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Short Citation:
Pacific Islands Fisheries Science Center, 2022: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the Hawaiian Archipelago from 2014-2019, https://www.fisheries.noaa.gov/inport/item/63093.

Item Identification

Title: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the Hawaiian Archipelago from 2014-2019
Short Name: SfM-Derived Coral Vital Rates Annotations
Status: On Going
Creation Date: 2020-11-10
Publication Date: 2022
Abstract:

The data described here are coral planar area measurements 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. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 1-3 years apart. In situ surveys, post-processing, and analysis were funded by NOAA Coral Reef Conservation Program (CRCP) and Ocean Acidification Program (OAP). Data collection was conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD).

Survey sites consisted of sites previously established by collaborators from Scripps Institution of Oceanography and new sites established in 2019 by NOAA ESD. During each survey, physical markings which identify each permanent survey site were either established or found using GPS coordinates previously collected. During image collection, the diver swam at a constant distance from the bottom of the reef while continuously capturing overlapping photographs, capturing approximately 100 m2 of reef habitat. The photographs were processed using Agisoft Metashape and Viscore, a custom visualization software, to generate 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections). Orthoprojections were uploaded to ArcGIS where corals were annotated and tracked over time to measure changes in vital rates (e.g. recruitment, mortality, growth).

In total, this dataset includes planar area and associated vital rates measurements for 5 coral species in 2 genera (Pocillopora and Porites) at 14 sites throughout the Hawaiian Archipelago.

Purpose:

The purpose of the SfM surveys of permanent sites throughout the Hawaiian Archipelago is to track coral vital rates (e.g. growth, mortality, recruitment) and how they vary across taxon, regions, and environmental gradients. This study leveraged SfM, an emerging photogrammetry technique, to allow efficient data collection alongside NCRMP essential efforts.

Other Citation Details:

Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 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 > Aquatic Habitat > Benthic Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Growth
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
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 Communities
ISO 19115 Topic Category 002
ISO 19115 Topic Category 007
ISO 19115 Topic Category 014
ISO 19115 Topic Category Biota
ISO 19115 Topic Category environment
ISO 19115 Topic Category oceans
NODC DATA TYPES THESAURUS CORAL
NODC DATA TYPES THESAURUS CORAL - COLONY SIZE
NODC DATA TYPES THESAURUS CORAL - SPECIES IDENTIFICATION
NODC INSTRUMENT TYPES THESAURUS Agisoft Metashape
NODC INSTRUMENT TYPES THESAURUS ArcGIS
NODC INSTRUMENT TYPES THESAURUS Viscore
NODC OBSERVATION TYPES THESAURUS derived products
NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS Ocean Acidification Program
NODC SEA AREA NAMES THESAURUS: NW Pacific
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None Ecosystem Sciences Division
None ESD
None NCRMP
None Pacific Islands Fisheries Science Center
None PIFSC
None RAMP
None Reef Assessment and Monitoring Program
None Scripps Institution of Oceanography
None SfM
None Structure from Motion

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Place Thesaurus Coastal Waters of Hawaii
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 > Kure Atoll (28N178W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Northwestern Hawaiian Islands (28N178W0000)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Pearl and Hermes Reef (27N176W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > 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 > Maui Island > Maui Island (20N156W0004)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands (28N178W0000)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001)
NODC SEA AREA NAMES THESAURUS North Pacific Ocean
NODC SEA AREA NAMES THESAURUS Papahanaumokuakea Marine National Monument

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
NODC INSTRUMENT TYPES THESAURUS photograph
NODC INSTRUMENT TYPES THESAURUS scale

Platform Keywords

Thesaurus Keyword
UNCONTROLLED
NODC PLATFORM NAMES THESAURUS HI'IALAKAI
NODC PLATFORM NAMES THESAURUS OSCAR ELTON SETTE

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 (site information, survey date and location, error vs. growth data), adult coral observations identified to the lowest taxonomic level possible (usually species) including initial and final size empirical size measurement.

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, PIFSC Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program and Ocean Acidification Program

Support Roles

Data Set Credit

CC ID: 991150
Date Effective From: 2019
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: 991152
Date Effective From: 2019
Date Effective To:
Contact (Person): Amir, Corinne
Email Address: corinne.amir@noaa.gov

Distributor

CC ID: 991153
Date Effective From: 2020
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: 991154
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: 991149
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: 991151
Date Effective From: 2019
Date Effective To:
Contact (Person): Oliver, Thomas
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: thomas.oliver@noaa.gov
Phone: (808)725-5444

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Northwestern Hawaiian Islands - Pearl and Hermes Atoll, Kure Atoll

Extent Group 1 / Geographic Area 1

CC ID: 991904
W° Bound: -178.341
E° Bound: -175.997
N° Bound: 28.385
S° Bound: 27.793

Extent Group 2

Extent Description:

Main Hawaiian Islands - Oahu Island, Maui Island, Hawaii Island

Extent Group 2 / Geographic Area 1

CC ID: 991906
W° Bound: -157.94
E° Bound: -155.058
N° Bound: 21.48
S° Bound: 19.244

Extent Group 3

Extent Group 3 / Time Frame 1

CC ID: 1171109
Time Frame Type: Range
Start: 2014-07-21
End: 2019-09-04

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) and Ocean Acidification Program (OAP). The analysis and interpretations presented here are solely that of the current authors.”

Data Access Procedure:

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

Data Access Constraints:

None

Data Use Constraints:

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

Example:

Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, 2020: National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected during Stratified Random Surveys (StRS) across the Hawaiian Archipelago from 2014 to 2019, https://www.fisheries.noaa.gov/inport/item/36155.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 991907
Download URL: https://accession.nodc.noaa.gov/0257945
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2020 - Present)
File Name: SfM_VitalRates_MHI_NWHI.csv
Description:

Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), and adult coral colony observations identified to the lowest taxonomic level possible (usually species) including initial and final size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Main Hawaiian Islands from 2014-2019. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division.

File Type: csv (comma-separated values)

URLs

URL 1

CC ID: 991156
URL: https://www.fisheries.noaa.gov/region/pacific-islands#science
Name: NOAA Fisheries Pacific Islands Region - Science Overview
URL Type:
Online Resource

URL 2

CC ID: 996723
URL: https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific
Name: Coral Reefs in the Pacific
URL Type:
Online Resource
File Resource Format: HTML
Description:

NOAA Fisheries Website

URL 3

CC ID: 996724
URL: https://coralreef.noaa.gov/
Name: NOAA Coral Reef Conservation Program
URL Type:
Online Resource
File Resource Format: HTML
Description:

NOAA Coral Reef Conservation Program (CRCP) website.

URL 4

CC ID: 1183073
URL: https://www.ncei.noaa.gov/data/oceans/coris/data/NOAA/ncrmp/Sfm_spiral_survey_drum_6in.stl
Name: Sfm_spiral_survey_drum_6in.stl
URL Type:
Other
File Resource Format: HTML
Description:

Click to download the .stl file for the printable 3D model of the 6 inch drum used to capture SfM spiral imagery at fixed sites.

URL 5

CC ID: 1183074
URL: https://www.ncei.noaa.gov/data/oceans/coris/data/NOAA/ncrmp/Sfm_spiral_survey_drum_8in.stl
Name: Sfm_spiral_survey_drum_8in.stl
URL Type:
Other
File Resource Format: HTML
Description:

Click to download the .stl file for the printable 3D model of the 8 inch drum used to capture SfM spiral imagery at fixed sites.

Technical Environment

Description:

A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. Mosaic images were created and scaled using Agisoft Metashape (version 1.2.5 build 2735). Models were further scaled using Viscore software. Sampling boundaries and coral demographic measurements were created in ArcMap (version 10.6.1). All statistics were performed in R (Version 3.6.1).

Data Quality

Representativeness:

The data set derived from the imagery is only as good as the images and image-derived products. All coral patches were delineated high resolution orthoprojections and raw imagery was referenced when determining patch perimeters.

Accuracy:

Survey sites were aligned atop one another to ensure coral patches could be followed through time and to ensure delineates were collected using the same orthorectified view which improves accuracy of planar area change measurements.

Coral species identification and size data were extracted by SfM image annotators that had been trained and tested on coral taxon identification and morphology. All annotators met a set of minimum standards for coral data collection.

Field Precision:

The average Ground Sample Distance (GSD, resolution/pixel) for the produced 3D Structure from Motion models was 0.21 cm/pix, allowing confident identification of coral species from the resulting high-resolution 2D orthoprojections.

Completeness Report:

SfM imagery was collected at 14 sites throughout the Hawaiian Archipelago across time intervals from several hours to 3 years. All sites were between 9-16m deep and and covered approximately 100 m2 of reef. Due to the labor-intensive and time-consuming nature of coral annotation, 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. Each site was sub-sampled by randomly distributing a minimum of 10 2.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated (n >/=30 for each target coral species). The target taxa species consisted of two genera - Pocillopora and Porites. Prior to analysis, coral colonies <19 cm2 were removed from the dataset. Additionally, all coral colonies that experienced full mortality in the second time point or were only observed in the second time point (i.e. coral recruits) are not included in this dataset.

Conceptual Consistency:

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

Quality Control Procedures Employed:

During annotation in ArcMap, the original JPEG imagery was viewed alongside the orthoprojection using the 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 in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing or duplicated coral colony ID, data in incorrect columns).

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 orthoprojections and scaled, oriented and aligned together using Viscore software. Next, the orthoprojections were imported into ArcMap for annotation. Orthoprojections were sub-sampled by randomly distributing quadrats throughout the orthoprojection. Quadrat location was conserved across all orthoprojections 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. The vital rates change in coral planar area of each coral colony was tracked by linking annotations of the same live coral across each time point. Data was exported from ArcMap and all statistics and figures were performed in R.

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: 997695
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
Source Contribution:

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.

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: 997696
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. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649

CC ID: 997698
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2021-10-01
Citation URL: https://repository.library.noaa.gov/view/noaa/32739
Citation URL Description:

Vital Rates Project Standard Operating Procedures and Error Estimates Pilot study

Source Contribution:

This document provides detailed procedures for collecting, processing, and annotating 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 rates data (e.g., growth,

mortality, recruitment, fission, and fusion) within coral communities over time. This pipeline consists of four key steps: (1) Image collection by SCUBA divers, (2) Generating 3-D models in Agisoft Metashape, (3) Generating 2D orthoprojections in CloudCompare, (4) Alignment of multi-year 2D orthoprojections and extraction of coral vital rates in ArcMap. 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.

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: 997697
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.

Process Steps

Process Step 1

CC ID: 997820
Description:

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.

Sites were imaged either in a gridded pattern as the diver swam 1.5 m off the seafloor, or in a circular pattern where the diver swam 1 m off the seafloor. In both cases, divers collected enough photographs to produce 60%-80% image overlap and completed two full passes of the site.

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

Process Step 2

CC ID: 998227
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 and aligned separately in Agisoft Metashape (AgiSoft Metashape Professional Version 1.6.1) and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019). The DPCs were then 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, as well as a corresponding scale grid, were exported from Viscore.

Process Contact: Amir, Corinne
Email Address: corinne.amir@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649

Process Step 3

CC ID: 998228
Description:

Orthoprojections of all time points from the same permanent site were uploaded to ArcMap for imagery annotation and scaled using the scale grid exported from Viscore. Due to the labor-intensive and time-consuming nature of annotation, 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 orthoprojections of the same site. Next, 10-30 2.5m2 quadrats were generated at random throughout the selected area and each labelled in numerical order.

Within the first 10 quadrats, all coral species on the target coral species list were annotated if their centroid was 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 orthoprojection with the 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). If one or several coral species on the target list did not reach n = 30 live patches within the first 10 quadrats. These species were identified and annotated in additional quadrats until a higher sample size could be reached.

Coral ID (to lowest taxonomic level), planar area, perimeter length, and a unique identifying number for each annotated coral were recorded in the ArcMap attribute table. The unique identifying numbers were used to track the fate of each coral colony. Corals identified within multiple time points were linked together using their unique identifying number within the ArcMap attribute table.

Process Contact: Amir, Corinne
Email Address: corinne.amir@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649

Process Step 4

CC ID: 998229
Description:

Annotations created in ArcMap were exported and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing coral unique identifier, data in incorrect columns). Before analysis, all corals patches < 19 cm2 and corals that were not present in both the initial and final time point were removed from the dataset.

Absolute change in coral patch area (cm2) and percentage change in coral patch area (delta cm2/initial cm2) were calculated in R. Additionally, outliers falling three standard deviations beyond a metric’s mean (area change, percent area change) were marked and removed from calculation of means and error bounds.

Process Contact: Oliver, Thomas
Phone (Voice): (808)725-5444
Email Address: thomas.oliver@noaa.gov
Source: Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity SfM Fixed Sites: SfM Derived Coral Annotations

Related Items

Item Type Relationship Type Title
Data Set (DS) Cross Reference Structure from Motion (SfM) benthic images collected from Fixed Sites across the Hawaiian Archipelago from 2016 - 2019

https://www.fisheries.noaa.gov/inport/item/63091

Catalog Details

Catalog Item ID: 63093
GUID: gov.noaa.nmfs.inport:63093
Metadata Record Created By: Brooke Olenski
Metadata Record Created: 2020-10-20 03:23+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-10-20 02:17+0000
Metadata Record Published: 2022-08-09
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2022-08-09
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2023-08-09