Carbonate Budgets, Structure-from-Motion Products, and Topographic Complexity Measurements From Restored and Non-Restored Areas of Coral Reefs in the Lower Florida Keys

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Frequently anticipated questions:

What does this data set describe?

Title:
Carbonate Budgets, Structure-from-Motion Products, and Topographic Complexity Measurements From Restored and Non-Restored Areas of Coral Reefs in the Lower Florida Keys
Abstract:
During the summers of 2022 and 2023, U.S. Geological Survey (USGS) researchers conducted underwater surveys aimed at quantifying the impact that past coral restoration by Mote Marine Laboratory had on the reef-accretion process. The surveys were conducted along paired transects representing restored and non-restored areas of eight offshore reefs and three patch-reef sites in the Lower Florida Keys. At each location on each reef, USGS researchers conducted photographic surveys (these images are published in an accompanying release by Johnson and others, 2025) to generate structure-from-motion (SfM) products (point clouds, orthomosaics, and digital surface models [DSMs]), which were used to quantify percent cover of corals and other benthos and topographic complexity. USGS researchers also conducted census surveys of bioeroding parrotfishes, urchins, and sponges at each site.
Supplemental_Information:
Following USGS data management protocols, these data were assigned the following field activity numbers (FANs), 2022-324-FA, 2022-353-DD, and 2023-311-FA. Additional survey and data details are available on the Coastal and Marine Geoscience Data System (CMGDS) at https://cmgds.marine.usgs.gov/.
  1. How might this data set be cited?
    Toth, Lauren T., 20250604, Carbonate Budgets, Structure-from-Motion Products, and Topographic Complexity Measurements From Restored and Non-Restored Areas of Coral Reefs in the Lower Florida Keys:.

    This is part of the following larger work.

    Toth, Lauren T., Johnson, Selena A., Lyons, Erin, Jenkins, Connor, Stathakopoulos, Anastasios, Bloomer, Sierra, Mallon, Jennifer, and Combs, Ian, 20250604, Carbonate Budgets, Structure-from-Motion Products, and Topographic Complexity Measurements From Restored and Non-Restored Areas of Coral Reefs in the Lower Florida Keys: U.S. Geological Survey data release doi.org/10.5066/P13HMEON, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -81.8783
    East_Bounding_Coordinate: -81.3626
    North_Bounding_Coordinate: 24.6216
    South_Bounding_Coordinate: 24.4517
    Description_of_Geographic_Extent: Lower Florida Keys
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 11-Jul-2022
    Ending_Date: 18-Jul-2023
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: tabular and raster digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.0001. Longitudes are given to the nearest 0.0001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is World Geodetic System 1984 (WGS 84).
      The ellipsoid used is WGS_1984.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257223563.
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    Coral reef restoration surveys: Comma-separated values (.csv) and Microsoft Excel (.xlsx) files describing reef site information, benthic composition, bioeroder abundance, carbonate budgets, and topographic complexity of coral reefs in the Lower Florida Keys. Reef surveys were conducted in areas of each reef with and without corals outplanted by Mote Marine Laboratory’s coral restoration program. Detailed attribute descriptions for these files are included data dictionary (Data_Dictionary_Coral_reef_restoration_surveys.docx). These metadata are not complete without this file.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.
    Entity_and_Attribute_Overview:
    Structure-from-motion data products: USGS researchers conducted photographic surveys to generate SfM products (point clouds, orthomosaics, and digital elevation models), which were used to quantify percent cover of corals and other benthos and topographic complexity. The SfM data are published in individual zipped folders, per study site (the eight offshore reefs and three patch-reef sites) and organized into sub-folders per data product: DEMs (.tif), orthomosaics (.tif), and point clouds (.las). These files can be opened in any software capable of opening Geographic Information System (GIS) files.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Lauren T. Toth
  2. Who also contributed to the data set?
    The collection of these data was funded by the U.S. Geological Survey Coastal/Marine Hazards and Resources Program and a Mote Marine Laboratory 'Protect Our Reefs' Grant.
  3. To whom should users address questions about the data?
    Lauren T Toth
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov

Why was the data set created?

The percent cover and census-survey data were used in an associated study (Toth and others, 2025) to quantify differences in carbonate budgets (gross carbonate production, bioerosion, and reef-accretion potential) between restored and non-restored areas of each reef. The SfM were also used to quantify the impact of restoration on topographic complexity at the offshore sites by measuring the impact of digitally removing outplanted coral colonies.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 17-Jul-2023 (process 1 of 6)
    Study locations: Surveys were conducted at eight offshore reefs and three patch-reef sites in the Lower Florida Keys where Mote Marine Laboratory researchers have been actively restoring coral populations in recent years. The reefs at Looe Key, Summerland Ledges, American Shoal, and Mote Site C were surveyed in the summer of 2022 (July 11-18) and the sites at Sand Key, Rock Key, Eastern Dry Rocks, Marker 32, Dog's Leg, Cat's Paw, and Cook Island were surveyed in the summer of 2023 (July 11-18). Restored and non-restored areas of the reef were surveyed at each site. For restored transects, SCUBA (self-contained underwater breathing apparatus) divers identified areas of the reef with a high density of outplanted corals and placed transects within those areas. Non-restored transects were placed on nearby areas of the reef (adjacent spurs or ledges for offshore reef sites) where no outplants were present. Person who carried out this activity:
    Lauren T. Toth
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov
    Data sources produced in this process:
    • Coral_reef_site_data.csv
    • Coral_reef_site_data.xlsx
    Date: 17-Jul-2023 (process 2 of 6)
    Photographic surveys for Structure-from-Motion (SfM): At each site, except for Summerland Ledges, 10–12 (approximately 10 x 2 meters [m] in size) photographic transects were surveyed by SCUBA divers using a downward facing Canon Powershot S120 camera in an underwater housing set to collect RAW image format in continuous shoot mode. Summerland Ledges is an experimental restoration site consisting of two 10 x 10 m restored area and one 10 x 10 m control plot. The two restored plots at Summerland Ledges were surveyed 2m from the reef base using a dual Nikon D7000 DSLR camera system and the control plot was surveyed using a Canon EOS R at the surface. The number of transects varied per site depending on the availability of restored or control reef. All images were collected 1-2m from the reef base using a double-lawnmower swim pattern ensuring 70-80% forward and lateral overlap between images. Prior to image acquisition, the diver used a metric field tape to delineate the sampling area then placed 3-4 coded 25-centimeter (cm) scalebar targets evenly throughout the transect areas to provide accurate scale for models. For more information about the photographic surveys and access to the associated imagery, refer to Johnson and others (2025). Person who carried out this activity:
    Selena A. Johnson
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8053 (voice)
    selenajohnson@usgs.gov
    Date: 2024 (process 3 of 6)
    Structure-from-motion data processing: SfM data products (point clouds, digital surface models, and orthomosaics) were generated using Agisoft Metasahpe Pro v2.0 or later generally following the protocols of Bayley and Mogg (2020). For a thorough description of the workflow and settings, refer to Toth and others (2025) supplemental information section. Briefly, the images from each transect were checked for proper orientation then uploaded into Metashape. Three-dimensional (3D) Models were then generated using the following basic steps: 1) align images into a sparse point cloud, 2) scale model and run initial bundle adjustment for lens calibration, 3) reduce number of low quality points in the model to improve accuracy, 4) orient and position the model in local coordinates, 5) generate dense 3D point cloud, 6) segment point cloud into classes: noise, reef base, canopy, and outplants, 7) filter point cloud based on segmentation classes to generate digital surface models (DSMs), 8) render orthomosaics and 9) export all SfM data products. The open-source R Multiscale DTM package (Ilich and others, 2023) was used to calculate structural complexity metrics from 1-centimeter (cm) resolution exports of the DSMs. The package calculates 15 metrics encompassing terrain attributes from five common terrain groups: slope, aspect, curvature, relative position, and roughness. For this study, four included Multiscale DTM roughness metrics were extracted with a 5x5 neighborhood window size: adjusted standard deviation, roughness index, and vector ruggedness. These metrics were found to be highly correlated so the analysis focused on vector ruggedness (VRM). The impact of restoration on average reef elevation (relative to the lowest point of each transect model) and overall surface area-to-planar-area ratio (rugosity) of the transects was also evaluated. SfM data are published in individual zipped folders, per study site (the eight offshore reefs and three patch-reef sites) and organized into sub-folders per data product: DEMs (Tagged Image File format, .tif), orthomosaics (.tif), and point clouds (LASer file, .las). Person who carried out this activity:
    Selena A. Johnson
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8053 (voice)
    selenajohnson@usgs.gov
    Data sources produced in this process:
    • Coral_reef_topographic_complexity_data.csv
    • Coral_reef_topographic_complexity_data.xlsx
    • AmericanShoal_SfMproducts.zip
    • CatsPaw_SfMproducts.zip
    • CookIsland_SfMproducts.zip
    • DogsLeg_SfMproducts.zip
    • EasternDryRocks_SfMproducts.zip
    • LooeKey_SfMproducts.zip
    • Marker32_SfMproducts.zip
    • RockKey_SfMproducts.zip
    • SandKey_SfMproducts.zip
    • SiteC_SfMproducts.zip
    • Summerland_SfMproducts.zip
    Date: 2023 (process 4 of 6)
    Quantifying percent cover of reef benthos: Percent cover of calcifying reef taxa (corals and crustose coralline algae) and other benthos were quantified by conducting point-count analysis of a 10 x 1 meter (m) belt transect within the two-dimensional (2D) orthomosaics described above using the online software, CoralNet (https://coralnet.ucsd.edu/). Briefly, 10, non-overlapping 1 x 1 m images were extracted from each orthomosaic and the benthos beneath each of 150 points were identified. All coral taxa were identified to species, except for Orbicella, Pseudodiploria, and Millepora spp. which were later pooled by genera. Other benthos, including crustose coralline algae, macroalgae, sponges, gorgonians, zoanthids, consolidated bare substrate (which was generally covered in turf algae), and unconsolidated substrate (sand and rubble) were identified categorically. Person who carried out this activity:
    Lauren T. Toth
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov
    Data sources produced in this process:
    • Coral_reef_percent_cover_data.csv
    • Coral_reef_percent_cover_data.xlsx
    Date: 2023 (process 5 of 6)
    Bioerosion census surveys: USGS researchers conducted census surveys of bioeroding parrotfish, sponges, and urchins following the ReefBudget v2 protocol (Perry and Lange, 2019) in the same reef areas where the structure-from-motion surveys were conducted. Divers recorded the number and size of bioeroding sponges (Cliona aprica, C. caribbaea, C. tenuis, C. varians, C. delitrix, and Siphonodictyon coralliphagum) and bioeroding urchins (Diadema antillarum, Echinometra lucunter, Ec. viridis, and Eucidaris tribuloides) along the same 10-m transects surveyed for structure-from-motion. Sponge surveys were conducted within a 1-m belts around the transects and urchin surveys were conducted within 2-m belts. Researchers also recorded the species, size, and life phase of bioeroding parrotfish (Sparisoma viride, Sp. aurofrenatum, Sp. rubripinne, Sp. chrysopterum, Scarus vetula, Sc. taeniopterus, Sc. iseri, Sc. guacamaia, Sc. coeruleus, and Sc. coelestinus) within 8–10 larger (25 x 4 m) belt-transects to estimate site-level parrotfish bioerosion. Note that because of the larger size of the parrotfish transects and their highly mobile nature, parrotfish surveys could not be conducted separately in restored and non-restored areas of the reefs. Person who carried out this activity:
    Lauren T. Toth
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov
    Data sources produced in this process:
    • Coral_reef_sponge_census_data.csv
    • Coral_reef_sponge_census_data.xlsx
    • Coral_reef_urchin_census_data.csv
    • Coral_reef_urchin_census_data.xlsx
    • Coral_reef_parrotfish_census_data.csv
    • Coral_reef_parrotfish_census_data.xlsx
    Date: 2024 (process 6 of 6)
    Calculating coral reef carbonate budgets: To calculate gross carbonate production (in kilograms per meter squared per year [kg m-2 y-1]), the percent cover of each reef calcifier (from the point count analysis) was multiplied by area-normalized taxon-specific calcification rates (Courtney and others, 2024) and summed for each transect. Microbioerosion along each transect was estimated by multiplying the total area of consolidated, non-calcifying reef substrate (from the point-count analysis) by the western Atlantic mean microbioerosion rate of 0.24 kg m-2 y-1 (Perry and Lange, 2019). Bioerosion by parrotfish, sponges, and urchins were estimated by multiplying by the species-, size-, and, for parrotfish, life-phase-specific bioerosion rates suggested in ReefBudget v2 (Perry and Lange, 2019). Those data were summed with microbioerosion to estimate total bioerosion. Total bioerosion was subtracted from gross carbonate production to estimate net carbonate production. Reef-accretion potential was estimated according to the following equation (Kinsey, 1985): Reef-accretion potential=(Net carbonate production)/(p(1-porosity)), where p is the density of calcium carbonate (2.9 grams per cubic centimeter; Kinsey, 1985) and porosity was estimated from cores of geologic reef framework in the Florida Keys built by branching or massive corals (for offshore and patch-reef sites, respectively; Toth and others, 2018). Person who carried out this activity:
    Lauren T. Toth
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    Research Physical Scientist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8029 (voice)
    ltoth@usgs.gov
    Data sources produced in this process:
    • Coral_reef_carbonate_budget_data.csv
    • Coral_reef_carbonate_budget_data.xlsx
  3. What similar or related data should the user be aware of?
    Toth, Lauren T., Johnson, Selena A., Lyons, Erin O., Spadaro, Jason, Stathakopoulos, Anastasios, Bloomer, Sierra K., Mallon, Jennifer, Jenkins, Connor M., Williams, Sara D., Combs, Ian, Craig, Zachary, and Muller, Erinn, 2025, Coral restoration can drive rapid increases in reef-accretion potential: Scientific Reports Unknown, Springer Nature, Online.

    Online Links:

    Johnson, Selena A., Toth, Lauren T., Jenkins, Connor M., and Lyons, Erin O., 20250604, Diver-based structure-from-motion imagery from coral reef restoration surveys in the Lower Florida Keys: July 2022 and July 2023: U.S. Geological Survey data release doi:10.5066/P1WHKTRD, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL.

    Online Links:

    Perry, Christopher T., and Lange, Ines D., 2019, ReefBudget: ReefBudget Caribbean v2: online resource and methodology: University of Exeter, Online.

    Online Links:

    Courtney, Travis A., Lange, Ines D., Pilly, S. Sannassy, Townsend, Joseph E., Chan, S., Perry, Christopher T., Kriegman, D. J., and Andersson, Andreas J., 20240807, Area-normalized scaling of ReefBudget calcification, macrobioerosion, and microbioerosion rates for use with CoralNet Version 2.0.: Zenodo, Online.

    Online Links:

    Toth, Lauren T., Stathakopoulos, Anastasios, and Kuffner, Ilsa B., 20180426, Descriptive core logs, core photographs, radiocarbon ages, and accretion data from Holocene reef cores collected throughout the Florida Keys reef tract: U.S. Geological Survey data release doi:10.5066/F7NV9HJX, U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, Petersburg, FL.

    Online Links:

    Kinsey, D. W., 1985, Metabolism, calcification and carbon production: 1 system level studies: Proceedings of the Fifth International Coral Reef Congress, Tahiti Volume 4, International Association for Biological Oceanography, Tahiti, French Polynesia.

    Other_Citation_Details: Pages 505-526
    Bayley, Daniel T.I., and Mogg, Andrew O.M., 20200829, A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry: Methods in Ecology and Evolution Volume 11, Issue 11, Wiley, Online.

    Online Links:

    Other_Citation_Details: Pages 1410-1420
    Ilich, Alexander R., Misiuk, Benjamin, Lecours, Vincent, and Murawski, Steven A., 20230526, MultiscaleDTM: An open-source R package for multiscale geomorphometric analysis: Transactions in GIS Volume 27, Issue 4, Wiley, Online.

    Online Links:

    Other_Citation_Details: Pages 1164-1204

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    No formal positional accuracy tests were conducted. The horizontal coordinates were collected in the World Geodetic System of 1984 (WGS 84) coordinate system.
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
    The data set is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints No access constraints. Please see 'Distribution Information' for details.
Use_Constraints These data are marked with a Creative Common CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
    Attn: USGS SPCMSC Data Management
    600 4th Street South
    Saint Petersburg, FL
    United States

    727-502-8000 (voice)
    gs-g-spcmsc_data_inquiries@usgs.gov
  2. What's the catalog number I need to order this data set? Coral_reef_site_data.csv, Coral_reef_site_data.xlsx, Coral_reef_sponge_census_data.csv, Coral_reef_sponge_census_data.xlsx, Coral_reef_urchin_census_data.csv, Coral_reef_urchin_census_data.xlsx, Coral_reef_parrotfish_census_data.csv, Coral_reef_parrotfish_census_data.xlsx, Coral_reef_percent_cover_data.csv, Coral_reef_percent_cover_data.xlsx, Coral_reef_carbonate_budget_data.csv, Coral_reef_carbonate_budget_data.xlsx, Coral_reef_topographic_complexity_data.csv, Coral_reef_topographic_complexity_data.xlsx, Data_Dictionary_Coral_reef_restoration_surveys.docx, *.tif, and *.las
  3. What legal disclaimers am I supposed to read?
    Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 04-Jun-2025
Metadata author:
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Attn: USGS SPCMSC Data Management
600 4th Street South
Saint Petersburg, FL
United States

727-502-8000 (voice)
gs-g-spcmsc_data_inquiries@usgs.gov
Metadata standard:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (FGDC-STD-001.1-1999)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Coral_reef_restoration_surveys_metadata.faq.html>
Generated by mp version 2.9.51 on Tue Jun 24 15:25:10 2025