Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014
Data Set (DS) | Pacific Islands Fisheries Science Center (PIFSC)GUID: gov.noaa.nmfs.inport:63093 | Updated: October 27, 2023 | Published / External
Summary
Short Citation
Pacific Islands Fisheries Science Center, 2024: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014, https://www.fisheries.noaa.gov/inport/item/63093.
Full Citation Examples
The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 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, starting as far back as 2014, 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. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time.
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 0.5 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.
In total, this dataset currently 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 and 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago.
Distribution Information
-
CSV - Comma Separated Values (Text)
Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Mariana Archipelago from 2014-2022. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division.
-
CSV - Comma Separated Values (Text)
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.
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PDF - Adobe Portable Document Format
Vital Rates Technical Memorandum
None
Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data.
Example:
Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, 2023: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014, https://www.fisheries.noaa.gov/inport/item/63093.
Controlled Theme Keywords
BENTHIC, biota, CORAL REEF, DOC/NOAA/NMFS/PIFSC/ESD, EARTH SCIENCE
Child Items
Type | Title |
---|---|
Entity | SfM Fixed Sites: SfM Derived Coral Annotations |
Contact Information
Point of Contact
Thomas Oliver
thomas.oliver@noaa.gov
(808)725-5444
Metadata Contact
Lori H Luers
lori.luers@noaa.gov
Extents
144.618287° W,
-154.806789° E,
28.455623° N,
-14.373615° S
2014-01-27 - Present
Timeframe of when imagery was collected for which annotations were derived. Each region (Mariana Archipelago, Hawaiian Archipelago, American Samoa & PRIAs) is typically sampled in different years.
Item Identification
Title: | Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014 |
---|---|
Short Name: | SfM-Derived Coral Vital Rates Annotations |
Status: | On Going |
Creation Date: | 2022-07-26 |
Publication Date: | 2023 |
Abstract: |
The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 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, starting as far back as 2014, 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. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time. 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 0.5 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. In total, this dataset currently 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 and 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago. |
Purpose: |
The purpose of the SfM surveys of permanent sites throughout the U.S. Pacific is to track coral vital rates (e.g. growth, mortality, recruitment) and how they vary across taxon, regions, and environmental gradients. This study leverages 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 |
---|---|
Global Change Master Directory (GCMD) Data Center Keywords |
DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce
|
Global Change Master Directory (GCMD) Science Keywords |
EARTH SCIENCE
|
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
|
ISO 19115 Topic Category |
biota
|
UNCONTROLLED | |
CoRIS Discovery Thesaurus | Numeric Data Sets > Benthic |
CoRIS Theme Thesaurus | EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat |
CoRIS Theme Thesaurus | EARTH SCIENCE > Biosphere > 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 |
CRCP Project | 31360 |
CRCP Project | NOAA Coral Reef Conservation Program |
ISO 19115 Topic Category | 002 |
ISO 19115 Topic Category | biota |
NODC DATA TYPES THESAURUS | CORAL |
NODC DATA TYPES THESAURUS | CORAL - COLONY SIZE |
NODC DATA TYPES THESAURUS | CORAL - SPECIES IDENTIFICATION |
NODC OBSERVATION TYPES THESAURUS | derived products |
NODC PROJECT NAMES THESAURUS | Coral Reef Conservation Program |
NODC PROJECT NAMES THESAURUS | CORAL REEF STUDIES |
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 | CNMI |
None | Commonwealth of the Northern Marianas Islands |
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 |
---|---|
Global Change Master Directory (GCMD) Location Keywords |
OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS
|
Global Change Master Directory (GCMD) Location Keywords |
OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > GUAM
|
Global Change Master Directory (GCMD) Location Keywords |
OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > NORTHERN MARIANA ISLANDS
|
UNCONTROLLED | |
CoRIS Place Thesaurus | Coastal Waters of Hawaii |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000) |
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) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Guam > Guam (13N144E0000) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Mariana Archipelago > Northern Mariana Islands ( CNMI ) (18N146E0000) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Maug Island > Maug Island (20N145E0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Pagan Island > Pagan Island (18N145E0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Saipan Island > Saipan Island (15N145E0002) |
NODC SEA AREA NAMES THESAURUS | North Pacific Ocean |
NODC SEA AREA NAMES THESAURUS | Papahanaumokuakea Marine National Monument |
NODC SEA AREA NAMES THESAURUS: | NW Pacific |
None | Main Hawaiian Islands |
None | Marianas |
None | MHI |
None | Northwestern Hawaiian Islands |
None | NWHI |
Instrument Keywords
Thesaurus | Keyword |
---|---|
UNCONTROLLED | |
NODC INSTRUMENT TYPES THESAURUS | Agisoft Metashape |
NODC INSTRUMENT TYPES THESAURUS | ArcGIS |
NODC INSTRUMENT TYPES THESAURUS | photograph |
NODC INSTRUMENT TYPES THESAURUS | scale |
NODC INSTRUMENT TYPES THESAURUS | TagLab |
NODC INSTRUMENT TYPES THESAURUS | Viscore |
Platform Keywords
Thesaurus | Keyword |
---|---|
UNCONTROLLED | |
NODC PLATFORM NAMES THESAURUS | HI'IALAKAI |
NODC PLATFORM NAMES THESAURUS | OSCAR ELTON SETTE |
NODC PLATFORM NAMES THESAURUS | RAINIER |
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 |
Maintenance Note: |
In 2022, T0 and T1_PatchName_G, StartingSize and EndingSize are not included in the dataset. Additionally, Shape_Length, Shape_Area and ColonyName have been added to the 2022 dataset. |
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 including initial and final empirical size measurements. |
Entity Attribute Detail URL: | https://www.fisheries.noaa.gov/inport/item/63094 |
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
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
Date Effective From: | 2019 |
---|---|
Date Effective To: | |
Contact (Person): | Amir, Corinne |
Email Address: | corinne.amir@noaa.gov |
Distributor
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
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
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
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 |
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Extent Group 1
Extent Description: |
The extent of area across the U.S. Pacific for which annotations are derived from fixed site SfM imagery: include the Hawaiian Archipelago, Mariana Archipelago, American Samoa, and Pacific Remote Island Areas. |
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Extent Group 1 / Geographic Area 1
W° Bound: | 144.618287 | |
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E° Bound: | -154.806789 | |
N° Bound: | 28.455623 | |
S° Bound: | -14.373615 |
Extent Group 1 / Time Frame 1
Time Frame Type: | Continuing |
---|---|
Start: | 2014-01-27 |
Description: |
Timeframe of when imagery was collected for which annotations were derived. Each region (Mariana Archipelago, Hawaiian Archipelago, American Samoa & PRIAs) is typically sampled in different years. |
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, 2023: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014, https://www.fisheries.noaa.gov/inport/item/63093. |
Metadata Access Constraints: |
None |
Metadata Use Constraints: |
None |
Distribution Information
Distribution 1
Start Date: | 2023-09-05 |
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End Date: | Present |
Download URL: | https://accession.nodc.noaa.gov/0282457 |
Distributor: | National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2020 - Present) |
File Name: | SfM_VitalRates_MARIAN_2022.csv |
Description: |
Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Mariana Archipelago from 2014-2022. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division. |
File Type (Deprecated): | csv (comma-separated values) |
Distribution Format: | CSV - Comma Separated Values (Text) |
Distribution 2
Start Date: | 2022-08-10 |
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End Date: | Present |
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 (Deprecated): | csv (comma-separated values) |
Distribution Format: | CSV - Comma Separated Values (Text) |
Distribution 3
Start Date: | 2021-10-01 |
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End Date: | Present |
Download URL: | https://repository.library.noaa.gov/view/noaa/32739 |
Distributor: | National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2020 - Present) |
File Name: | Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion SOP |
Description: |
Vital Rates Technical Memorandum |
File Type (Deprecated): | |
Distribution Format: | PDF - Adobe Portable Document Format |
URLs
URL 1
URL: | https://www.fisheries.noaa.gov/region/pacific-islands#science |
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Name: | NOAA Fisheries Pacific Islands Region - Science Overview |
URL Type: |
Online Resource
|
URL 2
URL: | https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific |
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Name: | Coral Reefs in the Pacific |
URL Type: |
Online Resource
|
File Resource Format: | HTML |
Description: |
NOAA Fisheries Website |
URL 3
URL: | https://coralreef.noaa.gov/ |
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Name: | NOAA Coral Reef Conservation Program |
URL Type: |
Online Resource
|
File Resource Format: | HTML |
Description: |
NOAA Coral Reef Conservation Program (CRCP) website. |
URL 4
URL: | https://www.ncei.noaa.gov/data/oceans/coris/data/NOAA/ncrmp/Sfm_spiral_survey_drum_6in.stl |
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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
URL: | https://www.ncei.noaa.gov/data/oceans/coris/data/NOAA/ncrmp/Sfm_spiral_survey_drum_8in.stl |
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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 using Agisoft Metashape. Sampling boundaries and coral demographic measurements were created using ArcGIS and TagLab. All statistics were performed in R. |
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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. |
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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. For the Mariana archipelago, imagery was collected at 10 sites at 3 and 5 year time intervals. All sites were between 9-16m deep and and cover 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 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated. The target taxa across both archipelagos consists of three genera - Pocillopora, Porites and Acropora. Prior to analysis, coral colonies <19 cm2 were removed from the dataset. In the Hawaiian archipelago dataset, all coral colonies that experienced full mortality in the final time point or were only observed in the final time point are not included in this dataset. |
Conceptual Consistency: |
The same method of annotation was used for all SfM imagery. |
Quality Control Procedures Employed: |
During coral annotation, 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 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 |
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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. Next, the orthoprojections were exported 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 changes in coral planar area of each coral colony was tracked by linking annotations of the same live coral across each time point. All statistics and figures were performed in R. |
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Sources
Amir C, Oliver T, Lamirand M, Couch C. 2023. Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-139, https://doi.org/10.25923/s2ym-tn10
Contact Role Type: | Originator |
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Contact Type: | Organization |
Contact Name: | Pacific Islands Fisheries Science Center |
Publish Date: | 2023-07-01 |
Citation URL: | https://repository.library.noaa.gov/view/noaa/50840 |
Citation URL Description: |
Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates |
Source Contribution: |
This document builds upon Rodriguez et al. 2022 and provides detailed procedures for annotating imagery using both ArcGIS and TagLab software in tandem. These procedures are designed to efficiently generate coral rates data (e.g., growth, mortality, recruitment, fission, and fusion) within coral communities over time. While this standard operating procedure is designed to meet ESD needs, we use commercially available software, making these methods adaptable based on programmatic capacity and needs. |
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
Contact Role Type: | Publisher |
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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.
Contact Role Type: | Publisher |
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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
Contact Role Type: | Originator |
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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
Contact Role Type: | Originator |
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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
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. Divers swam ~1m off the seafloor, collecting enough photographs to produce 60%-80% image overlap and complete two full passes of the site. |
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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
Description: |
Images for each site were evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. Following image quality control, each set of raw images were imported, aligned separately in Agisoft Metashape and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019). For the Hawaiian Archipelago dataset, 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 were exported from Viscore. For the Mariana Archipelago dataset, all scaling, orienting, alignment and 2D model creations were completed using Agisoft Metashape. |
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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
Description: |
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 0.5m2 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 fell within the quadrat. Corals were annotated by tracing the full perimeter of live coral tissue patches. During annotation, the original JPEG imagery was viewed alongside the orthoprojection 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, and sometimes outside the quadrats, until a higher sample size could be reached. Unique identifying numbers were assigned to each patch of live coral tissue link coral patches across time and to track fission/fusion events. |
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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
Description: |
Annotations 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. For the Hawaiian archipelago dataset, absolute change in coral patch area (cm2) was calculated in R. |
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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 |
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Platforms
Platform Unavailable Reason: | Not Applicable |
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Child Items
Rubric scores updated every 15m
Type | Title | |
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Entity | SfM Fixed Sites: SfM Derived Coral Annotations |
Related Items
Item Type | Relationship Type | Title |
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Data Set (DS) | Cross Reference |
Structure from Motion (SfM) benthic images collected from Fixed Sites across the U.S. Pacific since 2019 Source imagery used to generate vital rates annotations. |
Catalog Details
Catalog Item ID: | 63093 |
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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: | Lori H Luers |
Metadata Record Last Modified: | 2023-10-27 23:42+0000 |
Metadata Record Published: | 2023-09-11 |
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 |