...
- 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
...
Open the SHMSL application by double-clicking the icon on the desktop (Figure 2, below). The application will begin by initializing the Acuity AR700 laser, the Bartington MS2K point source susceptibility probe, and the Ocean Optics QE Pro spectrometer. Ask the PP Tech for assistance in changing the instrument's measurement parameters (see Setting Measurement Parameters). Once initialized, the logger is ready to measure a section.
Figure 2. IMS Icon
The Main Integrated Measurement System (IMS) control screen provides access to data acquisition functions and utilities as well as:
Current measurement parameters
...
The IMS immediately initializes the system hardware (Figure 3): the track system is initialized first, finding the home position for the Y- and then the Z-axes. Following that, the laser displacement sensor, magnetic susceptibility probe, and spectrometer are initialized (Figure 4).
Figure 3. IMS Initialization
Figure 4. IMS Application Main Screen.
Laboratory Apparatus
- GLAD® Plastic Wrap (crystal clear polyethylene)
...
This section is for advanced users only!
Each instrument sensor is set up through Instruments > Sensor Name > Setup (Figure 5). The parameters discussed in this section are common for all sensors on the SHMSL.
Figure 5. Setup Instrument Sensors
Instrument offset: track position of the laser where the center of the sensor is over the benchmarks zero edge.
Sensor/Contact width: physical width of the sensor that makes contact with the core's 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.
Description: instrument purpose; used in the System Information report.
...
- Standard name: standard's LIMS label_ID component value.
- Text ID: standard's LIMS text_ID component value.
- Standard's value: Value established by IODP is 48 +/- 2 SI
- Standard 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 Y-offset: lift position (Y-axis) when the MS sensor probe is in contact with the standard.
Figure 6. MS2K Parameters
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
Setting up the QE Pro parameters
...
The Ocean Optics QE Pro spectrometer can be set up using the screen shown in Figure 8. 
Figure 8. QE Pro Sensor Setup
Fixed Acquisition Parameters section
- Hi cut-off and Low cut-off: determine region of interest (ROI) in the spectrum.
- Bin size: width of each channel.
Figure 9. Illustration of high and low cut-off and bin size.
- Median filter rank: number of adjacent channels used to filter noise from the signal.
- Illuminant: = D65; International Commission on Illumination (CIE) standard illuminant used in color calculations (also called daylight illuminant).
- Geometry: = d/8; 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.
- Observer: = 10 Degree-2; indicates usage of CIE 1965 standard function in tristimulus calculations.
...
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
Setting the AR700 Parameters
The AR700 parameters are metadata and do not have an effect on the measurements. Their nominal values are shown in Figure 12.
Figure 12. AR700 Sensor Setup
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
...
- 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
...
- 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
...
- 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
...
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.
...
Note: For very soft sediments, it may be necessary to set the Touch Compression to 0.0 cm. 
Figure 20. Y-Axis Lift Setup
Setting Measurement Parameters
This section is for advanced users only!
Before measurement parameters can be set or changed the IMS must be unlocked. Note: Changing setup parameters can cause problems. Make sure you know what you are doing before changing any setup parameters.
Under File, select Unlock Setup as shown in Figure 21 below, then have the laboratory specialist type the unlock code into the keypad window (Note: this only has to be done if the setup has been locked, it usually remains unlocked).
Figure 21. IMS Control
To open the measurement editor, select DAQ > Measurement Editor as shown in Figure 22.
Figure 22. DAQ Control
Measurement Editor
In the Measurement Editor window, loaded instruments are shown in the Select Instrument fields. Click on an instrument to see its measurement parameters in the Instrument Parameters field.
Click the Instrument Parameters window to open the editor for that instrument. This will invoke the screen shown in Figure 23.
Figure 23. Measurement Editor Screen
The MS2K and QE Pro have similar editor screens (Figures 24 and 25, respectively). From each screen you can set the following parameters:
Interval (cm): set to 0.1 to 20 cm; intervals for both the MS and reflectance should either be the same or multiples of one another and whole number divisors of the distance between the sensors. If they are not whole number divisors, an inefficient landing schedule will be developed, taking much longer to analyze a core section.
Edge (cm): how close to measure to an edge (top and bottom of a section as well as edges of voids within the section). The distance is measured from the center of the sensor (MS2K sensor width = 4 mm or 10 mm, depending on orientation; QE Pro sensor width = 8 mm). Edge width = 1.0 cm works well.
Control (on/off): whether to measure a mounted control standard at the end of every section measurement.
Online (on/off): set the instrument online or offline.
...
Method: this is a selector between single or stacked (average) measurements.
Stack #: set the number of measurements to stack and average. 
Figure 24. MS2K Measurement Parameters
Figure 25. QE Pro Measurement Parameters
Click OK to save settings to the instrument configuration file and return to the Measurement Editor.
Only one parameter can be set for the laser, and that is Gap Detection Offset shown in Figure 26. 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 26. Gap Detection Offset
Running Samples
Core-half sections 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 (see Figure 33, below, but note that the sample must be laser-profiled before the wrap is applied).
...
- 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.
- Bring the endcap of the section half (usually A for archive half) to be measured to the SHMSL. Use the endcap rather than the label on the bottom of the section to scan the barcode for sample information, to prevent accidentally dropping the section half.
- 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 27).
Figure 27. Benchmark - 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.
- 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.
...
- Click the Start button (Figure 28) to open the Section Information screen (Figure 29).
- Figure 28. Start ScanFigure
Figure 29. Section Information Screen- Place the cursor in the SCAN text field (circled in black in Figure 29, above) so that the barcode information will be parsed appropriately. Pull the trigger on the barcode scanner; at the beep, the information will automatically fill for Expedition, Site, Hole, and so on.
- (Optional) Enter any comment needed into the Comment field.
- If material is missing from the top of the section, enter the distance in the Missing Top field (circled in red in Figure 29, above).
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. - Additional intervals can be specified for omission from measurement by clicking the Exclude Interval button (top left of Figure 29, above). Enter the top and bottom offsets of the areas to be excluded during the measurement pass as shown in Figure 30. The excluded intervals apply to all enabled sensors.
Figure 30. Exclude interval
- When the required minimum sample information has been entered, the Measure button becomes active. Click it to start the measurement. If the QE Pro does not require calibration (see Calibrating the Sensors, below), proceed to the next step.
- The sensor assembly will move down the track while the laser acquires a profile of the split surface of the section. 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; ask the PP tech for assistance in modifying them.)
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.
Figure 31. Laser Profile - After the surface profile is completed, the measured section length as determined by the laser is displayed (Figure 32). Apply GLAD® Plastic Wrap to the surface of sediment cores as demonstrated by the PP Tech (Figure 33). Adjust the displayed length if needed in the Scan Length field and click GO to start the section measurement.
Figure 32. Final Sample Preparation
IMPORTANT!!! Before pressing GO, it is necessary to cover the core section with GLAD® Plastic Wrap in order to avoid damage to the integration sphere. Any mud that gets inside the sphere will ruin it!
IMPORTANT! Do not cover the standards with GLAD® Plastic Wrap; they will give erroneous results if you do.
Figure 33. Wrapped Sample Ready to Analyze. - The measurement sequence begins. For efficiency, measurements begin at the bottom of the section and move upcore. Results are displayed during acquisition on instrument graphs on screen. Note that the QE Pro has several tabs that display different views of the color reflectance data. Tabs can be changed during the measurement sequence. The Normalized Spectra tab shows the corrected percent color reflectance being measured at each point.
Figure 34. Data Acquisition Screen - 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.
...