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Summary

Short Citation
Pacific Islands Fisheries Science Center, 2024: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021, https://www.fisheries.noaa.gov/inport/item/65764.
Full Citation Examples

Abstract

Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. This data includes coral species identification, bleaching extent and severity, colony diameter, perimeter, and planar size. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers and is documented and described separately. The data was collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands, and in subsequent years (2020, 2021) to assess recovery. The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. Two datasets are provided: an annotations file which provides coral demographic information of 6 target species at 12 fixed sites across 3 years, as well as a site metadata file which describes the site and surveys which were used to generate models for which annotation data was derived.

Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA). Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred.

Note an update in methodology: The data was collected in two stages. During the first stage of data collection that was completed in 2021, for each coral patch, (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded. In 2023 the methodology was updated for the second stage of data collection; the updated dataset includes measures of planar area and a "genet" (colony) identification column. The 2023 dataset was also collected following an update to the model process methodology (see Lineage). Users should refer to the most updated dataset published in 2023.

Distribution Information

  • CSV - Comma Separated Values (Text)

    Annotations of 3D coral models generated from patch level analysis in 2022 using imagery from follow-up surveys in 2021 and 2020 (Oahu only) to revisit fixed sites established in 2019 for bleaching assessment. A subset of metrics from 2019 was collected again, using an updated methodology described in the Lineage section.

  • CSV - Comma Separated Values (Text)

    List of coral species codes and their associated taxon names, as used in annotations dataset.

  • CSV - Comma Separated Values (Text)

    Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch/'genet' level information.

  • CSV - Comma Separated Values (Text)

    Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch level information.

  • CSV - Comma Separated Values (Text)

    Coral patch level SfM annotations observations from surveys conducted during the 2019 bleaching event in the Hawaiian Archipelago at fixed sites.

    ***NOTE: This data is outdated. Please refer to the dataset published in 2023 generated with an updated methodology to analyze time series effectively: BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021.csv

  • CSV - Comma Separated Values (Text)

    Reference table of full taxa names per taxa code.

Access Constraints:

None

Use Constraints:

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

Example:

Ecosystem Science Division; Pacific Islands Fisheries Science Center, 2023: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021, https://www.fisheries.noaa.gov/inport/item/65764.

Controlled Theme Keywords

BENTHIC, CORAL BLEACHING, CORAL REEF, DOC/NOAA/NMFS/PIFSC/ESD, environment

Contact Information

Point of Contact
Courtney S Couch
courtney.s.couch@noaa.gov

Metadata Contact
Lori H Luers
lori.luers@noaa.gov

Extents

Geographic Area 1

-158.0667° W, -155.830367° E, 21.47959° N, 19.42335° S

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

Time Frame 1
2019-10-08 - 2021-07-20

MHI 2019 bleaching surveys

Item Identification

Title: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021
Short Name: Bleaching & Recovery: 2019-2021 MHI Coral Observations
Status: On Going
Creation Date: 2021-11
Revision Date: 2023-09-14
Publication Date: 2023
Abstract:

Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. This data includes coral species identification, bleaching extent and severity, colony diameter, perimeter, and planar size. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers and is documented and described separately. The data was collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands, and in subsequent years (2020, 2021) to assess recovery. The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. Two datasets are provided: an annotations file which provides coral demographic information of 6 target species at 12 fixed sites across 3 years, as well as a site metadata file which describes the site and surveys which were used to generate models for which annotation data was derived.

Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA). Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred.

Note an update in methodology: The data was collected in two stages. During the first stage of data collection that was completed in 2021, for each coral patch, (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded. In 2023 the methodology was updated for the second stage of data collection; the updated dataset includes measures of planar area and a "genet" (colony) identification column. The 2023 dataset was also collected following an update to the model process methodology (see Lineage). Users should refer to the most updated dataset published in 2023.

Purpose:

The Hawaii Coral Bleaching Collaborative (HCBC) planned and executed a field survey response in 2019 that applied a structured, hypothesis-driven approach to document the extent of coral bleaching in the Hawaiian Archipelago, and laid the groundwork for tracking coral response and recovery through time. Fixed sites were revisited in 2020 and 2021 to examine survivorship, recovery, and growth following the 2019 bleaching event. The purpose of the Structure from Motion (SfM) surveys throughout the Main Hawaiian Islands is to efficiently and effectively collect coral demographic data.

This was funded by two CRCP Projects: #31283, #31361

titled 'Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities' and 'Hawai'i coral bleaching assessment and analysis'

Other Citation Details:

Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47

Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649

Keywords

Theme Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Data Center Keywords
DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce
Global Change Master Directory (GCMD) Science Keywords
EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC
Global Change Master Directory (GCMD) Science Keywords
EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF
Global Change Master Directory (GCMD) Science Keywords
EARTH SCIENCE > OCEANS > COASTAL PROCESSES > CORAL REEFS > CORAL BLEACHING
ISO 19115 Topic Category
environment
UNCONTROLLED
CoRIS Discovery Thesaurus Numeric Data Sets > Benthic
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals)
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral Communities
CoRIS Theme Thesaurus NEARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
CRCP Project 31283
CRCP Project 31361
CRCP Project Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities
CRCP Project Hawai'i coral bleaching assessment and analysis
NODC DATA TYPES THESAURUS CORAL
NODC DATA TYPES THESAURUS CORAL - COLONY SIZE
NODC DATA TYPES THESAURUS CORAL - SPECIES IDENTIFICATION
NODC OBSERVATION TYPES THESAURUS derived products
NODC OBSERVATION TYPES THESAURUS GIS product
NODC OBSERVATION TYPES THESAURUS in situ
NODC OBSERVATION TYPES THESAURUS survey - coral reef
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS National Coral Reef Monitoring Program
NODC PROJECT NAMES THESAURUS Ocean Acidification Program
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
None coral demography
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None DAR
None Department of Land and Natural Resources
None Division of Aquatic Resources
None DLNR
None Ecosystem Sciences Division
None ESD
None Pacific Islands Fisheries Science Center
None PIFSC
None SfM
None Structure from Motion

Spatial Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Location Keywords
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS
Global Change Master Directory (GCMD) Location Keywords
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > HAWAII ISLAND
Global Change Master Directory (GCMD) Location Keywords
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > LANAI
Global Change Master Directory (GCMD) Location Keywords
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > OAHU
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 > Honolulu > Oahu (21N157W0003)
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 > 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 > Oahu Island > Oahu (21N157W0003)
NODC SEA AREA NAMES THESAURUS Coastal Waters of Hawaii
NODC SEA AREA NAMES THESAURUS: Central Pacific Ocean
NODC SEA AREA NAMES THESAURUS: North Pacific Ocean

Instrument Keywords

Thesaurus Keyword
Global Change Master Directory (GCMD) Instrument Keywords
Computer > Computer
UNCONTROLLED
NODC INSTRUMENT TYPES THESAURUS photograph
NODC INSTRUMENT TYPES THESAURUS scale

Platform Keywords

Thesaurus Keyword
UNCONTROLLED
NODC PLATFORM NAMES THESAURUS VARIOUS SMALL VESSELS

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:

In 2023 this data was republished after 2019 - 2021 imagery was re-annotated with an updated methodology; refer to most recent published dataset (2023); prior to 2023 this metadata record described only the preliminary 2019 dataset, and was titled 'Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event'.

As more data is generated with this methodology, datasets will be added to this metadata record.

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

Dataset includes metadata for each Structure from Motion (SfM) survey site (survey date, geographic coordinates, depth); individual adult coral observations identified to the lowest taxonomic level possible (species) including morphology, maximum diameter, bleaching extent and bleaching severity.

Entity Attribute Detail URL: https://www.fisheries.noaa.gov/inport/item/65773
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: NOAA Fisheries Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program

Support Roles

Data Set Credit

CC ID: 1095601
Date Effective From: 2021
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: 1095603
Date Effective From: 2021
Date Effective To:
Contact (Person): Winston, Morgan S
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: morgan.winston@noaa.gov
Phone: (808)725-5480

Distributor

CC ID: 1095604
Date Effective From: 2021
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: 1273030
Date Effective From: 2022
Date Effective To:
Contact (Person): Luers, Lori H
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: lori.luers@noaa.gov

Originator

CC ID: 1095600
Date Effective From: 2019
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: 1095602
Date Effective From: 2019
Date Effective To:
Contact (Person): Couch, Courtney S
Email Address: courtney.s.couch@noaa.gov
View Historical Support Roles

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Hawaiian Archipelago October 8 2019 - July 20 2021

Extent Group 1 / Geographic Area 1

CC ID: 1095628
W° Bound: -158.0667
E° Bound: -155.830367
N° Bound: 21.47959
S° Bound: 19.42335
Description

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

Extent Group 1 / Time Frame 1

CC ID: 1095627
Time Frame Type: Range
Start: 2019-10-08
End: 2021-07-20
Description:

MHI 2019 bleaching surveys

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 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 NOAA Fisheries, Ecosystem Science Division (ESD) when using the data.

Example:

Ecosystem Science Division; Pacific Islands Fisheries Science Center, 2023: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021, https://www.fisheries.noaa.gov/inport/item/65764.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 1272701
Start Date: 2023-10
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0283598
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021
Description:

Annotations of 3D coral models generated from patch level analysis in 2022 using imagery from follow-up surveys in 2021 and 2020 (Oahu only) to revisit fixed sites established in 2019 for bleaching assessment. A subset of metrics from 2019 was collected again, using an updated methodology described in the Lineage section.

File Type (Deprecated): csv (comma-separated values)
Distribution Format: CSV - Comma Separated Values (Text)

Distribution 2

CC ID: 1273189
Start Date: 2023-10
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0283598
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: BLEACHING_SFM_TAXALIST_MHI_2019-2021.csv
Description:

List of coral species codes and their associated taxon names, as used in annotations dataset.

File Type (Deprecated): .csv
Distribution Format: CSV - Comma Separated Values (Text)

Distribution 3

CC ID: 1273190
Start Date: 2023-10
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0283598
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: SITE_METADATA_2019-2021_MHI
Description:

Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch/'genet' level information.

File Type (Deprecated): .csv
Distribution Format: CSV - Comma Separated Values (Text)

Distribution 4

CC ID: 1096123
Start Date: 2021-11-08
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0244392
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: 2019_SfMSiteMetadata.csv
Description:

Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch level information.

File Type (Deprecated): .csv
Distribution Format: CSV - Comma Separated Values (Text)

Distribution 5

CC ID: 1095607
Start Date: 2020-11-08
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0244392
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: ColonyLevelBleachingSfM2019.csv
Description:

Coral patch level SfM annotations observations from surveys conducted during the 2019 bleaching event in the Hawaiian Archipelago at fixed sites.

***NOTE: This data is outdated. Please refer to the dataset published in 2023 generated with an updated methodology to analyze time series effectively: BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021.csv

File Type (Deprecated): CSV
Distribution Format: CSV - Comma Separated Values (Text)

Distribution 6

CC ID: 1096124
Start Date: 2020-04-23
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0209239
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2021 - Present)
File Name: HCBC_2019_TaxaList.csv
Description:

Reference table of full taxa names per taxa code.

File Type (Deprecated): .csv
Distribution Format: CSV - Comma Separated Values (Text)

URLs

URL 1

CC ID: 1095608
URL: https://www.fisheries.noaa.gov/feature-story/surveys-assess-2019-hawaii-coral-bleaching-event
Name: Feature Story: Surveys to Assess the 2019 Hawaiʻi Coral Bleaching Event
URL Type:
Online Resource

Technical Environment

Description:

A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. A Nikon SL2 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25-0.50 m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape (version 1.6.2 build 10247). Models were further scaled using Viscore software. Sampling boundaries and coral demographic measurements were created in ArcGIS Pro (version 2.6.0).

Data Quality

Representativeness:

The data set derived from the imagery is only as good as the images themselves; Images with poor resolution, poor lighting, extraneous objects (fins, etc), or blur were excluded from analysis.

Accuracy:

Handheld GPS units were used to locate fixed sites and update site locations if needed.

Prior to conducting surveys, the SfM image collector was trained to swim in a back-and-forth or circular pattern to collect imagery with 60-80% overlap. Both classroom and field training were completed before any surveys were conducted. This training ensures that all SfM image collection was conducted consistently during the mission.

Coral demographic data was extracted by SfM image annotators that had been trained, underwent a series of calibration efforts and testing on coral taxon identification testing, morphology, and condition assessment. All annotators met a set of minimum standards for coral demographic data collection.

Completeness Report:

Of the fixed sites for which SfM imagery was collected at during the 2019 bleaching survey effort, a subset of these sites were annotated that included 5 from Hawaii Island, 5 from Oahu, and 2 from Lanai.

Conceptual Consistency:

The same method of annotation was used for all SfM imagery.

Quality Control Procedures Employed:

Prior to generating the 3D dense point clouds and 2D orthomosaics, the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. During annotation in ArcMap, the original JPEG imagery was viewed alongside the orthomosaic using Agisoft or Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcMap were quality controlled using a multi-stage process. Data were quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, % bleaching >100%).

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?:

NOAA IRC and NOAA Fisheries ITS resources and assets.

Lineage

Lineage Statement:

Benthic imagery was collected at permanent sites and generated into 3D dense point clouds (DPCs) using Agisoft Metashape software. DPCs from the same site, but different collection dates were converted into 2D orthomosaics and scaled, oriented and aligned together. Orthomosaics were sub-sampled by randomly distributing quadrats throughout the orthopmosaic. Quadrat location was conserved across all orthomosaics associated with the same permanent site. Target coral species were identified within each quadrat and their perimeters were annotated until a sufficient sample size of each species was recorded. Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred.

Sources

Burns J, Delparte D, Gates R, Takabayashi M. 2015. Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077

CC ID: 1095617
Contact Role Type: Publisher
Contact Type: Person
Contact Name: John Burns
Publish Date: 2015-07-07
Citation URL: https://doi.org/10.7717/peerj.1077
Citation URL Name: PeerJ
Citation URL Description:

This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems.

Couch CS, Oliver, TA, Suka R, Lamirand M, Asbury M, Amir C, Vargas-Ángel B, Winston M, Huntington B, Lichowski F, Halperin A, Gray A, Garriques J, & Samson J. 2021. Comparing coral colony surveys from in-water observations and structure-from-motion imagery shows low methodological bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943

CC ID: 1095619
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2021-05-28
Citation URL: https://doi.org/10.3389/fmars.2021.647943
Source Contribution:

This study provides the first quantified methodological comparison to validate the transition from standard in-water methods to SfM survey methods for estimates of coral colony-level surveys. Here, we quantitatively compare data generated from in-water surveys to SfM-derived metrics for assessing coral demography, bleaching, and diversity in the main Hawaiian Islands as part of NOAA’s National Coral Reef Monitoring Program. Our objectives were to compare between-method error to within-method

error, test for bias between methods, and identify strengths and weaknesses of both methods. Colony density, average colony diameter, average partial mortality,

prevalence of bleaching, species richness, and species diversity were recorded using both methods within the same survey areas. For all metrics, the magnitude of between-method error was comparable to the within-method error for the in-water method and between method error was significantly higher than within-method error for SfM for

one of the seven metrics. Our results also reveal that a majority of the metrics do not vary significantly between methods, nor did we observe a significant interaction between method and habitat type or method and depth. Exceptions include estimates of partial mortality, bleaching prevalence, and Porites juvenile density–though differences

between methods are generally small. Our study also highlights that SfM offers a unique opportunity to more rigorously quantify and mitigate inter-observer error by providing observers unlimited “bottom time” and the opportunity to work together to resolve difficult annotations.

Petrovic, V, Vanoni, DJ, Richter, AM, Levy, TE, & Kuester, F. 2014. Visualizing high resolution three-dimensional and two-dimensional data of cultural heritage sites. Mediterranean Archaeology and Archaeometry, 14(4), 93-100.

CC ID: 1095620
Contact Role Type: Publisher
Contact Type: Person
Contact Name: Vid Petrovic
Publish Date: 2014-01-01
Citation URL: https://escholarship.org/uc/item/58z4j8k2
Source Contribution:

The combination of 3D acquisition (terrestrial and airborne LiDAR, structured light, structure-from-motion) and 2D imaging (photographic, multispectral, panoramic, orthorectified, reflectance transformation) techniques allows the geometry, appearance and other aspects sites to be objectively documented. This study proposes a system for the direct visualization and analysis of such data, allowing the different aspects recorded to be layered together, and co-visualized with annotations and other relevant information. This study describes the required technical foundations, including gigapoint and gigapixel visualization pipelines that enable the dynamic layering of high-resolution imagery over massive minimally-processed LiDAR point clouds that serve as the base spatial layer. In particular, the study introduces the pointbuffer—a GPU-resident view-dependent point cache—as the foundation of our gigapoint pipeline, and outline the use of virtual texturing for draping of gigapixel imagery onto point clouds.

Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649

CC ID: 1096029
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2021-09-01
Citation URL: https://repository.library.noaa.gov/view/noaa/32739
Citation URL Name: NOAA Institutional Repository
Citation URL Description:

NOAA technical memorandum NMFS PIFSC

Source Contribution:

Here, we outline a method of directly measuring coral vital rates via structure-from-motion (SfM) photogrammetry — an image processing technique capable of reconstructing accurate, orthorectified representations of the seafloor and the coral communities that inhabit them. By leveraging SfM technology, NOAA’s U.S. National Coral Reef Monitoring Program (NCRMP) and partners are capable of generating accurate measures of coral vital rates from the scale of individual coral colonies with coverage of tens of sites and thousands of corals within a population.

In Section 1 of this technical memorandum, we provide a detailed set of Standard Operating Procedures for capturing, processing, and extracting data from SfM photogrammetry. In Section 2, we use this novel SfM approach and imagery collected at 14 sites across the Hawaiian Archipelago across time intervals from a few minutes to three years to determine how accurately we can measure coral vital rates.

Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47

CC ID: 1095616
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2019-12-30
Citation URL: https://doi.org/10.25923/h2q8-jv47
Citation URL Name: NOAA Institutional Repository
Citation URL Description:

NOAA technical memorandum NMFS PIFSC

Source Contribution:

This document provides detailed procedures for collecting and processing imagery using Structure-from-Motion techniques developed by Ecosystem Sciences Division (ESD) in collaboration with Scripps Institution of Oceanography and the University of Hawaii at Hilo. These procedures are designed to efficiently generate coral demographic and benthic community metrics across the broad spatial scale of the Pacific Rapid Assessment and Monitoring Program. This pipeline consists of four key steps: (1) Image collection by SCUBA divers, (2) Data management, post-processing, and QC, (3) Generating 3-D models and 2-D orthophotos in Agisoft Metashape, and (4) Extracting demographic data in ArcMap. This SOP is the result of comprehensive testing of different camera systems, collection techniques, and software. While the following procedures are designed to meet ESD needs, we primarily use commercially available cameras and software, making these methods adaptable based on programmatic capacity and needs.

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: 1095618
Publish Date: 2018-08-01
Citation URL: https://repository.library.noaa.gov/view/noaa/18267
Citation URL Name: NOAA Institutional Repository
Source Contribution:

Guidelines and procedures for implementation of sampling design, in situ survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018).

Winston M, Couch C, Ferguson M, Huntington B, Swanson D, Vargas-Ángel B. 2019. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA Tech. Memo. NOAA-TM-NMFS-PIFSC-92, 66 p. doi:10.25923/w1k2-0y84

CC ID: 1095615
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2020-01-31
Citation URL: https://doi.org/10.25923/ws5s-km69
Citation URL Name: NOAA Institutional Repository
Citation URL Description:

NOAA technical memorandum NMFS PIFSC

Source Contribution:

The objective of this document is to provide updates incorporated in 2019 to the guidelines and procedures for implementation of sampling design, survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018).

Process Steps

Process Step 1

CC ID: 1095622
Description:

SfM benthic surveys were conducted at fixed sites in the Main Hawaiian Islands during the 2019 bleaching event and during follow-up surveys in 2020 (Oahu only) and 2021. Imagery was collected using a digital camera in an underwater housing and white balance settings were adjusted in situ using a gray card.

Prior to image collection, each site was set up by placing at least two scale bars of known length, with ground control points (GCPs) at the end of each bar, 2-3 m away from the center of the survey area. At many sites, rebar caps with GCPs were also placed on the reference pins (36 in tall stainless steel rods used to mark the site). During plot set up, one diver drew a diagram of the plot, marking the location of each scale bar, reference pin, and distinctive benthic features. The depth and identification numbers of each scale bar were recorded in the diagram as well.

Divers swam ~1m off the seafloor, collecting enough photographs to produce 60%-80% image overlap and complete two full passes of the site.

Process Contact: Winston, Morgan S
Phone (Voice): (808)725-5480
Email Address: morgan.winston@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649

Process Step 2

CC ID: 1095623
Description:

Images for each site were evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. Following image quality control, each set of raw images were imported, aligned separately in Agisoft Metashape and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019).

Data collected before 2022 was only done for surveys conducted in 2019, and a subset of the metrics described in the Lineage Statement were collected. Different steps were also taken to prepare models for data collection. This pre-2022 collected data used DPCs that were imported into Viscore, a custom visualization software (Petrovic et al., 2014), where all DPCs from the same site, but from different time points, were scaled, oriented and aligned together using the GCP information. Each DPC was converted into a 2D orthorectified image (orthoprojection) and an identical top-down view of all othoprojections of the same site but different time points were exported from Viscore.

For data collected beginning in 2022, all scaling, orienting, alignment and 2D model creations were completed using Agisoft Metashape.

Process Contact: Winston, Morgan S
Phone (Voice): (808)725-5480
Email Address: morgan.winston@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649

Process Step 3

CC ID: 1095624
Description:

Due to the labor-intensive and time-consuming nature of annotation, in 2022 we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. To sub-sample each site, we selected the region where there was the most spatial overlap across all orthomosaics of the same site. Next, 10-30 2.5m2 quadrats were generated at random throughout the selected area and each labeled in numerical order.

Within the first 10 quadrats, all coral species on the target coral species list were annotated if their centroid fell within the quadrat. Corals were annotated by tracing the full perimeter of live coral tissue patches. During annotation, the original JPEG imagery was viewed alongside the orthomosaic to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges).

Following Rodriguez et al. (2021), if a coral species per site was found less than 10 times in the first 10 quadrats, the species was subsequently not recorded in future analyzed quadrats. Therefore, this data should be carefully analyzed and species density should not be calculated for these species with low sample size. If a species had low density at a given site, 20-40 patches were annotated. If a species was abundant at the site, at least 40 patches were annotated. See Rodriguez et al. (2021) for further information.

Unique identifying numbers were assigned to each patch of live coral tissue to link coral patches across time and to track fission/fusion events.

Process Contact: Winston, Morgan S
Phone (Voice): (808)725-5480
Email Address: morgan.winston@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649

Process Step 4

CC ID: 1095625
Description:

Annotations created in ArcGIS Pro were quality controlled using a multi-stage process. Data was exported from ArcGIS and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, data in incorrect columns, bleaching >100%). Coral patches composing the same colony or genet were assigned unique genet ID numbers.

Process Contact: Winston, Morgan S
Phone (Voice): (808)725-5480
Email Address: morgan.winston@noaa.gov

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Child Items

Related Items

Item Type Relationship Type Title
Data Set (DS) Cross Reference Hawaii Coral Bleaching Collaborative: surveys for percent and severity of bleached coral cover across the Hawaiian Archipelago from August 20 to December 7, 2019

Rapid visual assessments during the 2019 bleaching survey effort across the MHI.

Data Set (DS) Cross Reference Structure from Motion (SfM) benthic images collected from Fixed Sites across the U.S. Pacific since 2019

Source imagery that was annotated to generate this dataset is described and documented on this metadata record

Catalog Details

Catalog Item ID: 65764
GUID: gov.noaa.nmfs.inport:65764
Metadata Record Created By: Brooke Olenski
Metadata Record Created: 2021-11-03 00:40+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2023-10-17 16:12+0000
Metadata Record Published: 2023-10-04
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2021-12-14
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2022-12-14