Computed Tomography (CT) scans of vibracores from Searsville Lake, Jasper Ridge Biological Preserve, Stanford, California

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  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?
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   SeanPaul M. La Selle, Stegner, M. Allison, Nasr, Brandon M., Hadly, Elizabeth A., Barnosky, Anthony D., and Sherrod, Brian, 20230131, Computed Tomography (CT) scans of vibracores from Searsville Lake, Jasper Ridge Biological Preserve, Stanford, California: data release DOI:10.5066/P98CEB1B, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

   Online Links:

   • https://doi.org/10.5066/P98CEB1B
   • https://www.sciencebase.gov/catalog/item/6303faf1d34ed6dc5592a545

   This is part of the following larger work.
   SeanPaul M. La Selle, Stegner, M. Allison, Nasr, Brandon M., Hadly, Elizabeth A., Barnosky, Anthony D., and Sherrod, Brian, 2023, 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: data release DOI:10.5066/P98CEB1B, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

   Online Links:

   • https://doi.org/10.5066/P98CEB1B

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -122.23787
   East_Bounding_Coordinate: -122.23783
   North_Bounding_Coordinate: 37.40684
   South_Bounding_Coordinate: 37.40683
   

3. What does it look like?
4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 29-Oct-2018

   Ending_Date: 29-Oct-2018

   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 (2)
   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. 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. (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>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> (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 = 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 (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>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> (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)
   • SeanPaul M. La Selle
   • M. Allison Stegner
   • Brandon M. Nasr
   • Elizabeth A. Hadly
   • Anthony D. Barnosky
   • Brian Sherrod
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
   

   831-427-474 (voice)

   pcmsc_data@usgs.gov

Why was the data set created?

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: 18-Jun-2019 (process 1 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 segment scanned. Person who carried out this activity:
   

   SeanPaul La Selle

   U.S. Geological Survey, Pacific Coastal and Marine Science CEnter

   Geologist

   2885 Mission St.

   Santa Cruz, CA
   

   831-460-7574 (voice)

   slaselle@usgs.gov

   Date: 23-Feb-2023 (process 2 of 2)

   corrected typo in doi number (scochran@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 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.
3. How accurate are the heights or depths?
   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.
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 and the ruler alongside the TIFF images are not corrected for sediment compaction and are relative to the surface of the lakebed.

How can someone get a copy of the data set?

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?
   • Availability in digital form:

     Data format:

     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. in format TIFF Size: 200210

     Network links:

     https://www.sciencebase.gov/catalog/item/6303faf1d34ed6dc5592a545 https://doi.org/10.5066/P98CEB1B

   • Cost to order the data: None

Who wrote the metadata?

Dates:

Last modified: 23-Feb-2023

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)