Metadata:
  Identification_Information:
    Citation:
      Citation_Information:
        Originator: SeanPaul M. La Selle
        Originator: M. Allison Stegner
        Originator: Brandon M. Nasr
        Originator: Elizabeth A. Hadly
        Originator: Anthony D. Barnosky
        Originator: Brian Sherrod
        Publication_Date: 20230131
        Title: Computed Tomography (CT) scans of vibracores from Searsville Lake, Jasper Ridge Biological Preserve, Stanford, California
        Geospatial_Data_Presentation_Form: raster digital data
        Series_Information:
          Series_Name: data release
          Issue_Identification: DOI:10.5066/P98CEB1B
        Publication_Information:
          Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California
          Publisher: U.S. Geological Survey
        Online_Linkage: https://doi.org/10.5066/P98CEB1B
        Online_Linkage: https://www.sciencebase.gov/catalog/item/6303faf1d34ed6dc5592a545
        Larger_Work_Citation:
          Citation_Information:
            Originator: SeanPaul M. La Selle
            Originator: M. Allison Stegner
            Originator: Brandon M. Nasr
            Originator: Elizabeth A. Hadly
            Originator: Anthony D. Barnosky
            Originator: Brian Sherrod
            Publication_Date: 2023
            Title: Computed Tomography (CT) scans, photographs, X-ray Fluorescence (XRF) scans, grain size, and gamma-ray bulk density data of vibracores from Searsville Lake, Jasper Ridge Biological Preserve, Stanford, California
            Series_Information:
              Series_Name: data release
              Issue_Identification: DOI:10.5066/P98CEB1B
            Publication_Information:
              Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, California
              Publisher: U.S. Geological Survey
            Online_Linkage: https://doi.org/10.5066/P98CEB1B
    Description:
      Abstract: This portion of the data release presents computed tomography (CT) images from vibracores collected from Searsville Lake, Jasper Ridge Biological Preserve, Stanford, California in October 2018 (USGS Field Activity 2018-682-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.
      Purpose: Images were obtained to characterize sediment in vibracores. These data are intended for science researchers, students, policy makers, and the general public.
      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=2018-682-FA

        Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
    Time_Period_of_Content:
      Time_Period_Information:
        Range_of_Dates/Times:
          Beginning_Date: 20181029
          Ending_Date: 20181029
      Currentness_Reference: ground condition
    Status:
      Progress: Complete
      Maintenance_and_Update_Frequency: None planned
    Spatial_Domain:
      Bounding_Coordinates:
        West_Bounding_Coordinate: -122.23787
        East_Bounding_Coordinate: -122.23783
        North_Bounding_Coordinate: 37.40684
        South_Bounding_Coordinate: 37.40683
    Keywords:
      Theme:
        Theme_Keyword_Thesaurus: ISO 19115 Topic Category
        Theme_Keyword: geoscientificInformation
      Theme:
        Theme_Keyword_Thesaurus: USGS Thesaurus
        Theme_Keyword: limnology
        Theme_Keyword: core analysis
      Theme:
        Theme_Keyword_Thesaurus: Data Categories for Marine Planning
        Theme_Keyword: substrate
      Theme:
        Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords
        Theme_Keyword: sediment
      Theme:
        Theme_Keyword_Thesaurus: None
        Theme_Keyword: U.S. Geological Survey
        Theme_Keyword: USGS
        Theme_Keyword: Coastal and Marine Hazards and Resources Program
        Theme_Keyword: CMHRP
        Theme_Keyword: Pacific Coastal and Marine Science Center
        Theme_Keyword: PCMSC
      Theme:
        Theme_Keyword_Thesaurus: USGS Metadata Identifier
        Theme_Keyword: USGS:6303faf1d34ed6dc5592a545
      Place:
        Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
        Place_Keyword: Searsville Lake
        Place_Keyword: Jasper Ridge
        Place_Keyword: Stanford
        Place_Keyword: San Mateo County
        Place_Keyword: State of California
    Access_Constraints: None. Please see 'Distribution Info' for details.
    Use_Constraints: None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations.
    Point_of_Contact:
      Contact_Information:
        Contact_Person_Primary:
          Contact_Person: PCMSC Science Data Coordinator
          Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center
        Contact_Address:
          Address_Type: mailing and physical
          Address: 2885 Mission Street
          City: Santa Cruz
          State_or_Province: CA
          Postal_Code: 95060
        Contact_Voice_Telephone: 831-427-474
        Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
  Data_Quality_Information:
    Attribute_Accuracy:
      Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted
    Logical_Consistency_Report: The core depths listed in the Geotek software’s proprietary metadata files and the ruler alongside the TIFF images are not corrected for sediment compaction and are relative to the surface of the lakebed.
    Completeness_Report: 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.
    Positional_Accuracy:
      Horizontal_Positional_Accuracy:
        Horizontal_Positional_Accuracy_Report: The locations of samples were determined using a Garmin etrex 30x handheld global satellite navigation system (GNSS) receiver capable of receiving wide area augmentation system (WAAS) signals. The manufacturer reported accuracy for horizontal positions is 3-5 m while receiving WAAS signals.
      Vertical_Positional_Accuracy:
        Vertical_Positional_Accuracy_Report: Core location depths and water depths were not associated with a fixed vertical datum at the time of core collection. No formal positional accuracy tests were conducted, nor were they applicable for this dataset.
    Lineage:
      Process_Step:
        Process_Description: 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 segment scanned.
        Process_Date: 20190618
        Process_Contact:
          Contact_Information:
            Contact_Person_Primary:
              Contact_Person: SeanPaul La Selle
              Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science CEnter
            Contact_Position: Geologist
            Contact_Address:
              Address_Type: mailing and physical
              Address: 2885 Mission St.
              City: Santa Cruz
              State_or_Province: CA
              Postal_Code: 95060
            Contact_Voice_Telephone: 831-460-7574
            Contact_Electronic_Mail_Address: slaselle@usgs.gov
      Process_Step:
        Process_Description: corrected typo in doi number (scochran@usgs.gov)
        Process_Date: 20230223
  Spatial_Data_Organization_Information:
    Direct_Spatial_Reference_Method: Point
    Point_and_Vector_Object_Information:
      SDTS_Terms_Description:
        SDTS_Point_and_Vector_Object_Type: Point
        Point_and_Vector_Object_Count: 2
  Spatial_Reference_Information:
    Horizontal_Coordinate_System_Definition:
      Geographic:
        Latitude_Resolution: 0.00004
        Longitude_Resolution: 0.00001
        Geographic_Coordinate_Units: Decimal Degrees
      Geodetic_Model:
        Horizontal_Datum_Name: WGS_1984
        Ellipsoid_Name: WGS_1984
        Semi-major_Axis: 6378137.0
        Denominator_of_Flattening_Ratio: 298.257223563
  Entity_and_Attribute_Information:
    Detailed_Description:
      Entity_Type:
        Entity_Type_Label: zip files containing CT images
        Entity_Type_Definition: 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. The TIFF filenames ending in '_R' contain an embedded vertical scale on the left-hand side. Axial slices TIFFs and orthogonal view TIFFs are 16-bit images with a pixel size of 96 microns, or 104 pixels per centimeter.
        Entity_Type_Definition_Source: Producer defined
      Attribute:
        Attribute_Label: axial slice metadata file 'index.xml'
        Attribute_Definition:
          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>JRBP18-VC01B-650-801</Core-ID>
          <Image-Type>CT-Volume</Image-Type>
          <Processing-Stage>Acquired</Processing-Stage>
          <Section-Number>1</Section-Number>
          <Section-Depth units="cm">649.85</Section-Depth>
          <Total-Scanned-Length units="cm">151.10</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>JRBP2018-test</Name>
          </Recipe>
          </geoct-Recipe-Header-Section>
          <geoct-Acquisition-Section>
          <XRay-Source>
          <Model-Name>Thermo Kevex PSX10-65W</Model-Name>
          <XRay-Voltage units="kV">115.0</XRay-Voltage>
          <Spot-Size-Microns>77.000000</Spot-Size-Microns>
          </XRay-Source>
          <Geometry>
          <Source-Object-Distance units="mm">221.851</Source-Object-Distance>
          <Source-Detector-Distance units="mm">575.131</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">473.00</Horizontal-Position>
          <Vertical-Position units="pixels">370.00</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>17.000</Frame-Rate>
          <Pixel-Size units="mm">0.254</Pixel-Size>
          <Averaging>17</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>JRBP2018-test</Name>
          <Recipe-XML>
          <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\JRBP2018-test.xml" LastSavedUTC="20/05/2019 22:09:11">
          <EditPassword type="String"></EditPassword>
          <Recipe>
          <Name type="String">JRBP2018-test</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">2</ReconstructionThicknessPixels>
          <CentreOfRotation>
          <AutomaticCalculation type="Boolean">True</AutomaticCalculation>
          <InterpolateAlongVolume type="Boolean">False</InterpolateAlongVolume>
          <ManuallyEntered type="Boolean">False</ManuallyEntered>
          <NominalPositionPixels type="Double">462.48</NominalPositionPixels>
          <PresetTagFileValue type="Boolean">False</PresetTagFileValue>
          <VariableCentreVsSectionNumber>
          <Keys type="DoubleArray">1|2|15</Keys>
          <Values type="DoubleArray">462.59|462.58|462.48</Values>
          </VariableCentreVsSectionNumber>
          </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">-0.2</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">-4</Values>
          </XPixels>
          <YPixels>
          <Keys type="DoubleArray">1</Keys>
          <Values type="DoubleArray">-6</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>
        Attribute_Definition_Source: producer defined
        Attribute_Domain_Values:
          Unrepresentable_Domain: 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.
      Attribute:
        Attribute_Label: axial slice metadata file 'WholeCoreRecon.txt'
        Attribute_Definition:
          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 = JRBP18-VC01B-158-214
          Section number = 1
          Section Length = 56.09
          Core Depth At Top = 158.0
          X-Ray Voltage = 115 kV
          X-Ray Current = 450.1 uA
          X-Ray SpotSize = 77 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 = 473
          Source object distance = 221.73 mm
          Source detector distance = 575.01 mm
          Direction of rotation = clockwise
          Vertical centre = 473
          Voxel Size = 0.0959
          User set voxel size = 0
          Calculated Voxel size = 0.0959
          Helical Scan = 0

          RANGE
          -----

          Depth in section of first slice = 0.00 cm
          Slice interval = 0.0096 cm
          First Slice = 1
          Last Slice = 5928
          Minimum Intensity (Raw Floating Point)= -0.2
          Maximum Intensity (Raw Floating Point)= 5.000202
          Scale \$ Flip Complete = 1
          Scatter Adjustment Active = 0
          Horizontal centre = 473
        Attribute_Definition_Source: producer defined
        Attribute_Domain_Values:
          Unrepresentable_Domain: 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.
      Attribute:
        Attribute_Label: orthogonal view metadata files
        Attribute_Definition:
          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>JRBP18-VC01B-158-214</coreID>
          <section-number>1</section-number>
          <physical-width>9.07</physical-width>
          <physical-height>56.83</physical-height>
          <physical-top>158.0</physical-top>
          <pixels-per-CM>104.3</pixels-per-CM>
          <horizontal-resolution>104.3</horizontal-resolution>
          <pixel-width>946</pixel-width>
          <scan-lines>5928</scan-lines>
          <comments></comments>
          <camera-name>Thermo Kevex PSX10-65W</camera-name>
          <average-of>1</average-of>
          <filename>Orthogonal000.tif</filename>
          <x-ray-voltage>115</x-ray-voltage>
          <x-ray-current>450.1</x-ray-current>
          <x-ray-spot-size>77</x-ray-spot-size>
          <source-object-distance>221.73</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>
        Attribute_Definition_Source: producer defined
        Attribute_Domain_Values:
          Unrepresentable_Domain: 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.
  Distribution_Information:
    Distributor:
      Contact_Information:
        Contact_Person_Primary:
          Contact_Person: GS ScienceBase
          Contact_Organization: U.S. Geological Survey
        Contact_Address:
          Address_Type: mailing address
          Address: Denver Federal Center, Building 810, Mail Stop 302
          City: Denver
          State_or_Province: CO
          Postal_Code: 80225
          Country: United States
        Contact_Voice_Telephone: 1-888-275-8747
        Contact_Electronic_Mail_Address: sciencebase@usgs.gov
    Resource_Description: These data are available in TIFF format, including Geotek software-proprietary and CSDGM FGDC-compliant metadata.
    Distribution_Liability: 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.
    Standard_Order_Process:
      Digital_Form:
        Digital_Transfer_Information:
          Format_Name: TIFF
          Format_Information_Content: Downloadable zip files, ranging in size from 6.63 GB to 17.88 GB, contain folders with orthogonal and axial slice TIFF (.tif) images and associated software-proprietary metadata files (.xml). Zip file names correspond to the names of each core segment. For example ‘JRBP2018-VC01A-289-439cm_CT.zip’ contains CT TIFF images from the segment of vibracore VC01A with a top depth of 289 cm and bottom depth of 439 cm.
          File_Decompression_Technique: Zip
          Transfer_Size: 200210
        Digital_Transfer_Option:
          Online_Option:
            Computer_Contact_Information:
              Network_Address:
                Network_Resource_Name: https://www.sciencebase.gov/catalog/item/6303faf1d34ed6dc5592a545
                Network_Resource_Name: https://doi.org/10.5066/P98CEB1B
            Access_Instructions: Data can be downloaded using the Network_Resource_Name links. The first link points to a landing page with metadata and individual zipped data files of CT imagery. The second link points to the landing page for the entire data release.
      Fees: None
  Metadata_Reference_Information:
    Metadata_Date: 20230223
    Metadata_Contact:
      Contact_Information:
        Contact_Person_Primary:
          Contact_Person: PCMSC Science Data Coordinator
          Contact_Organization: U.S. Geological Survey, Pacific Coastal and Marine Science Center
        Contact_Address:
          Address_Type: mailing and physical
          Address: 2885 Mission Street
          City: Santa Cruz
          State_or_Province: CA
          Postal_Code: 95060
        Contact_Voice_Telephone: 831-427-4747
        Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
    Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
    Metadata_Standard_Version: FGDC-STD-001-1998