gov.noaa.nmfs.inport:63093 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) Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014 SfM-Derived Coral Vital Rates Annotations 2022-07-26 creation 2025-09 publication NOAA/NMFS/EDM 63093 https://www.fisheries.noaa.gov/inport/item/63093 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://coralreef.noaa.gov/ WWW:LINK-1.0-http--link NOAA Coral Reef Conservation Program NOAA Coral Reef Conservation Program (CRCP) website. download https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific WWW:LINK-1.0-http--link Coral Reefs in the Pacific NOAA Fisheries Website download https://www.fisheries.noaa.gov/region/pacific-islands#science WWW:LINK-1.0-http--link NOAA Fisheries Pacific Islands Region - Science Overview overview of NOAA Pacific islands jurisdiction download tableDigital Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649 The data described here are coral planar area measurements derived from the analysis of benthic photomosaic imagery collected at fixed sites across Pacific Island regions since 2014. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers. Imagery archival is documented separately here: https://www.fisheries.noaa.gov/inport/item/63091. All sites were surveyed at least twice and image collection intervals ranged from a few minutes (for error estimation) to 5 years apart. In situ surveys, post-processing, and analysis were funded by NOAA Coral Reef Conservation Program (CRCP) and Ocean Acidification Program (OAP). Data collection was conducted by the NOAA Fisheries, Ecosystem Sciences Division (ESD). Survey sites consisted of sites previously established by collaborators from Scripps Institution of Oceanography, starting as far back as 2014, and new sites established in 2019 by NOAA ESD. During each survey, physical markings which identify each permanent survey site were either established or found using GPS coordinates previously collected. During image collection, the diver swam at a constant distance from the bottom of the reef while continuously capturing overlapping photographs, capturing approximately 100 m2 of reef habitat. 3D dense point clouds (DPCs) and 2D orthorectified images (orthoprojections) derived from these photographs were used to to measure changes in coral vital rates (e.g. recruitment, mortality, growth) over time. Due to the labor-intensive and time-consuming nature of coral annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. Each site was sub-sampled by randomly distributing a minimum of 10 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated (n >/= 30 for each target coral species). The target taxa species vary by region and include Acropora, Montipora, Pocillopora, Porites. In total, this dataset includes planar area and associated vital rates measurements for 5 coral species in 2 genera (Pocillopora and Porites) at 14 sites throughout the Hawaiian Archipelago, 3 genera (Pocillopora, Porites and Acropora) at 10 sites throughout the Mariana Archipelago and 4 genera (Pocillopora, Porites, Acropora and Montipora) at 11 sites across American Samoa and Pacific Remote Islands and Atolls (PRIAs). The purpose of the SfM surveys of permanent sites throughout the U.S. Pacific is to track coral vital rates (e.g. growth, mortality, recruitment) and how they vary across taxon, regions, and environmental gradients. This study leverages SfM, an emerging photogrammetry technique, to allow efficient data collection alongside NCRMP essential efforts. NOAA Fisheries, PIFSC Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program and Ocean Acidification Program onGoing Oliver, Thomas (808)725-5444 1845 Wasp Blvd. Honolulu HI 96818 USA thomas.oliver@noaa.gov pointOfContact Amir, Corinne corinne.amir@noaa.gov custodian notPlanned In 2023, Surface_Area and nPatches have been added to the 2023 dataset. In 2022, T0 and T1_PatchName_G, StartingSize and EndingSize are not included in the dataset. Additionally, Shape_Length, Shape_Area and ColonyName have been added to the 2022 dataset. 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 > BENTHIC EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF theme Global Change Master Directory (GCMD) Science Keywords 17.0 OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > AMERICAN SAMOA OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > BAKER ISLAND OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HOWLAND ISLAND 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 NOAA Coral Reef Conservation Program theme CRCP Project Numeric Data Sets > Benthic theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat EARTH SCIENCE > Biosphere > Zoology > Corals EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Growth EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals) EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs EARTH SCIENCE > Oceans > Marine Biology > Coral Communities theme CoRIS Theme Thesaurus CORAL CORAL - COLONY SIZE CORAL - SPECIES IDENTIFICATION theme NODC DATA TYPES THESAURUS derived products theme NODC OBSERVATION TYPES THESAURUS CORAL REEF STUDIES Coral Reef Conservation Program Ocean Acidification Program theme NODC PROJECT NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division theme NODC SUBMITTING INSTITUTION NAMES THESAURUS (14S170W0042) COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000) COUNTRY/TERRITORY > Northern Mariana Islands > Asuncion Island > Asuncion Island (19N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Maug > Maug Island (20N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Pagan > Pagan Island (18N145E0001) COUNTRY/TERRITORY > Northern Mariana Islands > Saipan > Saipan Island (15N145E0002) 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 > Tutuila Island (14S170W0016) COUNTRY/TERRITORY > United States of America > American Samoa > Ofu Island > Ofu (14S169W0002) COUNTRY/TERRITORY > United States of America > American Samoa > Olosega Island > Olosega (14S169W0016) COUNTRY/TERRITORY > United States of America > American Samoa > Ta'u Island > Ta'u (14S169W0015) COUNTRY/TERRITORY > United States of America > American Samoa > Tutuila Island > Fagasa Bay (14S170W0014) COUNTRY/TERRITORY > United States of America > American Samoa > Tutuila Island > Fagatele Bay (14S170W0002) COUNTRY/TERRITORY > United States of America > Guam > Guam (13N144E0000) COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Kure Atoll (28N178W0001) 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 > 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) Coastal Waters of Hawaii OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000) OCEAN BASIN > Pacific Ocean > American Samoa > Manu'a Islands (14S170W0038) OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001) OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016) 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 > Maui Island > Maui Island (20N156W0004) 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 > Northwestern Hawaiian Islands (28N178W0000) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Kure Atoll (28N178W0001) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Northwestern Hawaiian Islands > Pearl and Hermes Reef (27N176W0001) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Asuncion Island > Asuncion Island (19N145E0001) OCEAN BASIN > Pacific Ocean > Western Pacific Ocean > Guam > Guam (13N144E0000) 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 > Saipan Island > Saipan Island (15N145E0002) place CoRIS Place Thesaurus Central Pacific Ocean Equatorial Pacific Ocean North Pacific Ocean Pacific Remote Islands Marine National Monument Papahanaumokuakea Marine National Monument Rose Atoll Marine National Monument South Pacific Ocean place NODC SEA AREA NAMES THESAURUS NW Pacific place NODC SEA AREA NAMES THESAURUS: Agisoft Metashape ArcGIS TagLab Viscore photograph scale instrument NODC INSTRUMENT TYPES THESAURUS HI'IALAKAI OSCAR ELTON SETTE RAINIER platform NODC PLATFORM NAMES THESAURUS CNMI CRED CREP Commonwealth of the Northern Marianas Islands Coral Reef Ecosystem Division Coral Reef Ecosystem Program ESD Ecosystem Sciences Division NCRMP PIFSC Pacific Islands Fisheries Science Center RAMP Reef Assessment and Monitoring Program Scripps Institution of Oceanography SfM Structure from Motion theme MHI Main Hawaiian Islands Marianas NWHI Northwestern Hawaiian Islands PMNM PRIA PRIMNM Pacific Remote Island Area Pacific Remote Islands Marine National Monument Papahānaumokuākea Marine National Monument place DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Structure From Motion project InPort otherRestrictions Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/63093. 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 Sciences Division, Pacific Islands Fisheries Science Center, 2023: Structure from Motion (SfM) Coral Vital Rates Annotations derived from Fixed Site Imagery across the U.S. Pacific since 2014, https://www.fisheries.noaa.gov/inport/item/63093. 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 Structure from Motion (SfM) benthic images collected from Fixed Sites across the U.S. Pacific since 2019 NOAA/NMFS/EDM 63091 crossReference NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 63093 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/63093.pdf WWW:LINK-1.0-http--link NOAA Data Management Plan (DMP) NOAA Data Management Plan for this record on InPort. information crossReference eng; US biota biota A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. Mosaic images were created using Agisoft Metashape. Sampling boundaries and coral demographic measurements were created using ArcGIS and TagLab. All statistics were performed in R. The extent of area across the U.S. Pacific for which annotations are derived from fixed site SfM imagery: include the Hawaiian Archipelago, Mariana Archipelago, American Samoa, and Pacific Remote Island Areas. 144.618287 -154.806789 -14.373615 28.455623 Timeframe of when imagery was collected for which annotations were derived. Each region (Mariana Archipelago, Hawaiian Archipelago, American Samoa & PRIAs) is typically sampled in different years. | Currentness: Ground Condition 2014-01-27 false eng false Spreadsheet SfM Fixed Sites: SfM Derived Coral Annotations Data Dictionary 2025-09-09 publication CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) PDF - Adobe Portable Document Format PDF - Adobe Portable Document Format 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/0257945 WWW:LINK-1.0-http--link SfM_VitalRates_MHI_NWHI.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), and adult coral colony observations identified to the lowest taxonomic level possible (usually species) including initial and final size measurement. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Main Hawaiian Islands from 2014-2019. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division. download https://accession.nodc.noaa.gov/0282457 WWW:LINK-1.0-http--link SfM_VitalRates_MARIAN_2022.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout the Mariana Archipelago from 2014-2022. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division. download https://repository.library.noaa.gov/view/noaa/32739 WWW:LINK-1.0-http--link Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion SOP Vital Rates Technical Memorandum download https://www.fisheries.noaa.gov/resource/document/measuring-coral-vital-rates-using-taglab-semi-automatic-coral-annotation-and WWW:LINK-1.0-http--link Measuring Coral Vital Rates Using TagLab SOP This standard operating procedure (SOP) provides a time savings comparison between manual annotation using the previous Vital Rates workflow (Rodriguez et al. 2021) and our TagLab-assisted Vital Rates workflow. We posit that, although TagLab remains an ongoing project of the Visual Computing lab and requires additional testing, it reduces personnel hours by 40%, making it a worthwhile approach to quantifying coral vital rates. Pacific Islands Fisheries Science Center technical memoranda are issued to promptly disseminate scientific and technical information to marine resource managers, scientists, and the general public. Their contents cover a range of topics, including biological and economic research, stock assessment, trends in fisheries, and other subjects. Administrative reports typically have not been reviewed outside the Center; therefore, they are considered informal publications. The material presented in administrative reports may later be published in the formal scientific literature after more rigorous verification, editing, and peer review. download https://accession.nodc.noaa.gov/0307802 WWW:LINK-1.0-http--link SFM_VitalRates_AMSM_PRIA_2023.csv Metadata for each Structure from Motion (SfM) survey site (site information, survey date and location), adult coral colony observations identified to the genus level and size measurements. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division and Scripps Institution of Oceanography throughout American Samoa and Pacific Remote Islands and Atolls (PRIAs) from 2014-2023. Imagery annotation was conducted by the NOAA Fisheries Ecosystem Sciences Division. download dataset Representativeness The data set derived from the imagery is only as good as the images and image-derived products. All coral patches were delineated high resolution orthoprojections and raw imagery was referenced when determining patch perimeters. Accuracy Survey sites were aligned atop one another to ensure coral patches could be followed through time and to ensure delineates were collected using the same orthorectified view which improves accuracy of planar area change measurements. Coral species identification and size data were extracted by SfM image annotators that had been trained and tested on coral taxon identification and morphology. All annotators met a set of minimum standards for coral data collection. Field Precision The average Ground Sample Distance (GSD, resolution/pixel) for the produced 3D Structure from Motion models was 0.21 cm/pix, allowing confident identification of coral species from the resulting high-resolution 2D orthoprojections. Completeness Report SfM imagery was collected at 14 sites throughout the Hawaiian Archipelago across time intervals from several hours to 3 years. For the Mariana archipelago, imagery was collected at 10 sites at 3 and 5 year time intervals. In American Samoa and PRIAs, 11 sites were selected with time points either 1 or 5 years apart. All sites were between 9-16m deep and and cover approximately 100 m2 of reef. Due to the labor-intensive and time-consuming nature of coral annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. Each site was sub-sampled by randomly distributing a minimum of 10 0.5 m2 quadrats throughout each orthoprojection. All corals whose centroid fell within the quadrat were annotated until a sufficient number of corals were annotated. The target taxa across all atolls and islands consist of four genera - Pocillopora, Porites, Montipora and Acropora. Prior to analysis, coral colonies <19 cm2 were removed from the dataset. In the Hawaiian archipelago dataset, all coral colonies that experienced full mortality in the final time point or were only observed in the final time point are not included in this dataset. Conceptual Consistency The same method of annotation was used for all SfM imagery. Benthic imagery was collected at permanent sites and generated into 3D dense point clouds (DPCs) using Agisoft Metashape software. DPCs from the same site, but different collection dates were converted into 2D orthoprojections and scaled, oriented and aligned together. Next, the orthoprojections were exported for annotation. Orthoprojections were sub-sampled by randomly distributing quadrats throughout the orthoprojection. Quadrat location was conserved across all orthoprojections associated with the same permanent site. Target coral species were identified within each quadrat and their perimeters were annotated. The changes in coral planar area of each coral colony was tracked by linking annotations of the same live coral across each time point. All statistics and figures were performed in R. Prior to image collection, each site was set up by placing at least two scale bars of known length, with ground control points (GCPs) at the end of each bar, 2-3 m away from the center of the survey area. At many sites, rebar caps with GCPs were also placed on the reference pins (36 in tall stainless steel rods used to mark the site). During plot set up, one diver drew a diagram of the plot, marking the location of each scale bar, reference pin, and distinctive benthic features. The depth and identification numbers of each scale bar were recorded in the diagram as well. Divers swam ~1m off the seafloor, collecting enough photographs to produce 60%-80% image overlap and complete two full passes of the site. Amir, Corinne corinne.amir@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. Following image quality control, each set of raw images were imported, aligned separately in Agisoft Metashape and used to build 3D dense point clouds (DPCs) following parameters described by Suka et al. (2019). For the Hawaiian Archipelago dataset, DPCs were then imported into Viscore, a custom visualization software (Petrovic et al., 2014), where all DPCs from the same site, but from different time points, were scaled, oriented and aligned together using the GCP information. Each DPC was converted into a 2D orthorectified image (orthoprojection) and an identical top-down view of all othoprojections of the same site but different time points were exported from Viscore. For the Mariana Archipelago dataset, all scaling, orienting, alignment and 2D model creations were completed using Agisoft Metashape. Amir, Corinne corinne.amir@noaa.gov processor Due to the labor-intensive and time-consuming nature of annotation, we used a randomized sub-sampling strategy that provided enough colony-level data across a wide range of size classes to fit robust demographic models. To sub-sample each site, we selected the region where there was the most spatial overlap across all orthoprojections of the same site. Next, 10-30 0.5m2 quadrats were generated at random throughout the selected area and each labelled in numerical order. Within the first 10 quadrats, all coral species on the target coral species list were annotated if their centroid fell within the quadrat. Corals were annotated by tracing the full perimeter of live coral tissue patches. During annotation, the original JPEG imagery was viewed alongside the orthoprojection to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthoprojection (e.g. under ledges). If one or several coral species on the target list did not reach n = 30 live patches within the first 10 quadrats. These species were identified and annotated in additional quadrats, and sometimes outside the quadrats, until a higher sample size could be reached. Unique identifying numbers were assigned to each patch of live coral tissue link coral patches across time and to track fission/fusion events. Amir, Corinne corinne.amir@noaa.gov processor Annotations were exported and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, missing coral unique identifier, data in incorrect columns). Before analysis, all corals patches < 19 cm2 and corals that were not present in both the initial and final time point were removed from the dataset. For the Hawaiian archipelago dataset, absolute change in coral patch area (cm2) was calculated in R. Oliver, Thomas (808)725-5444 thomas.oliver@noaa.gov processor Source Contribution: This document builds upon Rodriguez et al. 2022 and provides detailed procedures for annotating imagery using both ArcGIS and TagLab software in tandem. These procedures are designed to efficiently generate coral rates data (e.g., growth, mortality, recruitment, fission, and fusion) within coral communities over time. While this standard operating procedure is designed to meet ESD needs, we use commercially available software, making these methods adaptable based on programmatic capacity and needs. Amir C, Oliver T, Lamirand M, Couch C. 2023. Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-139, https://doi.org/10.25923/s2ym-tn10 2023-07-01 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/50840 WWW:LINK-1.0-http--link Source Citation URL Measuring coral vital rates using TagLab semi-automatic coral segmentation and temporal linking across fixed sites: standard operating procedures and time savings estimates information originator Source Contribution: This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems. 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 Source Citation URL information publisher Source Contribution: The combination of 3D acquisition (terrestrial and airborne LiDAR, structured light, structure-from-motion) and 2D imaging (photographic, multispectral, panoramic, orthorectified, reflectance transformation) techniques allows the geometry, appearance and other aspects sites to be objectively documented. This study proposes a system for the direct visualization and analysis of such data, allowing the different aspects recorded to be layered together, and co-visualized with annotations and other relevant information. This study describes the required technical foundations, including gigapoint and gigapixel visualization pipelines that enable the dynamic layering of high-resolution imagery over massive minimally-processed LiDAR point clouds that serve as the base spatial layer. In particular, the study introduces the pointbuffer—a GPU-resident view-dependent point cache—as the foundation of our gigapoint pipeline, and outline the use of virtual texturing for draping of gigapixel imagery onto point clouds. Petrovic, V, Vanoni, DJ, Richter, AM, Levy, TE, & Kuester, F. 2014. Visualizing high resolution three-dimensional and two-dimensional data of cultural heritage sites. Mediterranean Archaeology and Archaeometry, 14(4), 93-100. 2014-01-01 publication Vid Petrovic https://escholarship.org/uc/item/58z4j8k2 WWW:LINK-1.0-http--link Source Citation URL Source Citation URL information publisher Source Contribution: This document provides detailed procedures for collecting, processing, and annotating imagery using Structure-from-Motion techniques developed by Ecosystem Sciences Division (ESD) in collaboration with Scripps Institution of Oceanography and the University of Hawaii at Hilo. These procedures are designed to efficiently generate coral rates data (e.g., growth, mortality, recruitment, fission, and fusion) within coral communities over time. This pipeline consists of four key steps: (1) Image collection by SCUBA divers, (2) Generating 3-D models in Agisoft Metashape, (3) Generating 2D orthoprojections in CloudCompare, (4) Alignment of multi-year 2D orthoprojections and extraction of coral vital rates in ArcMap. While the following procedures are designed to meet ESD needs, we primarily use commercially available cameras and software, making these methods adaptable based on programmatic capacity and needs. Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Measuring Coral Vital Rates Using Structure-from-Motion Photogrammetry at Fixed Sites: Standard Operating Procedures and Error Estimates. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, https://doi.org/10.25923/a9se-k649 2021-10-01 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/32739 WWW:LINK-1.0-http--link Source Citation URL Vital Rates Project Standard Operating Procedures and Error Estimates Pilot study information originator 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: All SfM models produced in Agisoft after 2022 follow methodology included in this SOP. 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. Processing coral reef imagery using Structure-from-Motion photogrammetry : Standard operating procedures (2023 update) 2024-01-01 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/60890 WWW:LINK-1.0-http--link Source Citation URL The Pacific Islands Fisheries Science Center (PIFSC) has been testing, improving, and streamlining its Structure-from-Motion (SfM) processing pipeline to produce permanent digital records of coral reefs across the U.S. Pacific Islands and Territories. This SOP was developed in collaboration with Scripps Institution of Oceanography, the University of Hawai’i at Hilo and the Hawai’i Institute of Marine Biology to increase logistical efficiency in the field while continuing to produce streamlined coral demographic and benthic community data across the broad spatial scale of NCRMP. information originator otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None