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.
–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 negative numbers indicate red/magenta shading and positive numbers indicate green shading; and
• b* represents yellow to blue tinting, where negative numbers indicate yellow shading and positive 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 sensor.
–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.

Hardware

Instruments

The SHMSL system consists of the following hardware components (Figure 1):

• Bartington MS2K or MS2E (Note: MS2E is not generally recommended because of its very small read area) magnetic susceptibility contact probe
• Bartington MS2 meter, run in serial communications mode
• Ocean Optics QE Pro visible spectrum spectrophotometer
• Ocean Optics HL-2000 Halogen Light Source with Attenuator and TTL-Shutter
• Ocean Optics Multi-LED BluLoop Light Source
• Ocean Optics 30 mm integrating sphere, with a 10 mm aperture
• Acuity AccuRange AR700 Laser
• Barcode scanner
• Instrument platform
• Hardware abort switch

Figure 1. SHMSL Hardware

Bartington MS2K Probe Susceptibility Contact Probe

Bartington MS2 Probe Susceptibility Meter

Ocean Optics QE Pro Hamamatsu S7031-1006S Detector

Ocean Optics HL-2000 Halogen Light Source with Attenuator and TTL-Shutter

Ocean Optics Multi-LED BluLoop Light Source

Ocean Optics ISP-30-6-R-GT Integrating Sphere

Acuity AccuRange 700 Triangulating Laser Displacement Sensor

Laboratory Supplies

• GLAD® Plastic Wrap (crystal clear polyethylene)

Note: This analysis requires clear polyethylene film such as GLAD® Wrap. Other types of plastic wrap (e.g., Saran Wrap™) will not serve.

Standards

Color Reflectance

• Labsphere, Inc. Spectralon® white standard, certified at 99% reflectivity (Figure 2).
• Labsphere, Inc. diffuse color reflectance targets:
  • Grayscale: 99%, 50%, 20%, 2% reflectance  (Referred to as white, light grey, dark grey, and black)
  • Color: Red, Orange, Yellow, Green, Cyan, Blue, Purple, Violet (Figure 3).

Figure 2. WHITE Spectralon® Calibration Standard

Figure 3. Spectralon Diffuse Standards. 

Magnetic Susceptibility

The MS standards are used to check for drift, not to calibrate the meter or sensor. The JRSO puck is used to check drift instead of the Bartington standard because it is less sensitive to centering the sensor.

• Bartington-issued MS puck (note: user must center this standard carefully to get the correct reading)
• JRSO-created verification puck (~48 SIx10^-6; mounted on track)

Launching the IMS- SHMSL application

The IMS-SHMSL software can be launched from the Windows Start menu or from a desktop icon (Figure 4).

Figure 4. IMS Icon

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 5).

Figure 5. IMS Application Main Screen.

A Quick Introduction to the IMS Program Structure

IMS is a modular program. Individual modules are as follows:

• INST plug-in: code for each of the instruments
• MOTION plug-in: code for the motion control system
• DAQ Engine: code that organizes INST and MOTION plug-ins into a track system

The SHMSL system, specifically, is built with three INST modules (MS2, QEPro, AR700), two MOTION modules (X-axis, Y-axis), and one DAQ Engine module.

The IMS Main User Interface (IMS-UI) calls these modules, instructs them to initialize, and provides a user interface to their functionality.

Each module manages a configuration file that opens the IMS program at the same state it was when previously closed and provides utilities for the user to edit or modify the configuration data and calibration routines.

The four buttons on the IMS-UI window provide access to utilities/editors via dropdown menus as shown in Figure 6.

Figure 6. SHMSL IMS Menu Options

Initial Instrument Setup

SHMSL Configuration

Each instrument has a separate setup menu.  Configuration values should be set during initial setup and configuration 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 6). The QEPro Parameters window will open (Figure 7).  This window is divided into 4 sections: General Setup, Acquistion Parameters, White and Dark Standards, and Integration Time.

General Setup

• Instrument 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).
• Menu name: value that appears as the instrument's menu name.
• Full name: value that appears in instrument dialog boxes.

Acquisition Parameters section

• Hi 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 7)

• 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 7)
• 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 7)
• 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.

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: lift 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

• Integration time: time the CCD is exposed; if too short, noise will be high; if too long, the sensor will saturate and clip data.

• Starting integration time: beginning time (in seconds) value for WHITE calibration; set to 0.5 for new bulbs and up to 1 for aged bulbs. This setting has no effect on data from subsequent measurements.

• 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 throughput 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

Figure 7. QEPro Setup Window

Figure 8. Illustration of high and low cut-off and bin size.

MS2 Configuration

Select Instruments> MS2: Setup (Figure 6). The QEPro Parameters window will open (Figure 8).  This window is divided into 3 sections: General Setup, MS Correction Factor, and Select MS Control

General Setup

• Track and Sensor Type?: Select the type of MS sensor and the track (SHMSL- Point)
• Instrument offset: The x-axis distance of the laser where the center of the sensor is over the benchmarks zero edge.
• Contact width: Physical size of the contact surface
• Units: This value must match the front panel of the MS meter.  Set to SI per IODP standard practice
• Range: This value must match the range setting on the MS meter, 1 or 10
• 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 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
• Matching Constant: Value used to correc the sensor's output to a standard value

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

Figure 8: MS2 Setup Window

Laser Configuration

Select Instruments> Laser: Setup (Figure 6). The QEPro Parameters window will open (Figure 9).  

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

Figure 8: AR700 Setup Window

Setting Measurement Parameters

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

• Set the measurement interval for each instrument
• Calibrate the QE Pro Spectrophotometer

The user may adjust the measurement parameters for each instrument on the SHMSL by selecting DAQ> Measurement Editor (Figure 5).  The measurement editor window will open (Figure 9).

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.  

Figure 9. Main Measurement Editor Window

QE Pro Measurement Parameters

Settings available in the QE Pro Measurement editor (Figure 10) 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

Figure 10. QE Pro Measurement Parameters

MS Measurement Parameters

Settings available in the MS2 Measurement editor (Figure 11) 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
• Average: The number of measurements to average at a given position
• 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

Figure 11. MS Measurement Parameters

Laser Measurement Parameters

The user may use the Laser Measurement editor (Figure 12) 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 or less. For hard rock cores, the gap offset should be set between 20 and 30 mm.

Figure 12. Laser Measurement Parameters

Starting Measurements

Section halves are measured on the SHMSL as soon as possible after splitting so that drying and oxidation do not affect ephemeral sample properties such as color reflectance. Sample preparation includes scraping to clean the core surface and covering wet core samples with plastic wrap to prevent contamination of the contact sensors.

Preparing Samples

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 image first so SHMSL sensor marks 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 22).
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.
   
   

Figure 22. Benchmark location

Measuring Samples

To begin measuring, select Start from the main IMS SHMSL window (Figure 3).  The SHMSL Section Information window will open (Figure 23).

Figure 23. Section Information Screen

1. Place the cursor in the SCAN text field (Figure 23) so that the barcode information will be parsed appropriately. Scan the section label on the section half end cap.
   1. The Sample ID, LIMS ID and LIMS length will automatically parse.
   2. User also has the option to use the LIMS entry tab or the manual entry tab for entering sample information.  Be aware that samples must be named properly when using the Manual tab or the data files will not be uploaded to LIMS.
2. Select Measure
   
   1. The sensor assembly will move down the track while the laser acquires a profile of the split surface of the section (Figure 24).
      
      

      Figure 24. Laser Profile

      
      
      
   2. When the software has detected a gap, it will indicate regions that will not be measured by the MS and reflectance sensors on the screen in red.
             Note: (Gap detection parameters are configurable in the DAQ> Measurement Editor Laser window (Figure 12). 
   3. Acquisition of this profile is why the section is not yet wrapped in plastic wrap—sometimes the laser will profile the wrap rather than the sediment beneath it and give incorrect heights to the gap detection routine. 
      Add explanation of what the laser looks for to determine end of core
3. When the laser reaches the end of the section, the Section Length confirmation window will appear (Figure 25).
   1. Verify the section length, in centimeters, is correct. If the laser length is longer than the section, manually enter the correct length in the scan length field.

Figure 25. Section Length Confirmation Window

4. Apply GLAD® Plastic Wrap to the surface of sediment cores.

a. IMPORTANT!!! It is necessary to cover the core section with GLAD® PlasticWrap in order to avoid damage to the integration sphere. Any mud that gets inside the sphere will ruin it!

b. IMPORTANT! Do not cover the standards with GLAD® Plastic Wrap; they will give erroneous results if you do.

5.Select Go.  The measurement process will begin (Figure 26)

1. 1. For efficiency, measurements begin at the bottom of the section and move upcore.
      
   2. Results are displayed during acquisition on instrument graphs on screen. The QE Pro has several tabs that display different views of the color reflectance data (Figure 27). Tabs can be changed during the measurement sequence. The Corrected Spectra tab shows the corrected percent color reflectance being measured at each point.
   3. After the section has been measured, the logger takes measurements using the MS2K and WHITE standards as check standards if the control sample measurement was set up in the measurement parameters.

6. When the measurements are complete, the instruments will return to home and the sample information window will be displayed.  The user may now prepare the next section and continue measurements.

Figure 26. Main IMS- SHMSL Data Acquisition Display

Figure 27. Alternative displays for the spectrometer during measurements.  User may view the L*a*b* plot (left),  the hue-chroma plot (right), or one of the other available tabs.

Other Features

Additional features are available in the Sample Information window.  These include:

• Exclude Intervals: Intervals can be specified for omission (Figure 23). Enter the top and bottom offsets of the areas to be excluded during the measurement pass as shown in Figure 28. The excluded intervals apply to all enabled sensors.  A green indicator on the sample information entry window (Figure 23) will appear when intervals are set to be excluded.
  

Figure 28.  Exclude Intervals Window

• Missing Top:  When the top of the section is missing, typically due to whole round sampling, the value, in centimeters, of missing material can be entered into the Missing Top field (Figure 23).  The software will calculate the measurement offsets based off this entry.
• Fix My Scanner: Use this feature to reprogram the barcode scanner to properly parse section half labels for use with the SHMSL software.
  
• Measure Control Set:  This feature is used to trigger the QE Pro to measure the color reflectance standards.  See the Measure Control Set section under Instrument Calibration.
  

Instrument Calibration

Color Reflectance Spectrophotometer

The color reflectance spectrophotometer calibrates on a spectra, pure white (Spectralon® WHITE standard) (Figure 2), 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 or manually by the user.  The expiration time for the spectrometer calibration is set in the QEPro setup menu (Figure 5). 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.  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.  and data run without a calibration update will be flagged as calibration invalid in LIMS.

Automatic Calibration

1. If the QE Pro is out of calibration, the Instrument Calibration List screen will appear (Figure 13).
   
   

Figure 13. Instrument Calibration Prompt

2. Before beginning the calibration, ensure the WHITE standard is clean (Figure 2). If the Spectralon® standard appears even the least bit gray or discolored, contact the technician to clean or replace the standard! It may be useful to compare a clean, new piece of white paper to the standard—if the paper seems whiter, the standard is quite dirty.

a. The Spectralon® standard can be cleaned according to the Spectralon® Reflectance Standards Care and Handling Guidelines. Spectralon Standards Care and Handling.pdf.  Check that both lights are on and the shutters are open.  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).

3. Click the Calibrate button to begin the calibration process. The user may select Ignore Continue Measurement and skip the calibration, but the software will prompt the user for a calibration every time a measurement is started until the calibration is completed.

a. The logger moves the QE Pro integrating sphere over the WHITE calibration standard and lowers the sensor until it touches. The sensor begins the white calibration measurements (Figure 15) based on the set saturation level of the total response (Figure 5). 

b. The display includes:

• • 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.

4. When the white calibration is complete, the integration time will be displayed on the screen and the user will be prompted to Accept, Re-Start, or Abort the calibration (Figure 16). 

a. The integration time should be about 0.30 to 0.55 seconds for the current dual-light source configuration, assuming the bulbs are new. 

b.  If integration times increase to more than 1 second, alert the IODP technician. The halogen bulb or the LED source may need replacing.

5. Click Accept to accept the white calibratoin.  (Figure 15):

Figure 15. White Calibration Screen

Figure 16. White Calibration Integration Time Display

6. After the WHITE measurements are completed, the shutters on the light sources will close and the DARK measurement will acquire 20 measurements. The dark measurement is a baseline measurement that includes thermal noise of the system. On the screen (Figure 17):

1. • 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.

Figure 17. DARK Calibration Screen

6. When the dark calibration is complete, the user is prompted to Abort, Re-Start, or Accept the dark calibration (Figure 18).

Figure 18. Dark Calibration Completed Prompt

7. The final screen shows the normalization of spectra that will occur with the just-acquired calibration (note: low values are better than high values because of signal-to-noise ratio) (Figure 19). Ideally, the graph would display a straight line at zero value. However, a normalization factor is required to be applied to the XYZ and L*a*b* color indexes. Normalization amplifies the noise as well as the signal. If core flow allows, the data quality can be increased by averaging multiple measurements (in Measurement Editor increase the Average parameter).

Figure 19. Calibration Normalization Factor

8. Select Accept.  If this was an automatic calibration at the start of a measurement, the laser profile will start automatically, followed by the normal measurement sequence.

Manual Calibration

To perform calibration manually (not when specified by the software), select Instruments > QE Pro: Calibrate (Figure 5).  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.

Figure 20 demonstrates a calibration with an old light source. When the red end (500nm - 740nm) of the calibration is over the amount of counts the program will process, this might be for a number of reasons, a bad light, too much light bleed-in, or some other cause (I think it is only bleed in from the sphere not sitting flat or flush to the Spectralon standard-ADD). 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.

Figure 20 - White Calibration, bad lighting or bleed in.

Figure 21 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).

Figure 21 - White calibration, blue light (LED) turned off or other malfunction.

Measuring the Color Control Set

There are twelve color reflectance standards available in the physical properties lab in the drawers beneath the pycnometer (Figure 3).  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 22.
   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 22, 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 Standards section for more information about setting up the control set.
3. Select Start from the main IMS-SHMSL window (Figure 5).
4. Select Measure Control Set. 
5. 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 23).
   
   1. . 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.
6. After each standard has been measured, the data will automatically be saved to the C:/AUX_DATA/RSC/CNTRL folder as a .csv.

Figure 22 - Color Reflectance Control Set on SHMSL track.  The white square on the end of the standard holder should be against the white benchmark (red circle).

Figure 23 - IMS-SHMSL Display during control set measurements

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.

Utilities

Note: If material is missing at the top of the section, be sure the section half is positioned all the way up to the top of the rail. The software will add the missing top interval to all of the measurements in the database. For example, if a 150 cm section half has a missing 10 cm at the top, the yellow endcap should be placed against "0 cm" at the top of the instrument's rails. The user should enter 10.0 in the Missing Top (cm) field. The logger will measure the section, and all measurements will be placed at the correct offsets in the database.

Magnetic Susceptibility Utility

The SHMSL software also has a utility feature (shown in Figure 7, below) that allows the user to test the MS performance. The MS utility allows the user to zero the meter and to set it to continuous measurement.

Figure 7. MS2K Utility

Reflectance Utility

The software has a utility for the QE Pro that allows the user to run instantaneous or continuous measurements of the spectrum being acquired by the spectrometer. Different spectra (e.g., light standard, dark standard) can be overlaid and the user has a number of other options, as shown in Figure 10.

Figure 10. QE Pro Utility

Reflectance Standard Set Editor

The standards used for the calibration of the QE Pro (99% white Spectralon® standard and the "dark" standard, achieved by turning off the lights) are defined using the tool shown in Figure 11. Do not use this screen if you are not trained!

Figure 11. QE Pro Standard Editor

The AR700 configuration screen, shown in Figure 13, show the options available for the laser. These parameters are loaded to the AR700's on board memory and their values are returned in the AR700 Config Report panel (lower left). The utility can also be used to measure distances of a known metric to ensure that the laser is returning true distance values.

Figure 13. AR700 Configuration

Setting up the M-Drive Motion Control

This section is for advanced users only!

1. To access the motion controller setup window, select Motion > Setup (Figure 14).

Figure 14. M-Drive Motor Control

From the M-Drive Motion Setup window (Figure 15, five setup panels can be accessed:

• Track Configure: Motor and Track Options
• Track Configure: Limit and Home Switches
• Track Configure: Fixed Positions
• Motion Profiles
• Y-Axis Setup

Figure 15. M-Drive Motion Controls

Track Configure – Motor and Track Options

Before using this panel you should be familiar with the M-Drive hardware and command manuals. Values 1 thru 4 (shown in Figure 16, below) are used by IMS to set motion controller parameters and convert encoder pulses into ± position values in centimeters. The correct settings for the SHMSL are as follows:

X-Axis Track Motor Setup Settings

• Encoder Pulses/rev: 2048
• Screw Pitch: 2.00000E+0
• Gear Ratio: 4.00000
• Direction of Positive Motion: CCW for positive encoder counts

Y-Axis Track Motor Setup Settings

• Encoder Pulses/rev: 2048
• Screw Pitch: 1.00000E+0
• Gear Ratio: 1.00000
• Direction of Positive Motion: CW for positive encoder counts

Figure 16. Track Motor and Options
Once these values have been properly set you should never, never have to change them. This panel is only used for the initial setup.

Track Configure – Fixed Positions

The screen shown in Figure 17, below allows the user to configure the fixed positions of the track and the limit switches. The correct values are as follows for each axis:

X-Axis Fixed Position Settings

• Max Section Length: 160.0 cm
• Track Length: 200.0 cm
• Load Position: -4.0 cm
• Unload Position: 170.o cm
• All "PUSH Track Only" settings = OFF (or 0.0, as appropriate)

Y-Axis Fixed Position Settings

• Max Section Length: not configurable for this axis
• Track Length: not configurable for this axis
• Load Position: -3.0 cm
• Unload Position: -3.0 cm
• All "PUSH Track Only" settings = OFF.

Figure 17: Track Configuration

Track Configure – Limit & Home Switches

The screen shown in Figure 18 allows the user to configure the motion logic of the track. The SHMSL X-axis (down-core motion) and Y-axis (vertical sensor motion) are configured using this screen. As shown, the X-axis is "CW Look @ CCW Edge" logic (the first option). The Y-axis is "CCW Look @ CCW Edge" logic (the third option).

Figure 18. Limit and Home Switch Configuration

Track Configure – Motion Profile

The following table shows the motion profile settings for the SHMSL X and Y axes controlled by the interface shown in Figure 19, below.

Table: Motion Profile by Axis for SHMSL

Figure 19. Motion Profiles

Y-Axis Setup

Y-Axis Setup is found in the DAQ menu option as shown in Figure 22, below. The Y-Axis setup is used to define the working distance for the AR700 laser. The screen shown in Figure 20, below, shows a typical set of standoff values for the various parameters, but if anything is changed on the Y-axis mount, these values should be determined experimentally.

• To determine the distance to benchmark, click the "Get Benchmark Data" button. This value is normally between 46.1 to 46.5 mm.
• The Touch Down Offset value is 3.80 cm.
• The Safe Clearance value (usually set to 1.0 cm) is used to prevent the sensors from running into something (e.g., a tall rock piece) that is higher than the section half liner.
• The Touch Compression value (usually set to 0.5 cm) is used to push downward gently after the landing to flatten the sensors against the core section.

Note: For very soft sediments, it may be necessary to set the Touch Compression to 0.0 cm.

Figure 20. Y-Axis Lift Setup

Data Handling

After the core section has been measured, the software generates the following files/reports, which are uploaded into the LIMS upon acceptance (see LIMS Integration):
C:\data\IN

• Section half L* a* b* and XYZ data
• MS2K check standard result
• MS2K (MSPOINT) data file
• QE Pro white check standard result
• Laser profile file

C:\AUX_DATA\PROFILE
Laser profile data in 0.1 mm steps
C:\AUX_DATA\RSC\CALIB
White and Dark calibration spectral data per wavelength (380–900 in 2 nm steps)
C:\AUX_DATA\RSC\CNTRL
Raw spectra and normalized (% color reflectance) spectral data per wavelength (380–900 in 2 nm steps) for the white check standard at the end of a run
C:\AUX_DATA\RSC\RUN
Raw spectra and normalized (% color reflectance) spectral data per wavelength (380–900 in 2 nm steps) for the measured section

Quality Assurance/Quality Control

Analytical Batch

The analytical batch is defined by the number of samples run between each spectrometer calibration. Each sample in the batch run with the current calibration is associated with that calibration data in the LIMS. If a calibration problem is discovered, all samples in the batch can be identified and rerun.

Accuracy

Magnetic Susceptibility

Measure a well-characterized magnetic susceptibility control sample and compare results with true value and/or whole-core track results.

Reflectance

Measure a second standard, standard reference material, or characterize a material in-house to use as a control. Measuring the BCRA-calibrated tiles ensures the desired accuracy is being maintained. This should be done periodically throughout each expedition.

Precision

Run samples or standard reference materials more than once (separate measurement runs) and calculate the standard deviation. This should be done every ~20-section halves allowing for a comparison between runs and estimation of uncertainty based on precision.

LIMS Integration

LIMS Components

Results are stored in the LIMS database associated with an analysis code and an analysis component. Analysis codes and their components and units are listed below.

Magnetic Susceptibility

Color Reflectance Spectrophotometry

Uploading Data to LIMS

Uploading SHMSL data to the LIMS database is executed via the MegaUploadaTron application. 

The user must log in using database credentials to use MUT. Once the application is activated, it displays a table-like list of files in the C:\DATA\IN directory as shown in Figure 42, below. Files are ready to be uploaded if they have a green check mark next to them.

Once the Upload button is clicked or the Automatic Upload option is checked, files will be transferred to the LIMS database via MUT and then moved to the archive folder. The presence of files in the Archive folder is the indication that they have been uploaded to the database.

• Purple question marks on files in MUT indicates that MUT cannot identify them.
• Red and white X icons on files in MUT indicate errors associated with the files.

Please ask a technician for help if you see these indications.

Data Management

Once all sections for the Expedition have been sent through the track, all data needs to be placed in the appropriate folders on data1 (S:\data1). Be sure to include AUX_DATA.

1. Copy RSC files from archive and place them in the 7.1 Petrophysics SHMSL – RSC reflectance spectrophotometry colorimetry folder. Confirm relocation. Delete all RSC files off the local drive.
2. Copy MSPOINT files from archive an place them in the 7.2 Petrophysics SHMSL – MSPOINT point susceptibility folder. Confirm relocation. Delete all MSPOINT files off the local drive.
3. Copy PROFILE files from archive and place them in 7.3 Petrophysics SHMSL – PROFILE split section surface profile folder. Confirm relocation. Delete all PROFILE files off the local drive.

Health, Safety, & Environment

Safety

• Keep extraneous items and body parts away from the moving platform, belt, and motor.
• The track system has a well-marked emergency stop button to halt the system if needed.
• Do not look directly into the spectrometer light source.
• Do not look directly into the laser light source.
• Do not attempt to work on the system while a measurement is in progress.
• Do not lean over or onto the track.
• Do not stack anything on the track.
• This analytical system does not require personal protective equipment.

Pollution Prevention

This procedure does not generate heat or gases and requires no containment equipment.

Waste Management

Dispose of soiled GLAD® Plastic Wrap in an approved waste container.

Maintenance/Troubleshooting

Common Issues

Scheduled Maintenance
Daily

• Keep contact sensors and laser window clean by wiping with a Kimwipe.
• If necessary, use isopropyl alcohol to remove soil from sensors and laser window.
• Do not use any other solvent!

Annually

• Remove the end covers on the linear actuators and check if the motor belts need tightening.
• Examine the cable management system for abraded cables or other indications of wear.
• Remove the top covers of the linear actuators and check the ball screws to see if they need cleaning or additional lubrication.

When Needed

• If the reflectance standard becomes nicked or soiled, it can be smoothed, flattened, and cleaned.

Communication and Control Setup

Data communication and control is USB based and managed via National Instrument’s Measurement & Automation Explorer (NI-MAX). When you open NI-MAX and expand the Device and Interface section.  The correct communications setup can be found at IMS Hardware Communications Setup.

Vendor Information and Part Numbers

Reflectance Spectrometer

Vendor

Ocean Optics, Inc.
www.oceanoptics.com
info@OceanOptics.com
727-733-2447

Parts:

Spectrometer: PN QE PRO
Light source: PN HL-2000-FHSA or HL-2000-FHSA-LL
Spare bulb: PN HL-2000-B or HL-2000-LL-B
Reflectance standard: PN WS-1-SL

Magnetic Susceptibility Meter

Vendor:

Bartington Instruments, Ltd.
www.bartington.com
sales@bartington.com
44-1993-706565

Parts:

Meter: PN MS2
Sensor: PN MS2K

Laser Displacement Sensor

Vendor:

Acuity Laser Measurement
www.acuitylaser.com
702-616-6070

Parts:

Sensor: PN AR200

Related Documentation and Links

• AccuRange 700 laser displacement sensor data sheet: ar700-data-sheet.pdf
• Acuity Laser Measurement User Manual: ar700-users-manual.pdf
• Ocean Optics Halogen Light Source Operation Manual: hl2000fhsa.pdf
• Ocean Optics Fiber Optic Spectrometer Operation Manual: USB4000operatinginstructions.pdf
• Microscan MS-4 Ultra-Compact Imager data sheet: ms4spec.pdf
• Bartington MS2 Magnetic Susceptibility sensors data sheet: MS2 sensors D50020.pdf
• Bartington MS2 Magnetic Susceptibility system operation manual: OM0408 MS2.pdf
• "Environmental Magnetic Susceptibility Using the Bartington MS2 System": OM0409 J_Dearing_Handbook_iss7.pdf
• Hunt, R. W. (1998). Measuring Colour (3rd ed.). England: Fountain Press. ISBN 0-86343-387-1.. See pgs. 39–46 for the basis in human eye physiology of three-component color models, and 54–57 for chromaticity coordinates.
• Hunter Lab application note Vol 8. No. 1 http://www.hunterlab.com/appnotes/an04_96a.pdf