gov.noaa.nmfs.inport:65764 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 2026-03-04T19:17:21 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021 Bleaching & Recovery: 2019-2021 MHI Coral Observations 2021-11 creation 2023-09-14 revision 2023 publication NOAA/NMFS/EDM 65764 https://www.fisheries.noaa.gov/inport/item/65764 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://doi.org/10.3354/meps14918 WWW:LINK-1.0-http--link Publication: Survivorship and growth of corals in Hawai'i two years post-bleaching: signs of resilience Pomeroy MW, Couch CS, Oliver TA, McCarthy OS, Speare KE, Donovan MK (2025) Survivorship and growth of corals in Hawai‘i two years post-bleaching: signs of resilience. Mar Ecol Prog Ser 768:79-97 https://doi.org/10.3354/meps14918 download https://www.fisheries.noaa.gov/feature-story/surveys-assess-2019-hawaii-coral-bleaching-event WWW:LINK-1.0-http--link Feature Story: Surveys to Assess the 2019 Hawai'i Coral Bleaching Event Online Resource download tableDigital Pomeroy MW, Couch CS, Oliver TA, McCarthy OS, Speare KE, Donovan MK (2025) Survivorship and growth of corals in Hawai‘i two years post-bleaching: signs of resilience. Mar Ecol Prog Ser 768:79-97 https://doi.org/10.3354/meps14918 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 Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649 Coral adult demographic data described in this dataset are derived from the GIS analysis of benthic photomosaic imagery. This data includes coral species identification, bleaching extent and severity, colony diameter, perimeter, and planar size. The source imagery was collected using a Structure from Motion (SfM) approach during in-water surveys conducted by divers and is documented and described separately. The data was collected by the NOAA Pacific Islands Fisheries Science Center (PIFSC) Ecosystem Sciences Division (ESD; formerly the Coral Reef Ecosystem Division) and [on Hawaii Island] in partnership with State of Hawaii Department of Land and Natural Resources (DLNR), Division of Aquatic Resources (DAR) during the 2019 bleaching event in the Main Hawaiian Islands, and in subsequent years (2020, 2021) to assess recovery. The SfM surveys were conducted at fixed sites ranging in depth from 18-52'. Sites were photographed using underwater cameras for later processing using one of two SfM approaches: using a spiral swim pattern (where divers take images continuously in a circular pattern covering a circle of 12m diameter), or within a defined box where divers swam back and forth to cover a 10 x 10m area. The photographs were processed using Agisoft Metashape software to generate orthomosaic images that were analyzed in ArcGIS for adult coral colony demographic metrics. Data was collected for each site within at least 10 randomly generated 0.49m2 quadrats. Additional quadrats were analyzed if necessary until the sample sizes per species of interest were met. If a species had very low density at a given site (< 10 patches recorded within the first 10 quadrats), it was dropped from further observations. However, the data for these patches remains in the raw data in order to provide presence/absence data. Therefore, data should be carefully analyzed to ensure accurate species density calculations are done. Two datasets are provided: an annotations file which provides coral demographic information of 6 target species at 12 fixed sites across 3 years, as well as a site metadata file which describes the site and surveys which were used to generate models for which annotation data was derived. Six species were assessed: Montipora capitata (MCAP), Montipora patula (MPAT), Porites lichen (PLIC), Porites lobata (PLOB), Porites lutea (PLUT), and Pocillopora meandrina (PMEA). Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred. Note an update in methodology: The data was collected in two stages. During the first stage of data collection that was completed in 2021, for each coral patch, (>= 5cm in diameter), maximum diameter, ID (to lowest taxonomic level), morphology, bleaching extent (% of the patch with reduced pigmentation), and bleaching severity (1-3 from least to most severe) were recorded. In 2023 the methodology was updated for the second stage of data collection; the updated dataset includes measures of planar area and a "genet" (colony) identification column. The 2023 dataset was also collected following an update to the model process methodology (see Lineage). Users should refer to the most updated dataset published in 2023. The Hawaii Coral Bleaching Collaborative (HCBC) planned and executed a field survey response in 2019 that applied a structured, hypothesis-driven approach to document the extent of coral bleaching in the Hawaiian Archipelago, and laid the groundwork for tracking coral response and recovery through time. Fixed sites were revisited in 2020 and 2021 to examine survivorship, recovery, and growth following the 2019 bleaching event. The purpose of the Structure from Motion (SfM) surveys throughout the Main Hawaiian Islands is to efficiently and effectively collect coral demographic data. This was funded by two CRCP Projects: #31283, #31361 titled 'Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities' and 'Hawai'i coral bleaching assessment and analysis' NOAA Fisheries Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program onGoing Couch, Courtney S courtney.s.couch@noaa.gov pointOfContact Winston, Morgan S (808)725-5480 1845 Wasp Blvd. Honolulu HI 96818 USA morgan.winston@noaa.gov custodian asNeeded In 2023 this data was republished after 2019 - 2021 imagery was re-annotated with an updated methodology; refer to most recent published dataset (2023); prior to 2023 this metadata record described only the preliminary 2019 dataset, and was titled 'Colony-level annotations using Structure-from-Motion models from sites surveyed across the Main Hawaiian Islands during the 2019 bleaching event'. As more data is generated with this methodology, datasets will be added to this metadata record. DOC/NOAA/NMFS/PIFSC/ESD > Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 17.0 EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > BENTHIC EARTH SCIENCE > BIOSPHERE > ECOSYSTEMS > MARINE ECOSYSTEMS > REEF > CORAL REEF EARTH SCIENCE > OCEANS > COASTAL PROCESSES > CORAL REEFS > CORAL BLEACHING theme Global Change Master Directory (GCMD) Science Keywords 17.0 OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > HAWAII ISLAND OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > LANAI OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS > OAHU place Global Change Master Directory (GCMD) Location Keywords 20.8 Computer > Computer instrument Global Change Master Directory (GCMD) Instrument Keywords 17.2 31283 31361 Assessing impacts of Hawaii's 2019 coral bleaching event on coral recovery and coral communities Hawai'i coral bleaching assessment and analysis theme CRCP Project Numeric Data Sets > Benthic theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Condition EARTH SCIENCE > Biosphere > Zoology > Corals > Coral Diseases > Bleaching EARTH SCIENCE > Biosphere > Zoology > Corals > Scleractinia (stony corals) EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs EARTH SCIENCE > Oceans > Marine Biology > Coral EARTH SCIENCE > Oceans > Marine Biology > Coral Communities NEARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis theme CoRIS Theme Thesaurus CORAL CORAL - COLONY SIZE CORAL - SPECIES IDENTIFICATION theme NODC DATA TYPES THESAURUS GIS product derived products in situ survey - coral reef theme NODC OBSERVATION TYPES THESAURUS CORAL REEF STUDIES National Coral Reef Monitoring 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 COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii (21N160W0000) COUNTRY/TERRITORY > United States of America > Hawaii > Hawaii > Hawaii Island (19N155W0003) COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Oahu (21N157W0003) COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Lanai Island (20N156W0002 COUNTRY/TERRITORY > United States of America > Hawaii > Maui > Maui Island (20N156W0004 COUNTRY/TERRITORY > United States of America > Hawaiian Islands (21N157W0027) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands (21N157W0027) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii > Hawaii (21N160W0000 OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Hawaii Island > Hawaii Island (19N155W0003 OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Lanai Island > Lanai Island (20N156W0002) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Maui Island > Maui Island (20N156W0004) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003) place CoRIS Place Thesaurus Coastal Waters of Hawaii place NODC SEA AREA NAMES THESAURUS Central Pacific Ocean North Pacific Ocean place NODC SEA AREA NAMES THESAURUS: photograph scale instrument NODC INSTRUMENT TYPES THESAURUS VARIOUS SMALL VESSELS platform NODC PLATFORM NAMES THESAURUS CRED CREP Coral Reef Ecosystem Division Coral Reef Ecosystem Program DAR DLNR Department of Land and Natural Resources Division of Aquatic Resources ESD Ecosystem Sciences Division PIFSC Pacific Islands Fisheries Science Center SfM Structure from Motion coral demography theme DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Ocean and Climate Change project InPort otherRestrictions Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/65764. NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose. otherRestrictions Access Constraints: None otherRestrictions Use Constraints: Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data. Example: Ecosystem Science Division; Pacific Islands Fisheries Science Center, 2023: Coral Bleaching & Recovery Observations using Structure-from-Motion (SfM) Models from Main Hawaiian Islands Fixed Sites Surveyed from 2019 to 2021, https://www.fisheries.noaa.gov/inport/item/65764. 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 Hawaii Coral Bleaching Collaborative: surveys for percent and severity of bleached coral cover across the Hawaiian Archipelago from August 20 to December 7, 2019 NOAA/NMFS/EDM 59191 crossReference 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 65764 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/65764.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 environment A GPS unit is used to record the location of each Structure from Motion (SfM) survey site. A Nikon SL2 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25-0.50 m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape (version 1.6.2 build 10247). Models were further scaled using Viscore software. Sampling boundaries and coral demographic measurements were created in ArcGIS Pro (version 2.6.0). Hawaiian Archipelago October 8 2019 - July 20 2021 -158.0667 -155.830367 19.42335 21.47959 Main Hawaiian Islands (MHI), including Hawaii, Maui, Oahu, and Lanai. MHI 2019 bleaching surveys | Currentness: Ground Condition 2019-10-08 2021-07-20 false eng false Spreadsheet 2019-2021 MHI SfM Coral Observations: Data Dictionary 2023-10-04 publication 2019-2021 MHI SfM Coral Obs Annotations: Site Metadata 2023-10-04 publication CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) CSV - Comma Separated Values (Text) 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/0244392 WWW:LINK-1.0-http--link 2019_SfMSiteMetadata.csv Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch level information. download https://accession.nodc.noaa.gov/0209239 WWW:LINK-1.0-http--link HCBC_2019_TaxaList.csv Reference table of full taxa names per taxa code. download https://accession.nodc.noaa.gov/0244392 WWW:LINK-1.0-http--link ColonyLevelBleachingSfM2019.csv Coral patch level SfM annotations observations from surveys conducted during the 2019 bleaching event in the Hawaiian Archipelago at fixed sites. ***NOTE: This data is outdated. Please refer to the dataset published in 2023 generated with an updated methodology to analyze time series effectively: BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021.csv download https://accession.nodc.noaa.gov/0283598 WWW:LINK-1.0-http--link BLEACHING_SFM_PATCH_ANNOTATIONS_MHI_2019-2021 Annotations of 3D coral models generated from patch level analysis in 2022 using imagery from follow-up surveys in 2021 and 2020 (Oahu only) to revisit fixed sites established in 2019 for bleaching assessment. A subset of metrics from 2019 was collected again, using an updated methodology described in the Lineage section. download https://accession.nodc.noaa.gov/0283598 WWW:LINK-1.0-http--link SITE_METADATA_2019-2021_MHI Description of fixed sites surveyed using SfM methods to generate models that were annotated to derive coral patch/'genet' level information. download https://accession.nodc.noaa.gov/0283598 WWW:LINK-1.0-http--link BLEACHING_SFM_TAXALIST_MHI_2019-2021.csv List of coral species codes and their associated taxon names, as used in annotations dataset. download dataset Representativeness The data set derived from the imagery is only as good as the images themselves; Images with poor resolution, poor lighting, extraneous objects (fins, etc), or blur were excluded from analysis. Accuracy Handheld GPS units were used to locate fixed sites and update site locations if needed. Prior to conducting surveys, the SfM image collector was trained to swim in a back-and-forth or circular pattern to collect imagery with 60-80% overlap. Both classroom and field training were completed before any surveys were conducted. This training ensures that all SfM image collection was conducted consistently during the mission. Coral demographic data was extracted by SfM image annotators that had been trained, underwent a series of calibration efforts and testing on coral taxon identification testing, morphology, and condition assessment. All annotators met a set of minimum standards for coral demographic data collection. Completeness Report Of the fixed sites for which SfM imagery was collected at during the 2019 bleaching survey effort, a subset of these sites were annotated that included 5 from Hawaii Island, 5 from Oahu, and 2 from Lanai. 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 orthomosaics and scaled, oriented and aligned together. Orthomosaics were sub-sampled by randomly distributing quadrats throughout the orthopmosaic. Quadrat location was conserved across all orthomosaics associated with the same permanent site. Target coral species were identified within each quadrat and their perimeters were annotated until a sufficient sample size of each species was recorded. Annotations included coral species identification, maximum diameter measurement, planar area measurement, morphology, and, for sites surveyed in 2019, bleaching extent and bleaching severity. Each coral was annotated at the patch level, and patches composing individual colonies, also known as genets, were assigned a unique genet ID number. The same coral patches were tracked over each time point, unless mortality of a coral patch occurred. SfM benthic surveys were conducted at fixed sites in the Main Hawaiian Islands during the 2019 bleaching event and during follow-up surveys in 2020 (Oahu only) and 2021. Imagery was collected using a digital camera in an underwater housing and white balance settings were adjusted in situ using a gray card. 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. Winston, Morgan S (808)725-5480 morgan.winston@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). Data collected before 2022 was only done for surveys conducted in 2019, and a subset of the metrics described in the Lineage Statement were collected. Different steps were also taken to prepare models for data collection. This pre-2022 collected data used DPCs that were 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 data collected beginning in 2022, all scaling, orienting, alignment and 2D model creations were completed using Agisoft Metashape. Winston, Morgan S (808)725-5480 morgan.winston@noaa.gov processor Due to the labor-intensive and time-consuming nature of annotation, in 2022 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 orthomosaics of the same site. Next, 10-30 2.5m2 quadrats were generated at random throughout the selected area and each labeled 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 orthomosaic to see fine scale colony details, observe colonies from multiple angles and locate colonies not visible in the orthomosaic (e.g. under ledges). Following Rodriguez et al. (2021), if a coral species per site was found less than 10 times in the first 10 quadrats, the species was subsequently not recorded in future analyzed quadrats. Therefore, this data should be carefully analyzed and species density should not be calculated for these species with low sample size. If a species had low density at a given site, 20-40 patches were annotated. If a species was abundant at the site, at least 40 patches were annotated. See Rodriguez et al. (2021) for further information. Unique identifying numbers were assigned to each patch of live coral tissue to link coral patches across time and to track fission/fusion events. Winston, Morgan S (808)725-5480 morgan.winston@noaa.gov processor Annotations created in ArcGIS Pro were quality controlled using a multi-stage process. Data was exported from ArcGIS and quality controlled in R with specific queries to identify and correct data entry errors (e.g. misspelled species names, data in incorrect columns, bleaching >100%). Coral patches composing the same colony or genet were assigned unique genet ID numbers. Winston, Morgan S (808)725-5480 morgan.winston@noaa.gov processor Burns J, Delparte D, Gates R, Takabayashi M. 2015. Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 3:e1077 2015-07-07 publication John Burns https://doi.org/10.7717/peerj.1077 WWW:LINK-1.0-http--link PeerJ This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems. information publisher Source Contribution: This study provides the first quantified methodological comparison to validate the transition from standard in-water methods to SfM survey methods for estimates of coral colony-level surveys. Here, we quantitatively compare data generated from in-water surveys to SfM-derived metrics for assessing coral demography, bleaching, and diversity in the main Hawaiian Islands as part of NOAA’s National Coral Reef Monitoring Program. Our objectives were to compare between-method error to within-method error, test for bias between methods, and identify strengths and weaknesses of both methods. Colony density, average colony diameter, average partial mortality, prevalence of bleaching, species richness, and species diversity were recorded using both methods within the same survey areas. For all metrics, the magnitude of between-method error was comparable to the within-method error for the in-water method and between method error was significantly higher than within-method error for SfM for one of the seven metrics. Our results also reveal that a majority of the metrics do not vary significantly between methods, nor did we observe a significant interaction between method and habitat type or method and depth. Exceptions include estimates of partial mortality, bleaching prevalence, and Porites juvenile density–though differences between methods are generally small. Our study also highlights that SfM offers a unique opportunity to more rigorously quantify and mitigate inter-observer error by providing observers unlimited “bottom time” and the opportunity to work together to resolve difficult annotations. Couch CS, Oliver, TA, Suka R, Lamirand M, Asbury M, Amir C, Vargas-Ángel B, Winston M, Huntington B, Lichowski F, Halperin A, Gray A, Garriques J, & Samson J. 2021. Comparing coral colony surveys from in-water observations and structure-from-motion imagery shows low methodological bias. Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.647943 2021-05-28 publication Pacific Islands Fisheries Science Center https://doi.org/10.3389/fmars.2021.647943 WWW:LINK-1.0-http--link Source Citation URL Source Citation URL information originator Source Contribution: The combination of 3D acquisition (terrestrial and airborne LiDAR, structured light, structure-from-motion) and 2D imaging (photographic, multispectral, panoramic, orthorectified, reflectance transformation) techniques allows the geometry, appearance and other aspects sites to be objectively documented. This study proposes a system for the direct visualization and analysis of such data, allowing the different aspects recorded to be layered together, and co-visualized with annotations and other relevant information. This study describes the required technical foundations, including gigapoint and gigapixel visualization pipelines that enable the dynamic layering of high-resolution imagery over massive minimally-processed LiDAR point clouds that serve as the base spatial layer. In particular, the study introduces the pointbuffer—a GPU-resident view-dependent point cache—as the foundation of our gigapoint pipeline, and outline the use of virtual texturing for draping of gigapixel imagery onto point clouds. Petrovic, V, Vanoni, DJ, Richter, AM, Levy, TE, & Kuester, F. 2014. Visualizing high resolution three-dimensional and two-dimensional data of cultural heritage sites. Mediterranean Archaeology and Archaeometry, 14(4), 93-100. 2014-01-01 publication Vid Petrovic https://escholarship.org/uc/item/58z4j8k2 WWW:LINK-1.0-http--link Source Citation URL Source Citation URL information publisher Source Contribution: Here, we outline a method of directly measuring coral vital rates via structure-from-motion (SfM) photogrammetry — an image processing technique capable of reconstructing accurate, orthorectified representations of the seafloor and the coral communities that inhabit them. By leveraging SfM technology, NOAA’s U.S. National Coral Reef Monitoring Program (NCRMP) and partners are capable of generating accurate measures of coral vital rates from the scale of individual coral colonies with coverage of tens of sites and thousands of corals within a population. In Section 1 of this technical memorandum, we provide a detailed set of Standard Operating Procedures for capturing, processing, and extracting data from SfM photogrammetry. In Section 2, we use this novel SfM approach and imagery collected at 14 sites across the Hawaiian Archipelago across time intervals from a few minutes to three years to determine how accurately we can measure coral vital rates. Rodriguez C, Amir C, Gray A, Asbury M, Suka R, Lamirand M, Couch C, Oliver T. 2021. Extracting Coral Vital Rate Estimates at Fixed Sites Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-120, 80 p. p. doi: https://doi.org/10.25923/a9se-k649 2021-09-01 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/32739 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC 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: Guidelines and procedures for implementation of sampling design, in situ survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018). Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993. 2018-08-01 publication https://repository.library.noaa.gov/view/noaa/18267 WWW:LINK-1.0-http--link NOAA Institutional Repository Source Citation URL information Source Contribution: The objective of this document is to provide updates incorporated in 2019 to the guidelines and procedures for implementation of sampling design, survey methodology, and data entry for the monitoring of reef coral populations and benthic communities as part of the Pacific RAMP led by ESD (Swanson et al. 2018). Winston M, Couch C, Ferguson M, Huntington B, Swanson D, Vargas-Ángel B. 2019. Ecosystem Sciences Division Standard Operating Procedures: Data Collection for Rapid Ecological Assessment Benthic Surveys, 2018 Update. NOAA Tech. Memo. NOAA-TM-NMFS-PIFSC-92, 66 p. doi:10.25923/w1k2-0y84 2020-01-31 publication Pacific Islands Fisheries Science Center https://doi.org/10.25923/ws5s-km69 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information originator otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None