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1. Click the Start button (Figure 28) to open the Section Information screen (Figure 29).
   
   
   Figure 28. Start ScanFigure 
   
   
   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.
      
      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.) 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
   
   
4. 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.
5. 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
6. 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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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.
      
      
      Figure 36. White Calibration Screen
      
      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):
   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.
      
      
      
      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).
   
   
   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.
   
   
   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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