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

Metadata also available as - [Questions & Answers] - [Parseable text] - [XML]

Metadata:

Identification_Information
Data_Quality_Information
Spatial_Data_Organization_Information
Spatial_Reference_Information
Entity_and_Attribute_Information
Distribution_Information
Metadata_Reference_Information

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:

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

This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/ScienceBase/DR_P98CEB1B/JRBP2018-CT-metadata.html>