Table of Contents

I. Introduction

The Section Half Multisensor Core Logger succeeded the Archive-Half Multisensor Track (AMST) in the physical properties laboratory. The SHMSL simultaneously measures spectral reflectance and magnetic susceptibility on core section halves. Data generated from these sensors are used to augment the core descriptions.

Reflectance Spectrometry

–Percent reflectance plotted against depth supports lithology descriptions.
–Color parameters can provide a detailed time series of relative changes in the composition of the core material and can be used to correlate sections from core to core or hole to hole and to analyze cyclicity of lithologic changes.
–Spectral data can be used to estimate the abundances of certain compounds.

• Visible range provides semiquantitative estimates of hematite and goethite with better sensitivity than XRD.

• Near-infrared or near-ultraviolet ranges allow estimates of carbonate, opal, organic matter, chlorite, and some combinations of clay minerals.

Magnetic Susceptibility

Magnetic Susceptibility can be used to confirm whole-round core section magnetic susceptibility measurements. The SHMSL can measure magnetic susceptibility at a similar sampling point spacing to the whole-round measurements, or the user can select a completely different frequency of analysis.
MS data is used for correlation with other age-depth proxy measurements.

Theory of Operation

A split and scraped core section in a half-core liner is placed on the core track, where a barcode scanner is used to scan the section ID (from the end cap) and imports sample information from the LIMS. The electronics platform moves along a track above the core section, recording the sample height in the core liner using a laser sensor. The laser establishes the location of bottom of the section. When this step is finished, the track will pull up out of the way of the user in order to facilitate the covering of the core section with GLAD® Plastic Wrap. When the user covers the core section and answers the prompt, the platform reverses the direction of movement, moving from bottom to top while recording point magnetic susceptibility and spectral reflectance data at user-specified data acquisition intervals (generally 2–10 cm).

Reflectance Spectrometry

–Measured from 380 to 900 nm at 2 nm intervals using both an LED and a halogen light source, covering a wavelength range through the visible spectrum and slightly into the infrared domain. Currently only 390nm to 732nm is being recorded.  Waiting to hear back from Bill Mills.
–Scanning the entire wavelength range takes ~5 s per data acquisition offset. 
–Data are generated using the CIELAB L*a*b* color system:

• L* represents lightness, where 0 yields black and 100 indicates diffuse white;

• a* represents magenta to green tinting, where positive numbers indicate red/magenta shading and negative numbers indicate green shading; and

• b* represents yellow to blue tinting, where positive numbers indicate yellow shading and negative number indicate blue shading.

–Data are also stored and returned as CIELAB Tristimulus XYZ values. The definition of X, Y, and Z is complex and the reader should refer to reference materials for an explanation. Refer to the related documentation section below.
–Finally data are stored and returned as RGB values to facilitate comparison with the imaging logger RGB values; note however that the sampling interval is quite different between the imaging logger and the integration sphere.

Magnetic Susceptibility

–Measured at the same data acquisition rate as spectral reflectance using a contact probe with a flat 15 mm diameter Bartington magnetic susceptibility sensor. This is typically an MS2K sensor, but MS2E is available if very small intervals are needed. See Section C.3 for a full description of the sensors.
–The sensor can be configured for different integration times (1 Hz or 0.1 Hz) and different numbers of replicate measurements. Our standard conditions are 3 measurements at 1 Hz measurement frequency for each offset. These three results are averaged and uploaded to the database. Thermal drift is effectively eliminated by zeroing the meter before each section.
–Data are reported in dimensionless instrument units (SI). In order to use these data as SI magnetic susceptibility units, the appropriate volume correction must be applied, which varies by sensor type. The user should not use the cgs setting so that the data set is consistent with previous measurements and with the whole-round logger results.

II. Procedures

A. Preparing the Instrument

1. Double-click the MUT icon on the desktop (Figure 1a) and login using ship credentials. For more information on data uploading see the "Uploading Data to LIMS" section below.

2. Double-click the IMS icon (Figure 1b). IMS initializes the instrument. Once initialized, the logger is ready to measure the first section.

At launch, the program begins the following initialization process:

• Tests all instrument communications

• Reloads configuration values

• Homes the X and Y axis

After successful initialization, the main IMS- SHMSL window will appear (Figure 2).

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The IMS Control panel (Figure 3): Provides access to utilities/editors via drop-down menus.

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START button will allow the user to begin measurements. Section Information window (Figure 4) will pop up.

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Prior to measuring a section half on the SHMSL, the user must:

• Calibrate the QE Pro Spectrophotometer

• Set the measurement interval for each instrument.

B. Instrument Calibration

a) Color Reflectance Spectrophotometer

The color reflectance spectrophotometer calibrates on a spectra, pure white (Spectralon® WHITE standard) (See Important Notes for further information), and the black is acquired with the lights off and the shutters, but closed still on the white Spectralon standard.  The spectrometer calibration can be triggered automatically (typically every 6 hours) or manually by the user.  The expiration time for the spectrometer calibration is set in the QEPro setup menu (Figure 16). Before running the first sample, the software will check the status of the spectrometer calibration. If the calibration has expired, a prompt will appear asking the user to begin an automatic calibration (Figure 5).  It is recommended that the user calibrate every time the software prompts the user.

There is an option to ignore the calibration, but the calibration prompt will reappear with every run until the calibrations are completed. Data run without a calibration update will be flagged as calibration invalid in LIMS.

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Automatic Calibration

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  • Max Counts: current highest value

  • Target Counts: percent saturation value as set in the instrument parameters (range = 32,000 counts)

  • Integration Time: measurement period where the highest wavelength count is equal to or exceeds 80 percent of the spectrophotometer's range.

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   • Temperature: should remain below 50°C; note that the TEC temperature is usually about -9 degrees C; accessed through the QE Pro Utilities screen.

   • Spectral Mean: mean of the entire spectrum (at the line across the display plot). This should be only about 200 counts higher than the Dark Pixel count. With plastic wrap, it should not exceed 500 counts

   • Dark Pixels: 20 pixels that have been deliberately masked to allow no light. These counts represent the thermal noise of the spectrophotometer.

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Manual Calibration

To perform calibration manually (not when specified by the software), select Instruments > QE Pro: Calibrate (Figure 3).  The QEPro will move to the white standard and begin the calibration process.  Follow the automatic procedure from step 4 to complete the calibration.  This should be performed when a bulb is changed or other hardware configuration changes.

Recognizing a Bad Calibration

The following information is provided to assist scientists and technicians in evaluating the QE Pro calibration.  Always verify the lights are on and the shutters are open.  Two dots of light should be visible exiting the integration sphere.

• Figure 12, demonstrates a calibration with an old light source. When the 500nm - 740nm end of the calibration spectrum is over the amount of counts the program will process, this might be for a number of reasons, but most likely the LED light is dim or off. The blue end of the spectrum is within the correct amount of counts and maintains the right curve with the spike around 400 wavelength and a dip into the 420-430 range. The first thing to check is the age of the LED light source, if it is older than 1 month it should be replaced. 

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• Figure 13 demonstrates a calibration with the LED turned off (i.e., the shutter did not close properly). You'll notice the left side of the graph, the blue side, does not show the proper peaks, whereas the red side of the graph is at 180K counts. Make sure the LED light is in TTL mode and properly connected to the QE Pro, and lastly that the shutter is opening.  If you look at the white standard while the integrating sphere is over it you should see two dots of light, one blue (LED) and one yellowish (Halogen).
  
  

Measuring the Color Control Set

There are twelve color reflectance standards available in the physical properties lab in the drawers beneath the pycnometer.  The black standard is not typically used in the control set.

Measuring the Control Set:

1. Set the standard holder on the track as seen in Figure 14.

   1. The standard holder has a white block on one end.  This white block should be against the white benchmark on the track for proper positioning (Figure 14, red circle).

2. Place the color standards in the sample holder. 

   1.  The order and position of the standards are set under the Instruments > QE Pro: Edit Standards menu.  See the Utilities: QEPro Edit Control Set section for more information about setting up the control set.

3. Select Start from the main IMS window (Figure 2).

4. Select Measure Control Set. 

   1. The QE Pro will begin moving down the track and collecting measurements on each standard. The data for each standard will be displayed on the screen (Figure 15).

   2. . If the QE Pro does not properly touch down on the standards, the positions may need to be edited in the Instruments > QE Pro: Edit Standards.  Also verify that the standard holder is against the benchmark.

5. After each standard has been measured, the data will automatically be saved to the C:/AUX_DATA/RSC/CNTRL folder as a .csv

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b) Magnetic Susceptibility Meter

The point magnetic susceptibility meter is calibrated by the manufacturer (Bartington, Ltd.). The probe is zeroed in air before the core section is measured, so drift is not a significant factor. It is not necessary to calibrate the MS2K or MS2E probes (or the MS2C loops on the whole-round loggers), but the calibration check standard can be used to demonstrate consistent results.

C. Set Measurement Parameters

a) Instrument Setup

Each instrument has a separate setup menu.  Configuration values should be set during initial setup by the technician and scientists.  The general instrument setup should not change unless there have been changes to the hardware.

QEPro Configuration

Select Instruments> QEPro: Setup (Figure 3). The QEPro Parameters window will open (Figure 16).  This window is divided into 4 sections: General Setup, Acquisition Parameters, White and Dark Standards, and Integration Time.

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General Setup

• Instrument X offset: The x-axis distance of the laser where the center of the sensor is over the benchmarks zero edge.

• Sensor Width:  Physical size of the sensor area

• Contact Width: Physical size of the contact surface

• Analysis name: LIMS analysis component (must match LIMS component exactly).

• Instrument group: LIMS instrument group logger name (i.e., SHMSL).

• Model: Model name of the sensor (from manufacturer).

• S/N: Serial number of the sensor (from manufacturer).

• Manufacturer's Name: Name of the manufacturer of the QEPro spectrometer.

• Menu name: value that appears as the instrument's menu name.

• Full name: value that appears in instrument dialog boxes.

Acquisition Parameters section

• High Cut-off:  Used to define the upper limit of the region of interest (ROI) in the spectrum.  The spectrum above this value will not be saved or used in calculations. (Figure 17)

• Low Cut-off: Used to define the lower limit of the region of interest (ROI) in the spectrum.  The spectrum below this value will not be saved or used in calculations. (Figure 17)

• Median Filter Rank: Number of adjacent channels used to filter noise from the signal.

• Bin size: The width (nm) of each bin that the spectrum is recorded in. (Figure 17)

• Illuminant: The Daylight Illuminant Standard for L*a*b calculations;  International Commission on Illumination (CIE) standard illuminant used in color calculations (also called daylight illuminant)

• Geometry: References integration sphere measurement technique: illumination from a diffuse light source viewed 8° from normal (d/8); includes a gloss trap to exclude spectral reflections.

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White and Dark calibration Section

• White Label ID: LIMS label_ID component value (STND-White).

• White Text ID: LIMS text_ID component value (WHITE).

• Dark Label ID name: LIMS label_ID component value (STND-Dark).

• Dark Text ID: LIMS text_ID component value (DARK).

• Standard X-offset: Track position (X-axis; in cm) of laser when the center of the integration sphere sensor is over the center of the white standard.

• Standard Y-offset:Llift position (Y-axis) when the integration sphere is in contact with the White or Dark standard (same value for both).

• Calibration expire: Time in hours between calibrations.  The user will be given a warning when the calibration time has expired.

• Previous Timestamp: Time and date of last calibration (read only).

• Remaining time: Clock displays of the time remaining until the next calibration is needed (read only).

Integration time section

• Start Time: The integration time used to determine the white standard saturation point

• % Saturation: Used by WHITE calibration to determine sample integration time by calculating the integration time required to reach the specified saturation (70%–95%). Note: if cores are light colored, increase throughout by using a low saturation level; if cores are dark colored, use a high saturation level to improve signal-to-noise ratio.

• Step Time: The time step used to determine the White Standard's saturation point

• White: Stack: The number of measurements to stack for the final White calibration

• Dark: Stack:  The number of measurements to stack for the final Dark calibration

MS3 Configuration

Select Instruments> MS3: Setup (Figure 3). The QEPro Parameters window will open (Figure 18).  This window is divided into 3 sections: General Setup, MS Correction Factor, and Select MS Control

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General Setup

• Track and Sensor Type: Select the type of MS sensor and the track (SHMSL- Point)

• Instrument X Offset: The x-axis distance to the sensor, where the center of the sensor is over the benchmarks zero edge

• Contact Width: Physical size of the contact surface

• Analysis name: LIMS analysis component (must match LIMS component exactly).

• Instrument group: LIMS instrument group logger name (i.e., SHMSL).

• Meter Model: Model name of the sensor (from manufacturer).

• Meter S/N: Serial number of the sensor (from manufacturer).

• Sensor Model: Sensor's Model of the active sensing component.

• Sensor S/N: Sensor's Serial Number of the active sensing component.

• Manufacturer's Name: The name of the manufacturer of the MS sensor

• Menu name: Value that appears as the instrument's menu name.

• Full name: Value that appears in instrument dialog boxes.

MS Correction Factor

These values are used when attempting to match data between multiple sensors. Default values are 1.

• Correction Factor: A correction factor provided by the Bartington. Typically 1.

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  • For standard-frequency loops (80 and 90 mm, 565 Hz), this value is 1.000.

  • For 10% high loops (80 mm only, 621 Hz), this value is 0.908.

  • For 10% low loops (80 mm only, 513 Hz), this value is 1.099.

  • For 20% low loops (90 mm only, 452 Hz), this value is 1.174.

Select MS Control (Point Only)

• Standards: Name of the standard being used.

• Label ID: The label ID used to identify the standard.

• Text ID: Unique identifier for the standard in the database.

• Standard's X offset: Track position (X-axis) of the laser when the center of the MS sensor probe is over the center of the standard.

• Standard's Y offset: Lift position (Y-axis) when the MS sensor probe is in contact with the standard.

• Standard's Value:  The standard's accepted/given value.  Value established by IODP is 48 +/- 2 SI.

Laser Configuration

Select Instruments> Laser: Setup (Figure 3). The AR700 Parameters window will open (Figure 19). 

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General Setup

• Analysis name: LIMS analysis component (must match LIMS component exactly).

• Instrument group: LIMS instrument group logger name (i.e., SHMSL).

• Model: model name of the sensor (from manufacturer).

• S/N: serial number of the sensor (from manufacturer).

• Manufacturer's Name: The name of the manufacturer of the laser.

• Menu Name: Laser

• Full name: value that appears in instrument dialog boxes.

Profile Parameters

• Tray Depth: Measure from the White Benchmanrk to the bottom of the tray (mm)

• Liner Thickness: Measure from the White Benchmark to the bottom of the tray (mm)

b) Set Measurement Parameters

The user may adjust the measurement parameters for each instrument on the SHMSL by selecting DAQ> Measurement Editor (Figure 3).  The measurement editor window will open (Figure 20).

To edit the settings for a particular instrument, select the instrument from the list on the left side of the window and then click within the Instrument Parameters block on the right side of the screen.  A window, like in Figure 21, will open.

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QE Pro Measurement Parameters

Settings available in the QE Pro Measurement editor (Figure 21) include:

• Interval: The measurement interval in centimeters.

• Edge: The interval of core to exclude at the start and end of a section and at the edges of gaps in the core.

• Method: Select to take a single measurement at the time set by the white calibration or to stack multiple measures and average using the measurement time set by the white calibration.

• Stack: The number of measurements to average at a given position.

• Control: Control ON will measure the white standard as a control each time a section is measured.

• Online?: Suspend measurements with the QE Pro.

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MS Measurement Parameters

Settings available in the MS3 Measurement editor (Figure 22) include:

• Interval: The measurement interval in centimeters.

• Edge: The interval of core to exclude at the start and end of a section and at the edges of gaps in the core.

• Meas. Time: Integration time used for a measurement.

• Zero Meas. Time: Integration Time used for zeroing the meter (air blank).

• Control: Control ON will measure the MS standard as a control each time a section is measured

• Online?: Suspend measurements with the MS point sensor

• Drift Correction: Applies a two-point drift correction to the data. A measurement is taken before the laser profile and another after measuring the standard, at the end of the test.

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Laser Measurement Parameters

The user may use the Laser Measurement editor (Figure 23) to set the gap offset. This is the height below the benchmark which will be tagged by the system as a gap and will therefore not be measured. For piston cores, the recommended gap offset should be set to 10 mm to 13 mm. For hard rock cores, the gap offset should be set between 20 and 30 mm.

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D. Preparing Sections

1. Use a spatula or smear slide to clean the cut surface of the core by lightly scraping away any material that was smeared across the surface during core splitting.  Take the SHIL and X-Ray image first so SHMSL sensor footprints will not be in the image.

2. Bring the endcap of the section half (usually A for archive half) to be measured to the SHMSL, you will use the endcap to scan the barcode for sample information.

3. Place the archive section in the core tray with the blue endcap up against the benchmark. The benchmark is the white square at the head of the rails that hold the section halves (Figure 24). If material is missing at the top of the section, section half should be positioned all the way up to the top of the rail.

4. Adjust the section so that it is as flat as possible with respect to the plane of the benchmark. There is a limit to how much the sensor heads can float when they land on a tilted section.

5. Do not wrap the cores yet. The Acuity AR700 laser cannot reliably see through the plastic to measure an accurate profile of the section half surface.
   
   

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Note: This analysis requires clear polyethylene film such as GLAD® Wrap. Other types of plastic wrap will not serve.

E. Making a Measurement

1. Select Start from the main IMS SHMSL window (Figure 2).  The SHMSL Section Information window will open (Figure 4).