Computed Tomography (CT) scans of sediment cores collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA

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Frequently anticipated questions:

What does this data set describe?

Title:
Computed Tomography (CT) scans of sediment cores collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA
Abstract:
This dataset includes computed tomography (CT) scans of sediment cores collected from Cargill Marsh, South San Francisco Bay, California on June 21, 2022, and December 14, 2023. The cores were collected with hand driven push cores to assess sediment accumulation on the marsh. CT images are provided in the original 16-bit grayscale TIFF format.
Supplemental_Information:
Cores were collected, analyzed, and archived by USGS, Pacific Coastal and Marine Science Center. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Information about the data collection field activities can be found at: http://cmgds.marine.usgs.gov/fan_info.php?fan=2022-643-FA http://cmgds.marine.usgs.gov/fan_info.php?fan=2023-681-FA
  1. How might this data set be cited?
    Joanne C. T. Ferreira, Nowacki, Daniel J., and SeanPaul M. La Selle, 20240711, Computed Tomography (CT) scans of sediment cores collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA: data release DOI:10.5066/P15AORBR, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    Joanne C. T. Ferreira, Nowacki, Daniel J., and SeanPaul M. La Selle, 2024, Sediment core data collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA: data release DOI:10.5066/P15AORBR, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, CA.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: Ferreira, J.C.T., Nowacki, D.J., and La Selle, S.M., 2024, Sediment core data collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA: U.S. Geological Survey data release, https://doi.org/10.5066/P15AORBR.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -122.13863
    East_Bounding_Coordinate: -122.13845
    North_Bounding_Coordinate: 37.59074
    South_Bounding_Coordinate: 37.58864
  3. What does it look like?
    ct_color_enhanced_RC02_60-70cm.png (PNG)
    Preview of a CT image from core RC02, with a false colormap applied to CT intensity values. Color enhanced image has identical information as the grey scale images in the zipped file.
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 21-Jun-2022
    Ending_Date: 14-Dec-2023
    Currentness_Reference:
    Ground conditions at time data were collected
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: raster digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (6)
    2. What coordinate system is used to represent geographic features?
      Vertical_Coordinate_System_Definition:
      Depth_System_Definition:
      Depth_Datum_Name: Local surface
      Depth_Resolution: 1.0
      Depth_Distance_Units: centimeters
      Depth_Encoding_Method: Attribute values
  7. How does the data set describe geographic features?
    cargill_cores_ct.zip
    A zip file containing 6 TIFF files of CT images and their respective software-proprietary XML files. (Source: Producer defined)
    orthogonal CT image metadata XML file
    This Geotek software-proprietary XML file contains information on CT scan acquisition settings and reconstruction settings. The following attributes and example attribute values are provided: <geotek-image> <image-type>giCTOrthogonalView</image-type> <coreID> CAR22-RC02</coreID> <section-number>1</section-number> <physical-width>8.70</physical-width> <physical-height>102.65</physical-height> <physical-top>0.01</physical-top> <pixels-per-CM>108</pixels-per-CM> <horizontal-resolution>108</horizontal-resolution> <pixel-width>940</pixel-width> <scan-lines>5496</scan-lines> <comments> Enter Comments Here</comments> <camera-name> Thermo Kevex PSX10-65W</camera-name> <average-of>1</average-of> <filename>XZ_CAR22-RC02-0-50cm.TIF</filename> <x-ray-voltage>130</x-ray-voltage> <x-ray-current>330</x-ray-current> <x-ray-spot-size>63</x-ray-spot-size> <source-object-distance>220.64</source-object-distance> <source-detector-distance>591.85</source-detector-distance> <detector-CCD-mode> 2x2</detector-CCD-mode> <image-enhancement-filter>Enabled=False,WindowCount=2,Window=400,SigmaA=0.1,SigmaV=0.0005,Weight=0.4,Window=100,SigmaA=0.1,SigmaV=0.0005,Weight=1,Reduction=0.85</image-enhancement-filter> <is-a-sync-scan-image>0</is-a-sync-scan-image> </geotek-image> (Source: producer defined) These Geotek software-proprietary XML files contain information on CT scan acquisition settings and image scaling information. The values in the example provided may be different for each scan. Please contact the PCMSC data coordinator for more information on the contents of these XML files.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Joanne C. T. Ferreira
    • Daniel J. Nowacki
    • SeanPaul M. La Selle
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    PCMSC Science Data Coordinator
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    2885 Mission Street
    Santa Cruz, CA

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

Why was the data set created?

These cores were collected to measure sediment accumulation as part of a study to quantify sediment fluxes and changes in marsh morphology on marshes in southern San Francisco Bay.

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: 2023 (process 1 of 2)
    Sediment cores were collected from the marsh environment on Cargill Marsh in Eden Landing Environmental Reserve, Alameda County, California using a Russian corer (a hand-held, side-filling peat auger). At each core site, two adjacent cores holes were used to sample sediment in 50 cm intervals with a 10 cm overlapping section resulting in undisturbed sediment cores of 90 cm length. Cores were transported back to the USGS Pacific Coastal and Marine Science Center for imaging, and subsequently sectioned in two cm samples for Cesium-137 analyses. Not all segments of the cores were analyzed.
    Date: 2023 (process 2 of 2)
    CT scans were acquired at the USGS Pacific Coastal and Marine Science Center core facility using a Geotek Rotating X-Ray CT (RXCT) Scanner system, running acquisition software version XCT4. Rotational x-ray images were acquired with a Thermo Kevex PSX10-65W x-ray source every 0.2 degrees at 130 kilovolts (kV) and 330 microamperes. Core segments were scanned in batches of two to three segments. Rotational images were reconstructed into axial slice TIFFs using Geotek’s Reconstructor Software. Once reconstructed, the axial slice TIFFs were imported into GeoTek's Image Viewer software and a representative two-dimensional orthogonal view was selected. TIFFs are provided in 16-bit unsigned integer, single channel format. Scaling information is embedded in the TIFF files and also provided in the associated XML files. File names correspond to the names of the cores within each scan. For example, ‘2022-643-FA_CAR-RC02-0-50cm.TIF' corresponds to the CT image of core segments collected during field activity 2022-643-FA,'CAR' refers to the Cargill Marsh, and 'RC-02' to the core location within the marsh. '0-50cm' or '40-90cm' refers to the depth of the core relative to the surface of the marsh. Photographic images of these cores are available in a separate section of this data release.
  3. What similar or related data should the user be aware of?
    Joanne C. T. Ferreira, Lacy, Jessica R., McGill, Samantha C., WinklerPrins, Lukas T., Nowacki, Daniel J., Stevens, Andrew W., and Tan, Angela C., 2023, Hydrodynamic and sediment transport data from Whale's Tail South marsh and adjacent waters in South San Francisco Bay, California 2021-2022.

    Online Links:

    Joanne C. T. Ferreira, and Nowacki, Daniel J., 2024, Information on sediment cores collected from Cargill Marsh, South San Francisco Bay, California during field activities 2022-643-FA and 2023-681-FA.

    Online Links:

    Other_Citation_Details:
    Core location information for these CT scans have been published in a separate section in this data release

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

  1. How well have the observations been checked?
    Quality control of attribute accuracy was conducted during field data collection and processing workflows. No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    A RTK GPS system was used for obtaining latitude and longitude point locations during the field activity with centimeter accuracy. As each core site required two adjacent cores to complete the 90 cm length, the horizontal position accuracy of 50 cm is reasonable.
  3. How accurate are the heights or depths?
    Core depth values are relative to the top of sediment surface at the time of core collection. Coring-induced compaction, if any, was not determined. No formal vertical accuracy tests were conducted.
  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 consistency 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 Info' for details.
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
    United States

    831-427-4747 (voice)
    pcmsc_data@usgs.gov
  2. What's the catalog number I need to order this data set? CT images are provided in a zip archive (Cargill_cores_ct.zip) with CSDGM FGDC compliant metadata. Please contact the PCMSC Data Coordinator about availability of full 3D CT scan volumes.
  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?
    • Availability in digital form:
      Data format: Zip file contains CT core imagery in TIFF format and associated proprietary metadata in XML format. in format TIFF, XML (version Geotek RXCT Scanner system, software version XCT4) Size: 48.5
      Network links: https://doi.org/10.5066/P15AORBR
    • Cost to order the data: None.

  5. What hardware or software do I need in order to use the data set?
    CT images can be viewed with any standard image software. Proprietary metadata XML files can be viewed with any standard text editing software.

Who wrote the metadata?

Dates:
Last modified: 11-Jul-2024
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_P15AORBR/cargill_marsh_ct_metadata.faq.html>
Generated by mp version 2.9.51 on Thu Jul 18 15:07:15 2024