gov.noaa.nmfs.inport:67851 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 2026-03-04T19:17:25 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) Coral Reef Structural Complexity derived from Structure-from-Motion (SfM) imagery collected at Stratified-Random Sites (StRS) across the U.S. Pacific since 2019 SfM Structural Complexity StRS US Pacific 2022-11 creation 2025 publication NOAA/NMFS/EDM 67851 https://www.fisheries.noaa.gov/inport/item/67851 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://github.com/jmadinlab/Asburyetal_2023 WWW:LINK-1.0-http--link GitHub Repository for R Scripts used in Structural Complexity Analysis 'GEOLOGICAL AND ENVIRONMENTAL FACTORS SHAPE REEF HABITAT STRUCTURE IN THE MAIN HAWAIIAN ISLANDS' 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 Webiste 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/10.1111/geb.13691 WWW:LINK-1.0-http--link Geological age and environments shape reef habitat structure Published 2022 results using structural complexity dataset from the Hawaiian islands. download https://repository.library.noaa.gov/view/noaa/60890 WWW:LINK-1.0-http--link Processing Coral Reef Imagery Using Structure-from-Motion Photogrammetry: Standard Operating Procedures (2023 Update) Published 2023 Standard Operating Procedures to collect and reconstruct Digital Elevation models and orthomosaics from coral reef photos using Structure from Motion photogrammetry methods. download https://repository.library.noaa.gov/view/noaa/71123 WWW:LINK-1.0-http--link Linking fish biomass and coral reefs structural complexity across the Mariana Archipelago Published technical memorandum using the 2022 structural complexity dataset from the Mariana Archipelago. download https://doi.org/10.1038/s41559-020-1281-8 WWW:LINK-1.0-http--link A geometric basis for surface habitat complexity and biodiversity This study presents a geometric basis for surface habitats that unifies ecosystems and spatial scales. download https://doi.org/10.1111/2041-210X.70027 WWW:LINK-1.0-http--link habtools: An R package to calculate 3D metrics for surfaces and objects habtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow. download https://www.fisheries.noaa.gov/region/pacific-islands#science WWW:LINK-1.0-http--link NOAA Fisheries Pacific Islands Region - Science Overview Online Resource download tableDigital Torres-Pulliza D, Oliver T, Weible R, Lichowski F, Kindinger T, Gajdzik L & Couch C (2025). Linking fish biomass and coral reefs structural complexity across the Mariana Archipelago (PIFSC Technical Memoranda Series, TM-PIFSC-180). Pacific Islands Fisheries Science Center. https://doi.org/10.25923/epgn-3x74 Schiettekatte N, Asbury M, Chen GK, Dornelas M, Reichert J, Torres-Pulliza D, Zawada KJA, Madin JS (2025). habtools: An R package to calculate 3D metrics for surfaces and objects. Methods Ecol Evol 16, 895-903. https://doi.org/10.1111/2041-210X.70027 Torres-Pulliza D, Charendoff J, Couch C, 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). https://doi.org/10.25923/CYDJ-Z260 Asbury M, Schiettekatte NMD, Couch CS, Oliver T, Burns JHR, Madin JS (2023). Geological age and environments shape reef habitat structure. Global Ecology and Biogeography 32, 1230–1240. https://doi.org/10.1111/geb.13691 Torres-Pulliza D, Dornelas MA, Pizarro O, Bewley M, Blowes SA, Boutros N, Brambilla V, Chase TJ, Frank G, Friedman A, Hoogenboom MA, Williams S, Zawada KJA, Madin JS (2020). A geometric basis for surface habitat complexity and biodiversity. Nature Ecology & Evolution, 4, 1495-1501p. https://doi.org/10.1038/s41559-020-1281-8 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. https://doi.org/10.25923/h2q8-jv47 The data described here are structural complexity estimates derived from Structure-from-Motion (SfM) benthic habitat imagery from diver transect surveys conducted at stratified-random sites (StRS) by the Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD) as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The coral reef photos, collected by scuba divers, are used to generate 3-dimensional models, digital elevation models (DEMs) and orthomosaics using Agisoft Metashape photogrammetric software. The digital elevation models were analyzed in R studio to derive estimates of habitat structural complexity, using metrics such as: rugosity, fractal dimension, and height range, among others. The source imagery is archived and described separately at https://www.fisheries.noaa.gov/inport/item/63095. The SfM surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. Sites were imaged using underwater cameras along 3x20m (3x13m for sites deeper than 18m) transects across the U.S. Pacific Island areas beginning in 2019. Please refer to the Lineage section for SOPs -- 2019 and 2022 have slightly different processing steps. Complexity metrics were estimated for each site within five or six 4m2 DEM sampling plots, which can then be averaged for the site. Rugosity is measured as the ratio between surface area and planar area within a sampling plot, Fractal dimension is measured using the variation or standard deviation method (see Lineage section below), and height range is measured as the difference between the deepest and shallowest point within a sampling plot. A stratified random sampling (StRS) design was employed to survey the coral reef ecosystems across the U.S. Pacific Regions (Hawaiian Archipelago, Mariana Archipelago, American Samoa, and the Pacific Remote Island Areas). The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0-30 m depth range. The stratification scheme included island, sub-island sector, reef zone, and depth in all regions, as well as habitat structure type. Allocation of sampling effort was proportional to the strata hardbottom area. The StRS design effectively reduces estimated variance by sampling more sites with larger hardbottom area and variance. 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 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 U.S. Pacific is to efficiently and effectively collect benthic data. Estimates of habitat structural complexity will expand our understanding of how structure influences coral reef ecology, function, and services. NOAA Fisheries, ESD and funded by the NOAA CRCP onGoing Oliver, Thomas (808)725-5444 1845 Wasp Blvd. Honolulu HI 96818 USA thomas.oliver@noaa.gov pointOfContact Torres-Pulliza, Damaris damaris.torres-pulliza@noaa.gov custodian asNeeded This record will be updated as datasets continue to be derived from SfM models for other regions. In 2023, a dataset was generated for the Mariana Archipelago and appended to 2019 data from the Main Hawaiian Islands. 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 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 31360 31525 743 NOAA Coral Reef Conservation Program Pacific National Coral Reef Monitoring Program theme CRCP Project Geographic Information > Digital Elevation Model Map Images > Coral Mapping Map Images > Topography Numeric Data Sets > Benthic theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis EARTH SCIENCE > Oceans > Bathymetry/Seafloor Topography > Rugosity EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Rugosity EARTH SCIENCE > Oceans > Marine Biology > Coral theme CoRIS Theme Thesaurus CORAL - CENSUS theme NODC DATA TYPES THESAURUS photograph computer theme NODC INSTRUMENT TYPES THESAURUS derived products 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 place NODC SEA AREA NAMES THESAURUS Central Pacific Ocean North Pacific Ocean place NODC SEA AREA NAMES THESAURUS: OSCAR ELTON SETTE platform NODC PLATFORM NAMES THESAURUS Agisoft American Samoa CNMI CRED CREP Complexity metrics Coral Reef Ecosystem Division Coral Reef Ecosystem Program ESD Ecosystem Sciences Division Fractal dimension Guam Height range Mariana Archipelago PIFSC Pacific Islands Fisheries Science Center Pacific Remote Island Areas Reef Assessment and Monitoring Program Reef habitat complexity Rugosity SfM Structure from Motion digital elevation model theme 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]: Coral Reef Structural Complexity derived from Structure-from-Motion (SfM) imagery collected at Stratified-Random Sites (StRS) across the U.S. Pacific since 2019 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/67851. 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: Ecosystem Science Division; Pacific Islands Fisheries Science Center, 2022: Structure from Motion (SfM) Structural Complexity derived from Stratified Random Site (StRS) Imagery across the US Pacific since 2019, https://www.fisheries.noaa.gov/inport/item/67851. 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: 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 67851 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/67851.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 2019 MHI: A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. A Nikon SL2 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25-0.50 m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape (version 1.2.5 build 2735). All structural complexity metrics were extracted in R (Version 3.6.1). 2022 MARI: A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. A Canon SL2/3 DSLR digital camera with a 18 mm camera lens and 6 in dome port in an Ikelite underwater housing was used to take photographs of each site. Three to four coded scale bars 0.25 m long were used underwater to provide scale to the 3D model reconstructions. Digital Elevation Models and orthomosaics were created using Agisoft Metashape Professional (version 2.0). All structural complexity metrics were extracted in R (Version 4.4.3). -160.2518 -154.8042 19.07632 22.20357 Extent of imagery used to generate the 2019 structural complexity dataset, at sites across the Main Hawaiian Islands (MHI), including Hawaii, Kauai, Maui, Oahu, Molokai, Niihau, Kahoolawe, and Lanai during the 2019 MHI NCRMP mission (SE1902_MHI_Leg3). Date range of structure-from-motion (SfM) imagery collected used to produce this structural complexity dataset during the 2019 NCRMP cruise to the Main Hawaiian Islands. | Currentness: Ground Condition 2019-04-21 2019-08-06 144.1498 146.840346 12.75505 20.974233 Extent of imagery used to generate SfM-derived complexity dataset, at sites across Guam and the Commonwealth of the Northern Mariana Islands (CNMI), together forming the Mariana Archipelago, during the 2022 Rainier Integrates Charting, Hydrography, and Reef Demographics (RICHARD) NCRMP mission (RA2201_Leg3-7). Vessel: NOAA Ship Rainier Project Number: RA-22-01 Project Title: Rainier Integrates Charting, Hydrography, and Reef Demographics (RICHARD) Area of Operation: Guam and the Northern Mariana Islands | Currentness: Ground Condition 2022-04-14 2022-08-09 Bounding coordinate for Pacific-wide dataset. 144.634585 -154.804172 -14.559759 28.457971 Bounding coordinates that include US Pacific Islands region. More specific geographic information is included for 2019 and 2022 in this metadata record. More recent data are captured in these coordinates. Structural complexity dataset will be updated as more data is collected, and starts in 2019 in the Main Hawaiian Islands. | Currentness: Ground Condition 2019-04-21 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 derived structural complexity Data Dictionary 2025-12-18 publication 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/0268310 WWW:LINK-1.0-http--link ESD_SfM_StructuralComplex_MHI_2019.csv DEPRECATED- data is now under a singular Pacific-wide file as described. Structural complexity dataset generated by extracting data from digital elevation models developed from 1imagery collected at StRS across the Main Hawaiian Islands during the 2019 NCRMP mission. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site information. download https://accession.nodc.noaa.gov/0268310 WWW:LINK-1.0-http--link ESD_SfM_StructuralComplexity_Pacific_2022.csv Coral reef structural complexity dataset generated by extracting metrics from digital elevation models developed from imagery collected during the National Coral Reef Monitoring Program surveys across the U.S. Pacific Islands regions. Data generated includes three metrics of habitat structural complexity (rugosity, fractal dimension, and height range) and also includes site-level information. This data file will be updated as more data is collected and derived for different Pacific Islands regions. Currently data includes: stratified random sites across Guam and CNMI during the 2022 NCRMP mission, as well as in 2019 in the Hawaiian archipelago. Currently data includes: stratified random sites surveyed as part of NCRMP across Guam and CNMI in 2022, as well as the Hawaiian archipelago in 2019. 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. The SfM models are processed to attain reprojection errors lower than 0.5 pixels, allowing confident estimations of habitat structural complexity from the resulting digital elevation model. Field Precision Ground Sample Distance (GSD, resolution/pixel) for the produced 3D models was 0.014 - 0.034 cm/pix. Completeness Report Habitat structural complexity is estimated from all imaged NCRMP sites whose SfM-derived digital elevation models meet the accuracy and sampling criteria. Conceptual Consistency The same method of estimation 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 image maps using Agisoft Metashape software. Resulting digital elevation models are used to estimate three habitat structural complexity metrics: rugosity, fractal dimension, and height range. 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 Nikon SL2 or Canon SL3 digital 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. Torres-Pulliza, Damaris damaris.torres-pulliza@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. Images with compromised color tones (i.e. no white balance, dark, over exposed, etc.) were corrected using Adobe Lightroom. Image adjustments were batch run per site for consistent correction. Once the images have been collected, quality checked, and organized, they are processed to digitally reconstruct the 3D geometry of a coral reef scene through SfM using Agisoft Metashape. First, the raw imagery was imported into Agisoft Metashape Professional software where images were aligned and used to build 3D dense point clouds (DPCs) following parameters described by Torres-Pulliza et al. (2023). Two digital elevation models (DEM) were generated for each survey site and exported at a 0.002m resolution, one with default interpolation methods and one with interpolation methods disabled. Default interpolation was desired to acquire a DEM with no holes and was the product used for structural complexity metrics extraction. To avoid areas where limited data was interpolated, a non-interpolated DEM was extracted for use of the accurate reconstruction boundary. No analysis was performed on the non-interpolated DEM, but was used as a guide to trim the interpolated DEM. The interpolated digital elevation models were used to quantify coral reef surface complexity through metrics such as Rugosity, Fractal dimension and height range, among others. Torres-Pulliza, Damaris damaris.torres-pulliza@noaa.gov processor In statistical software R v3.6.1, both digital elevation models (DEMs) were imported. Interpolated DEMs were clipped by the extent of the non-interpolated model to avoid inaccurate edges. Specifically, the non-interpolated DEM was aggregated with an aggregation factor of 100 to smooth the edges, and converted to a polygon. The resulting polygon was used to crop the interpolated DEM, thereby removing the distorted edges. Each belt was subsampled to more easily sample across belts that varied slightly in model straightness and width. Five or six 2 x 2m boxes were placed on each belt transect by randomly pulling coordinates from a normal distribution and only boxes that were fully within the bounding area were used (i.e., containing no NA values). Random boxes were continuously placed until five were achieved. Plots that were too thin for the 2 x 2m boxes were removed (14 sites). DEMs were spatially rectified to a known local reference system; however, the natural slope of some sites yielded inaccurate height range values (i.e., difference between maximum z and minimum z) when analyzing the subsetted sample box. To resolve this issue, tilt of sample boxes were corrected by updating the z values to reflect the residuals. Scripts modified from Torres-Pulliza et al. (2020) were used to calculate three structural complexity metrics: rugosity, height range, fractal dimension (variation method). The three metrics were extracted from each 2 x 2m box; Rugosity and height range were calculated at a resolution of 1 cm, while fractal dimension was calculated over a range of 1 cm to 2 m (thus over 2 orders of magnitude). Rugosity was calculated as the ratio between surface area and planar area. Height range was calculated as the difference between the deepest and shallowest point in the box. Fractal dimension was calculated using the variation method; each box was divided into squares with side lengths 2.00, 1.00, 0.64, 0.32, 0.16, 0.08, 0.04, 0.02, 0.01 m and height ranges within each grid at each scale were calculated and averaged for that scale. The slope was calculated for each box by fitting a line to the log of side lengths versus the log of mean height and fractal dimension was calculated by 3 - slope. See Torres-Pulliza et al. (2025) for an alternative sampling strategy and data extraction in R. Asbury, Mollie mollie.asbury@noaa.gov processor Asbury M, Schiettekatte, NMD, Couch CS, Oliver T, Burns JHR, Madin JS (2023). Geological age and environments shape reef habitat structure. Global Ecology and Biogeography 32, 1230-1240. https://doi.org/10.1111/geb.13691 2023-04-28 publication Mollie Asbury https://onlinelibrary.wiley.com/doi/abs/10.1111/geb.13691 WWW:LINK-1.0-http--link Global Ecology and Biogeography Asbury et al. (2023) detail methods used to extract complexity metrics from the 2019 MHI SfM belts. information originator 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 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://doi.org/10.25923/h2q8-jv47 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator Source Contribution: 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. Further, while this SOP focuses on belt transects, the procedures described here apply to building SfM models from photos collected using a variety of photogrammetric survey patterns or research applications beyond Rapid Ecological Assessments (REA). For example, ESD uses the same SfM pipeline to process photos collected following the spiral survey pattern over fixed sites to support monitoring impacts of coral bleaching events, extract benthic parameters to estimate reef carbonate budget, quantify reef 3D complexity, and assess temporal coral vital rates. Torres-Pulliza D, Charendoff J, Couch C, 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). https://doi.org/10.25923/CYDJ-Z260 Damaris Torres-Pulliza https://doi.org/10.25923/cydj-z260 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator Torres-Pulliza D, Dornelas MA, Pizarro O, Bewley M, Blowes SA, Boutros N, Brambilla V, Chase TJ, Frank G, Friedman A, Hoogenboom MO, Williams S, Zawada KJA, & Madin JS. (2020). A geometric basis for surface habitat complexity and biodiversity. Nature Ecology & Evolution, 4, 1495-1501. 2020-08-24 publication Damaris Torres-Pulliza https://doi.org/10.1038/s41559-020-1281-8 WWW:LINK-1.0-http--link Nature Ecology & Evolution This study presents a geometric basis for surface habitats that unifies ecosystems and spatial scales. The theory is framed by fundamental geometric constraints between three structure descriptors surface height, rugosity and fractal dimension and explains 98% of surface variation in a structurally complex test system: coral reefs. information originator Source Contribution: Torres-Pulliza et al. (2025) provides detailed procedures for complexity metrics extraction using the 2022 Mariana Archipelago SfM belts. Torres-Pulliza D, Oliver T, Weible R, Lichowski F, Kindinger T, Gajdzik L, Couch C (2025). Linking fish biomass and coral reefs structural complexity across the Mariana Archipelago (PIFSC Technical Memoranda Series, TM-PIFSC-180). Pacific Islands Fisheries Science Center. 2025-05-01 publication Damaris Torres-Pulliza https://doi.org/10.25923/epgn-3x74 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None