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Contents

Manual Information

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.

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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

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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

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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.
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Figure 26. Gap Detection Offset

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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).

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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.
2. 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.
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 27).Image Modified
   Figure 27. Benchmark
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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1. Click the Start button (Figure 28) to open the Section Information screen (Figure 29).
   

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   Figure 28. Start ScanFigure 
   

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   Figure 29. Section Information Screen
   1. 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.
   2. (Optional) Enter any comment needed into the Comment field.
   3. 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.
   4. 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.
      

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      Figure 30. Exclude interval
2. 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.
3. 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.)

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1.  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. 
   

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   Figure 31. Laser Profile
   
   
2. 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.
   

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   Figure 32. Final Sample

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1. 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!

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

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   Figure 33. Wrapped Sample Ready to Analyze.
2. 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.
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   Figure 34. Data Acquisition Screen
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.

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Calibrating the Sensors

Before running the first sample, the software will check the status of each instrument's calibration. If any instrument needs calibration, a prompt will appear listing out of date calibrations. It is recommended that the user select every instrument that needs calibration and click the Calibrate button before continuing. There is an option to ignore one or all calibrations (click Cancel), but the calibration list 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.

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The color reflectance spectrophotometer calibrates on two spectra, pure white (Spectralon® WHITE standard) and pure black (DARK standard – lights off), mounted in the track's bench. Color calibration is required approximately every 6 hours. The control program will notify when calibration is due and automatically open the Calibrate routine.
Note: a calibration may be run at any time, even if the mandatory period has nod elapsed.
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Figure 35. WHITE Spectralon® Calibration Standard

1. If the QE Pro is out of calibration, the Instrument Calibration List screen will appear.
2. Before beginning the calibration, ensure the WHITE standard is clean (Figure 35). 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!
   1. The Spectralon® standard can be cleaned according to the Spectralon® Reflectance Standards Care and Handling Guidelines, found in the Cumulus database under SHMSL>Diffuse Color Standards.
3. Click the Calibrate ALL CHECKED Instruments button to begin the calibration process. The logger moves the QE Pro integrating sphere over the WHITE calibration standard and lowers the sensor until it touches. The sensor takes some preliminary measurements to establish the integrating time based on an 80% saturation level of the total response (see Figure 36, below). These measurements take about 0.30 to 0.55 seconds for the current dual-light source configuration, assuming the bulbs are new.
   Note: If integration times increase to more than 1 second, alert the IODP technician. The halogen bulb or the LED source may need replacing.
4. Click Accept to accept the suggested integration time. The logger will then take 20 measurements of the WHITE standard at the calculated integration time. On the screen (Figure 37):
   1. Max Counts: current highest value
   2. Target Counts: percent saturation value as set in the instrument parameters (range = 32,000 counts)
   3. Integration Time: measurement period where the highest wavelength count is equal to or exceeds 80 percent of the spectrophotometer's range.Image Added
      

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1. 1. Figure 36. White Calibration Screen
      

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      Figure 37. Integration Time
2. 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 38):
   1. Temperature: should remain below 50°C; note that the TEC temperature is usually about -9¿C (accessed through the QE Pro Utilities screen.
   2. 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.
   3. 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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      Figure 38. DARK Calibration Screen
2. 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). 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).
   

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   Figure 39. Calibration Normalization Factor
2. If this was a mandatory calibration the laser profile will start automatically, followed by the normal measurement sequence.

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1. Time: Calibration expiration time can be set in the Instrument Setup screens. Calibration expiration can be set from 1 to 24 h (default = 6 h). The time trigger is independent of number of samples run.
   

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   Figure 40. Calibration Time Trigger
2. Core number or section number change: Set this option in Track > Calibrate Setup.
3. Manual override.

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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

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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

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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.

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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.

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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.

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Uploading Data to LIMS

As with most laboratory data, uploading SHMSL data to the LIMS database is executed via the MUT application. Look for an icon on the bottom menu of the Desktop (shown by the red triangle below in Figure 41) or the more prominent "Puppy" MUT Icon (usually on the Desktop). Double-click on one of these application launchers.  

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Figure 41. MUT Icons
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.

Figure 42. SHMSL MUT Screen
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.

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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.

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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.

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

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Maintenance/Troubleshooting

Common Issues

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

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Vendor Information and Part Numbers

Reflectance Spectrometer

Vendor

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

Parts:

Sensor: PN AR200

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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