gov.noaa.nmfs.inport:68015 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) Corallivory, or coral predation, data derived from Structure-from-Motion imagery and in-situ surveys of coral reefs off of O'ahu, Hawai'i from 2021 to 2022 SfM Corallivory Oahu 2023 creation 2023 publication NOAA/NMFS/EDM 68015 NOAA NCEI 10.25921/hqq9-w471 https://www.fisheries.noaa.gov/inport/item/68015 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://console.cloud.google.com/storage/browser/nmfs_odp_pifsc/PIFSC/ESD/ARP/Photogrammetric%20Imagery/CRCP_Projects/Corallivory_Oahu_2022 WWW:LINK-1.0-http--link Source SfM Imagery for Corallivory Estimates Access to SfM imagery used in this analysis via Google Cloud Bucket. nmfs_odp_pifsc/PIFSC/ESD/ARP/Photogrammetric Imagery/CRCP_Projects/Corallivory_Oahu_2022 This folder contains raw structure-from-motion (SfM) imagery at sites off of O'ahu in 2022 (.jpg), and their complementary site metadata (.csv). A total of 39, 3x20m transects were haphazardly placed and imaged using a standard structure-from-motion methodology. download https://www.fisheries.noaa.gov/region/pacific-islands#science WWW:LINK-1.0-http--link NOAA Fisheries Pacific Islands Region - Science Overview Landing page for PIFSC download https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific WWW:LINK-1.0-http--link Coral Reefs in the Pacific NOAA Fisheries Website download https://www.coris.noaa.gov/monitoring/ WWW:LINK-1.0-http--link National Coral Reef Monitoring Program NOAA National Coral Reef Monitoring Program (NCRMP) website. download tableDigital Escontrela Dieguez D, Lee R, Kindinger TL, Couch CS, Charendoff J. 2023. Quantifying corallivory from Structure-from-motion models. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-149, 8182 p. doi: 10.25923/c64k-gh75 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 The data described here are raw corallivory, or coral predation, data from in situ visual surveys as well as derived corallivory data from Structure-from-Motion (SfM) imagery collected during diver transect surveys between 2021 and 2022. These surveys were conducted by a graduate student researcher from the University of Hawaii at Manoa, and funded by NOAA's Coral Reef Conservation Program (CRCP), with support from scientists of the Ecosystem Sciences Division (ESD) at the Pacific Islands Fisheries Science Center (PIFSC) of NOAA. This data was funded by CRCP Project number 31349 titled: 'Determining whether herbivore-focused management strategies enhance critical ecosystem functions provided by fishes'. The source SfM imagery will be accessible via Google Cloud bucket (see URLs). 39 sites off of O'ahu, Hawai'i were established for this project. At each site, a 3x20m haphazardly placed transect was surveyed and imaged using underwater cameras. Along each transect, seven 1x1m quadrats spaced 3m apart were first surveyed for corallivory bite marks. After the survey was conducted, the same 3x20m transect was imaged using an underwater camera. Photographs were processed using Agisoft Metashape software to generate 2D orthomosaics. These orthomosaics were uploaded to ArcGIS Pro to be annotated for corallivory estimates. In water bite counts and estimates derived from SfM annotations will be compared with visual survey data to better understand the accuracy at which SfM annotations capture corallivory. Corallivory, or coral predation, is an important ecological process on coral reefs. Corallivores can, for example, mediate coral species distributions on coral reefs. However, when left unchecked, corallivores can cause mass mortality of corals. Corallivores can also transmit diseases and can cause reductions in coral growth and reproduction as corals redirect limited metabolic resources to wound healing. Moreover, corallivory can act synergistically or additively with other stressors, further exacerbating the threats corals face. Better tools are needed to rapidly and accurately assess coral reefs for excess predation in order to enact timely management interventions when needed. Past monitoring techniques for corallivory have included in situ surveys, which are accurate but expensive, and analysis of 2D benthic imagery, which is fast but inaccurate. SfM techniques allow for the surveying of broader spatial extents as underwater time can be reallocated from conducting surveys at one location to gathering images for different models at different sites. Moreover, as opposed to 2D benthic imagery, SfM models allow annotators to view the coral reef in 3D making annotations more accurate as they are less likely to miss bite marks that may otherwise be hidden. Having a tool to rapidly assess corallivory, such as this SfM technique, will allow managers to enact timely management interventions if or when excess corallivory is detected. NOAA Fisheries, Ecosystem Sciences Division and funded by NOAA's Coral Reef Conservation Program completed Shantz, Andrew andrew.shantz@noaa.gov pointOfContact Lee, Roseanna roseanna.lee@noaa.gov custodian notPlanned 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 > ECOLOGICAL DYNAMICS > SPECIES/POPULATION INTERACTIONS > SPECIES PREDATION 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 > HAWAIIAN ISLANDS > OAHU place Global Change Master Directory (GCMD) Location Keywords 20.8 CAMERA > CAMERA instrument Global Change Master Directory (GCMD) Instrument Keywords 17.2 31349 Determining whether herbivore-focused management strategies enhance critical ecosystem functions provided by fishes theme CRCP Project Numeric Data Sets > Benthic theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Feeding Scars On Hard Coral > COTS EARTH SCIENCE > Biosphere > Zoology > Corals > Feeding Scars On Hard Coral > Fish EARTH SCIENCE > Biosphere > Zoology > Corals > Feeding Scars On Hard Coral > Gastropod EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Damage Assessment > Biological EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Quadrat Monitoring > In Situ EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis > Quadrat Monitoring > Photograph Analysis EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs theme CoRIS Theme Thesaurus CORAL images theme NODC DATA TYPES THESAURUS derived products in situ theme NODC OBSERVATION TYPES THESAURUS CORAL REEF STUDIES Coral Reef Conservation 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 > Honolulu > Oahu (21N157W0003) OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Hawaiian Islands > Oahu Island > Oahu (21N157W0003) place CoRIS Place Thesaurus Central Pacific Ocean Coastal Waters of Hawaii North Pacific Ocean place NODC SEA AREA NAMES THESAURUS: photograph instrument NODC INSTRUMENT TYPES THESAURUS CRED CREP Coral Reef Ecosystem Division Coral Reef Ecosystem Program Corallivory ESD Ecosystem Sciences Division PIFSC Pacific Islands Fisheries Science Center SfM Structure from Motion theme DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian Structure From Motion project InPort otherRestrictions Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: Corallivory, or coral predation, data derived from Structure-from-Motion imagery and in-situ surveys of coral reefs off of O'ahu, Hawai'i from 2021 to 2022 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/68015. 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: Corallivory Estimates derived from Structure-from-Motion Imagery and in-situ Surveys around Oahu, HI from 2021 to 2022 from 2010-06-15 to 2010-08-15. NOAA National Centers for Environmental Information, https://www.fisheries.noaa.gov/inport/item/68015. 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 NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 68015 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/68015.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 was used to record the location of each Structure from Motion (SfM) survey site. A Canon SL2 DSLR digital camera in an Ikelite underwater housing was used to take photographs of each site. Coded markers 0.25-0.50 m long were used underwater to provide a scale for the mosaic imagery. Mosaic images were created and scaled using Agisoft Metashape Professional (version 1.8.1). Corallivory estimates were made using ArcGIS Pro (version 3.0.1). Oahu, Hawaii June 2021 - October 2022 -158.2251 -157.691881 21.268008 21.649219 Extent of sites where in-situ corallivory data and imagery for Structure-from-Motion was collected across O'ahu in 2021-2022. | Currentness: Ground Condition 2021-06-29 2022-10-28 false eng false Data Table CORALLIVORY_INSITU_DATADICTIONARY_OAHU_2023 2025-08-05 publication CORALLIVORY_SFM_DATADICTIONARY_OAHU_2023 2025-08-05 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) 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/0286084 WWW:LINK-1.0-http--link coral_code_lookup.CSV Lookup table for coral species codes used by the NOAA Fisheries Ecosystem Sciences Division. download https://accession.nodc.noaa.gov/0286084 WWW:LINK-1.0-http--link bite_category_code_lookup.CSV Lookup table for bite category codes used by the NOAA Fisheries Ecosystem Sciences Division. download https://accession.nodc.noaa.gov/0286084 WWW:LINK-1.0-http--link corallivory_insitu_data_OAHU_2021-2022.csv Corallivory dataset from in situ corallivory estimate surveys across Oahu in 2021-2022. Datafile includes metadata for each Structure from Motion (SfM) survey site (site name, survey date, and location) and site characteristics (depth and habitat type). Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division in partnership with the University of Hawaii at Manoa. download https://accession.nodc.noaa.gov/0286084 WWW:LINK-1.0-http--link corallivory_sfm_data_OAHU_2021-2023.csv Corallivory dataset from Structure from Motion (SfM) derived corallivory estimates from surveys across Oahu in 2021-2022. Surveys were conducted by the NOAA Fisheries Ecosystem Sciences Division in partnership with the University of Hawaii at Manoa. *Note - While the in situ data includes sea star and Drupella corallivory data, the SfM derived estimates dataset does not include these types of predation because they require a different annotation methodology in ArcGIS Pro. Moreover, because they were encountered so infrequently while conducting in situ surveys, the decision was made not to annotate these predation types. download https://accession.nodc.noaa.gov/0286084 WWW:LINK-1.0-http--link corallivory_image_metadata.CSV Metadata for the corallivory SfM imagery which includes; the date the images were collected, site name, and latitude and longitude of the site. Source imagery is accessible via Google Cloud bucket which will be updated under the 'URLs' section of this metadata record. 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 haphazardly selected sites and mark site locations. All SfM images were collected by one individual who was trained to swim in a back-and-forth pattern to collect imagery with 60-80% overlap. Coral demographics and corallivory data were extracted by SfM image annotators who were trained and underwent a series of calibration trainings. All annotators proved to be proficient in identifying coral taxon and bite mark categories. Completeness Report At each of the 39 sites where SfM imagery was collected, in situ surveys were completed and corallivory was annotated. Conceptual Consistency The same method of estimation was used for all SfM imagery. Structure from Motion (SfM) techniques are increasingly being used to extract coral health metrics. In 2021 and 2022, new methods were developed, executed and tested to extract corallivory estimates from SfM models at sites around Oahu, Hawaii. At each site, a 3x20m haphazardly placed transect was surveyed for corallivory marks and imaged using underwater cameras. Seven 1x1m quadrats spaced 3m apart were first surveyed for corallivory bite marks along each transect. Spray painted fishing weights were used to mark placement of each quadrat. After the survey was completed, the same 3x20m transect was imaged using an underwater camera. Photographs were processed using Agisoft Metashape software to generate 2D orthomosaics. These orthomosaics were uploaded to ArcGIS Pro and were annotated for corallivory bite marks. Most of the surveys were conducted with SCUBA, with the exception of a few shallow sites where surveys were conducted with snorkeling gear. Sites were accessed either by boat or from shore. Divers used diver propulsion vehicles (DPVs) to search for appropriate places to conduct the surveys. Transect locations were selected haphazardly. Because of the nature of the study, sites were selected with different levels of coral cover and rugosity. Transects (20m) were laid out parallel to shore in order to ensure the same depth was maintained throughout the transect. This is with the exception of spur and groove sites where transects were laid along the top of the groove. Once the transect was deployed, three ground control points were placed 0.5 meters from the transect line at 0, 10 and 20 meters and depth measurements were taken at each point. Other metadata such as surveyor codes and reef habitat type were also recorded. Escontrela-Dieguez, Daniela daniela.escontreladieguez@noaa.gov processor Along each transect, seven 1mx1m quadrats were surveyed for corallivory, or coral predation bite marks. Quadrats were spaced out every 3m starting at the 1m mark (with some exceptions). Every time a quadrat was surveyed, a fishing weight, spray painted pink, was placed in the middle of the quadrat along the edge facing the 0m mark. Within each quadrat, the surveyor recorded coral species, bite mark category, overlap score, and healing condition. Descriptions of these can be found in Appendix 1 of the "Quantifying Corallivory from Structure-from-Motion Model" SOP. Escontrela-Dieguez, Daniela daniela.escontreladieguez@noaa.gov processor Once the in water survey was completed, SfM images were taken along the entire transect, covering a total area of 20mx3m. A Canon SL2 with Ikelite underwater housing was used to take the pictures. Before image collection began, the camera was white balanced using an 18% gray card. Pointing the camera straight down, the diver took continuous photographs of the reef along the transect, making three passes on each side of the transect. Detailed methods regarding image collecting for SfM models, including camera settings, can be found in the "Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures" SOP. Couch, Courtney S courtney.s.couch@noaa.gov processor Images were sorted and assessed for quality before model building began. Any gray card photos or images with blue water or fins were stored in a separate folder. Once an initial quality control was completed, Agisoft was used to build the 3D point cloud and 2D orthomosaic for each transect. Once these were built, underlying images were linked to the 3D point cloud in Viscore. Detailed methods for image processing and model building can be found in the "Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures" SOP Couch, Courtney S courtney.s.couch@noaa.gov processor Before annotations began, a geodatabase was created. A geodatabase is used to create the attribute domains which will provide annotators with standard drop down menus to pick from. Next, the 2D orthomosaic was imported into ArcGIS Pro. Transect lines and quadrats were then added, using the pink fishing weight as a reference for their placement. The geodatabase was then added to the project. The models were annotated for fish predation using the multipoint tool. A new line was created in the attribute table for each new coral species/bite mark category/healing condition combination within each quadrat. Once all the models were annotated, the annotations data was extracted from ArcGIS Pro. Detailed descriptions of the bite mark categories, healing conditions, and overlap scores and step by step instructions for setting up models in ArcGIS Pro and doing annotations can be found in the "Quantifying Corallivory from Structure-from-Motion Model" SOP. Escontrela-Dieguez, Daniela daniela.escontreladieguez@noaa.gov processor Source Contribution: This document provides detailed procedures for quantifying corallivory from Structure-from-Motion (SfM) models developed by Ecosystem Sciences Division (ESD) in collaboration with the University of Hawaii at Manoa. These procedures are designed to produce quality corallivory estimates for benthic communities in Hawaii. This pipeline consists of the following steps: (1) Model generation, (2) Setting up ArcGIS Pro, and (3) Extracting corallivory data using ArcGIS Pro. This SOP is the result of comprehensive testing of different 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. Escontrela Dieguez D, Lee R, Kindinger TL, Couch CS, Charendoff J. 2023. Quantifying corallivory from Structure-from-motion models. U.S. Dept. of Commerce, NOAA Technical Memorandum NMFS-PIFSC-149, 8182 p. doi: 10.25923/c64k-gh75 Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/55821 WWW:LINK-1.0-http--link Source Citation URL Source Citation URL information publisher Source Contribution: This document provides detailed procedures for collecting and processing imagery using Structure-from-Motion techniques developed by Ecosystem Sciences Division (ESD) in collaboration with Scripps Institution of Oceanography and the University of Hawaii at Hilo. These procedures are designed to efficiently generate coral demographic and benthic community metrics across the broad spatial scale of the Pacific Rapid Assessment and Monitoring Program. This pipeline consists of four key steps: (1) Image collection by SCUBA divers, (2) Data management, post-processing, and QC, (3) Generating 3-D models and 2-D orthomosaics in Agisoft Metashape, and (4) Extracting demographic data in ArcMap. This SOP is the result of comprehensive testing of different camera systems, collection techniques, and software. While the following procedures are designed to meet ESD needs, we primarily use commercially available cameras and software, making these methods adaptable based on programmatic capacity and needs. Suka R, Asbury M, Couch C, Gray A, Winston M, Oliver T. 2019. Processing Photomosaic Imagery of Coral Reefs Using Structure-from-Motion Standard Operating Procedures. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-93, 54 p. doi:10.25923/h2q8-jv47 2019-12-30 publication Pacific Islands Fisheries Science Center https://repository.library.noaa.gov/view/noaa/22753 WWW:LINK-1.0-http--link NOAA Institutional Repository NOAA technical memorandum NMFS PIFSC information publisher otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None