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1. 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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   Figure32Figure32. Final Sample Preparation 
   
   IMPORTANT!!! Before pressing GO, 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!
   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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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):
   • 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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     Figure 36. White Calibration Screen
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     Figure 37. Integration Time
5. 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):
   • Temperature: should remain below 50°C; note that the TEC temperature is usually about -9¿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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     Figure 38. DARK Calibration Screen
6. 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
7. 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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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.
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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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