71550 NCRMP: US Pacific Coral Demography Data Set Published / External 71549 Pacific-wide Benthic Project On Going 2024 2024 The data described here result from benthic coral demographic surveys within belt transects of specified length and width for two life stages (juveniles and adults) across the US Pacific since 2013. This data is 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 Mariana Archipelago, American Samoa, Pacific Remote Island Areas, and the Hawaiian Archipelago since 2013. This metadata record replaces those previously separated by region (Catalog ID: 22790, 36164,36165,36166). The in-situ diver coral demographic surveys are part of the Rapid Ecological Assessment (REA) surveys for corals and fish conducted during ESD-led NCRMP missions. From 2013 to 2017, a two-stage stratified random sampling (StRS) design was used to survey the coral reef ecosystems across sub-island sectors and three depth strata (shallow: 0-6m, mid: 6-18m and deep: >18m). Starting in 2018 a one-stage StRS design was employed. 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. Starting in 2023 coral demographic data was also derived by the GIS analysis of benthic Structure from Motion (SfM) imagery. The source imagery was collected during in-water surveys conducted by divers, and is documented separately here: https://www.fisheries.noaa.gov/inport/item/63095.During each SfM 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. At depths of 0-18m, SfM surveys were conducted over a 3 x 20m area and at depths >18m, 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. The data provide information on adult coral colony counts, morphology, size, partial mortality (old and recent dead), presence and causation of disease and other compromised health conditions, including bleaching. Juvenile colony surveys include morphology and size. Taxonomic identification of adult colonies is to the lowest taxonomic level possible and genus level for juveniles. Some segment observations were repeated for internal quality control starting in 2019, and indicated with a repeat segment flag and transectnum = -999; use column OG_OR_RPT_SEG to filter for only original segments. Refer to data dictionaries for details on column conditions. The raw data also include individual observations of crustose coralline algae diseases and Alcyonarian disease type and lesion size as well as the presence of other Anthozoans, such as other cnidarians including Alcyonareans, Zoantharians, Corallimorpharians, and Antipatharians (does not apply to PMNM surveys conducted in 2014 and 2015 or surveys conducted after 2017). 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. This metadata record consolidates four metadata records for coral demography from different Pacific Islands Regions which are be referenced under 'Related Items' Taxa codes/names and their genera can be updated over time. See reference table for taxonomic name changes. 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 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. https://doi.org/10.25923/cydj-z260 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. https://doi.org/10.25921/5QSA-Z057 NOAA Theme Global Change Master Directory (GCMD) Science Keywords EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC Theme Global Change Master Directory (GCMD) Science Keywords EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF Theme ISO 19115 Topic Category biota Spatial Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA Spatial Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS Spatial Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > UNITED STATES MINOR OUTLYING ISLANDS Spatial Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > GUAM Spatial Global Change Master Directory (GCMD) Location Keywords OCEAN > PACIFIC OCEAN > WESTERN PACIFIC OCEAN > MICRONESIA > NORTHERN MARIANA ISLANDS Theme CRCP Project 743 Theme CRCP Project National Coral Reef Monitoring Program Theme CoRIS Discovery Thesaurus Numeric Data Sets > Benthic Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Ecological Dynamics > Species Richness Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Coral Colony Size and Condition Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Rapid assessment studies Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals) Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > BioDiversity Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Coral Communities Theme CoRIS Theme Thesaurus NEARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis Theme ISO 19115 Topic Category 002 Theme ISO 19115 Topic Category biota Theme NODC DATA TYPES THESAURUS CORAL Theme NODC DATA TYPES THESAURUS CORAL - CENSUS Theme NODC DATA TYPES THESAURUS CORAL - COLONY SIZE Theme NODC DATA TYPES THESAURUS CORAL - SPECIES IDENTIFICATION Theme NODC OBSERVATION TYPES THESAURUS GIS product Theme NODC OBSERVATION TYPES THESAURUS derived products Theme NODC OBSERVATION TYPES THESAURUS in situ Theme NODC OBSERVATION TYPES THESAURUS laboratory analysis Theme NODC OBSERVATION TYPES THESAURUS survey Theme NODC OBSERVATION TYPES THESAURUS survey - biological Theme NODC OBSERVATION TYPES THESAURUS survey - coral reef Theme NODC OBSERVATION TYPES THESAURUS survey - swimmer/diver Theme NODC OBSERVATION TYPES THESAURUS visual observation Theme NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES Theme NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program Theme NODC PROJECT NAMES THESAURUS National Coral Reef Monitoring Program Theme NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division Theme CRED Theme CREP Theme Coral Belt Survey Theme Coral Demography Theme Coral Disease Theme Coral Reef Ecosystem Division Theme Coral Reef Ecosystem Program Theme ESD Theme Ecosystem Sciences Division Theme PIFSC Theme Pacific Islands Fisheries Science Center Theme RAMP Theme Reef Assessment and Monitoring Program Theme SfM Theme Structure from Motion Theme belt transect Temporal Triennial Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Aguihan > Aguihan Island (Aguijan) (14N145E0006) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Northern Mariana Islands > Northern Mariana Islands ( CNMI ) (18N146E0000) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Rota > Rota Island ( Luta ) (14N145E0007) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Sarigan Island > Sarigan Island (16N145E0003) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Northern Mariana Islands > Tinian > Tinian Island (14N145E0005) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Swains Atoll (11S171W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii (21N160W0000) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Kauai Island (22N159W0001 Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Molokai Island (21N157W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > French Frigate Shoals (24N166W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Lisianski Island (25N173W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Northwestern Hawaiian Islands (28N178W0000) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Pearl and Hermes Reef (27N176W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Kalawao > Kahoolawe Island (20N156W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Kauai > Niihau Island (21N160W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Lanai Island (20N156W0002 Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Maui Island (20N156W0004 Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaiian Islands (21N157W0027) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Baker Island (00N176W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Howland Island (00S176W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Johnston Atoll (16N169W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Baker Island > Baker Island (00N176W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands (21N157W0027) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii > Hawaii (21N160W0000 Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii Island > Hawaii Island (19N155W0003 Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kahoolawe Island > Kahoolawe Island (20N156W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Kauai Island > Kauai Island (22N159W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Lanai Island > Lanai Island (20N156W0002) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Maui Island > Maui Island (20N156W0004) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Molokai Island > Molokai Island (21N157W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Niihau Island > Niihau Island (21N160W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Howland Island > Howland Island (00S176W0001 Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Johnston Atoll > Johnston Atoll (16N169W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands (28N178W0000) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > French Frigate Shoals (24N166W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Lisianski Island (25N173W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Aguihan Island Reefs > Aguihan Island (Aguijan) (14N145E0006) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Mariana Archipelago > Northern Mariana Islands ( CNMI ) (18N146E0000) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Maug Island > Maug Island (20N145E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Pagan Island > Pagan Island (18N145E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Rota Island > Rota Island ( Luta ) (14N145E0007) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Saipan Island > Saipan Island (15N145E0002) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Sarigan Island > Sarigan Island (16N145E0003) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Tinian Island Reefs > Tinian Island (14N145E0005) Spatial NODC SEA AREA NAMES THESAURUS Coastal Waters of Hawaii Spatial NODC SEA AREA NAMES THESAURUS Equatorial Pacific Ocean Spatial NODC SEA AREA NAMES THESAURUS Marianas Trench Marine National Monument Spatial NODC SEA AREA NAMES THESAURUS Northwest Pacific Spatial NODC SEA AREA NAMES THESAURUS Pacific Remote Islands Marine National Monument Spatial NODC SEA AREA NAMES THESAURUS Papahanaumokuakea Marine National Monument Spatial NODC SEA AREA NAMES THESAURUS Rose Atoll Marine National Monument Spatial NODC SEA AREA NAMES THESAURUS South Pacific Ocean Spatial NODC SEA AREA NAMES THESAURUS: Central Pacific Ocean Spatial NODC SEA AREA NAMES THESAURUS: North Pacific Ocean Spatial American Samoa Spatial CNMI Spatial Commonwealth of the Northern Marianas Islands Spatial MHI Spatial Main Hawaiian Islands Spatial Marianas Spatial NWHI Spatial Northwestern Hawaiian Islands Spatial PMNM Spatial PRIA Spatial PRIMNM Spatial Pacific Remote Island Areas Instrument NODC INSTRUMENT TYPES THESAURUS photograph Instrument NODC INSTRUMENT TYPES THESAURUS scale Platform NODC PLATFORM NAMES THESAURUS HI'IALAKAI Platform NODC PLATFORM NAMES THESAURUS OSCAR ELTON SETTE Platform NODC PLATFORM NAMES THESAURUS RAINIER Platform NODC PLATFORM NAMES THESAURUS small boat Pacific Islands Fisheries Science Center Honolulu HI USA Data Set CSV Files Annually As more data are generated, we will continue to update this record. Table (digital) Dataset includes metadata for each survey site (site information, survey date and location); site characteristics (depth, reef type, habitat); data collection method (Diver or SfM); individual adult and juvenile coral 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. The raw data also include individual observations of crustose coralline algae diseases and Alcyonarian disease recorded disease type and lesion size (does not apply to surveys conducted after 2017). Finally, the third type of raw data include presence of other Anthozoans, such as other cnidarians including Alcyonareans, Zoantharians, Corallimorpharians, and Antipatharians (does not apply to PMNM surveys conducted in 2014 and 2015 or surveys conducted after 2017). Juvenile Coral Annotations Data Dictionary https://www.fisheries.noaa.gov/inport/item/63244 Adult Coral Annotations Data Dictionary https://www.fisheries.noaa.gov/inport/item/63239 Reference table for genus and species codes data dictionary https://www.fisheries.noaa.gov/inport/item/72887 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. NOAA Fisheries, ESD and funded by the NOAA CRCP 71560 Published / External On Going This entity describes the columns in the dataset for coral belt observations (adult) Data View Yes GISDAT This entity describes the columns in the dataset for coral belt observations (adult) Note a repeat segment flag was included to mark those repeated for internal review. If using data without repeats, filter for transectnum = 1 (transectnum 1 with repeat segment flag -1 means it was the original segment, transectnum 2 with repeat segment flag -1 means it was a repeated segment). 2 MISSIONID TEXT 30 Yes No Active Mission identifier. 3 REGION TEXT 20 Yes No Active Code for REGION_NAME. 4 REGION_NAME TEXT 30 No No Active The name of the region surveyed in the Pacific Islands region: American Samoa, Pacific Remote Island Areas, Mariana Archipelago, main Hawaiian Islands, Northwestern Hawaiian Islands. 5 ISLANDCODE TEXT 15 No No Active 3-letter code for ISLAND. 6 ISLAND TEXT 150 No No Active Name of island or atoll surveyed in the Pacific Islands region (REGION_NAME). 7 SITE TEXT 150 Yes No Active The code for the site surveyed at the island or atoll (ISLAND). Combines a 3-letter island code (ISLANDCODE) with a 2-5 digit site number. 8 LATITUDE NUMERIC 22 No No 38 Active Latitude in decimal degrees, WGS84, for the given SITE. 9 LONGITUDE NUMERIC 22 No No Active Longitude in decimal degrees, WGS84 for the given SITE. 11 REEF_ZONE TEXT 150 No No Active The zone for the given SITE (Forereef, Backreef, Protected Slope, Lagoon). 12 HABITAT_CODE TEXT 50 No No Active 3-letter code for HABITAT_TYPE. Habitat determination described in the 2018 SOP by Swanson et. al. 13 HABITAT_TYPE TEXT 30 No No Active Habitat type (e.g., aggregate reef, reef rubble, pavement) for the given SITE. 14 SITE_MIN_DEPTH NUMERIC 22 No No 5 0 Active Minimum SITE depth (ft). NULL if depth values were not recorded. When SFM derived, depth values will be the minimum and maximum depths of the scalebars recorded by divers at time of survey. 15 SITE_MAX_DEPTH NUMERIC 22 No No 5 0 Active Maximum SITE depth (ft). NULL if depth values were not recorded. When SFM derived, depth values will be the minimum and maximum depths of the scalebars recorded by divers at time of survey. 16 DEPTH_BIN TEXT 60 No No Active Classification of depth (shallow, mid, deep) based on midpoint between minimum and maximum depths of transect(s) of a given SITE. Shallow: >0-6 m, Mid: >6-18 m, Deep: >18-30 m 18 SITEVISITID NUMERIC 22 Yes No Active Unique identifier created each time a SITE is surveyed on a DATE_. 19 DATE_ DATE 7 Yes No Active Local date the survey was conducted. 20 OBS_DAY NUMERIC 22 No No Active Numeric day the survey was conducted (DATE_). 21 OBS_MONTH NUMERIC 22 No No 38 Active Numeric month the survey was conducted (DATE_). 22 OBS_YEAR NUMERIC 22 No No Active 4-digit year the survey was conducted (DATE_). 30 TRANSECTNUM NUMERIC No No Active Unique identifier for each transect surveyed within a SITE. A value of -999 denotes a transect with a repeated segment. 31 OG_OR_RPT_SEG NUMERIC No No Active Flag to indicate original segments (0), or those that were repeats of the segment and can be excluded (-1) 32 REPEAT_SEGMENT_YN NUMERIC 22 No No Active Flag (-1) to indicate that a re-survey of the same site/segment was done by an additional diver. This marks both the original segment that was repeated, and the replicate itself. This flag was added starting 2019 and will be null for prior years. 33 SEGMENT TEXT 150 No No Active Segment number (0,5,10,or 15). Segments are within a TRANSECT and are typically 1 x 2.5 m in size and situated 2.5 m apart. 34 SEGLENGTH NUMERIC 22 No No 28 8 Active Segment length (m). 35 SEGWIDTH NUMERIC 22 No No 38 8 Active Segment width (m). 37 COLONYID NUMERIC 22 No No 38 0 Active Coral colony identifier. NULL if no colony was observed, indicated with TAXONCODE/SPECIES = 'AAAA'. 38 COLONYLENGTH NUMERIC 22 No No 38 8 Active Length of adult coral colony (cm). Required if colony observed. Value -9 is a placeholder and represents a missing value. Length of adult Scleractinian (hard/stony) coral colonies >= 5 cm unless flagged as a fragment (FRAGMENT_YN = -1). 39 MORPHOLOGY TEXT 50 No No Active Coral morphology type (branching, columnar, encrusting, etc.). Required if colony observed. 40 MORPH_CODE TEXT 5 No No Active Code for MORPHOLOGY. 41 FRAGMENT_YN NUMERIC No No Active Flag to indicate observation is a coral fragment (-1), as opposed to a whole coral colony (0). Collection of this data began in 2017 and will be null prior. 42 OLDDEAD NUMERIC 22 No No 5 0 Active Percentage of older dead coral (0-100%), as opposed to recently dead coral recorded in RECENTDEAD. Required. Value -9 is a placeholder and represents a missing value. Sum of OLDDEAD + RECENTDEAD_1 + RECENTDEAD_2 + RECENTDEAD_3 should not exceed 100. 44 RECENTDEAD_1 NUMERIC No No Active Percentage of recently dead (freshly denuded skeleton not fouled by algae) coral (0-100%), as opposed to older dead coral recorded in OLDDEAD. Value -9 is a placeholder and represents a missing value. Sum of OLDDEAD + RECENTDEAD_1 + RECENTDEAD_2 + RECENTDEAD_3 should not exceed 100. 45 RECENT_GENERAL_CAUSE_CODE_1 TEXT 4 No No Active Code for RECENT_GENERAL_CAUSE_DESC_1. 46 RECENT_GENERAL_CAUSE_DESC_1 TEXT No No Active General cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_1. Required if RECENTDEAD_1 > 0. 47 RECENT_SPECIFIC_CAUSE_CODE_1 TEXT 4 No No Active Code for RECENT_SPECIFIC_CAUSE_DESC_1. 48 RECENT_SPECIFIC_CAUSE_DESC_1 TEXT No No Active Specific cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_1. Required if RECENTDEAD_1 > 0. 49 RECENTDEAD_2 NUMERIC 22 No No 5 0 Active Percentage of recently dead (freshly denuded skeleton not fouled by algae) coral (0-100%). Only used if more than one cause of coral mortality was observed. Sum of OLDDEAD + RECENTDEAD_1 + RECENTDEAD_2 + RECENTDEAD_3 should not exceed 100. 50 RECENT_GENERAL_CAUSE_CODE_2 TEXT 4 No No Active Code for RECENT_GENERAL_CAUSE_DESC_2. 51 RECENT_GENERAL_CAUSE_DESC_2 TEXT No No Active General cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_2. Required if RECENTDEAD_2 > 0. 52 RECENT_SPECIFIC_CAUSE_CODE_2 TEXT 4 No No Active Code for RECENT_SPECIFIC_CAUSE_DESC_2. 53 RECENT_SPECIFIC_CAUSE_DESC_2 TEXT No No Active Specific cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_2. Required if RECENTDEAD_2 > 0. 54 RECENTDEAD_3 NUMERIC No No Active Percentage of recently dead (freshly denuded skeleton not fouled by algae) coral (0-100%). Only used if more than two causes of coral mortality were observed. Added in 2018. Sum of OLDDEAD + RECENTDEAD_1 + RECENTDEAD_2 + RECENTDEAD_3 should not exceed 100. 55 RECENT_GENERAL_CAUSE_CODE_3 TEXT No No Active Code for RECENT_GENERAL_CAUSE_DESC_3. 56 RECENT_GENERAL_CAUSE_DESC_3 TEXT No No Active General cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_3. Required if RECENTDEAD_3 > 0. 57 RECENT_SPECIFIC_CAUSE_CODE_3 TEXT No No Active Code for RECENT_SPECIFIC_CAUSE_DESC_3. 58 RECENT_SPECIFIC_CAUSE_DESC_3 TEXT No No Active Specific cause of recently dead (freshly denuded skeleton not fouled by algae) coral recorded in RECENTDEAD_3. Required if RECENTDEAD_3 > 0. 63 CONDITION_1 TEXT No No Active Code for CONDITION_1_DESC. 64 CONDITION_1_DESC TEXT No No Active Condition/disease observed affecting the coral colony (e.g., bleaching, infection, infestation, pigmentation response, growth anomaly, etc.), but which does not cause RECENT DEAD. 65 EXTENT_1 NUMERIC No No Active Extent of condition/disease observed on coral colony (5-100). Required when CONDITION_1 is recorded. Sum of EXTENT_1, EXTENT_2 and EXTENT_3 must not exceed 100. Value -9 is a placeholder and represents a missing value. 66 SEVERITY_1 NUMERIC No No Active Severity of condition/disease observed on coral colony (scale of 1-5 from least to most severe). Required only when CONDITION_1 = Environmental / Thermal Bleaching (condition code = BLE or BLP). Value -9 is a placeholder and represents a missing value. 67 CONDITION_2 TEXT No No Active Code for CONDITION_2_DESC. 68 CONDITION_2_DESC TEXT No No Active Condition/disease observed affecting the coral colony (e.g., bleaching, infection, infestation, pigmentation response, growth anomaly, etc.), but which does not cause RECENT DEAD. 68 EXTENT_2 NUMERIC No No Active Extent of condition/disease observed on coral colony (5-100). Required when CONDITION_2 is recorded. Sum of EXTENT_1, EXTENT_2 and EXTENT_3 must not exceed 100. 69 SEVERITY_2 NUMERIC No No Active Severity of condition/disease observed on coral colony (scale of 1-3 from least to most severe). Required only when CONDITION_2 = Environmental / Thermal Bleaching (condition code = BLE or BLP). 70 CONDITION_3 TEXT No No Active Code for CONDITION_3_DESC. 71 CONDITION_3_DESC TEXT No No Active Condition/disease observed affecting the coral colony (e.g., bleaching, infection, infestation, pigmentation response, growth anomaly, etc.), but which does not cause RECENT DEAD. Only used if more than two coral conditions/diseases were observed. 72 EXTENT_3 NUMERIC No No Active Extent of condition/disease observed on coral colony (5-100). Required when CONDITION_3 is recorded. Sum of EXTENT_1, EXTENT_2 and EXTENT_3 must not exceed 100. 73 SEVERITY_3 NUMERIC No No Active Severity of condition/disease observed on coral colony (scale of 1-5 from least to most severe). Required only when CONDITION_3 = Environmental / Thermal Bleaching (condition code = BLE or BLP). 74 TAXONCODE TEXT 150 No No Active 4-letter code for TAXONNAME when recorded. Code AAAA represents a SEGMENT that was surveyed and no individual colonies were found. Note taxonomic codes and names may be updated; refer to column TAXONCODE_2024 for the most recent taxoncode. 75 TAXONCODE_2024 TEXT No No Active Taxoncode of coral colony using the most recent taxoncode. Taxoncodes that were updated are noted in the reference table for genus and species codes. Note updated genus codes can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genus codes changed. 76 TAXONNAME TEXT 765 No No Active Scientific name of observed organism to the finest taxonomic resolution that divers can identify a colony to, either to species or genus level identification (see RANK). Null if no colony was observed with taxoncode 'AAAA' 77 RANK TEXT 20 No No Active Lowest defined rank in taxonomic hierarchy, from the World Registry of Marine Species (WoRMS) database. NULL if TAXONCODE = 'UNKN'. 78 PHYLUM TEXT 255 No No Active Taxonomic classification: Phylum of observed organism (TAXONNAME). 79 CLASS TEXT 60 No No Active Taxonomic classification: Class of observed organism (TAXONNAME). 80 S_ORDER TEXT 255 No No Active Taxonomic classification: Order of observed organism (TAXONNAME). 81 FAMILY TEXT 255 No No Active Taxonomic classification: Family of observed organism (TAXONNAME). 82 GENUS_CODE TEXT 12 No No Active 4-letter code for GENUS. Note updated genus codes can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genus codes were updated. 83 GENUS TEXT 300 No No Active Taxonomic classification: Genus name of observed organism (TAXONNAME). NULL if TAXONNAME = Unknown Scleractinian. Note updated genera can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genera were updated. 84 SCIENTIFIC_NAME TEXT 255 No No Active Taxonomic classification: the true scientific name (genus and species) of the observed organism (TAXONNAME). If NULL, organism not identified to species taxonomic level (see RANK). 85 APHIAID TEXT 20 No No Active Aphia ID from the World Registry of Marine Species (WoRMS) database. Null if organism not identified to species taxonomic level (see RANK). If value = 0, the species does not exist in WoRMS. 86 SURVEYMETHOD TEXT No No Active Data collection method for belt transects to indicate diver or SfM-based surveys. Collecting demographic data with SfM imagery (GIS) began in 2023. 87 EX_BOUND NUMERIC No No Active Flag (-1) to indicate a coral with a max diameter that expands past image boundaries if observation comes from an SfM survey. Will be null for data not derived via SfM. 71561 Published / External Completed Data Table Yes GISDAT This entity describes the columns in the dataset for coral belt observations (juvenile) Note a repeat segment flag was included to mark those repeated for internal review. If using data without repeats, filter for transectnum = 1 (transectnum 1 with repeat segment flag -1 means it was the original segment, transectnum 2 with repeat segment flag -1 means it was a repeated segment). 2 MISSIONID TEXT 30 Yes No Active Mission Identifier. 3 REGION TEXT 20 Yes No Active Code for REGION_NAME. 4 REGION_NAME TEXT 30 No No Active The name of the region surveyed in the Pacific Islands region: American Samoa, Pacific Remote Island Areas, Mariana Archipelago, main Hawaiian Islands, Northwestern Hawaiian Islands. 5 ISLANDCODE TEXT 15 No No Active 3-letter code for ISLAND. 6 ISLAND TEXT 150 No No Active Name of island or atoll surveyed in the Pacific Islands region (REGION_NAME). 7 SITE TEXT 150 Yes No Active The code for the site surveyed at the island or atoll (ISLAND). Combines a 3-letter island code (ISLANDCODE) with a 2-4 digit site number. 8 LATITUDE NUMERIC 22 No No Active Latitude in decimal degrees, WGS84, for the given SITE. 9 LONGITUDE NUMERIC 22 No No 38 Active Longitude in decimal degrees, WGS84 for the given SITE. 10 REEF_ZONE TEXT 150 No No Active The zone for the given SITE (Forereef, Backreef, Protected Slope, Lagoon). 11 HABITAT_TYPE TEXT 30 No No Active Habitat type (e.g., aggregate reef, reef rubble, pavement) for the given SITE. NULL if data were not recorded. 11 HABITAT_CODE Text No No Active 3-letter code for habitat type (e.g. aggregate reef, reef rubble, pavement). NULL if data were not recorded. 12 SITE_MIN_DEPTH NUMERIC 22 No No 5 0 Active Minimum SITE depth (ft). NULL if depth values were not recorded. When SFM derived, depth values will be the minimum and maximum depths of the scalebars recorded by divers at time of survey. 13 SITE_MAX_DEPTH NUMERIC 22 No No 5 0 Active Maximum SITE depth (ft). NULL if depth values were not recorded. When SFM derived, depth values will be the minimum and maximum depths of the scalebars recorded by divers at time of survey. 14 DEPTH_BIN TEXT 60 No No Active Classification of depth (shallow, mid, deep) based on midpoint between minimum and maximum depths of transect(s) for the given SITE. Shallow: >0-6 m, Mid: >6-18 m, Deep: >18-30 m 15 SITEVISITID NUMERIC 22 Yes No 38 Active Unique identifier created each time a SITE is surveyed on a DATE_. 16 DATE_ DATE 7 Yes No Active Local date the survey was conducted. 17 OBS_DAY NUMERIC 22 No No 38 Active Numeric day the survey was conducted (DATE_). 18 OBS_MONTH NUMERIC 22 No No Active Numeric month the survey was conducted (DATE_). 19 OBS_YEAR NUMERIC 22 No No 38 Active 4-digit year the survey was conducted (DATE_). 22 SURVEYMETHOD TEXT No No Active Data collection method for belt transects for diver or SfM-based surveys. Collecting demographic data with SfM imagery (GIS) began in 2023. 25 TRANSECTNUM NUMERIC No No Active Unique identifier for each transect surveyed within a SITE. A value of -999 denotes a transect with a repeated segment. 27 SEGMENT TEXT 150 No No Active Segment number (0,5,10, or 15). Segments are within a TRANSECT and are typically 1 x 1 m in size and situated 2.5 m apart. 28 REPEAT_SEGMENT_YN NUMERIC 22 No No Active Flag (-1) to indicate that a re-survey of the same site/segment was done by an additional diver. This marks both the original segment that was repeated, and the replicate itself. This flag was added starting 2019 and will be null for prior years 28 OG_OR_RPT_SEG NUMERIC No No Active Flag to indicate original segments (0), or those that were repeats of the segment and can be excluded (-1) 29 SEGLENGTH NUMERIC 22 No No 28 8 Active Segment length (m). 30 SEGWIDTH NUMERIC 22 No No 38 8 Active Segment width (m), usually 1 m. 32 COLONYID NUMERIC 22 No No 28 0 Active Coral colony identifier. NULL if TAXONCODE/SPECIES = 'AAAA' indicating no colony observed. 33 COLONYLENGTH NUMERIC 22 No No 38 8 Active Length of juvenile coral colony (<=5 cm). Required. Value -9 is a placeholder and represents a missing value. 34 COLONYWIDTH NUMERIC 22 No No Active Width of juvenile coral colony (<=5 cm). Required. Value -9 is a placeholder and represents a missing value. ESD stopped recording COLONYWIDTH in 2018. 35 MORPHOLOGY TEXT 50 No No Active Coral morphology type (branching, columnar, encrusting, etc.). Required. Not recorded in 2013. 35 MORPH_CODE TEXT No No Active Code for coral morphology type (branching, columnar, encrusting, etc.). Not recorded in 2013. 36 TAXONCODE TEXT 150 No No Active 4-letter code for TAXONNAME at time of observation. Code AAAA represents a SEGMENT that was surveyed and no individual colonies were found. Note taxoncodes may have been updated in reference table. 36 TAXONCODE_2024 TEXT No No Active Taxoncode of coral colony using the most recent taxoncode. Taxoncodes that were updated are noted in the reference table for genus and species codes. Note updated genus codes can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genus codes changed. 37 TAXONNAME TEXT 765 No No Active Scientific name of observed organism to the finest taxonomic resolution that divers can identify a colony to, either to species or genus level identification (see RANK). Taxonname is for the TAXONCODE. Updates to taxon names are noted in the reference table. 38 RANK TEXT 20 No No Active Lowest defined rank in taxonomic hierarchy, from the World Registry of Marine Species (WoRMS) database. 39 PHYLUM TEXT 255 No No Active Taxonomic classification: Phylum of observed organism (TAXONNAME). 40 CLASS TEXT 60 No No Active Taxonomic classification: Class of observed organism (TAXONNAME). 41 S_ORDER TEXT 255 No No Active Taxonomic classification: Order of observed organism (TAXONNAME). 42 FAMILY TEXT 255 No No Active Taxonomic classification: Family of observed organism (TAXONNAME). 43 GENUS_CODE TEXT 12 No No Active 4-letter code for GENUS. Note updated genus codes can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genus codes changed. 44 GENUS TEXT 300 No No Active Taxonomic classification: Genus name of observed organism (TAXONNAME). Note updated genera can be looked up using the reference table; for taxoncodes 'MVAL', 'MONS', 'MCUR', or 'MANN', genera changed. 45 SCIENTIFIC_NAME TEXT 255 No No Active Taxonomic classification: the true scientific name (genus and species) of the observed organism (TAXONNAME). If NULL, organism not identified to species taxonomic level (see RANK). 46 APHIAID TEXT 20 No No Active Aphia ID from the World Registry of Marine Species (WoRMS) database. Null if organism not identified to species taxonomic level (see RANK). If value = 0, species does not exist in WoRMS. 72887 Published / External Data Table Reference table for genus and species codes; includes former and current coral species codes. 1 TAXONCODE TEXT No No Active 4-letter code for TAXONNAME 2 TAXONNAME TEXT No No Active Scientific name of observed organism to the finest taxonomic resolution that divers can identify a colony to, either to species or genus level identification (see RANK). 3 GENUS TEXT No No Active Taxonomic classification: Genus name or lowest classification possible of observed organism (TAXONNAME). NULL if TAXONNAME = Unknown Scleractinian 4 RANK TEXT No No Active Lowest defined rank in taxonomic hierarchy. Multi-species and multi-genus complexes are identified in RANK. 5 GENUSCODE TEXT No No Active 4-letter code for GENUS. 6 NEW_TAXONCODE TEXT No No Active Updated 4-letter code for TAXONNAME if taxon was reclassified. Data Set Credit 2013 Organization NOAA Coral Reef Conservation Program CRCP 1305 East West Highway 10th Floor Silver Spring MD 20910-3281 (301) 713-3155 https://coralreef.noaa.gov Link to the NOAA Coral Reef Conservation Program website Online Resource Data Steward 2023 Person Charendoff, Jonathan jonathan.charendoff@noaa.gov Distributor 2023 Organization NOAA National Centers for Environmental Information NCEI ncei.info@noaa.gov https://ror.org/04r0wrp59 https://www.ncei.noaa.gov/contact NCEI Contact Information Information for contacts at NCEI. Online Resource Metadata Contact 2023 Person Luers, Lori H lori.luers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA Originator 2013 Organization Pacific Islands Fisheries Science Center PIFSC pifsc.info@noaa.gov https://ror.org/02apffz65 1845 Wasp Blvd. Honolulu HI 96818 USA 808-725-5360 https://www.pifsc.noaa.gov Pacific Island Fisheries Science Center homepage Online Resource 8:00 a.m. - 4:30 p.m. Point of Contact 2023 Person Oliver, Thomas thomas.oliver@noaa.gov https://orcid.org/0000-0002-0684-1287 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5444 Ground Condition U.S. Pacific Island Areas 144.634585 -154.804172 28.457971 -14.559759 Range 2013-08-02 2013-10-29 Main Hawaiian Islands 2013: Hawaii, Kauai, Lanai, Maui, Molokai, Niihau, Oahu Range 2014-03-16 2014-08-26 Mariana Archipelago 2014: Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guam, Guguan, Maug, Pagan, Rota, Saipan, Sarigan, Tinian, Wake PNMN 2014: French Frigate Shoals, Lisianski, Midway Range 2015-01-29 2015-08-21 American Samoa and Pacific Remote Island Areas 2015: Baker, Howland, Jarvis, Johnston, Kingman, Palmyra, Ofu & Olosega, Rose, Swains, Tau, Tutuila. PMNM 2015: French Frigate Shoals, Kure, Laysan, Lisianski, Maro, Midway, Pearl and Hermes Range 2016-05-01 2016-09-27 Hawaiian Archipelago 2016: Hawaii, Maui, Kahoolawe, Lanai, Molokai, Oahu, Kauai, Niihau, French Frigate Shoals, Kure, Lisianski, Pearl and Hermes American Samoa and Pacific Remote Island Areas 2016: Jarvis, Rose Range 2017-04-02 2017-09-27 Mariana Archipelago 2017: Agrihan, Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guam, Guguan, Jarvis, Maug, Pagan, Rota, Saipan, Sarigan, Tinian, Wake. PMNM 2017: French Frigate Shoals, Kure, Laysan, Lisianksi, Midway, Pearl and Hermes. Range 2018-06-08 2018-08-11 American Samoa and Pacific Remote Island Areas 2018: Baker, Howland, Jarvis, Kingman, Palmyra, Ofu & Olosega, Rose, Swains, Tau, Tutuila Range 2019-04-21 2019-08-06 Main Hawaiian Islands 2019: Hawaii, Maui, Kahoolawe, Molokai, Lanai, Oahu, Kauai, Niihau Range 2022-05-10 2022-06-01 Mariana Archipelago 2022: Asuncion, Guam, Maug, Pagan, Rota, Saipan, Tinian Range 2023-03-15 2023-08-08 American Samoa and Pacific Remote Island Areas 2023. Islands visited: Tutuila, Ofu and Olosega, Tau, Swains, Rose Atoll, Howland, and Baker Islands. Range 2024-05-13 2024-08-27 MP2404, SE2406 Includes data from shore-based O'ahu missions MP2404 and NOAA ship surveys in the Main Hawaiian Islands and Northwestern Hawaiian Islands in SE2406 Custom Unclassified Not applicable Not applicable 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 Ocean Acidification Program (OAP). The analysis and interpretations presented here are solely that of the current authors. Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive. None Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data. Example: Pacific Islands Fisheries Science Center, 2023: National Coral Reef Monitoring Program: Stratified Random Surveys (StRS) of Coral Demography (Adult and Juvenile Corals) across the US Pacific since 2013, https://www.fisheries.noaa.gov/inport/item/71550. None None https://accession.nodc.noaa.gov/0298217 2023 Organization NOAA National Centers for Environmental Information https://ror.org/04r0wrp59 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 it is recommended that analysis is performed at that level. This table also indicates any changes to taxonomic codes that are present in the original data. csv (comma-separated values) CSV - Comma Separated Values (Text) https://accession.nodc.noaa.gov/0298217 2023 Organization NOAA National Centers for Environmental Information https://ror.org/04r0wrp59 NCRMP_CORAL_ADU_OBS_2013-2024.csv Metadata for each survey site (site information, survey date, and location), site characteristics (depth, reef type, habitat), data collection method (Diver or SfM) 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 across the US Pacific from 2013 to present. Note a repeat segment flag was included in 2019 to mark those repeated for internal review. To use without repeats, filter for OG_OR_RPT= 0 or filter out TRANSECTNUM = -999. Analysis is recommended at genus level; note any changes to genus codes using the reference table provided. CSV - Comma Separated Values (Text) 90MB https://accession.nodc.noaa.gov/0298217 2023 Organization NOAA National Centers for Environmental Information https://ror.org/04r0wrp59 NCRMP_CORAL_JUV_OBS_2013-2024.csv Metadata for each survey site (site information, survey date and location), site characteristics (depth, reef type, habitat), data collection method (diver or SfM), and individual juvenile coral colony observations identified to the lowest taxonomic level possible (genus) including morphology and empirical size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division across the US Pacific from 2013 to present. Note a repeat segment flag was included in 2019 to mark those repeated for internal review. To use without repeats, filter for OG_OR_RPT_SEG = 0 or TRANSECTNUM = -999. Analysis is recommended at genus level; note any changes to genus codes using the reference table provided. CSV - Comma Separated Values (Text) 15MB ftp://ftp.nodc.noaa.gov/nodc/archive/arc0101/0157633/ Benthic Monitoring Briefs since 2016 Online Resource PDF NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (ESD) Benthic Monitoring Briefs available for FTP download for surveys starting in 2016. Monitoring briefs provide timely release of a summary overview of monitoring effort and preliminary data following a research expedition led by ESD, including Pacific Reef Assessment and Monitoring Program cruises and other missions. This type of report is intended as an initial and provisional summary of the data collected, and the information contained in these briefs is subject to change. https://repository.library.noaa.gov/view/noaa/22060 Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update Online Resource PDF SOPs for Benthic REA Surveys from 2018 https://repository.library.noaa.gov/view/noaa/22753 Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures Online Resource PDF SOP for data collection from Structure from Motion surveys. https://www.coris.noaa.gov/monitoring/ National Coral Reef Monitoring Program Online Resource HTML NOAA National Coral Reef Monitoring Program (NCRMP) website. https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific Coral Reefs in the Pacific Online Resource HTML NOAA Fisheries Website https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific#survey-methods Survey Methods Online Resource NOAA Fisheries, Pacific Islands website https://www.fisheries.noaa.gov/region/pacific-islands#science NOAA Fisheries Pacific Islands Region - Science Overview Online Resource NOAA Fisheries Website PIFSC Oracle database view: V_NCRMP_CORAL_OBS_E and V_NCRMP_CORAL_OBS_F For SfM-derived coral demography starting in 2023, a Canon SL2 or SL3 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25 m long were used underwater to provide a scale and depth for each mosaic. Orthomosaic images were created using Agisoft Metashape (version 1.8.0 or later). The custom software 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). The data set derived from the SfM 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. This data should be assessed at the genus level due to variabilities in identifying at genus or species level. Observations were made by experienced benthic survey personnel who have been trained, undergone a series of calibration surveys and coral taxon identification testing, and have met a set of minimum standards for colony assessment and taxon identification in each region. The accuracy of species and genus level identification was high. The lowest taxonomic level of coral identification was genus except for a select number of species that were consistently identified to species by all divers conducting the surveys. The number of species may change for each survey year depending on the experience and training of the benthic divers. The list of coral species is included for each survey year. In other words, the individual records within each data set may include many more species than encompassed by the lists; however, these were not consistently identified across all surveys so these records should be assessed at the genus level. 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. Handheld GPS units were used to locate random sites and mark site locations. The taxon code AAAA is included where the segment was surveyed and no individual colonies were found in both the juvenile and adult colony records. These are true zeros. The value -9 is a placeholder or missing value for the fields: colony length, colony width (juveniles), extent, and severity. 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. 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. Periodic examination of the data is conducted throughout each mission to check for diver bias or other discrepancies. While data are collected by divers and from SfM imagery, the same methods were applied to both survey types. Quality control of the data occurred at a few stages from data entry to data ingestion into the Oracle database. Observations, including species identification, are periodically checked during expeditions for consistency between and among divers. Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by individual divers checking entry errors at a separate time. Following a mission, the data is then run through rigorous quality control checks by the data management team before the data are migrated to the Oracle database. The data is quality controlled against the physical data sheets following data entry. There are also several queries in the MS Access / Oracle database to flag errors based on pre-defined criteria. Given the size of the data set, there remains some possibility of typographical or other errors. Prior to generating the 3D dense point clouds and 2D orthomosaics , the JPEG imagery was 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. During annotation in ArcGIS, the original JPEG imagery was viewed alongside the orthomosaic using the Viscore Image View feature to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic. Annotations created in ArcGIS were quality controlled using a multi-stage process. Data were first 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 were 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 were identified for a given annotator, that annotator reviewed and corrected each site if they did find errors. Yes Unknown Yes No Unknown NCEI-MD Unknown The data is captured in several locations: physical data sheets, MS Access cruise database, and PIFSC Oracle database. The physical data sheets are housed at PIFSC. The MS Access cruise database is regularly backed up by the cruise data manager while at sea. The PIFSC Oracle database is regularly backed up by PIFSC ITS. Coral demographic data has been collected at stratified-random sites (StRS) across US Pacific Island Regions for the National Coral Reef Monitoring Program (NCRMP) since 2013. The methodology for selecting StRS and analyzing this data can be found in the sources listed below. The methodology has continued to evolve. Starting in 2023, some data was collected with GIS analysis alongside in-water diver surveys. 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. 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 Person John Burns Publisher 2015-07-07 https://doi.org/10.7717/peerj.1077 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. 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 Organization Pacific Islands Fisheries Science Center Originator 2021-05-28 https://www.frontiersin.org/articles/10.3389/fmars.2021.647943/full Frontiers Journal Comparing Coral Colony Surveys From In-Water Observations and Structure-From-Motion Imagery Shows Low Methodological Bias 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. 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. Person Vid Petrovic Publisher 2014-01-01 https://escholarship.org/uc/item/58z4j8k2 Mediterranean Archaeology and Archaeometry VISUALIZING HIGH RESOLUTION THREE-DIMENSIONAL AND TWO-DIMENSIONAL DATA OF CULTURAL HERITAGE SITES 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. 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 Organization Pacific Islands Fisheries Science Center Originator 2019-12-30 https://repository.library.noaa.gov/view/noaa/22753 NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC 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. 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 https://repository.library.noaa.gov/view/noaa/18267 NOAA Institutional Repository Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys 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). Includes details on how to determine habitat types. 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. https://doi.org/10.25923/cydj-z260 Organization NMFS PIFSC ESD Originator 2024-04-01 https://doi.org/10.25923/cydj-z260 NOAA technical memorandum NMFS PIFSC 2023 updated SOP for processing imagery using SfM.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. Starting 2023, coral demography began being measured via SfM in addition to in-situ diver surveys. Imagery must be processed to create SfM models that then get annotated. 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 Organization Pacific Islands Fisheries Science Center Originator 2020-01-31 https://repository.library.noaa.gov/view/noaa/23951 NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC 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). 1 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). Person Oliver, Thomas thomas.oliver@noaa.gov https://orcid.org/0000-0002-0684-1287 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5444 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 2 At each site, benthic Rapid Ecological Assessment (REA) surveys were conducted within one 10 sq. meter belt transect. Transects were 18 meters in length. Adult coral colonies (>=5 cm) were surveyed within four (1.0 x 2.5 m) segments at 5 meter increments along the 18 meter transect in the following manner: 0-2.5 m (segment 1); 5.0-7.5 m (segment 3); 10-12.5 m (segment 5); and 15-17.5 m (segment 7). All colonies whose center fell within 0.5 m on either side of each transect line were identified to lowest taxonomic level possible (species or genus), measured for size (maximum diameter to nearest cm), and morphology was noted. In addition, partial mortality and condition of each colony was assessed. Partial mortality was estimated as percent of the colony in terms of old dead and recent dead. The cause of recent mortality was identified if possible. The condition of each colony including disease (not attributed to recent tissue loss) and bleaching was noted along with the extent (percent of colony affected) and level of severity (range from moderate to acute). The lowest taxonomic level of coral identification was genus except for a select number of species consistently identified to species by all divers conducting the surveys. The number of species may change for each survey year depending on the experience and training of the benthic divers conducting the surveys. The list of coral species is included for each survey year. Juvenile coral colonies (<5 cm) were surveyed within three (1.0 x 1.0 m) segments along the same transect: 0-1.0 m (segment 1); 5.0-6.0 m (segment 3); and 10.0-11.0 m (segment 5). Juvenile colonies were distinguished in the field by a distinct tissue and skeletal boundary (not a fragment of a larger colony). Each juvenile colony was identified to lowest taxonomic level (genus or species) and measured for size by recording both the maximum and perpendicular diameter to the nearest 2 mm. Person Oliver, Thomas thomas.oliver@noaa.gov https://orcid.org/0000-0002-0684-1287 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5444 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 3 Structure from Motion (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. Person Charendoff, Jonathan jonathan.charendoff@noaa.gov 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 4 SfM 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 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. Person Charendoff, Jonathan jonathan.charendoff@noaa.gov 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 5 In ArcGIS, each SfM 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). Person Charendoff, Jonathan jonathan.charendoff@noaa.gov 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 6 SfM derived 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. Person Charendoff, Jonathan jonathan.charendoff@noaa.gov 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 7 Raw data from in situ and SfM surveys include individual colony records with the corresponding physical data which reflect the description of the site. An individual colony record for adult corals includes colony species/genus identification, morphology, maximum diameter (cm), percent old dead, percent recent dead, cause of recent dead general category, cause of recent dead specific category, condition, extent and severity. Juvenile coral colony records include colony species/genus identification, morphology, maximum diameter (cm) and perpendicular diameter (cm). For species level identification of adult and juvenile corals, check the species list to ensure species identification across all divers conducting the surveys. The physical data for all records includes the following: region, island, site, date (day, month, year), latitude (dd), longitude (dd), transect, segment, segment length, segment width, minimum depth (ft), maximum depth (ft), and survey type. Person Oliver, Thomas thomas.oliver@noaa.gov https://orcid.org/0000-0002-0684-1287 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5444 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 Not Applicable Not Applicable 71560 Entity 71561 Entity 72887 Entity 22790 Data Set Cross Reference 36164 Data Set Cross Reference 36165 Data Set Cross Reference 36166 Data Set Cross Reference 63095 Data Set Cross Reference 25260 Data Set Cross Reference 63097 Data Set Cross Reference gov.noaa.nmfs.inport:71550 Lori Luers 2023-11-28T21:17:03 Lori Luers 2026-07-02T21:20:35 2024-10-22 Pacific Islands Fisheries Science Center PIFSC 1845 Wasp Blvd. Honolulu HI 96818 USA 808-725-5300 https://www.pifsc.noaa.gov 8:00 a.m. - 4:30 p.m. 1001 Public No No 2022-05-11 1 Year 2023-05-11