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

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.

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

Dataset includes metadata for each Structure from Motion (SfM) survey site (site name, survey date and location); site characteristics (depth and habitat type); and individual in situ and SfM corallivory observations where coral was identified to the lowest taxonomic level possible (usually species) and bite marks were characterized in six different categories.

There are two data dictionaries:

1. In-situ corallivory estimates

https://www.fisheries.noaa.gov/inport/item/68016

2. SfM derived corallivory estimates

https://www.fisheries.noaa.gov/inport/item/70037

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.

Oahu, Hawaii June 2021 - October 2022

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NOAA Ecosystem Science Division (ESD) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

ESD welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. ESD has a very diverse set of field activities that generates large volumes of data using an array of data collection protocols.

The following recommendations are for your consideration as you use this data:

1) Data analyses should take all field exigencies into account. The most effective way to do this would be active collaboration with ESD principal investigators.

2) In all presentations, product releases, or publications using data generated by ESD, proper acknowledgement of both ESD and the individuals responsible for data collection is expected. Citing the DOI (if available) is preferred, a non-DOI example is listed below.

3) If you collect or generate data for the same study areas, ESD requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the ESD Data Management Team of any errors and discrepancies that are discovered during the course of using these data. They are further urged to bring to the attention of the Team all problems and difficulties encountered in using these data. This information is necessary in order to improve the collections and to facilitate more efficient and economical data processing and retrieval. The users are asked to supply copies of any missing data that may be located, and to provide information as to significant subsets and special aggregations of data that are developed in using the material provided.

Example citation:

"This publication makes use of data products provided by the Ecosystem Science Division (ESD), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Ocean Acidification Program (OAP). The analysis and interpretations presented here are solely that of the current authors.”

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

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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.

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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).

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.

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.

At each of the 39 sites where SfM imagery was collected, in situ surveys were completed and corallivory was annotated.

The same method of estimation was used for all SfM imagery.

Prior to generating the 3D dense point clouds and 2.5D digital elevation model , the JPEG imagery was evaluated for image quality and images deemed unsatisfactory (e.g. overexposed, images of blue water or images of divers, or images not taken perpendicular to the reef) were removed from the image set. Once images were uploaded to Agisoft, the "Estimate Image Quality" feature was used to further eliminate images with an image quality of less than 0.5. In some instances, if the majority of the images had a quality score of less than 0.5, images were eliminated with a quality of less than 0.4.

NOAA IRC and NOAA Fisheries ITS resources and assets.

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.