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Summary

Short Citation
Pacific Islands Fisheries Science Center, 2024: 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.
Full Citation Examples

Abstract

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 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). 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.

Distribution Information

  • PDF - Adobe Portable Document Format

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

  • CSV - Comma Separated Values (Text)

    Benthic community data generated from automated annotation of benthic photoquadrat images by a trained robot in CoralNet that were collected at random and permanent survey sites across the Pacific Remote Island Areas and American Samoa in 2018 by the Pacific Islands Fisheries Science Center Ecosystem Sciences Division as part of the National Coral Reef Monitoring Program.

Access Constraints:

None

Use Constraints:

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

Example:

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 in 2018, https://www.fisheries.noaa.gov/inport/item/57610.

Controlled Theme Keywords

biota

Contact Information

Point of Contact
Bernardo Vargas-Angel
bernardo.vargasangel@noaa.gov
(808)725-5423

Metadata Contact
Annette M DesRochers
annette.desrochers@noaa.gov
(808)725-5461

Extents

Geographic Area 1

-176.626077° W, -159.971695° E, 6.451465° N, -0.382607° S

Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra) of the Pacific Remote Island Areas.

Geographic Area 2

-171.092425° W, -168.141129° E, -11.045273° N, -14.558022° S

American Samoa, including Tutuila, Ta`u, Ofu and Ologega, and Swains islands, and Rose Atoll.

Time Frame 1
2018-06-08 - 2018-06-15

Time frame of benthic images collected during ASRAMP 2018, Leg 1 to Howland and Baker islands of the PRIA that were analyzed for benthic community data.

Time Frame 2
2018-06-19 - 2018-07-18

Time frame of benthic images collected during ASRAMP 2018, Leg 2 to the islands of American Samoa that were analyzed for benthic community data.

Time Frame 3
2018-07-28 - 2018-08-11

Time frame of benthic images collected during ASRAMP 2018, Leg 3 to Jarvis, Palmyra and Kingman of the PRIA that were analyzed for benthic community data.

Item Identification

Title: Benthic Cover from Automated Annotation of Benthic Images Collected at Coral Reef Sites in the Pacific Remote Island Areas and American Samoa in 2018
Short Name: Benthic Cover - Robot
Status: On Going
Creation Date: 2019-09
Publication Date: 2019
Abstract:

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 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). 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.

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.

Supplemental Information:

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 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.

Keywords

Theme Keywords

Thesaurus Keyword
ISO 19115 Topic Category
biota
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 > 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 > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Rapid Assessment Studies
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
NODC DATA TYPES THESAURUS BENTHIC COMMUNITIES
NODC DATA TYPES THESAURUS BENTHIC SPECIES
NODC DATA TYPES THESAURUS BENTHIC SPECIES - TAXA IDENTITIES
NODC INSTRUMENT TYPES THESAURUS machine-learning algorithm
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 automated annotation
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None Ecosystem Sciences Division
None ESD
None image analysis
None Pacific Islands Fisheries Science Center
None PIFSC
None RAMP
None Reef Assessment and Monitoring Program
None stratified random
None StRS

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Swains Atoll (11S171W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > Ofu Island > Ofu (14S169W0002)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > Olosega Island > Olosega (14S169W0016)
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 > Kingman Reef (06N162W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016)
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 > 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 > Manu'a Group > Ofu (14S169W0002)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega (14S169W0016)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012)
NODC Sea Area Names Thesaurus Equatorial Pacific Ocean
NODC Sea Area Names Thesaurus Pacific Remote Islands Marine National Monument
NODC Sea Area Names Thesaurus Rose Atoll Marine National Monument
NODC Sea Area Names Thesaurus South Pacific Ocean
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:

Created September 2019 for benthic data generated by robot from images collected in 2018.

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

Raw benthic community data include metadata for each survey (where, when, who); site characteristics (depth, reef zone); unique image name, and individual point observations of benthic elements identified to benthic taxa group, referred to as "Tier 1", which includes hard coral, soft coral, macroalgae, turf algae, crustose coralline algae, invertebrates, mobile fauna, and sediment.

Entity Attribute Detail URL: https://www.fisheries.noaa.gov/inport/item/57660
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: 876305
Date Effective From: 2018
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

Data Steward

CC ID: 876306
Date Effective From: 2018
Date Effective To:
Contact (Person): Couch, Courtney S
Email Address: courtney.s.couch@noaa.gov

Distributor

CC ID: 876307
Date Effective From: 2019
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: 876309
Date Effective From: 2018
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: 876310
Date Effective From: 2018
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: 876311
Date Effective From: 2018
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:

Pacific Remote Island Areas (PRIA) including Baker, Howland, and Jarvis islands, Kingman Reef, and Palmyra atoll, and the islands and atolls of American Samoa.

Extent Group 1 / Geographic Area 1

CC ID: 876334
W° Bound: -176.626077
E° Bound: -159.971695
N° Bound: 6.451465
S° Bound: -0.382607
Description

Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra) of the Pacific Remote Island Areas.

Extent Group 1 / Geographic Area 2

CC ID: 876335
W° Bound: -171.092425
E° Bound: -168.141129
N° Bound: -11.045273
S° Bound: -14.558022
Description

American Samoa, including Tutuila, Ta`u, Ofu and Ologega, and Swains islands, and Rose Atoll.

Extent Group 1 / Time Frame 1

CC ID: 876331
Time Frame Type: Range
Start: 2018-06-08
End: 2018-06-15
Alternate Start As Of Info: HA1801
Description:

Time frame of benthic images collected during ASRAMP 2018, Leg 1 to Howland and Baker islands of the PRIA that were analyzed for benthic community data.

Extent Group 1 / Time Frame 2

CC ID: 876332
Time Frame Type: Range
Start: 2018-06-19
End: 2018-07-18
Alternate Start As Of Info: HA1801
Description:

Time frame of benthic images collected during ASRAMP 2018, Leg 2 to the islands of American Samoa that were analyzed for benthic community data.

Extent Group 1 / Time Frame 3

CC ID: 876333
Time Frame Type: Range
Start: 2018-07-28
End: 2018-08-11
Alternate Start As Of Info: HA1801
Description:

Time frame of benthic images collected during ASRAMP 2018, Leg 3 to Jarvis, Palmyra and Kingman of the PRIA 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: 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.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 876315
Download URL: https://accession.nodc.noaa.gov/0157633
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2019 - 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 (Deprecated): PDF
Distribution Format: PDF - Adobe Portable Document Format

Distribution 2

CC ID: 876312
Download URL: https://accession.nodc.noaa.gov/0204646
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2019 - Present)
File Name: BIA_CNET_ROBOT_2018.csv
Description:

Benthic community data generated from automated annotation of benthic photoquadrat images by a trained robot in CoralNet that were collected at random and permanent survey sites across the Pacific Remote Island Areas and American Samoa in 2018 by the Pacific Islands Fisheries Science Center Ecosystem Sciences Division as part of the National Coral Reef Monitoring Program.

File Date/Time: 2019-10-02 00:00:00
File Type (Deprecated): csv (comma-separated values)
Distribution Format: CSV - Comma Separated Values (Text)

URLs

URL 1

CC ID: 876316
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

URL 2

CC ID: 876317
URL: https://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 3

CC ID: 876318
URL: https://coralnet.ucsd.edu/
Name: CoralNet
URL Type:
Online Resource
File Resource Format: HTML
Description:

CoralNet Home Page

Technical Environment

Description:

PIFSC Oracle database view: CoralNet: MV_BIA_CNET_ANALYSIS_DATA_ROB

Data Quality

Accuracy:

Data sets derived from the machine-learning, image annotation tool, CoralNet, are highly reliable within the stipulated taxonomic context (Tier 1). Substantial effort is required to manually annotate benthic images, which is expensive and leads to lags before data are available.

Human, expert-analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program 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.

As image acquisition is relatively straightforward, the capacity of fully-automated image analysis tools to minimize the need for resource-intensive human analysts creates the opportunity to dramatically increase the quantity and consistency of coral reef benthic data available to researchers and managers.

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

Comparability:

Permanent transects/plots 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 for the site and 10 points 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 complete to the functional/taxa group level (Tier 1).

Survey sites in which less than 15 images were collected are discarded from the analysis.

Conceptual Consistency:

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

Quality Control Procedures Employed:

Machine-generated fully-automated benthic estimates of site-level coral cover (Tier 1) 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).

Pre- and post-automated benthic image analysis quality control procedures include spot checks for:

1- Image quality integrity: focus, white balance, distance from bottom (too high or too low)

2- image inventory completeness (all images acquired for each island are included in the analysis)

3- Duplicate sites

4- Complete and coherent upload of imagery to CoralNet

5- Integrity and completeness of robot-generated image annotations

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 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:

Protocol describing the automated annotation of benthic images to generate benthic community data. Still photographs (30 per survey site) collected during photoquadrat surveys at random and permanent sites in coral reef habitats by the PIFSC Ecosystem Sciences Division were later annotated by a human-trained robot in CoralNet.

Sources

Ayotte, P., K. McCoy, A. Heenan, I. Williams, and J. Zamzow. 2015. Coral Reef Ecosystem Division standard operating procedures: data collection for Rapid Ecological Assessment fish surveys. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-15-07, 33 p. doi: 10.7289/V5SN06ZT.

CC ID: 877197
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center, PIFSC
Publish Date: 2015-12-21
Citation URL: https://dx.doi.org/10.7289/V5SN06ZT
Citation URL Name: NOAA Institutional Repository
Source Contribution:

Survey protocol for reef fish surveys.

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: 876325
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

Lozada-Misa P., B. D. Schumacher, and B. Vargas-Ángel. 2017. Analysis of benthic survey images via CoralNet: a summary of standard operating procedures and guidelines. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-17-02, 175 p. doi:10.7289/V5/AR-PIFSC-H-17-02.

CC ID: 876324
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:

Protocol to annotate benthic images using CoralNet.

Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993.

CC ID: 877173
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center, PIFSC
Publish Date: 2018-08-01
Citation URL: https://doi.org/10.25923/39jh-8993
Citation URL Name: NOAA Institutional Repository
Source Contribution:

Survey protocol for coral demographic surveys

Williams ID, Couch CS, Beijbom O, Oliver TA, Vargas-Angel B, Schumacher BD and Brainard RE (2019) Leveraging Automated Image Analysis Tools to Transform Our Capacity to Assess Status and Trends of Coral Reefs. Front. Mar. Sci. 6:222. doi:10.3389/fmars.2019.00222.

CC ID: 878150
Contact Role Type: Originator
Contact Type: Organization
Contact Name: NOAA Pacific Islands Fisheries Science Center
Publish Date: 2019-04-30
Citation URL: https://doi.org/10.3389/fmars.2019.00222
Citation URL Name: Frontiers in Marine Science: Ocean Observation
Citation URL Description:

Ocean Observation, a specialty section of Frontiers in Marine Sciences, aims to progress our understanding of the ocean and of its role in a changing environment. Frontiers provides online free and open access to all of its research publications.

Source Contribution:

Research study to assess the feasibility/capacity of machine-learning to generate benthic data from photographs for coral reef ecosystems.

Process Steps

Process Step 1

CC ID: 877149
Description:

RANDOM SURVEY SITES:

A stratified random sampling (StRS) design was employed to select the random sites surveyed for reef fish and corals. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0-30 m depth range. The stratification scheme included island, reef zone, and depth. Sampling effort was allocated based on strata area and sites were randomly located within strata. 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.

Photoquadrat surveys conducted during surveys for reef fish (Ayotte et al. 2015) occur along one 30-m transect that spans the length of two stationary point count (SPC) cylinders used to assess fish abundance (30 images total, Rep A). Benthic photos are taken at 1-m intervals along the right hand side of the 30-m transect line.

Photoquadrat surveys conducted during coral demographic surveys (Swanson et al. 2018) occur along two, independent 18-m transects. Photos of the benthic substrate are taken at 1-m intervals starting at meter one, along the left hand side of each 18-m transect (15 images/transect, 30 images total, Rep A and B).

Process Contact: Williams, Ivor D
Phone (Voice): (808)725-5427
Email Address: ivor.williams@noaa.gov

Process Step 2

CC ID: 876327
Description:

PERMANENT SURVEY SITES:

Permanent sites were chosen in hard-bottom habitat at ~15-m depths, and a subset of the permanent sites called climate stations were established at north, south, east, and west points around each of the islands and atolls. A minimal suite of climate monitoring activities are conducted at permanent sites, whereas a full complement of activities are conducted at climate stations.

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 transect, generating 30 photographs per survey site.

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

Process Step 3

CC ID: 876328
Description:

IMAGE PROCESSING:

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 guarantee that all photoquadrat sites have the respective correct metadata.

Post image analysis quality control steps include spot checks of the machine-generated output data for completeness and adequate analysis of optical data.

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

Process Step 4

CC ID: 876329
Description:

AUTOMATED ANNOTATION OF BENTHIC IMAGES:

Benthic habitat images were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015). 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.

Process Contact: Vargas-Angel, Bernardo
Phone (Voice): (808)725-5423
Email Address: bernardo.vargasangel@noaa.gov
Source: Lozada-Misa P., B. D. Schumacher, and B. Vargas-Ángel. 2017. Analysis of benthic survey images via CoralNet: a summary of standard operating procedures and guidelines. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-17-02, 175 p. doi:10.7289/V5/AR-PIFSC-H-17-02.

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Child Items

Related Items

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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

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Human-annotated benthic cover for permanent sites, PRIA

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Images Collected During Photoquadrat Surveys at Climate Stations across the Pacific Remote Island Areas since 2014

Source images

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

Source images

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Images Collected from Stratified Random Sites (StRS) across American Samoa since 2015

Source images

Data Set (DS) Cross Reference National Coral Reef Monitoring Program: Benthic Images Collected from Stratified Random Sites (StRS) across the Pacific Remote Island Areas since 2014

Source images

Catalog Details

Catalog Item ID: 57610
GUID: gov.noaa.nmfs.inport:57610
Metadata Record Created By: Annette M DesRochers
Metadata Record Created: 2019-09-17 23:03+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2023-10-17 16:12+0000
Metadata Record Published: 2019-11-25
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2019-11-25
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2020-11-25