In situ sediment profile images from south San Francisco Bay, California, 2023-2025

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Frequently anticipated questions:

What does this data set describe?

Title:
In situ sediment profile images from south San Francisco Bay, California, 2023-2025
Abstract:
In situ images of the sediment-water interface and sediment profiles were collected to characterize the top layer of the sediment bed (less than 15 cm sediment depth) prior to dredged material placement and post dredge material placement in south San Francisco Bay, California. Several sites within the placement area, as well as sites outside of the placement area, and near time-series stations were collected. The photos were acquired during four separate trips: August 2023 (pre-placement), October 2023 (pre-placement), January 2023 (post-placement), and February (greater than 1 year post-placement). The sediment profile imaging system consisted of a Blackfly S Board-level BFS-GE-50S5C0BD2 camera that incorporates a Sony IMX264 sensor and has an m12-mount type wide-angle 4.4 mm lens. The resulting field of view was approximately 7x15 cm at the window, with a resolution of 0.0667 mm per pixel when the vertically (portrait) oriented window of the housing was pushed into the sediment bed. The camera was secured horizontally in Sediment Profile Imaging (SPI) camera waterproof housing from OceanInstruments, which was lowered to the bay floor at the different stations and pushed from above into the sediment bed using a rigidly attached pole. The images captured using the system show a profile view which includes a surface view of the sediment bed where the window was above the water-sediment interface, and/or a high-resolution sediment profile where the window extended vertically down into the sediment bed and was flush with the sediment. The maximum depth below the water-sediment interface recorded by the sediment profile imaging camera was approximately 15 cm.
Supplemental_Information:
Additional information about the field activity or activities from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2023-655-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
  1. How might this data set be cited?
    McGill, Samantha C., and Hatcher, Gerald A., 20250820, In situ sediment profile images from south San Francisco Bay, California, 2023-2025: data release DOI:10.5066/10.5066/P14D723N, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    McGill, Samantha C., Lacy, Jessica R., Stevens, Andrew W., Allen, Rachel M., Dartnell, Peter, Thede, Joanne C., Tan, Angela C., and Hatcher, Gerald A., 2025, Oceanographic and hydrographic monitoring data of a shallow-water placement of dredged sediment in south San Francisco Bay, California, 2023-2025: data release DOI:10.5066/P14D723N, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: McGill, S.C., Lacy, J.R., Stevens, A.W., Allen, R.M., Dartnell, P., Thede, J.C., Tan, A.C., and Hatcher, G.A., 2025, Hydrodynamic, bathymetric, and sediment transport data spanning dredge material placement in south San Francisco Bay, California, 2023-2025: U.S. Geological Survey data release, https://doi.org/10.5066/P14D723N.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -122.181326
    East_Bounding_Coordinate: -122.141708
    North_Bounding_Coordinate: 37.606221
    South_Bounding_Coordinate: 37.577274
  3. What does it look like?
    sediment_profile_image_collage.png (PNG)
    Multiple images of the bed in south San Francisco Bay captured by the camera as well as a photograph of the camera used to acquire bay floor images and the camera system setup showing a scientist adjusting the push pole to prepare the system for image collection.
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 15-Aug-2023
    Ending_Date: 26-Mar-2025
    Currentness_Reference:
    ground condition at time data were collected
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: comma-delimited text
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      Indirect_Spatial_Reference:
      The location information for the images is available in the EXIF headers of the images.
    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 0.000001. Longitudes are given to the nearest 0.000001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is WGS_1984.
      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:
    There are no additional attributes besides the tags described in data quality section associated with these images.
    Entity_and_Attribute_Detail_Citation: USGS Field Activity 2023-655-FA

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Samantha C. McGill
    • Gerald A. Hatcher
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Attn: PCMSC Science Data Coordinator
    2885 Mission Street
    Santa Cruz, CA

    831-427-4747 (voice)
    pcmsc_data@usgs.gov

Why was the data set created?

Characterization of the sediment bed prior to the placement of dredged material as well as during different times after the placement provides insight on how the dredge sediments have impacted the local environment, including impacts to the local benthic community. These images provide general insight into how the benthos are evolving as a result of the placed dredged material. These data were collected as part of a collaborative study with USGS Western Ecological Research Center monitoring the pilot project conducted by US Army Corps of Engineers San Francisco District. The study investigated the transport, impacts, and evolution of strategically placed dredged material in a shallow subtidal region adjacent to a marsh. Goals of this study were to assess the potential use of shallow-water placement for marsh management and restoration while gaining insight into local sediment transport adjacent to marshes in the shallows of South San Francisco Bay. These data are intended for researchers, students, policy makers, and the general public.

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: 10-Feb-2025 (process 1 of 4)
    In situ images of the sediment-water interface were collected to characterize the sediment bed in south San Francisco Bay prior to dredged material placement and post dredge material placement. Images were collected at various sites during four separate trips: August 15th, 2023, October 18th, 2023, January 4th, 2024, and February 10th, 2025. Image collection sites were either within the placement area, outside of the placement area, or near time-series stations were collected. The sediment profile imaging system consisted of a Blackfly S Board-level BFS-GE-50S5C0BD2 camera that incorporates a Sony IMX264 sensor and has an m12-mount type wide-angle 4.4 mm lens. The resulting field of view was approximately 7x15 cm at the window, with a resolution of 0.0667 mm per pixel when the vertically (portrait) oriented window of the housing was pushed into the sediment bed. The camera was secured horizontally in Sediment Profile Imaging (SPI) camera waterproof housing from OceanInstruments, which was lowered to the bay floor at the different stations and pushed from above into the sediment bed using a rigidly attached pole. The images captured using the system show a profile view which includes a surface view of the sediment bed where the window was above the water-sediment interface, and/or a high-resolution sediment profile where the window extended vertically down into the sediment bed and was flush with the sediment. The maximum depth below the water-sediment interface recorded by the sediment profile imaging camera was approximately 15 cm. A laptop that was running a custom software was used to record images from the camera and record the positions from the GPS resulting in a log file that contained the image file name, acquisition time, and position of the survey vessel at the time of image acquisition. TIFF file names were typically assigned the name of either a time-series or sediment core sampling station (X1, P1, and so on) that the images were collected near. If the image was not captured near a time-series or core sampling station, a general descriptor of the location (for example, near shore) was used. File names also include the datetime that the image was collected.
    Date: 26-Mar-2025 (process 2 of 4)
    A calibration image of a ruler grid was collected using the camera. This image can be used for scaling images of the bed, where the sediment was flush with the camera housing.
    Date: 04-Apr-2025 (process 3 of 4)
    Images were inspected to remove any of very poor quality (for example, completely washed out or dark), images that might provide some level of characterization of the bay floor were retained. The positions and times in the log file were later written to the EXIF header of each image using the command-line 'exiftool' software. Additional known and required EXIF imagery headers were written to each image using the command-line 'exiftool' software.
    Date: 04-Apr-2025 (process 4 of 4)
    The Images were organized into collections based on survey date (August 2023, October 2023, January 2024, February 2025). The calibration image is in its own collection (Calibration Image). The images were uploaded as TIFF files onto to the Imagery Data System (https://cmgds.marine.usgs.gov/idsviewer/) where they can be previewed and downloaded.
  3. What similar or related data should the user be aware of?

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

  1. How well have the observations been checked?
    Information about the acquisition times and positions is recorded to the image metadata (EXIF) header for each image. The positions of the images were determined using one of three ways: 1) U-blox-Neo-M9N logged on a laptop, 2) Garmin GPSmap 76CS logged onto a laptop, or 3) Ship navigation system (Garmin GPSmap XSV chartplotter and Garmin GPS19x antenna or Garmin Echomap UHD2 64sv and inbuilt GPS antenna). A laptop running a custom software was used to view and record images from the camera and record the positions from the GPS resulting in a log file that contained the image file name, acquisition time, and position of the survey vessel at the time of image acquisition. The positions and times in the log file were later written to the EXIF header of each image using the command-line 'exiftool' software. The positions stored in the EXIF are in the WGS84 (G1150) coordinate reference system and times are all in Coordinated Universal Time (UTC).
  2. How accurate are the geographic locations?
    The location of each image was determined using one of the following GPS systems: 1) U-blox-Neo-M9N logged on a laptop with a manufacturer accuracy of 2 meters, 2) Garmin GPSmap 76CS logged onto a laptop with an accuracy of 3 meters, or 3) Ship navigation system: Garmin GPSmap XSV chartplotter and Garmin GPS19x antenna or Garmin Echomap UHD2 64sv and inbuilt GPS antenna, both have an accuracy of 3 meters. The exact location recorded by the GPS system was always on deck, while the camera was lowered off the side of the vessel which may have introduced an addition error or offset of up to 2 meters.
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
    Dataset 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
Use_Constraints USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator(s) of the dataset and in products derived from these data.
  1. Who distributes the data set? (Distributor 1 of 1)
    U.S. Geological Survey - CMGDS
    2885 Mission Street
    Santa Cruz, CA

    1-831-427-4747 (voice)
    pcmsc_data@usgs.gov
  2. What's the catalog number I need to order this data set? The bay floor images from all four surveys are available in TIFF format. The images from each survey (August 2023, October 2023, January 2024, February 2025) as well as the calibration image are all available on the Coastal and Marine Hazards and Resources Program’s (CMHRP) Imagery Data System (IDS).
  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 on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 20-Aug-2025
Metadata author:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Attn: PCMSC Science Data Coordinator
2885 Mission Street
Santa Cruz, CA

831-427-4747 (voice)
pcmsc_data@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/CMGDS_DR_tool/DR_P14D723N/DMP23_sediment_profile_images_metadata.faq.html>
Generated by mp version 2.9.51 on Tue Sep 2 13:32:13 2025