documented to ensure improved performance and consistent imagery analysis results produced by multiple analysts.

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.

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: 1076688
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: 1076691
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: 1072056
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
Citation URL Description:

The NOAA Fisheries, Ecosystem Sciences Division benthic image analysis SOP using CoralNet.

Process Steps

Process Step 1

CC ID: 1072055
Description:

The benthic photoquadrat imagery that are collected as part of the Climate Station surveys are analyzed by 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. CPCe or CoralNet assigns 10 random points per photo and the benthic elements falling directly underneath each point is identified to three functional group levels: Tier 1 (e.g. hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g. Hard coral by morphology = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g. Hard coral by genus and morphology; Macroalgae by genus or grouped genera). 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 2

CC ID: 1072057
Description:

Raw survey data includes unique image name and individual point observations identified at three functional group levels of benthic cover with the corresponding physical data which reflect the description of the site. The physical data for all records includes the following: region, island, site, date (day, month, year), latitude (dd), longitude (dd), reef zone, habitat type, depth category, minimum depth and maximum depth.

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity Benthic Image analysis classification scheme
Entity Benthic_Cover

Related Items

Item Type Relationship Type Title
Data Set (DS) Cross Reference 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

Benthic cover/community metrics derived from image analysis also performed in the Hawaiian Archipelago but at stratified-random sites (StRS) rather than fixed climate stations.

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across American Samoa since 2015

Same surveys conducted in different region.

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Cover from Annotated Benthic Images Collected During Photoquadrat Surveys at Climate Stations across the Mariana Archipelago since 2014

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Data Set (DS) Cross Reference 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

Same surveys conducted in different region.

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Images Collected from Climate Stations across the Hawaiian Archipelago since 2013

Source imagery used to produce the annotations in this data package.

Catalog Details

Catalog Item ID: 36146
GUID: gov.noaa.nmfs.inport:36146
Metadata Record Created By: Troy T Kanemura
Metadata Record Created: 2016-12-30 15:16+0000
Metadata Record Last Modified By: Sarah Kunkel
Metadata Record Last Modified: 2022-10-20 03:55+0000
Metadata Record Published: 2021-07-30
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2021-07-30
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2022-07-30