gov.noaa.nmfs.inport:63097 eng UTF8 dataset CSV Files Pacific Islands Fisheries Science Center 808-725-5300 1845 Wasp Blvd. Honolulu HI 96818 USA https://www.pifsc.noaa.gov WWW:LINK-1.0-http--link Website Website for this organization information 8:00 a.m. - 4:30 p.m. resourceProvider Luers, Lori H 1845 Wasp Blvd. Honolulu HI 96818 USA lori.luers@noaa.gov pointOfContact 2026-03-04T19:17:26 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) Structure from Motion (SfM) Coral (Adult and Juvenile) Annotations derived from Stratified Random Site (StRS) Imagery across the US Pacific from 2019 to 2023 for methods comparison SfM StRS Comparison Benthic Annotations 2023 creation 2024-03 revision 2025 publication NOAA/NMFS/EDM 63097 NOAA NCEI 2025-09-30 inForce https://doi.org/10.25921/ggt2-sk81 https://www.fisheries.noaa.gov/inport/item/63097 WWW:LINK-1.0-http--link Full Metadata Record View the complete metadata record on InPort for more information about this dataset. information Pacific Islands Fisheries Science Center 808-725-5360 1845 Wasp Blvd. Honolulu HI 96818 USA pifsc.info@noaa.gov https://www.pifsc.noaa.gov WWW:LINK-1.0-http--link Pacific Islands Fisheries Science Center Website Pacific Island Fisheries Science Center homepage information 8:00 a.m. - 4:30 p.m. originator https://www.fisheries.noaa.gov/region/pacific-islands#science WWW:LINK-1.0-http--link NOAA Fisheries Pacific Islands Region - Science Overview NOAA Fisheries Website download https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific WWW:LINK-1.0-http--link Coral Reefs in the Pacific NOAA Fisheries Website download https://www.coris.noaa.gov/monitoring/ WWW:LINK-1.0-http--link National Coral Reef Monitoring Program NOAA National Coral Reef Monitoring Program (NCRMP) website. download https://doi.org/10.25923/8r7f-t404 WWW:LINK-1.0-http--link 2023 Methods Comparison Tech Memo Publication utilizing the data describes in this record download tableDigital Winston M, Couch C, Ferguson M, Huntington B, Swanson D, Vargas-Angel B. 2019. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA Tech. Memo. NOAA-TM-NMFS-PIFSC-92, 66 p. doi:10.25923/w1k2-0y84 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 Couch CS, Oliver, TA, Suka R, Lamirand M, Asbury M, Amir C, Vargas-Angel B, Winston M, Huntington B, Lichowski F, Halperin A, Gray A, Garriques J, & Samson J. 2021. Comparing coral colony surveys from in-water observations and structure-from-motion imagery shows low methodological bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943 Charendoff J.A., Couch C, Oliver T, Lamirand M, Amir C, Basden I, Torres-Pulliza D, Asbury M, Winston M, Huntington B, Lichowski F, Osborn N, Ehrenberg J, Garriques J, Samson J. 2023. Comparing coral demographic surveys from in situ observations and structure-from-motion photogrammetry on high diversity reefs shows low methodological bias but highlights persistent areas of concern. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-153,52 52 p. doi:10.25923/8r7f-t404 Coral adult and juvenile coral colony demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers, and is documented separately here: https://www.fisheries.noaa.gov/inport/item/63095. The data were collected as part of the NOAA Pacific Islands Fisheries Science Center (PIFSC) and Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) led National Coral Reef Monitoring Program (NCRMP) missions around the US Pacific from 2019 for method comparison. Refer to Lineage and URLs for links to publication. The SfM surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. Surveys were conducted at sites randomly stratified across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). These sites represent a broad range of depths (1-25 m), habitat types (aggregate reef, patch reef, pavement, rock and boulder and rubble), coral cover, and diving conditions. Allocation of sampling effort was proportional to strata area and variance in coral density. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site to site comparisons should be used with caution. During each survey, an 18m transect line was deployed along the isobath and photographed using underwater cameras while swimming in a back and forth swim pattern for later processing using an SfM approach. At depths of 1-20 m, SfM surveys were conducted over a 3 x 20m area and at depths > 20m, a 3 x 13m area was surveyed, both with the transect running down the middle of the survey area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for juvenile and adult coral colony demographic metrics. Data was collected for each site within four 2.5m2 segments, each 1m wide, along the transect (at 0-2.5m, 5-7.5m, 10-12.5m, and 15-17.5m). At deeper sites where a 3 x 13m area was surveyed, only the first three segments were analyzed in ArcGIS. For each adult coral colony (> 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), and estimated percent old mortality were recorded. Bleaching extent (% of living tissue with reduced pigmentation) and severity were also recorded. Juvenile coral colonies (0.7 to 5cm maximum diameter) were recorded within the first 1 m2 of the first 3 segments. For juvenile colonies, only ID and maximum diameter were recorded. The National Coral Reef Monitoring Program (NCRMP) details a long-term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various Coral Reef Conservation Coral Reef Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. The purpose of the Structure from Motion (SfM) surveys throughout the US Pacific is to efficiently and effectively collect coral demographic data. SfM-derived data collection occurred along the same transects as in situ diver coral demographic surveys as a means to compare the use of SfM as a tool for quantifying coral demographic metrics in comparison to traditional visual in situ assessments. NOAA Fisheries, ESD and funded by the NOAA CRCP completed Couch, Courtney S courtney.s.couch@noaa.gov pointOfContact Charendoff, Jonathan jonathan.charendoff@noaa.gov custodian asNeeded As more imagery is collected and datasets are generated, we will continue to update this record. DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 17.0 EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF theme Global Change Master Directory (GCMD) Science Keywords 17.0 OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > UNITED STATES MINOR OUTLYING ISLANDS OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > GUAM OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > NORTHERN MARIANA ISLANDS place Global Change Master Directory (GCMD) Location Keywords 20.8 743 National Coral Reef Monitoring Program theme CRCP Project Numeric Data Sets > Benthic theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals) EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs EARTH SCIENCE > Oceans > Marine Biology > Coral EARTH SCIENCE > Oceans > Marine Biology > Coral Communities NEARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis theme CoRIS Theme Thesaurus CORAL CORAL - COLONY SIZE CORAL - SPECIES IDENTIFICATION theme NODC DATA TYPES THESAURUS GIS product derived products in situ laboratory analysis survey - coral reef theme NODC OBSERVATION TYPES THESAURUS CORAL REEF STUDIES Coral Reef Conservation Program National Coral Reef Monitoring Program theme NODC PROJECT NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division theme NODC SUBMITTING INSTITUTION NAMES THESAURUS COUNTRY/TERRITORY > Northern Mariana Islands > Aguihan > Aguihan Island (Aguijan) (14N145E0006) COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Northern Mariana Islands > Northern Mariana Islands ( CNMI ) (18N146E0000) COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Rota > Rota Island ( Luta ) (14N145E0007) COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002) COUNTRY/TERRITORY > Northern Mariana Islands > Sarigan Island > Sarigan Island (16N145E0003) COUNTRY/TERRITORY > Northern Mariana Islands > Tinian > Tinian Island (14N145E0005) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Swains Atoll (11S171W0001) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016) COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000) COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii (21N160W0000) COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003) COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Kauai Island (22N159W0001 COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Molokai Island (21N157W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > French Frigate Shoals (24N166W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Lisianski Island (25N173W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Northwestern Hawaiian Islands (28N178W0000) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Pearl and Hermes Reef (27N176W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Kalawao > Kahoolawe Island (20N156W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Kauai > Niihau Island (21N160W0001) COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Lanai Island (20N156W0002 COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Maui Island (20N156W0004 COUNTRY/TERRITORY > United States of America > Hawaiian Islands (21N157W0027) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Baker Island (00N176W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Howland Island (00S176W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Johnston Atoll (16N169W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001) COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001) OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000) OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001) OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001) OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Baker Island > Baker Island (00N176W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands (21N157W0027) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii > Hawaii (21N160W0000 OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii Island > Hawaii Island (19N155W0003 OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kahoolawe Island > Kahoolawe Island (20N156W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kauai Island > Kauai Island (22N159W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Lanai Island > Lanai Island (20N156W0002) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Maui Island > Maui Island (20N156W0004) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Molokai Island > Molokai Island (21N157W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Niihau Island > Niihau Island (21N160W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Howland Island > Howland Island (00S176W0001 OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Johnston Atoll > Johnston Atoll (16N169W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands (28N178W0000) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > French Frigate Shoals (24N166W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Lisianski Island (25N173W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001) OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013) OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014) OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Aguihan Island Reefs > Aguihan Island (Aguijan) (14N145E0006) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Mariana Archipelago > Northern Mariana Islands ( CNMI ) (18N146E0000) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Maug Island > Maug Island (20N145E0001) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Pagan Island > Pagan Island (18N145E0001) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Rota Island > Rota Island ( Luta ) (14N145E0007) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Saipan Island > Saipan Island (15N145E0002) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Sarigan Island > Sarigan Island (16N145E0003) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Tinian Island Reefs > Tinian Island (14N145E0005) place CoRIS Place Thesaurus Coastal Waters of Hawaii Equatorial Pacific Ocean Marianas Trench Marine National Monument Northwest Pacific Pacific Remote Islands Marine National Monument Papahanaumokuakea Marine National Monument Rose Atoll Marine National Monument South Pacific Ocean place NODC SEA AREA NAMES THESAURUS Central Pacific Ocean North Pacific Ocean place NODC SEA AREA NAMES THESAURUS: photograph scale instrument NODC INSTRUMENT TYPES THESAURUS OSCAR ELTON SETTE RAINIER platform NODC PLATFORM NAMES THESAURUS CRED CREP Coral Demography Coral Reef Ecosystem Division Coral Reef Ecosystem Program ESD Ecosystem Sciences Division PIFSC Pacific Islands Fisheries Science Center RAMP Reef Assessment and Monitoring Program SfM Structure from Motion theme American Samoa CNMI Commonwealth of the Northern Marianas Islands MHI Main Hawaiian Islands Marianas NWHI Northwestern Hawaiian Islands PMNM PRIA PRIMNM Pacific Remote Island Areas place DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Structure From Motion project InPort otherRestrictions Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: Structure from Motion (SfM) Coral (Adult and Juvenile) Annotations derived from Stratified Random Site (StRS) Imagery across the US Pacific from 2019 to 2023 for methods comparison [Data Date Range], https://www.fisheries.noaa.gov/inport/item/63097. NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose. otherRestrictions Access Constraints: None otherRestrictions Use Constraints: Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data. Example: Pacific Islands Fisheries Science Center, 2023: National Coral Reef Monitoring Program: Structure from Motion (SfM) Coral (Adult and Juvenile) Annotations derived from Stratified Random Site (StRS) Imagery across the US Pacific since 2019, https://www.fisheries.noaa.gov/inport/item/63097. otherRestrictions 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. unclassified Not applicable Not applicable National Coral Reef Monitoring Program: Coral demographic data (adult and juvenile corals, species, colony length, condition, etc.) collected during Stratified Random Surveys (StRS) across the US Pacific since 2013 derived from in-situ diver surveys and structure-from-motion imagery NOAA/NMFS/EDM 71550 crossReference National Coral Reef Monitoring Program: Stratified Random Surveys (StRS) of Coral Demography (Adult and Juvenile Corals) across the Hawaiian Archipelago since 2013 NOAA/NMFS/EDM 36164 crossReference National Coral Reef Monitoring Program: Stratified Random Surveys (StRS) of Coral Demography (Adult and Juvenile Corals) across the Mariana Archipelago since 2014 NOAA/NMFS/EDM 36165 crossReference National Coral Reef Monitoring Program: Structure from motion (SfM) benthic images collected at Stratified Random Sites (StRS) across the US Pacific from 2019 NOAA/NMFS/EDM 63095 crossReference NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 63097 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/63097.pdf WWW:LINK-1.0-http--link NOAA Data Management Plan (DMP) NOAA Data Management Plan for this record on InPort. information crossReference eng; US biota biota A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. In 2019, a Canon SL2 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25-0.50 m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape (version 1.2.5 build 2735). Models were further scaled using the custom software Viscore. Sampling boundaries and coral demographic measurements were created in ArcMap (version 10.6.1). All statistics were performed in R (Version 3.6.1). Starting in 2022, a Canon SL2 or SL3 DSLR camera in an ikelite housing was used to take photographs of each site. Coded markers 0.25 m long were used underwater to provide scale and depth information for each mosaic. Orthomosaic images were created using Agisoft Metashape (version 1.8.0 or later). Viscore was used for accessing raw imagery. Sampling boundaries and coral demographic measurements were created in ArcGIS Pro (version 2.8.0 or later). All statistics were performed in R (Version 4.1.2 or later). U.S. Pacific Island Areas 144.618287 -154.806789 -14.373615 28.455623 Main and Northwestern Hawaiian Islands 2019 | Currentness: Ground Condition 2019-04-21 2019-10-31 Mariana Archipelago 2022 | Currentness: Ground Condition 2022-04-14 2022-08-09 American Samoa 2023 | Currentness: Ground Condition 2023-03-30 2023-04-20 The NOAA National Coral Reef Monitoring Program (NCRMP) details a long term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various NOAA Coral Reef Conservation Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The PIFSC Ecosystem Sciences Division (ESD) at NOAA Fisheries is leading biological monitoring in the U.S. Pacific Islands Region. The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). Innovative analysis techniques are then used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time. false eng false Data Table SfM Stratified Random: SfM Derived Adult Coral Annotations 2025-09-17 publication SfM Stratified Random: SfM Derived Juvenile Coral Annotations 2025-09-17 publication CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) NOAA National Centers for Environmental Information ncei.info@noaa.gov https://www.ncei.noaa.gov/contact WWW:LINK-1.0-http--link NCEI Contact Information Information for contacts at NCEI. information distributor https://accession.nodc.noaa.gov/0253468 WWW:LINK-1.0-http--link SfM_Adult_demographic_MHI_2019.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. download https://accession.nodc.noaa.gov/0253468 WWW:LINK-1.0-http--link SfM_Juvenile_Demographic_MHI_2019.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the main Hawaiian Islands beginning in 2019 during REA surveys. download https://accession.nodc.noaa.gov/0308012 WWW:LINK-1.0-http--link SfM_Adult_demographic_AS-PRIA_2023.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the American Samoa in 2023 during REA surveys. download https://accession.nodc.noaa.gov/0280938 WWW:LINK-1.0-http--link SfM_Juvenile_demographic_MARI_2022.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago in 2022 during REA surveys. download https://accession.nodc.noaa.gov/0280938 WWW:LINK-1.0-http--link REFERENCE_GENUS_SPCODE.csv Lookup table for species and taxon codes used by the NOAA Fisheries Ecosystem Sciences Division across the US Pacific. Note: 'AAAA' is used to denote no colonies observed. Genus is provided as analysis can be performed at that level. download https://accession.nodc.noaa.gov/0280938 WWW:LINK-1.0-http--link SfM_Adult_demographic_MARI_2022.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual adult coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology, empirical size measurement, and all other recorded colony attributes including partial mortality and condition. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout the Marianas Archipelago beginning in 2022 during REA surveys. download https://accession.nodc.noaa.gov/0308012 WWW:LINK-1.0-http--link SfM_Juvenile_demographic_AS-PRIA_2023.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (usually species) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division throughout American Samoa in 2023 during REA surveys. download dataset Representativeness The data set derived from the imagery is only as good as the images themselves; Images with poor resolution, poor lighting, extraneous objects (fins, etc), or blur were excluded from analysis. Accuracy Handheld GPS units were used to locate random sites and mark site locations. Prior to conducting surveys, the SfM image collector was trained to swim in a back-and-forth pattern to collect imagery with 60-80% overlap. Both classroom and field training were completed before any surveys were conducted. This training ensures that all SfM image collection was conducted consistently during the mission. Coral demographic data was extracted by SfM image annotators that had been trained, underwent a series of calibration efforts and testing on coral taxon identification testing, morphology, and condition assessment. All annotators met a set of minimum standards for coral demographic data collection. 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 orthomosaics. Completeness Report Only sites from shallow water (0 to 30 meter depth range) hard-bottom habitats were annotated. At deep sites, bottom time is limited and therefore survey area is reduced from 3 x 20 m to 3 x 13 m. Therefore, shallower sites, 4 2.5 m2 segments were annotated and for deeper sites (>30 m) 3 2.5m2 segments were annotated along the central transect line. Within each 2.5 m2 segment, only 1m2 of the segment was sampled for juvenile demographic metrics and for all sites, regardless of depth, only the first three segments along the transect line were annotated. Main Hawaiian Islands 2019: SfM imagery was collected at all benthic REA survey sites but only at a subset of the Fish REA survey sites (145 SfM collections out of 300 sites total). Of the 145 sites where SfM imagery was collected, 104 sites were analyzed for juvenile and adult coral demographics via SfM. Marianas Archipelago 2022: SfM imagery was collected at a subset of benthic and Fish REA survey sites (303 SfM collections out of 480 sites total). Of the 303 sites where SfM imagery was collected, 102 sites were analyzed for juvenile and adult coral demographics via SfM. American Samoa/Pacific Remote Island Areas 2023: SfM imagery was collected at a subset of benthic and Fish REA survey sites (178 SfM collections out of 374 sites total). Of the 178 sites where SfM imagery was collected, 75 sites were analyzed for juvenile and adult coral demographics via SfM. Conceptual Consistency The same method of annotation was used for all SfM imagery. The benthic SfM survey methodology, employed by the NOAA Ecosystem Sciences Division (ESD), began in 2019. Benthic imagery is collected at stratified random sites and generated into orthomosaic images using Agisoft Metashape software. Orthomosaics are imported into ArcGIS for annotation. Annotation of SfM belt orthomosaics is modelled after in situ diver adult and juvenile coral belt surveys employed by the PIFSC Ecosystem Sciences Division and includes coral species identification, maximum diameter measurement, partial mortality estimates, and disease and condition identification. A stratified random sampling (StRS) design was employed to survey the coral reef ecosystems through the U.S. Pacific regions. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats. The stratification scheme included island, reef zone, and depth in all regions, as well as habitat structure type in the Main Hawaiian Islands. The habitat structure types included simple, complex, and coral-rich. Depth categories of shallow (0-6 m), mid (> 6-18m) and deep (>18-30 m) were also incorporated into the stratification scheme. Allocation of sampling effort was proportional to strata area and variance in coral density. Sites were randomly selected within each stratum. A geographic information system (GIS) and digital spatial databases of benthic habitats (NOAA National Centers for Coastal Ocean Science NCCOS), reef zones (IKONOS satellite imagery, NDGC 1998) bathymetry (NDGC 1998, CREP benthic mapping data), and marine reserve boundaries (NOAA) were used to facilitate spatial delineation of the sampling survey domain, strata, and sample units. Map resolution was such that the survey domain could be overlain by a grid using a GIS with individual cells of size 50 m by 50 m in area. A one-stage sampling scheme following Cochran (1977) was employed. Grid cells containing at least 10% hard-bottom reef habitats were designated as primary sample units (referred to as sites). Couch, Courtney S courtney.s.couch@noaa.gov processor SfM benthic surveys were conducted by both the fish and benthic teams to record the benthic community composition. A 3 x 20 m plot was visually established centered on a transect line (at sites >18 m, a 3 x 13 m plot was visually established). 3-4 ground control points (GCPs) were placed within the plot for scale. White balance settings were adjusted in situ using a 15% gray card. JPEG images were collected using a Canon SL2 or SL3 DSLR camera in an underwater housing with a dome port. Images were collected at each site by swimming in a back-and-forth motion 1 m above the substrate capturing images continuously to achieve a 60-80% overlap. Suka, Rhonda (808)725-5494 rhonda.suka@noaa.gov processor 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. Imagery was color and exposure corrected using Adobe Lightroom if white balance was not achieved in situ or a substantial number of images were dark, respectively. Image adjustments were batch run per site for consistent correction. The Structure from Motion (SfM) approach produces an accurately scaled, two-dimensional (2D) orthomosaic model created from the overlapping imagery. Raw imagery was imported into Agisoft Metashape software (AgiSoft Metashape Professional Version 1.6.1 or later) where images were aligned and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019). DPCs were then imported into Viscore, a visualization software (Petrovic et al., 2014) where they were scaled and oriented using the GCP information. The ground sample distance (GSD) of the scaled DPC, which estimates the resolution per pixel by measuring the size of each pixel on the ground, ranged from 2-4 mm/pix. A geometrically accurate 2D projection of the DPC (orthoorthomosaic) is exported from Metashape and uploaded into ArcGIS for annotation. Suka, Rhonda (808)725-5494 rhonda.suka@noaa.gov processor In ArcGIS, each site was set up for annotation by manually digitizing the transect and segments as a shapefile using the same sampling design as the PIFSC ESD-led in situ coral demography surveys, and setting up the attribute table in a geodatabase to mirror the in situ visual survey database (Swanson et al. 2018; Winston et al. 2019). To record and extract data from the orthomosaic, each coral colony was annotated following the in situ visual survey methods. Each colony was measured by digitizing a line across the maximum diameter of the colony. Coral ID (to lowest taxonomic level), estimated percent old mortality, and bleaching extent and severity were recorded. During annotation, the original JPEG imagery was viewed alongside the orthomosaic with the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges). Suka, Rhonda (808)725-5494 rhonda.suka@noaa.gov processor Annotations created in ArcGIS are quality controlled using a multi-stage process. Data are first exported from ArcGIS and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing segments, data in incorrect columns, partial mortality >100%). Then data are summarized to the segment-level by annotator to identify potential issues (e.g. anomalously high or low mean values for specific metrics relative to other annotators). If issues are identified for a given annotator, that annotator reviews and corrects each site if they did find errors. The third stage involves annotators reviewing a subset (10% of the annotated segments) of randomly selected segments (stratified by annotator) that they did not originally annotate and recording errors (e.g. species misidentification, missing or incorrect conditions, and missing colonies) to establish individual annotator error rates for each metric. If an annotator had greater than error rate for a given metric all of that annotator's sites were reviewed and corrected for the metric in question by a different annotator. In addition, a subset of the segments across sites were annotated twice by SfM annotators to further quantify inter-annotator error. Couch, Courtney S courtney.s.couch@noaa.gov processor 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 2015-07-07 publication John Burns https://doi.org/10.7717/peerj.1077 WWW:LINK-1.0-http--link PeerJ 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. information publisher Charendoff J.A., Couch C, Oliver T, Lamirand M, Amir C, Basden I, Torres-Pulliza D, Asbury M, Winston M, Huntington B, Lichowski F, Osborn N, Ehrenberg J, Garriques J, Samson J. 2023. Comparing coral demographic surveys from in situ observations and structure-from-motion photogrammetry on high diversity reefs shows low methodological bias but highlights persistent areas of concern. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-153,52 52 p. doi:10.25923/8r7f-t404 2023-12-01 publication Pacific Islands Fisheries Science Center https://doi.org/10.25923/8r7f-t404 WWW:LINK-1.0-http--link Comparing Coral Demographic Surveys From In Situ Observations and Structure-From-Motion Photogrammetry on High Diversity Reefs Shows Low Methodological Bias but Highlights Persistent Areas of Concern NOAA Tech Memo information originator Source Contribution: This study provides the first quantified methodological comparison to validate the transition from standard in-water methods to SfM survey methods for estimates of coral colony-level surveys. Here, we quantitatively compare data generated from in-water surveys to SfM-derived metrics for assessing coral demography, bleaching, and diversity in the main Hawaiian Islands as part of NOAA’s National Coral Reef Monitoring Program. Our objectives were to compare between-method error to within-method error, test for bias between methods, and identify strengths and weaknesses of both methods. Colony density, average colony diameter, average partial mortality, prevalence of bleaching, species richness, and species diversity were recorded using both methods within the same survey areas. For all metrics, the magnitude of between-method error was comparable to the within-method error for the in-water method and between method error was significantly higher than within-method error for SfM for one of the seven metrics. Our results also reveal that a majority of the metrics do not vary significantly between methods, nor did we observe a significant interaction between method and habitat type or method and depth. Exceptions include estimates of partial mortality, bleaching prevalence, and Porites juvenile density–though differences between methods are generally small. Our study also highlights that SfM offers a unique opportunity to more rigorously quantify and mitigate inter-observer error by providing observers unlimited “bottom time” and the opportunity to work together to resolve difficult annotations. Couch CS, Oliver, TA, Suka R, Lamirand M, Asbury M, Amir C, Vargas-Ángel B, Winston M, Huntington B, Lichowski F, Halperin A, Gray A, Garriques J, & Samson J. 2021. Comparing coral colony surveys from in-water observations and structure-from-motion imagery shows low methodological bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943 2021-05-28 publication Pacific Islands Fisheries Science Center https://www.frontiersin.org/articles/10.3389/fmars.2021.647943/full WWW:LINK-1.0-http--link Frontiers Journal Comparing Coral Colony Surveys From In-Water Observations and Structure-From-Motion Imagery Shows Low Methodological Bias information originator 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. 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. 2014-01-01 publication Vid Petrovic https://escholarship.org/uc/item/58z4j8k2 WWW:LINK-1.0-http--link Mediterranean Archaeology and Archaeometry VISUALIZING HIGH RESOLUTION THREE-DIMENSIONAL AND TWO-DIMENSIONAL DATA OF CULTURAL HERITAGE SITES information publisher 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, 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 2019-12-30 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/22753 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator Source Contribution: Guidelines and procedures for implementation of sampling design, in situ survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018). Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993. 2018-08-01 publication https://repository.library.noaa.gov/view/noaa/18267 WWW:LINK-1.0-http--link NOAA Institutional Repository Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys information Source Contribution: This SOP is the result of comprehensive testing of different camera systems, data collection methods, and software. The objective of this SOP revision is to provide updates incorporated in 2022 to Suka et al. (2019), including: updated model building parameters in Agisoft Metashape; refined steps to reduce error in model geometry; standardized parameters to generate consistent SfM products; and updated methods to extract demographic metrics that migrate from ArcMap to ArcGIS Pro. Torres-Pulliza D, Charendoff J, Couch CS, Suka R, Gray A, Lichowski F, Amir C, Lamirand M, Asbury M, Winston M, Basden I, Oliver T 2024. Processing Coral Reef Imagery Using Structure-from-Motion Photogrammetry: Standard Operating Procedures (2023 Update) U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-159, 91 p. 2024-04-01 publication NMFS PIFSC ESD https://doi.org/10.25923/cydj-z260 WWW:LINK-1.0-http--link NOAA technical memorandum NMFS PIFSC 2023 Updated SOP for Processing imagery using SfM information originator Source Contribution: The objective of this document is to provide updates incorporated in 2019 to the guidelines and procedures for implementation of sampling design, survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018). Winston M, Couch C, Ferguson M, Huntington B, Swanson D, Vargas-Ángel B. 2019. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA Tech. Memo. NOAA-TM-NMFS-PIFSC-92, 66 p. doi:10.25923/w1k2-0y84 2020-01-31 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/23951 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None