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Short Citation:
Pacific Islands Fisheries Science Center, 2022: Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event, https://www.fisheries.noaa.gov/inport/item/65764.

Item Identification

Title: Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event
Short Name: Bleaching: 2019 MHI Colony-level annotations
Creation Date: 2021-11
Abstract:

Coral adult colony demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. The data were 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.

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. For each adult coral colony 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.

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. The purpose of the Structure from Motion (SfM) surveys throughout the Main Hawaiian Islands is to efficiently and effectively collect coral demographic data.

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
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
ISO 19115 Topic Category 007
ISO 19115 Topic Category environment
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/GIS product/survey - coral reef
NODC OBSERVATION TYPES THESAURUS in situ
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
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
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: None Planned
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.

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: 1095605
Date Effective From: 2019
Date Effective To:
Contact (Person): Olenski, Brooke
Email Address: brooke.olenski@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

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Hawaiian Archipelago April 21 - October 31, 2019

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: 2019-11-13
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; COPY INPORT RECORD CITATION HERE (keep ESD).

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

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 in 2019 using SfM methods to generate models that were annotated to derive coral colony patch level information.

File Type: .csv

Distribution 2

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

File Type: CSV

Distribution 3

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: .csv

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 random sites and mark site locations.

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 13 from Hawaii Island, 5 from Oahu, 1 from Maui, and 1 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 orthroprojections , 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 orthoprojection 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 orthoprojection. 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:

The benthic SfM survey methodology, employed by the NOAA Ecosystem Sciences Division (ESD), began in 2019. Benthic imagery is collected and generated into orthomosaic images using Agisoft Metashape software. Orthomosaics are scaled using Viscore software and imported into ArcGIS for annotation. Annotation of SfM orthomosaics collected during the 2019 bleaching event included coral species identification, maximum diameter measurement, morphology, bleaching extent and bleaching severity.

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 collected at fixed sites during the 2019 bleaching event in the Main Hawaiiian Islands. A 10x10m or 12m diameter circular plot was visually established. 3-4 ground control points (GCPs) were placed within the plot for scale. White balance settings were adjusted in situ using a 15% gray card. JPEG images were collected using a Nikon SL2 digital camera in an underwater housing with a dome port. Images were collected at each site by swimming in a back-and-forth or circular motion 1m above the substrate capturing images continuously to achieve a 60-80% overlap.

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.

The Structure from Motion (SfM) approach produces an accurately scaled, two-dimensional (2D) orthomosaic model created from the overlapping imagery. Raw imagery was imported into Agisoft Metashape software where images were aligned and used to build 3D dense point clouds (DPCs) following parameters described by Rodriguez et al. (2021). DPCs were then imported into Viscore, a visualization software (Petrovic et al., 2014) where they were scaled and oriented using the GCP information. The ground sample distance (GSD) of the scaled DPC, which estimates the resolution per pixel by measuring the size of each pixel on the ground, ranged from 2-4 mm/pix. A geometrically accurate 2D projection of the DPC (orthoprojection) and scale grid are exported from Viscore and uploaded into ArcGIS Pro for annotation.

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:

In ArcGIS Pro, each site was set up for annotation by scaling the orthoprojection using the scale grid exported from Viscore, manually digitizing quadrats as a shapefile, and setting up the attribute table in a geodatabase. To record and extract data from the orthoprojection image, each coral colony patch >= 5cm was annotated. Each patch was measured by digitizing a line across the maximum diameter of the colony. Coral ID (to lowest taxonomic level), morphology, and bleaching extent and severity were recorded. During annotation, the original JPEG imagery was viewed alongside the orthoprojection with the Agisoft or Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection (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.

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 were exported from ArcMap 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%).

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

Related Items

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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: 2022-10-20 02:17+0000
Metadata Record Published: 2021-12-14
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