USGS Archive of Computed tomography (CT) Scans of Coral Cores

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What does this data set describe?

Title: USGS Archive of Computed tomography (CT) Scans of Coral Cores
Abstract:
This data release presents computed tomography (CT) imagery generated from coral core samples curated within the U.S. Geological Survey (USGS) Coral-Core Archive. These data were collected as part of ongoing USGS coral-reef research activities and include samples originating from multiple locations and collection efforts. A Geotek Rotating X-ray CT (RXCT) system was used to acquire x-ray images and perform CT reconstructions of archived coral cores.
The full three-dimensional CT dataset 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.
This data release allows future expansions of the archive to incorporate CT imagery scanned under the same consistent methodology from additional coral cores, locations, and collection efforts.
Supplemental_Information:
Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Additional information about the field activity or activities from which these data were derived is available online at: https://cmgds.marine.usgs.gov/services/activity.php?fan=1991-301-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1980-302-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1989-301-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1977-301-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1980-300-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=2020-620-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1982-301-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=09CGS02 https://cmgds.marine.usgs.gov/services/activity.php?fan=12CBC01 https://cmgds.marine.usgs.gov/services/activity.php?fan=1975-303-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=08CGS01 https://cmgds.marine.usgs.gov/services/activity.php?fan=1983-302-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1991-302-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=08CGS02 https://cmgds.marine.usgs.gov/services/activity.php?fan=1979-300-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1991-305-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1974-300-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=11CGS01 https://cmgds.marine.usgs.gov/services/activity.php?fan=1986-304-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=2018-331-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=12CBC03 https://cmgds.marine.usgs.gov/services/activity.php?fan=1983-300-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=2018-301-DD https://cmgds.marine.usgs.gov/services/activity.php?fan=1978-303-FA https://cmgds.marine.usgs.gov/services/activity.php?fan=1978-302-FA
  1. How might this data set be cited?
    Oberle, Ferdinand K.J., Toth, Lauren T., Prouty, Nancy G., Padgett, Jason S., Santos, Brook, Jacobs, Jessica A., Bloomer, Sierra K., Bagheri, Kian, Williams, Breanna N., Stathakopoulos, Anastasios, and Rich, Lily H., 20260209, USGS Archive of Computed tomography (CT) Scans of Coral Cores: data release DOI:10.5066/P139Y9H4, U.S. Geological Survey, Pacific Coastal and Marine Science Center, Santa Cruz, California.

    Online Links:

    Other_Citation_Details:
    Suggested Citation: Oberle, F.K., Toth, L.T., Prouty, N.G., Padgett, J.S., Santos, B., Jacobs, J.A., Bloomer, S.K., Bagheri, K., Williams, B.N., Stathakopoulos, A., and Rich, L.H., 2026, USGS Archive of Computed tomography (CT) Scans of Coral Cores: U.S. Geological Survey data release, https://doi.org/10.5066/P139Y9H4.
  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -169.6668
    East_Bounding_Coordinate: -64.6902
    North_Bounding_Coordinate: 27.9167
    South_Bounding_Coordinate: -14.1850
  3. What does it look like?
    OberleCoral.gif (GIF)
    Three-dimensional view of a coral core created from reconstructed CT scans.
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 01-Jan-1978
    Ending_Date: 31-Jul-2022
    Currentness_Reference:
    Ground condition 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 (358)
    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 0.0001. Longitudes are given to the nearest 0.0001. 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
    The name of each zip file corresponds to the core id. The latitude, longitude, and water depth for each core id can be found in Ofu_CoralCores_CoreLocations. Each zip file contains 2 subfolders 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 slice TIFFs and orthogonal view TIFFs are 16-bit images of CT intensity with a pixel size of 76 microns, or 131.21 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>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-ApplicationReconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> <geotek-ct-stack-section> <geotek-ct-stack-header> <_002265_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <Name>002265{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Name> <Date>22.06.2022 09.51.47</Date> </_002265_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <_006795_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <Name>006795{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Name> <Date>22.06.2022 09.54.03</Date> </_006795_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <_011325_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <Name>011325{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Name> <Date>22.06.2022 09.57.06</Date> </_011325_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <_015855_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <Name>015855{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Name> <Date>22.06.2022 10.00.09</Date> </_015855_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <_020385_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> <Name>020385{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Name> <Date>22.06.2022 10.03.11</Date> </_020385_E38804CA-6A6F-4BDD-83F5-28CAF46307A0> </geotek-ct-stack-header> <geotek-ct-stack Name="002265{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}" Date="22.06.2022 09.51.47"> <geoct-Identification-Section> <Core-ID>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">0.00</Section-Depth> <Depth-in-Section units="cm">2.2650</Depth-in-Section> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <Start-Time>22.06.2022 09.51.47</Start-Time> <End-Time>22.06.2022 09.51.55</End-Time> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-Application>Reconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.13.17</DateTime> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <Section-Depth>22.65</Section-Depth> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> <Min-Value>-0.0875082</Min-Value> <Max-Value>0.7626445875</Max-Value> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.13.17</DateTime> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> </geotek-ct-stack> <geotek-ct-stack Name="006795{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}" Date="22.06.2022 09.54.03"> <geoct-Identification-Section> <Core-ID>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">4.53</Section-Depth> <Depth-in-Section units="cm">6.7950</Depth-in-Section> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <Start-Time>22.06.2022 09.54.03</Start-Time> <End-Time>22.06.2022 09.54.58</End-Time> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-Application>Reconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.13.48</DateTime> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <Section-Depth>67.95</Section-Depth> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> <Min-Value>-0.240834</Min-Value> <Max-Value>1.3946246925</Max-Value> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.13.48</DateTime> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> </geotek-ct-stack> <geotek-ct-stack Name="011325{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}" Date="22.06.2022 09.57.06"> <geoct-Identification-Section> <Core-ID>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">9.06</Section-Depth> <Depth-in-Section units="cm">11.3250</Depth-in-Section> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <Start-Time>22.06.2022 09.57.06</Start-Time> <End-Time>22.06.2022 09.58.01</End-Time> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-Application>Reconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.14.17</DateTime> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <Section-Depth>113.25</Section-Depth> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> <Min-Value>-0.251271</Min-Value> <Max-Value>1.182254697</Max-Value> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.14.17</DateTime> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> </geotek-ct-stack> <geotek-ct-stack Name="015855{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}" Date="22.06.2022 10.00.09"> <geoct-Identification-Section> <Core-ID>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">13.59</Section-Depth> <Depth-in-Section units="cm">15.8550</Depth-in-Section> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <Start-Time>22.06.2022 10.00.09</Start-Time> <End-Time>22.06.2022 10.01.04</End-Time> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-Application>Reconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.14.47</DateTime> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <Section-Depth>158.55</Section-Depth> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> <Min-Value>-0.23904</Min-Value> <Max-Value>1.122973905</Max-Value> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.14.47</DateTime> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> </geotek-ct-stack> <geotek-ct-stack Name="020385{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}" Date="22.06.2022 10.03.11"> <geoct-Identification-Section> <Core-ID>J2-1419-PC01</Core-ID> <Scan-ID>SectionCircularCT</Scan-ID> <Image-Type>CT-Volume</Image-Type> <Processing-Stage>Recon</Processing-Stage> <Section-Number>1</Section-Number> <Section-Depth units="cm">18.12</Section-Depth> <Depth-in-Section units="cm">20.3850</Depth-in-Section> <Total-Scanned-Length units="cm">22.65</Total-Scanned-Length> <Start-Time>22.06.2022 10.03.11</Start-Time> <End-Time>22.06.2022 10.04.06</End-Time> <User-Comments>Enter Comments Here</User-Comments> <Firmware-Version>M067</Firmware-Version> <Windows-Version>Win64</Windows-Version> <Logger-Type-Desc>RXCT</Logger-Type-Desc> <Generated-From-Application>MSCLXCT</Generated-From-Application> <SVN-Version>SVN12394</SVN-Version> <Build-Date>2021-08-24</Build-Date> <Project></Project> <Client></Client> <Location></Location> <Image-Data-Type>UInt16</Image-Data-Type> <Reconstruction-Summary> <Generated-From-Application>Reconstructor;SVN12998;2021-12-17</Generated-From-Application> <Angle-Offset-Deg units="degrees">0.000</Angle-Offset-Deg> <Image-Pixel-Size-X units="microns">83.442</Image-Pixel-Size-X> <Image-Pixel-Size-Y units="microns">83.442</Image-Pixel-Size-Y> <Image-Pixel-Size-Z units="microns">83.442</Image-Pixel-Size-Z> <Image-Dimension-X units="pixels">940</Image-Dimension-X> <Image-Dimension-Y units="pixels">940</Image-Dimension-Y> <Image-Dimension-Z units="pixels">2714</Image-Dimension-Z> <Image-Scalar units="">0.000E+000</Image-Scalar> <Image-Offset units="">0.000E+000</Image-Offset> </Reconstruction-Summary> </geoct-Identification-Section> <geoct-Recipe-Header-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.15.15</DateTime> </Recipe> </geoct-Recipe-Header-Section> <geoct-Acquisition-Section> <Projection-File_Structure>XCT5</Projection-File_Structure> <XRay-Source> <Model-Name>Thermo Kevex PSX10-65W</Model-Name> <XRay-Voltage units="kV">130.0</XRay-Voltage> <XRay-Current units="uA">325.0</XRay-Current> <Spot-Size-Microns>62.000000</Spot-Size-Microns> </XRay-Source> <Filter> <Material>Cu 0.125 mm</Material> <Thickness units="mm">0.125</Thickness> </Filter> <Geometry> <Source-Object-Distance units="mm">315.625</Source-Object-Distance> <Source-Detector-Distance units="mm">960.775</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-Offset units="pixels">-5.00</Horizontal-Offset> <Vertical-Offset units="pixels">0.50</Vertical-Offset> </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</Start-Angle> <Step units="degrees">0.2</Step> <End-Angle units="degrees">360</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> <Serial-No>A06S04-1005</Serial-No> <Frame-Rate>15.000</Frame-Rate> <Pixel-Size units="mm">0.254</Pixel-Size> <Averaging>1</Averaging> <Pixel-Scan-Height>748</Pixel-Scan-Height> <Pixel-Scan-Width>940</Pixel-Scan-Width> <Image-Slope>1.8361E-005</Image-Slope> <Image-Offset>0.0000E+000</Image-Offset> </Detector> </geoct-Acquisition-Section> <geoct-Processing-Section> <Fluctuation-Correction> <Mode>Off</Mode> <Frames-To-Average>0</Frames-To-Average> <Region-Of-Interest> <Index>1</Index> <Top-Pixel-Position units="pixels">23</Top-Pixel-Position> <Bottom-Pixel-Position units="pixels">102</Bottom-Pixel-Position> <Left-Pixel-Position units="pixels">574</Left-Pixel-Position> <Right-Pixel-Position units="pixels">663</Right-Pixel-Position> <Target-Intensity>100.00</Target-Intensity> </Region-Of-Interest> </Fluctuation-Correction> <Centre-Rotation> <COR-Selection-Method>Calculated</COR-Selection-Method> <Use-Interpolation>No</Use-Interpolation> <Centre-Of-Rotation-Values> <Section-Depth>203.85</Section-Depth> <COR-Geometry-Calculated>511.34</COR-Geometry-Calculated> </Centre-Of-Rotation-Values> </Centre-Rotation> </geoct-Processing-Section> <geoct-Post-Process-Section> <Output-Scaling> <Auto-Mode>Yes</Auto-Mode> <Min-Value>-0.2489</Min-Value> <Max-Value>1.3796513035</Max-Value> </Output-Scaling> </geoct-Post-Process-Section> <geoct-Recipe-Section> <Recipe Latest="True"> <Name>TN403</Name> <DateTime>23.06.2022 12.15.15</DateTime> <Recipe-XML> <Geotek Description="Geotek Reconstructor Recipe" FileName="C:\Geotek\Settings\Reconstructor\Recipes\Ozette-whole.xml" LastSavedUTC="16/06/2022 23:00:48"> <EditPassword type="String"></EditPassword> <Recipe> <Name type="String">Ozette-whole</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> <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> <Reconstruction> <CentreOfRotation> <AutomaticCalculation type="Boolean">True</AutomaticCalculation> <ManualValue type="DoubleArray">0</ManualValue> </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</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">5</FilterSizePixels> </RingFilter> <YawAdjustment> <EnableYaw type="Boolean">False</EnableYaw> <YawDegrees type="Double">0</YawDegrees> </YawAdjustment> <OffsetOfCore> <XPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">-5</Values> </XPixels> <YPixels> <Keys type="DoubleArray">2</Keys> <Values type="DoubleArray">5</Values> </YPixels> </OffsetOfCore> </Reconstruction> </RotationalReconstruction> </Recipe> </Geotek> </Recipe-XML> </Recipe> </geoct-Recipe-Section> <Version-Number>5</Version-Number> <Core-GUID>{E38804CA-6A6F-4BDD-83F5-28CAF46307A0}</Core-GUID> </geotek-ct-stack> </geotek-ct-stack-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 = J2-1419-PC01 Section number = 1> <Section Length = 22.65> <Core Depth At Top = 0> <X-Ray Voltage = 130 kV> <X-Ray Current = 325 uA> <X-Ray SpotSize = 62 microns> <Camera Name = Thermo Kevex PSX10-65W><Average Of = 1> <Detector Mode = 2x2> <Comments = Enter Comments Here> <GEOMETRY><--------> <Mode = cone beam Last angle = 360°> <Offset angle= 0°> <Clock wise = 1> <Pixel size = 0.25 mm> <Centre of rotation = 511.34> <Source object distance = 315.63 mm> <Source detector distance = 960.78 mm> <Direction of rotation = clockwise> <Vertical centre = 374.5> <Voxel Size = 0.0828> <User set voxel size = 0> <Calculated Voxel size = 0.0828> <Helical Scan = 0> <RANGE> <-----> <Depth in section of first slice = 0.00 cm> <Slice interval = 0.0083 cm> <First Slice = 1><Last Slice = 2849> <Minimum Intensity (Raw Floating Point)= 0> <Maximum Intensity (Raw Floating Point)= 5.000321> <Scale & Flip Complete = 1> <Scatter Adjustment Active = 0><Horizontal centre = 465> (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>J2-1419-PC01</coreID> <section-number>1</section-number> <physical-width>7.78</physical-width> <physical-height>23.59</physical-height> <physical-top>0</physical-top> <pixels-per-CM>120.77</pixels-per-CM> <horizontal-resolution>120.77</horizontal-resolution> <pixel-width>940</pixel-width> <scan-lines>2849</scan-lines> <comments>Enter Comments Here</comments> <camera-name>Thermo Kevex PSX10-65W</camera-name> <average-of>1</average-of> <filename>Orthogonal000.tif</filename> <x-ray-voltage>130</x-ray-voltage> <x-ray-current>325</x-ray-current> <x-ray-spot-size>62</x-ray-spot-size> <source-object-distance>315.63</source-object-distance> <source-detector-distance>960.78</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.
    USGS_CT_scanned_coral_cores_09_29_2025.csv
    Comma Separated Value (CSV) file containing information supporting the core data. (Source: Producer defined)
    count
    Sequential number assigned to each coral core record in the dataset. (Source: Producer defined)
    Range of values
    Minimum:1
    Maximum:358
    Units:Unitless
    core_id
    Unique identifier for the coral core, following the project-specific naming convention (such as year, region, site, and core number). (Source: Producer defined) Unique identifier for the coral core, following the project-specific naming convention (such as year, region, site, and core number).
    FAN
    Unique U.S. Geological Survey field activity number (FAN) assigned to fieldwork activities. (Source: Producer defined) Unique U.S. Geological Survey field activity number.
    region
    General geographic region where the coral core was collected (such as Florida, Caribbean). (Source: Producer defined) General geographic region where the coral core was collected (such as Florida, Caribbean).
    location
    Broader locality descriptor within the region, indicating the coastal or reef area of sampling. (Source: Producer defined) Broader locality descriptor within the region, indicating the coastal or reef area of sampling.
    site
    Specific reef site or sampling station where the coral core was extracted. (Source: Producer defined) Specific reef site or sampling station where the coral core was extracted.
    approximate_core_length_cm
    Field measured or estimated total length of the coral core in centimeters. (Source: Producer defined)
    Range of values
    Minimum:9
    Maximum:223
    Units:centimeters
    Resolution:1
    species
    Scientific name or genus-level designation of the coral species from which the core was taken. (Source: Producer defined) Scientific name or genus-level designation of the coral species from which the core was taken.
    latitude
    Latitude coordinate (decimal degrees, WGS84) representing the core collection location. (Source: Producer defined)
    Range of values
    Minimum:-14.1850
    Maximum:27.9167
    Units:Decimal Degrees
    Resolution:0.0001
    longitude
    Longitude coordinate (decimal degrees, WGS84) representing the core collection location. (Source: Producer defined)
    Range of values
    Minimum:-169.6668
    Maximum:-64.6902
    Units:Decimal Degrees
    Resolution:0.0001
    r_squared
    R-squared (coefficient of determination) is a statistical measure that quantifies how well the calibration regression model relating CT image intensity to material density fits the observed data. It represents the proportion of variance in material density that is explained by the regression model. (Source: Producer defined)
    Range of values
    Minimum:0.951461462
    Maximum:1.000000000
    Units:unitless
    Resolution:0.000000001
    Entity_and_Attribute_Overview:
    Zip files contain TIFF image files and Geotek software-proprietary metadata files. A comma-delimited text file with supporting location and coral species information for the core image files is included (USGS_CT_scanned_coral_cores.csv).
    Entity_and_Attribute_Detail_Citation: U.S. Geological Survey

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Ferdinand K.J. Oberle
    • Lauren T. Toth
    • Nancy G. Prouty
    • Jason S. Padgett
    • Brook Santos
    • Jessica A. Jacobs
    • Sierra K. Bloomer
    • Kian Bagheri
    • Breanna N. Williams
    • Anastasios Stathakopoulos
    • Lily H. Rich
  2. Who also contributed to the data set?
    The cores contained within the USGS CT Coral-Core Archive represents the legacy of more than 50 years of coral-reef research at the U.S. Geological Survey. Numerous USGS researchers have contributed to these invaluable collections over the years. In particular, we are indebted to the work of J. Harold Hudson, who led the collection of most of the cores in the St. Petersburg Coastal and Marine Science Center archive, and his close collaborators Eugene Shinn and Robert Halley. This research was financially supported by the U.S. Department of Interior, U.S. Geological Survey (USGS) through the Coastal and Marine Hazards and Resources Program and the National Park Service-USGS Water Quality Partnership Program. We thank Ian Moffitt and Valentine Vaeoso from the National Park of American Samoa and Josh Logan and Cordell Johnson from the USGS for field work assistance during the collection of cores from Ofu Island, American Samoa. Thank you to Curt Storlazzi from the USGS for a thorough and timely review and two anonymous reviewers for constructive input.
  3. To whom should users address questions about the data?
    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

Why was the data set created?

Images were obtained to characterize coral 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: 31-Jul-2022 (process 1 of 4)
    Coral Cores presented in this archive were collected between September 7, 1974, and July 31, 2022. Coral cores were extracted from coral reefs from around the world using a combination of submersible pneumatic and electric drilling systems. All cores were collected by divers in variable water depths using handheld underwater drills fitted with hollow diamond-tipped core barrels, cylindrical cores were drilled vertically along the coral growth axis to recover continuous records of skeletal accretion. Recovered coral cores were typically 5–10 cm in diameter and ranged in length from 0.09 to 3.07 meters. All coral cores were labeled top and bottom on site before storing.
    Date: 20-Nov-2023 (process 2 of 4)
    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 375 microamperes. Each core was scanned individually with a set of standards. The RXCT acquisition and reconstruction settings were kept consistent across all scans. 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. Axial slice TIFF images are organized into a subfolder folder named 'SliceViews', and orthogonal TIFF images are in the subfolder 'OrthogonalViews'. The 'SliceViews' subfolder also contains a Geotek software-proprietary XML file that contains information on CT scan acquisition settings and reconstruction settings. Additionally, the 'SliceViews' subfolder also contains a Geotek software-proprietary TXT file with information on CT scan acquisition settings and image scaling information. The 'OrthogonalViews' subfolders contain one XML file per TIFF image with Geotek software-proprietary information on CT scan acquisition settings and image scaling information. These folders are compressed into single zip files with filenames corresponding to each core scanned. Person who carried out this activity:
    Ferdinand Oberle
    USGS
    Research Geologist
    2885 Mission Street
    Santa Cruz, CA

    831-460-7589 (voice)
    foberle@usgs.gov
    Date: 29-Sep-2025 (process 3 of 4)
    To ensure CT intensities are comparable between scans, we calculated mean CT intensities in 3-dimensional regions of interest within co-scanned coral standards of known bulk density. A linear regression of CT intensity versus bulk density was calculated and the resulting coefficient of determination (r squared) from this fit was used as a metric of calibration quality. Scans with calibration r squared value below 0.95 were flagged as unreliable and triggered reprocessing or rescanning. The final r squared values are provided in the CSV data sheet of this data release. The reconstructed axial slices of each scan can be used to select a 3-dimensional region of interest and calculate mean CT intensity values for each standard. Bulk density of the included coral standards are: Siderastrea siderea (1.571 grams per cubic centimeter), Pseudodiploria strigosa (1.513 grams per cubic centimeter), Porites lobata (1.218 grams per cubic centimeter), three Orbicella subspecies (1.181 grams per cubic centimeter; 1.065 grams per cubic centimeter; 1.024 grams per cubic centimeter) and Colpophyllia natans (0.867 grams per cubic centimeter).
    Date: 29-Sep-2025 (process 4 of 4)
    A CSV data sheet was created recording all coral cores that were scanned under this project. The data sheet includes the following attributes: Count, Core ID, Region, Location Name, Site Name, Approximate Core Length as originally reported in field observations (cm), Coral Species, Latitude, Longitude, and r-squared.
  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?
    No formal positional accuracy tests were conducted.
  3. How accurate are the heights or depths?
    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?
    Relative variability in CT density was consistent with visual changes in coral composition.

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
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. These data are marked with a Creative Common CC0 1.0 Universal License. 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 - ScienceBase
    Denver Federal Center, Building 810, Mail Stop 302
    Denver, CO

    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 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: Downloadable zip files, ranging in size from 11.28 GB to 62.67 GB, contain folders with orthogonal and axial slice TIFF (.tif) images and associated software-proprietary metadata files (.xml). Zip file names correspond to the core id. For example 'C-2022-AS-FA-CH64.zip' contains all CT TIFF images and associated metadata from core C-2022-AS-FA-CH64. USGS_CT_scanned_coral_cores_09_29_2025.csv contains the location information, core length, species, and r-squared for each core id. in format TIFF, XML, comma-delimited text (version Geotek RXCT Scanner system, software version XCT4) Size: 287780
      Network links: https://www.doi.org/10.5066/P139Y9H4
    • Cost to order the data: None.

Who wrote the metadata?

Dates:
Last modified: 09-Feb-2026
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/ScienceBase/DR_P139Y9H4/USGSCoralCores_CT_Archive.faq.html>
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