Computed tomography (CT) scans of push cores from Loki's Castle and Favne vent fields, Mohns Ridge

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Frequently anticipated questions:

What does this data set describe?

Title:
Computed tomography (CT) scans of push cores from Loki's Castle and Favne vent fields, Mohns Ridge
Abstract:
This portion of the data release presents computed tomography (CT) images from push cores collected from Loki's Castle and Favne vent fields, on the Mohns Ridge, in the Norwegian Sea. These data were collected in 2018 and 2019 (USGS Field Activity 2018-691-DD and 2019-624-FA). A Geotek Rotating X-Ray CT (RXCT) system was used to acquire x-ray images and perform CT reconstructions of unsplit core segments. The full three-dimensional data set consists of individual axial slices which are reconstructed images in TIFF format. These axial slices are oriented perpendicular to the long axis of the core. Two-dimensional orthogonal views are also provided that illustrate representative downcore slabs of each core. Geotek software-proprietary XML files are provided in each folder containing axial slices and orthogonal views, containing more image-scaling and information on x-ray system settings and reconstruction parameters.
Supplemental_Information:
Additional information about the field activities from which these data were derived is available online at: https://cmgds.marine.usgs.gov/fan_info.php?fan=2018-691-DD https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-624-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?
    Gartman, Amy, 20240110, Computed tomography (CT) scans of push cores from Loki's Castle and Favne vent fields, Mohns Ridge: data release DOI:10.5066/P96D02FG, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    This is part of the following larger work.

    Gartman, Amy, Au, Manda V., and Payan, Denise, 2023, Computed tomography (CT) scans, photographs, X-ray fluorescence (XRF) scans, geochemistry, X-ray diffraction (XRD), and gamma-ray bulk density data of push cores from Loki's Castle and Fauna vent fields, Mohns Ridge: data release DOI:10.5066/P96D02FG, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: Gartman, A., Au, M.V., and Payan, D., 2024, Computed tomography (CT) scans, photographs, X-ray fluorescence (XRF) scans, geochemistry, X-ray diffraction (XRD), and gamma-ray bulk density data of push cores from Loki's Castle and Favne vent fields, Mohns Ridge: U.S. Geological Survey data release, https://doi.org/10.5066/P96D02FG.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: 3.8318
    East_Bounding_Coordinate: 8.1661
    North_Bounding_Coordinate: 73.5678
    South_Bounding_Coordinate: 72.7556
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 18-Jul-2018
    Ending_Date: 30-Jun-2019
    Currentness_Reference:
    ground condition
  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 (16)
    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 0.00004. Longitudes are given to the nearest 0.00001. 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?
    zip files containing CT images
    Each zip file contains 2 sub-folders named 'SliceViews' and 'OrthogonalViews'. The 'SliceViews' folder contains TIFF files of each axial slice and two Geotek software-proprietary metadata files, 'index.xml' and 'WholeCoreRecon.txt'. The 'index.xml' file is generated during reconstruction and contains detailed acquisition and reconstruction metadata. The 'WholeCoreRecon.txt' file summarizes x-ray settings, the source and detector geometry, and core depth information. In the 'OrthogonalViews' folder, 4 TIFF files and their respective Geotek software-proprietary metadata .xml files are included. The 'Orthogonal000' and 'Orthogonal090' components of the TIFF filenames signify two-dimensional downcore views of slabs that are orthogonal to each other. Axial slices TIFFs and orthogonal view TIFFs are 16-bit images with a pixel size of 96 microns, or 104 pixels per centimeter. (Source: Producer defined)
    axial slice metadata file 'index.xml'
    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-ct-recon> <geoct-Identification-Section> <Core-ID>GS18ROV26PC01</Core-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Acquired</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">0</Section-Depth> <Total-Scanned-Length units="cm">48.19</Total-Scanned-Length> <User-Comments></User-Comments> <Firmware-Version></Firmware-Version> <Windows-Version></Windows-Version> <Logger-Type-Desc></Logger-Type-Desc> <Generated-From-Application></Generated-From-Application> <SVN-Version></SVN-Version> <Build-Date></Build-Date> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>AmyG</Name> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">120.0</XRay-Voltage> <Spot-Size-Microns>39.000000</Spot-Size-Microns> </XRay-Source> <Geometry> <Source-Object-Distance units="mm">277.733</Source-Object-Distance> <Source-Detector-Distance units="mm">575.011</Source-Detector-Distance> <Detector-in-Plane units="degrees">-90.000</Detector-in-Plane> <Detector-Tilt units="degrees">0.000</Detector-Tilt> <Detector-Skew units="degrees">0.000</Detector-Skew> <Offset-Angle units="degrees">0.000</Offset-Angle> <Beam-Centre> <Horizontal-Position units="pixels">472.00</Horizontal-Position> <Vertical-Position units="pixels">369.00</Vertical-Position> </Beam-Centre> <User-Defined-Pixel-Size> <Enabled>No</Enabled> <Position-One units="pixels">0</Position-One> <Position-Two units="pixels">0</Position-Two> <Distance units="mm">0.0</Distance> <Is-Crosscore>No</Is-Crosscore> </User-Defined-Pixel-Size> </Geometry> <Motor-Movements> <Rotation> <Start-Angle units="degrees">0.000</Start-Angle> <Step units="degrees">0.200</Step> <End-Angle units="degrees">360.000</End-Angle> <Clockwise-Direction>1</Clockwise-Direction> <Start-Stop-Acquisition>0</Start-Stop-Acquisition> </Rotation> </Motor-Movements> <Detector> <Model-Name>Varian-2520DX</Model-Name> <Mode>2x2</Mode> <Frame-Rate>10.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>10</Averaging> <Pixel-Scan-Height>960</Pixel-Scan-Height> <Pixel-Scan-Width>768</Pixel-Scan-Width> </Detector> </geoct-Acquisition-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>AmyG</Name> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\AmyG.xml" LastSavedUTC="12/02/2019 00:50:45"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">AmyG</Name> <Type type="String">CT Rotational Reconstruction</Type> <ReconstructedOutput> <IncludeVolumeSinograms type="Boolean">False</IncludeVolumeSinograms> <IncludeVolumeSlices type="Boolean">False</IncludeVolumeSlices> <OutputAlongsideRawProjections type="Boolean">True</OutputAlongsideRawProjections> <OutputFolderPostFix type="String"></OutputFolderPostFix> <OutputFolderPrefix type="String"></OutputFolderPrefix> </ReconstructedOutput> <RotationalReconstruction> <Reconstruction> <ReconstructionThicknessPixels type="Int64">5</ReconstructionThicknessPixels> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <InterpolateAlongVolume type="Boolean">False</InterpolateAlongVolume> <ManuallyEntered type="Boolean">False</ManuallyEntered> <PresetTagFileValue type="Boolean">False</PresetTagFileValue> </CentreOfRotation> <CuppingCorrection> <AutomaticCalculation type="Boolean">False</AutomaticCalculation> <CorrectionFactors type="DoubleArray">0.7|0|0|0</CorrectionFactors> <EnableCorrection type="Boolean">True</EnableCorrection> </CuppingCorrection> <IntensityRange> <ManualIntensityMaximum type="Double">5</ManualIntensityMaximum> <ManualIntensityMinimum type="Double">-5</ManualIntensityMinimum> <SetManually type="Boolean">True</SetManually> </IntensityRange> <PitchAdjustment> <EnablePitch type="Boolean">False</EnablePitch> <PitchDegrees type="Double">0</PitchDegrees> </PitchAdjustment> <ReconFilter> <EnableFilter type="Boolean">True</EnableFilter> <FilterLevel type="Cardinal">150</FilterLevel> </ReconFilter> <RingFilter> <EnableFilter type="Boolean">True</EnableFilter> <FilterSizePixels type="Double">20</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">1</Keys> <Values type="DoubleArray">-36</Values> </XPixels> <YPixels> <Keys type="DoubleArray">1</Keys> <Values type="DoubleArray">120</Values> </YPixels> </OffsetOfCore> </Reconstruction> <Projections> <CropFilter> <EnableCrop type="Boolean">False</EnableCrop> <LeftRightPixels type="Double">0</LeftRightPixels> <TopBottomPixels type="Double">0</TopBottomPixels> </CropFilter> <NormalisationReference> <EnableReference type="Boolean">False</EnableReference> <ReferenceValue type="Point">X=0,Y=0</ReferenceValue> </NormalisationReference> <NormalisationRegions> <EnableRegions type="Boolean">False</EnableRegions> <PixelLocations type="StringArray"></PixelLocations> </NormalisationRegions> <SpotFilter> <EnableFilter type="Boolean">True</EnableFilter> <FilterSizePixels type="Double">5</FilterSizePixels> </SpotFilter> </Projections> </RotationalReconstruction> </Recipe> </Recipe-XML> </Recipe Latest="True"> </geoct-Recipe-Section> </geotek-ct-recon> (Source: producer defined) These Geotek software-proprietary XML files contain information on CT scan acquisition settings and reconstruction settings. 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.
    axial slice metadata file 'WholeCoreRecon.txt'
    This Geotek software-proprietary TXT file contains information on CT scan acquisition settings and image scaling information. The following attributes and example attribute values are provided: CORE INFO --------- Version Number = 6 Core ID = GS18ROV26PC01-AG Section number = 1 Section Length = 48.19 Core Depth At Top = 0 X-Ray Voltage = 120 kV X-Ray Current = 234.7 uA X-Ray SpotSize = 39 microns Camera Name = Thermo Kevex PSX10-65W Average Of = 1 Detector Mode = 2x2 Comments = GEOMETRY -------- Mode = cone beam Last angle = 360° Offset angle= 0° Clock wise = 1 Pixel size = 0.25 mm Centre of rotation = 472 Source object distance = 277.73 mm Source detector distance = 575.01 mm Direction of rotation = clockwise Vertical centre = 369 Voxel Size = 0.1201 User set voxel size = 0 Calculated Voxel size = 0.1201 Helical Scan = 0 RANGE ----- Depth in section of first slice = 0.00 cm Slice interval = 0.012 cm First Slice = 1 Last Slice = 4119 Minimum Intensity (Raw Floating Point)= -0.3516 Maximum Intensity (Raw Floating Point)= 4.893821 Scale \$ Flip Complete = 1 Scatter Adjustment Active = 0 Horizontal centre = 472 (Source: producer defined) These Geotek software-proprietary TXT files contain information on CT scan acquisition settings. 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 TXT files.
    orthogonal view metadata files
    These Geotek software-proprietary XML files contain information on CT scan acquisition settings and image scaling information. Each orthogonal TIFF file is accompanied by an XML file with the same filename. The following attributes and example attribute values are provided: <geotek-image> <image-type>giCTOrthogonalView</image-type> <coreID>GS18ROV26PC01-AG</coreID> <section-number>1</section-number> <physical-width>11.34</physical-width> <physical-height>49.47</physical-height> <physical-top>0</physical-top> <pixels-per-CM>83.26</pixels-per-CM> <horizontal-resolution>83.26</horizontal-resolution> <pixel-width>944</pixel-width> <scan-lines>4119</scan-lines> <comments></comments> <camera-name>Thermo Kevex PSX10-65W</camera-name> <average-of>1</average-of> <filename>Orthogonal000.tif</filename> <x-ray-voltage>120</x-ray-voltage> <x-ray-current>234.7</x-ray-current> <x-ray-spot-size>39</x-ray-spot-size> <source-object-distance>277.73</source-object-distance> <source-detector-distance>575.01</source-detector-distance> <detector-CCD-mode>2x2</detector-CCD-mode> <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)
    • Amy Gartman
  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?

Images were obtained to characterize sediment in push cores. These data are intended for science 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: 04-Jul-2019 (process 1 of 2)
    Samples are push cores and were pushed into sediment by the ROV’s manipulator arm. Once recovered, shipboard cores were frozen (2018-691-DD) or refrigerated (2019-624-FA) until return to shore. Samples were donated from Field Activity 2018-691-DD, and no USGS attendees were present. Amy Gartman attended 2019-624-FA.
    Date: 17-May-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 115 kilovolts (kV) and 450 microamperes. Each core segment was scanned individually. 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 representative two-dimensional orthogonal views were selected. A ruler was added to the orthogonal TIFF images using the GeoTek Add Ruler software, which exported the final TIFF and software-proprietary XML files, appending 'R' to the file name. Axial slice TIFF images are organized into a subfolder folder named ‘SliceViews’, and orthogonal TIFF images are in the subfolder ‘OrthogonalViews’. These folders are compressed into single zip files with filenames corresponding to each core scanned. Person who carried out this activity:
    Amy Gartman
    U.S. Geological Survey, Pacific Coastal and Marine Science Center
    Research Oceanographer
    2885 Mission St.
    Santa Cruz, CA

    831-460-7562 (voice)
    agartman@usgs.gov
  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?
    No formal attribute accuracy tests were conducted
  2. How accurate are the geographic locations?
    The locations of samples were determined using the ROV's Ultra Short Baseline Positioning (USBL) navigation. Accuracy for this depth is approximately 20-50 m.
  3. How accurate are the heights or depths?
    The vertical accuracy was determined with the ROV's altimeter, which is accurate to less than 1 m. No formal positional 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?
    The core depths listed in the Geotek software’s proprietary metadata files are not corrected for sediment compaction and are relative to the surface of the sediment.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints None. 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. 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)
    GS ScienceBase
    U.S. Geological Survey
    Denver Federal Center, Building 810, Mail Stop 302
    Denver, CO
    United States

    1-888-275-8747 (voice)
    sciencebase@usgs.gov
  2. What's the catalog number I need to order this data set? These data are available in TIFF format, including Geotek software-proprietary and CSDGM FGDC-compliant metadata.
  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.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 10-Jan-2024
Metadata author:
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
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/ScienceBase/DR_P96D02FG/LokiFavne-CT-metadata.faq.html>
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