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Short Citation:
Pacific Islands Fisheries Science Center, 2022: Benthic cover derived from structure from motion images collected during marine debris surveys at coral reef sites entangled with derelict fishing nets at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands from missions in 2018 and 2021, https://www.fisheries.noaa.gov/inport/item/59172.

Item Identification

Title: Benthic cover derived from structure from motion images collected during marine debris surveys at coral reef sites entangled with derelict fishing nets at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands from missions in 2018 and 2021
Short Name: SfM Debris: benthic cover
Status: Completed
Creation Date: 2020-03-30
Revision Date: 2022-04-20
Publication Date: 2022
Abstract:

The benthic cover and fishing-net related data described in this dataset are derived from the GIS analysis of benthic orthophotos. The source imagery was collected by snorkelers using a Structure from Motion (SfM) approach during swim surveys in search of derelict fishing nets. Surveys were conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD) at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands (NWHI). Initial surveys occurred from September 24 - October 3, 2018 during an ESD-led marine debris removal mission aboard the NOAA Ship Oscar Elton Sette, and follow-up surveys occurred from September 13-14, 2021 on a joint mission with non-profit organization Papahanaumokuakea Marine Debris Project aboard the M/V IMUA.

During the 2018 mission, fishing nets were located during swim surveys and selected for SfM if the net was interacting with coral or hard substrate, the depth of the net was within ~1 - 4 m of the surface, and the area of the net fit within the 9 sq. meter SfM survey plot. During the SfM survey, a permanent 3 x 3 m plot was established around the center of the fishing net, and the net was photographed using a back and forth swim pattern ("before" photos) for later processing using a SfM approach. The net was then removed, the volume of net removed was estimated and recorded, and the same area was photographed again in the same way ("after" photos). A nearby (>50 m distant) paired control site was also photographed using the same method ("control" photos).

During the 2021 mission, we attempted to relocate all paired sites where "after" and "control" photos were taken in 2018 and if found, we reimaged the permanent 3 x 3m plot using the same SfM approach. Only a subset of 2018 sites were successfully relocated in 2021 (12 "after" sites, 8 "control" sites), and five new nearby "control" sites had to be established to fulfill our paired study design.

The photographs from each site were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for benthic cover using a random point approach. In 2018, the number of points at net-impacted sites were constrained to the net coverage area and were scaled to the net area to ensure an equal point density among replicate net-impact sites. The same number of points were randomly assigned to the 3 by 3 m paired control site. In 2021, twenty random points were assigned to each orthophoto within the 2018 net polygon. Each point was classified into one of seven benthic categories: turf algae, macroalgae, sand, bare substrate, Porites compressa, sponge, or crustose coralline algae (CCA). In 2021, turf and macroalgae categories were merged into a single algae category and all coral species were assigned the coral category. The annotated points for each site were converted to percent cover for each benthic category. Fishing net size (sq. m) and degree of fouling were also calculated from the initial "before" orthophotos. Analyses were conducted to compare the benthic composition of net sites to control sites and to determine if fouling or net size contributed to these differences.

Purpose:

The purpose of the Structure from Motion (SfM) surveys at Pearl and Hermes Atoll is to understand how derelict fishing nets alter the benthic community composition of the reef, how these impacts last over time once the net is removed or if the benthic community can recover. In addition, we investigated how net size and fouling level may vary the severity of this impact. This study leveraged SfM, an emerging photogrammetry technique, to allow efficient data collection alongside marine debris survey and removal efforts.

Other Citation Details:

Suka R, Huntington B, Morioka J, O'Brien K, Acoba T (2020) Successful application of a novel technique to quantify negative impacts of derelict fishing nets on Northwestern Hawaiian Island reefs. Mar Pollut Bull 157:111312. https://doi.org/10.1016/j.marpolbul.2020.111312

Supplemental Information:

The Papahanaumokuakea Marine National Monument (PMNM) includes the 1200 nautical mile chain of atolls and islets known as the Northwestern Hawaiian Islands (NWHI) that are geographically positioned as a repository for marine debris. Marine debris circulates within the North Pacific Subtropical Gyre until it encounters the atolls of the NWHI. The Ecosystem Sciences Division (ESD) at NOAA Fisheries has conducted both ship- and shore-based missions in the NWHI to survey for and remove derelict fishing gear and many other types of marine debris. Exploratory and opportunistic efforts began in 1996 that evolved into ~annual cruises.

Keywords

Theme Keywords

Thesaurus Keyword
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 > MARINE ENVIRONMENT MONITORING > MARINE SUBMERGED DEBRIS
ISO 19115 Topic Category
environment
UNCONTROLLED
CoRIS Discovery Thesaurus Numeric Data Sets > Benthic
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Algal Cover
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Crustose Coralline Algae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Fleshy Macroalgae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Vegetation > Algae > Turf Algae
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Damage Assessment > Marine Debris
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Sponges
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Bathymetry/Seafloor Topography > Hard Seafloor Substrate
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Coral Cover
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral
ISO 19115 Topic Category 007
ISO 19115 Topic Category environment
NODC DATA TYPES THESAURUS DEBRIS
NODC DATA TYPES THESAURUS REEF AND/OR BOTTOM REGIME - PERCENT COVER
NODC OBSERVATION TYPES THESAURUS derived products
NODC OBSERVATION TYPES THESAURUS in situ
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
None benthic cover
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None derelict fishing gear
None Ecosystem Sciences Division
None ESD
None fishing nets
None marine debris
None Marine Debris Program
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
CONTINENT > NORTH AMERICA > UNITED STATES OF AMERICA > HAWAII
Global Change Master Directory (GCMD) Location Keywords
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS
UNCONTROLLED
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 > Pearl and Hermes Reef (27N176W0001)
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 > Pearl and Hermes Reef (27N176W0001)
NODC SEA AREA NAMES THESAURUS North Pacific Ocean
NODC SEA AREA NAMES THESAURUS Papahanaumokuakea Marine National Monument
None NWHI
None Pearl and Hermes
None PHR
None PMNM

Instrument Keywords

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

Platform Keywords

Thesaurus Keyword
UNCONTROLLED
NODC PLATFORM NAMES THESAURUS M/V IMUA
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 File
Maintenance Frequency: None Planned
Data Presentation Form: Table (digital)
Entity Attribute Overview:

Dataset includes metadata for each Structure from Motion (SfM) survey (site information, survey date, and location); area, weight, and fouling level of fishing net surveyed and removed from the reef; and percentage of benthic cover by category. For 2018 data, seven categories were used (bare substrate, crustose coralline algae, macroalgae, the coral species Porites compressa, sand, turf algae, and sponges). In 2021, turf and macroalgae were merged into a single algae category and Porites compressa/Montipora sp. were merged into a single category named coral.

Entity Attribute Detail URL: https://www.fisheries.noaa.gov/inport/item/59257
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

Support Roles

Data Steward

CC ID: 1168410
Date Effective From: 2021
Date Effective To:
Contact (Person): Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Contact Instructions:

Email preferred

Distributor

CC ID: 1168411
Date Effective From: 2021
Date Effective To:
Contact (Person): Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Contact Instructions:

Email preferred

Distributor

CC ID: 901608
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: 901603
Date Effective From: 2021
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: 901605
Date Effective From: 2018
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 1168413
Date Effective From: 2022
Date Effective To:
Contact (Person): Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Contact Instructions:

Email preferred

View Historical Support Roles

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Pearl and Hermes Atoll, Northwestern Hawaiian Islands

Extent Group 1 / Geographic Area 1

CC ID: 901638
W° Bound: -175.8211335
E° Bound: -175.7880926
N° Bound: 27.89404863
S° Bound: 27.82745706
Description

Geographic extent of marine debris structure from motion surveys conducted at Pearl and Hermes Atoll.

Extent Group 1 / Vertical Extent 1

CC ID: 903548
CRS Type: Vertical
EPSG Code: EPSG:8051
EPSG Name: MSL depth (ft)
See Full Coordinate Reference System Information
Vertical Minimum: 2.0
Vertical Maximum: 15.0

Extent Group 1 / Time Frame 1

CC ID: 1168414
Time Frame Type: Range
Start: 2021-09-13
End: 2021-09-14
Description:

Time frame of marine debris Structure from Motion (SfM) surveys at Pearl and Hermes Atoll during the 2021 mission.

Extent Group 1 / Time Frame 2

CC ID: 901637
Time Frame Type: Range
Start: 2018-09-24
End: 2018-10-03
Description:

Time frame of marine debris structure from motion surveys conducted at Pearl and Hermes Atoll during the 2018 mission.

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

NOAA Ecosystem Sciences 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 Sciences Division, Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA). 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 Use Constraints:

These marine debris survey data act as a proxy for area surveyed and have not been screened for accuracy based on environmental conditions or GPS accuracy. NOAA can not be held liable for use of these data in a manner other than for perusal of preliminary marine debris data for scientific research on coral reef ecosystems. When using this data, please credit the NOAA Fisheries, Ecosystem Sciences Division.

Suggested citation:

Pacific Islands Fisheries Science Center, 2022: Benthic cover derived from structure from motion images collected during marine debris surveys at coral reef sites entangled with derelict fishing nets at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands from missions in 2018 and 2021, https://www.fisheries.noaa.gov/inport/item/59172.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 1168415
Download URL: https://accession.nodc.noaa.gov/0253462
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2020 - Present)
File Name: SfM_MarineDebris_BenthicCover_PHR_2021.csv
Description:

Benthic cover data from marine debris surveys conducted at coral reef sites entangled with derelict fishing nets at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands in 2021. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division. Data include fishing net area and weight, and percent benthic cover data derived from structure from motion images collected during the marine debris surveys.

File Date/Time: 2022-04-21 14:58:00
File Type: csv (comma-separated values)
File Size: 3 KB

Distribution 2

CC ID: 902855
Start Date: 2020-05-13
End Date: Present
Download URL: https://accession.nodc.noaa.gov/0209247
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2020 - Present)
File Name: SFM_MarineDebris_BenthicCover_PHR_2018.csv
Description:

Benthic cover data from marine debris surveys conducted at coral reef sites entangled with derelict fishing nets at Pearl and Hermes Atoll in the Northwestern Hawaiian Islands in 2018. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division. Data include fishing net area and weight, and percent benthic cover data derived from structure from motion images collected during the marine debris surveys and processed using a structure from motion approach.

File Date/Time: 2020-04-29 00:00:00
File Type: csv (comma-separated values)

URLs

URL 1

CC ID: 901610
URL: https://www.fisheries.noaa.gov/pacific-islands/marine-debris-research-and-removal-northwestern-hawaiian-islands
Name: Marine Debris Research and Removal in the Northwestern Hawaiian Islands
URL Type:
Online Resource
Description:

Information about marine debris research and removal efforts in Northwestern Hawaiian Islands by Pacific Islands Fisheries Science Center

URL 2

CC ID: 901744
URL: https://noaa.maps.arcgis.com/apps/MapTour/index.html?appid=852aeea527834cfbbc53248850065b4a
Name: 2018 Marine Debris Removal and Assessment in the Northwestern Hawaiian Islands
URL Type:
Online Resource
Description:

Story map about marine debris removal efforts in 2018 with images and captions describing work that was conducted.

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 0.5-m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape (version 1.2.5 build 2735). Plot boundaries, net boundaries and benthic characteristics were created in ArcMap (version 10.6.1). All statistics were performed in R (Version 3.6.1).

Data Quality

Representativeness:

Derelict fishing nets tend to accumulate in certain locations inside the lagoon creating a spatial gradient from where net impacts are common, to locations where nets have never been observed. Our aim was to survey the lagoon equally across this gradient of high to low net prevalence to avoid bias in our impact assessment. We identified this prevalence gradient by plotting the locations of each net found between 2006 and 2014 during prior removal missions onto a 30 m x 30 m grid of all hard reef substrate areas within the lagoon. We then categorized each grid cell by the total number of surveys that occurred within the cell and the number of nets found within each grid cell. Based on this net prevalence information, five spatial zones were defined.

The data set derived from the image analysis is as good as the mosaic image itself; points that fell within areas of low contrast, shadow, obstruction, or blur were discarded. In 2018, new random points were generated so that each point could be analyzed for percent cover.

Accuracy:

Prior to conducting surveys, researchers are trained to identify debris type and estimate/measure debris size, along with other ecological metrics. Both classroom and field training were completed for all researchers (experienced and inexperienced alike) before any surveys were conducted. This training ensures that all marine debris surveys are conducted consistently by all researchers during the mission.

A single experienced researcher was designated to collect all the Structure from Motion imagery and set up the plots. The images were collected by swimming a crosshatch pattern rather than a single pass to ensure no gaps occurred in the image collection.

Field Precision:

The size of nets removed from net-impact sites ranged from 0.48 m2 to 4.46 m2 (mean area = 2.0 m2). The Ground Sample Distance (GSD, resolution/pixel) for the produced 3D Structure from Motion models ranged from 0.000122 to 0.000618 m/pix with an error of 1.11 to 3.03 pix, allowing confident identification of benthic species and net boundaries from the resulting high-resolution 2D photomosaics.

Completeness Report:

A minimum of three nets were selected for each Structure from Motion survey from each of the five zones if the net also fit within the additional selection criteria ( > 75% hard substrate within ~1-4 m depths and fits within 3 x 3 m structure from motion survey plot).

A paired control site was selected for each net within the same zone ( > 50 m away from net-impact site for independence). Four control sites were deemed unusable as they did not meet the study design requirements for matching spatial zone or habitat type (i.e. > 75% hard substrate). In these cases, an existing control site within the same zone was used as a paired control. In total, 20 net-impact sites and 16 control sites were surveyed in 2018, and 12 of each net-impact and control sites were surveyed in 2021.

Images that were blurred or had unnecessary objects (e.g., dive fins) were removed.

Conceptual Consistency:

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

Quality Control Procedures Employed:

Size estimates of debris in water were verified against the more accurate volume estimates of the nets once removed from the shallow coral reef environments and hauled onto the small boats.

Each image set was evaluated for image quality. Images deemed unsatisfactory were removed from the image set.

The benthic category assigned to each random point across each mosaic were verified by an expert. Any points that fell onto an unidentifiable area (i.e., shadow) were discarded and re-generated (for the 2018 data).

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:

Marine debris removal has been conducted by the Pacific Islands Fisheries Science Center's Ecosystem Sciences Division at the atolls, reefs and islands of Northwestern Hawaiian Islands since 1996. Standardized data collection has been implemented since 1999. Swim surveys are typically used in the comparatively high-relief and patchy lagoonal reef habitats. Survey areas are chosen based on regional reef morphology and past accumulation records.

At each Structure from Motion (SfM) data collection site, a permanent 3 x 3 m plot was established around the center of the entangled fishing net in 2018. SfM images were taken underwater before and after net removal. The same method was also used at the paired control sites. Sites were relocated and reimaged in 2021.

We used Agisoft Metashape software to generate orthomosaic images of each site from the photographs captured. Using 2018 orthomosaics, the planar net area (square meters) was calculated by delineating the net boundary in ArcGIS. In addition, the degree of fouling was estimated for each net based on the percent of the net surface area that was covered by fouling organisms.

Using the orthomosaics from the "after" (impact) and "control" sites, benthic cover was assessed using a random point approach within the boundary of the net and at the paired control site. Each point was classified into an appropriate benthic category. The annotated points for each site were converted to percent cover. For both years, analyses were conducted to compare the benthic composition of net sites to control sites. In 2018, analyses were carried out to determine if fouling or net size contributed to these differences, and in 2021, analyses were conducted to track changes in benthic composition at net impacted sites three years after removal.

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: 901988
Publish Date: 2015-07-07
Citation URL: https://doi.org/10.7717/peerj.1077
Citation URL Name: PeerJ
Source Contribution:

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure from Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. 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.

Dameron, O. J., Parke, M., Albins, M. A., & Brainard, R. (2007). Marine debris accumulation in the Northwestern Hawaiian Islands: an examination of rates and processes. Marine Pollution Bulletin, 54(4), 423-433.

CC ID: 901615
Publish Date: 2007-01-10
Citation URL: https://doi.org/10.1016/j.marpolbul.2006.11.019
Citation URL Name: Marine Pollution Bulletin
Source Contribution:

Large amounts of derelict fishing gear accumulate and cause damage to shallow coral reefs of the Northwestern Hawaiian Islands (NWHI). To facilitate maintenance of reefs cleaned during 1996–2005 removal efforts, we identify likely high-density debris areas by assessing reef characteristics (depth, benthic habitat type, and energy regime) that influence sub-regional debris accumulation. Previously cleaned backreef and lagoonal reefs at two NWHI locations were resurveyed for accumulated debris using two survey methods. Accumulated debris densities and weights were found to be greater in lagoonal reef areas. Sample weight-based debris densities are extrapolated to similar habitats throughout the NWHI using a spatial ‘net habitat’ dataset created by generalizing IKONOS satellite derivatives for depth and habitat classification. Prediction accuracy for this dataset is tested using historical debris point data. Annual NWHI debris accumulation is estimated to be 52.0 metric tonnes. For planning purposes, individual NWHI atolls/reefs are allotted a proportion of this total.

Donohue, M. J., Boland, R. C., Sramek, C. M., & Antonelis, G. A. (2001). Derelict fishing gear in the Northwestern Hawaiian Islands: diving surveys and debris removal in 1999 confirm threat to coral reef ecosystems. Marine pollution bulletin, 42(12), 1301-1312.

CC ID: 901619
Publish Date: 2001-12-04
Citation URL: https://doi.org/10.1016/s0025-326x(01)00139-4
Citation URL Name: Marine Pollution Bulletin
Source Contribution:

Marine debris threatens Northwestern Hawaiian Islands' (NWHI) coral reef ecosystems. Debris, a contaminant, entangles and kills endangered Hawaiian monk seals (Monachus schauinslandi), coral, and other wildlife. We describe a novel multi-agency effort using divers to systematically survey and remove derelict fishing gear from two NWHI in 1999. 14 t of derelict fishing gear were removed and debris distribution, density, type and fouling level documented at Lisianski Island and Pearl and Hermes Atoll. Reef debris density ranged from 3.4 to 62.2 items/km2. Trawl netting was the most frequent debris type encountered (88%) and represented the greatest debris component recovered by weight (35%), followed by monofilament gillnet (34%), and maritime line (23%). Most debris recovered, 72%, had light or no fouling, suggesting debris may have short oceanic circulation histories. Our study demonstrates that derelict fishing gear poses a persistent threat to the coral reef ecosystems of the Hawaiian Archipelago.

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: 901840
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.

Suka R, Huntington B, Morioka J, O’Brien K, Acoba T (2020) Successful application of a novel technique to quantify negative impacts of derelict fishing nets on Northwestern Hawaiian Island reefs. Mar Pollut Bull 157:111312

CC ID: 902857
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2020-06-01
Citation URL: https://doi.org/10.1016/j.marpolbul.2020.111312
Citation URL Name: Marine Pollution Bulletin
Citation URL Description:

Marine Pollution Bulletin is concerned with the rational use of maritime and marine resources in estuaries, the seas and oceans, as well as with documenting marine pollution and introducing new forms of measurement and analysis. A wide range of topics are discussed as news, comment, reviews and research reports, not only on effluent disposal and pollution control, but also on the management, economic aspects and protection of the marine environment in general.

Source Contribution:

The remote and uninhabited Northwestern Hawaiian Islands (NWHI) contain 70% of the shallow water coral reefs in the United States and are regularly exposed to derelict fishing nets. These nets snag on the shallow reefs, damaging or killing benthic communities. However, no data exist to quantify this impact. Here we use a novel application of photogrammetry, Structure-from-Motion (SfM), to calculate benthic cover from mosaic images at net-impact and control sites. Net-impact sites had significantly higher cover of bare substrate, sand, and crustose coralline algae and significantly lower coral and macroalgae cover compared to control sites. These differences were unrelated to net size and fouling. Our study demonstrates the utility of using SfM to efficiently quantify impacts of derelict fishing nets. Revisiting these sites will be essential to document how the reef recovers to further our understanding of the lasting impacts of derelict fishing nets on coral reef habitats.

Suka R, Morioka J, Huntington B, O'Brien K, Acoba T. 2020. 2018 Marine Debris Removal and Assessment in the Northwestern Hawaiian Islands. Pacific Islands Fisheries Science Center, PIFSC Special Publication, SP-20-001, 8 p. https://doi.org/10.25923/f19b-je14.

CC ID: 901620
Contact Role Type: Originator
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center
Publish Date: 2020-01-01
Citation URL: https://doi.org/10.25923/f19b-je14
Citation URL Name: NOAA Institutional repository
Citation URL Description:

Booklet summarizing marine debris removal and research efforts in the Northwestern Hawaiian Islands in 2018 by Pacific Islands Fisheries Science Center

Source Contribution:

The Papahānaumokuākea Marine National Monument (PMNM) includes all of the Northwestern Hawaiian Islands (NWHI) and encompasses 1,508,870 km2 (582,578 mi2) of the Pacific Ocean. Within the boundaries of the monument lie coral reefs, atolls, shoals, and seamounts, including 70% of all shallow-water coral reef habitats (<200 m) in the United States. The PMNM was named a World Heritage site in 2010 by the 34th session of the World Heritage Committee in recognition of its cultural and natural values (World Heritage Committee 2010). The extensive coral reefs found in the PMNM are home to more than 7,000 marine species, one-quarter of which are found only in the Hawaiian Archipelago (PMNM Webmaster 2019). Many of the islands and shallow-water environments in the PMNM are important habitats for rare species, such as the green sea turtle (listed as threatened under the U.S. Endangered Species Act) and Hawaiian monk seal (listed as endangered under the International Union for Conservation of Nature Red List and as endangered under the U.S. Endangered Species Act). The PMNM contains only 15 km2 of emergent land, but 14 million seabirds representing 22 species use this land as breeding and nesting grounds (PMNM Webmaster 2019). Land areas provide a home for four species of birds found nowhere else in the world, including one of the world’s most endangered ducks—the Laysan duck (PMNM Webmaster 2019).

Process Steps

Process Step 1

CC ID: 901622
Description:

This step describes the initial site survey in 2018. The swim survey method was developed for surveys in lagoonal, reticulated reef areas. During swim surveys, two or more divers swim across reefs to search for debris while being directed by personnel in small boats to follow pre-planned routes and are coordinated for maximum visual area covered. Survey areas and routes are chosen based on regional reef morphology and past accumulation records. Based on this net prevalence information, five spatial zones were defined. A minimum of three nets in each of the five zones were surveyed using a Structure from Motion (SfM) approach if the net also fit within the additional selection criteria (< 75% hard substrate and within ~1-4 m depths).

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Source: Dameron, O. J., Parke, M., Albins, M. A., & Brainard, R. (2007). Marine debris accumulation in the Northwestern Hawaiian Islands: an examination of rates and processes. Marine Pollution Bulletin, 54(4), 423-433.

Process Step 2

CC ID: 901623
Description:

At each impact site established in 2018, a permanent 3 x 3 m plot was established around the center of the net by securing zip ties to the reef at each corner of the plot and taking a GPS location at the center. Depth measurements were recorded at each corner of the plot. Only nets that fit within the plot were selected for this study to allow rapid data collection of the Structure from Motion (SfM) imagery. In 2018, SfM images were taken underwater before net removal to record the extent of the reef covered by net.

In both years, images were collected by snorkeling in a cross-hatch pattern over the plot at 1 m above the substrate to achieve image overlap of at least 60% (~580 images per site). JPEG images were collected using a Nikon SL2 digital camera in an underwater housing.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Source: 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

Process Step 3

CC ID: 901990
Description:

This step only occurred in 2018 when the net impact sites were established.

Fishing nets were disentangled from the reef by hand or carefully cut using knives to free the net from the benthos in order to minimize impacts to the underlying habitat. Once removed and loaded into the cargo area of the small boat, the volume of each net removed from the reef was estimated and recorded.

A second series of "after" images were collected in the same manner as the first series of "before" images (i.e., before the fishing net was removed from the reef).

The volume of each fishing net removed from the reef was estimated when brought aboard the small boat. At the end of the marine debris survey, which could include one to several structure-from-motion surveys, or when the small boat reached its capacity, the small boat returned to the ship and the boat’s entire debris load was weighed and recorded. The estimated volume of each net was used to determine the percentage each net contributed to the boat's entire load, and weights for each net were calculated based on the percentage.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov

Process Step 4

CC ID: 901624
Description:

In 2018, a paired control site was selected for each net impacted site within the same zone (≥ 50 m away from net-impact site for independence). The same photogrammetry method was also used at the paired control sites (3 x 3 m plot).

In 2021, each paired control site was relocated and reimaged. When the old control site could not be found, a new paired control site was established using the same criteria and reimaged.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov

Process Step 5

CC ID: 901625
Description:

The Structure from Motion (SfM) approach produces an accurately scaled, two-dimensional (2D) orthomosaic model created from the overlapping imagery. We used Agisoft Metashape software (version 1.2.5 build 2735) to generate the orthomosaic following parameters published by Burns et al., 2015.

Process Contact: Lichowski, Frances
Phone (Voice): (808)725-5476
Email Address: frances.lichowski@noaa.gov
Source: 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

Process Step 6

CC ID: 901991
Description:

This step was only completed at net impacted sites surveyed in 2018.

From the pre-net removal ("before") orthomosaics, the planar net area (square meters) was calculated by delineating the net boundary with a polygon shapefile and using the Calculate Geometry tool in ArcMap v10.6.1. In addition, the degree of fouling was estimated for each net based on the percent of the net surface area that was covered by fouling organisms. Fouling scores ranged from 1 to 3, where 1 = Light: 1-40% of net surface area covered, 2 = Moderate: 41-75% of net surface area covered, and 3 = Heavy: >75% of net surface area covered (adapted from Donohue et al., 2001). Four nets were classified as fouling level 1, eight nets as fouling level 2, and eight nets as fouling level 3.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov
Source: Donohue, M. J., Boland, R. C., Sramek, C. M., & Antonelis, G. A. (2001). Derelict fishing gear in the Northwestern Hawaiian Islands: diving surveys and debris removal in 1999 confirm threat to coral reef ecosystems. Marine pollution bulletin, 42(12), 1301-1312.

Process Step 7

CC ID: 901626
Description:

For each SfM site surveyed, benthic cover was assessed using a random point approach and the stitched together orthomosaic in ArcMap 10.6.1.

In 2018, using the post-net removal ("after") orthomosaics, benthic cover was assessed within the boundary of the net (based on the net boundary shapefile). The number of points at net-impacted sites was scaled to the net size to ensure an equal point density (mean point density = 10.9 points/m2 ± 0.40 SE) among replicate net-impact sites. Using the paired "control" orthomosaic, the same number of points were randomly assigned to the 3 x 3 m paired control site. Each point was classified into one of seven benthic categories: turf algae, macroalgae, sand, bare substrate, Porites compressa, sponge, and crustose coralline algae (CCA). The annotated points for each site were converted to percent cover (number of points for a given category/total number of points x 100) for each benthic category.

In 2021, orthomosaics from net-impacted sites and paired controls were assessed for benthic cover using much of the same methodology. For each impact site, a shapefile of the net boundary delineated by Suka et al. in 2020 was overlaid and repositioned on the recent orthophotos to align with the original location of the derelict net. For control sites, the same boundary shapefile was overlaid in the center of the orthophoto. The benthic cover at each control and impact site site was assessed from 20 random points placed within the net boundary shapefile of each orthophoto. The benthic feature under each point was then classified into one of six benthic categories: algae (grouping turf and macroalgae), sand, bare, coral, sponge, and crustose coralline algae (CCA) and then converted to percent cover for the site.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov

Process Step 8

CC ID: 901992
Description:

This process step occurred only with the 2018 data.

To test whether derelict fishing nets impact benthic assemblages regardless of net size or level of fouling, all net-impact and control sites were compared using both multivariate and univariate techniques. Differences in the benthic assemblage between control and net-impact sites were visualized using an ordination plot generated from non-metric multi-dimensional scaling (nMDS) performed on Bray-Curtis distances using untransformed cover data. Assemblage differences indicated by the nMDS were tested for significance using a permutational analysis of variance (PERMANOVA) with treatment (net-impacts or control) as a fixed factor. PERMANOVA models used 999 permutations and the assumption of equal dispersion among the treatment groups was confirmed. To determine which specific categories drove the difference in the benthic assemblage between net-impact and control sites, we ran paired t-tests (or the non-parametric equivalent based on Shapiro-Wilk tests of normality) on the paired difference for each of the seven benthic cover categories.

Process Contact: Huntington, Brittany
Phone (Voice): (808)725-5438
Email Address: brittany.huntington@noaa.gov

Process Step 9

CC ID: 901993
Description:

This processing step was only conducted with the 2018 data.

To test whether the impact of derelict nets on the benthos differed depending on the net size or level of fouling, a distance-based redundancy analysis (db-RDA) was performed. However, in this analysis control sites were excluded (as control sites have no associated derelict net) and only the net-impacted sites were analyzed (n=20). As with PERMANOVA, db-RDA is a method for carrying out constrained ordinations on data using non-Euclidean distance measures, such as Bray Curtis distance. The results of db-RDA can reveal whether a matrix of explanatory variables has some significant impact on the dissimilarities derived from the community composition data as a whole. The db-RDA model considered fouling level (ordinal) and net size (continuous) as explanatory variables. Although db-RDA does not make explicit assumptions about the distribution of the explanatory variables, net size and fouling level were evaluated for skew and co-linearity prior to executing the analysis.

All data analyses were conducted in R Version 3.6.1. PERMANOVA and dbRDA analyses were conducted using the vegan package. Non-parametric paired t-test were carried out using the coin package.

Process Contact: Huntington, Brittany
Phone (Voice): (808)725-5438
Email Address: brittany.huntington@noaa.gov

Process Step 10

CC ID: 1168569
Description:

This processing step was only done with the 2021 data.

Paired t-tests were used to compare the 2021 impact relative to unimpacted control sites, as well as how benthic cover changed over time at the impact sites from 2018 to 2021. Lastly, we assess if control sites remained stable over time using an unpaired t-test (as control sites in 2018 were not identical to those used in 2021). For each comparison, benthic cover values were extremely left skewed and thus arcsin square root transformed.

Percent cover data was generated using ArcMap v10.6.1. All data analyses were conducted in R Version 3.6.1. (R Core Team, 2019). Paired t-test analyses were conducted using the rstatix package version 0.7.0.

Process Contact: Halperin, Ariel
Email Address: ariel.halperin@noaa.gov

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 Debris: Benthic Cover entities

Catalog Details

Catalog Item ID: 59172
GUID: gov.noaa.nmfs.inport:59172
Metadata Record Created By: Rhonda Suka
Metadata Record Created: 2020-03-30 22:26+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-10-20 02:17+0000
Metadata Record Published: 2022-05-09
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2022-05-09
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2023-05-09