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1. Insert the calibration standard into the holder and tighten the set screw.  Center the standard in the holder by using your fingers on either side.  Wiggle the standard and tighten more if necessary; it is important that the sample does not slip.  Do not overtighten the screw, as it will cause the holder to break.
2. Close the coils and put on the shield.
3. Check the calibration standard settings by clicking Settings> Calibration Standard.  The magnetization and volume values should match the values written on the cube. Then select OK.
4. Open the calibration dialog box by selecting Execute > Calibration (Figure 5). 
5. Select Start.  As the standard runs, keep your hand on the spacebar. This is the kill switch/emergency stop and will need to be hit if the sample slips in the spinner and begins to scrape the side.  Listen for this as the spinner operates.
   1. The displayed Phase and Gain should be the “current” values. Gain should be within ±15% from the nominal value for the corresponding speed; Phase should be ±20° from nominal. If so, click Save. Otherwise, redo the calibration.
6. Remove the calibration standard from the spinner.  Make sure the screw head is flush with the holder or just below the edge.

Figure 5: Calibration dialogue box.

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1. Click Execute > Holder Correction. The Holder Correction dialogue box will open (Figure 6).
2. Make sure the holder is empty, the screw is flush with the edge of the holder, the coils are closed, and the shield is in place.
3. Click Start in the dialogue box and wait for measurement to complete.
   1. There is an error associated with this process. The program tends to overflow (error E9) and then say that it is completed even when it hasn’t gone through all three positions. See the appendix for help with this issue.
4. If all of the values are highlighted in green, then select Save.  If the values are highlighted red or are blank, remeasure.

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Figure 6: Holder Correction dialogue box after successful measurement. 

Preparing Samples

1. For Japanese style cubes, no special preparation is needed, simply install the cube into the holder with the arrow pointed up and left (Figure 7, red arrow). An orientation correction will be applied during sample information entry.
2. For hard rock samples, there are two options for installing the cube into the holder.

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• Install the cube into the spinner as seen in Figure 9, with the added arrow pointing up and left. The reason for this is the differing coordinate systems between the JR 6A and IODP.  See the figure on the side of the spinner from the Methods section of Expedition 342.  The coordinate systems will be discussed further in Appendix A.
• With this option 2, there is no need for further coordinate corrections.

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Figure 7: Japanese cube sample placement.

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Figure 8: Added arrow to hard rock sample.

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Figure 9: Hard rock sample in automatic holder of spinner. 

Measuring Samples

1. Securely install the sample into the holder, close the coils, and put on the shield.
2. Click File > New to create a .jr6 file and to set the file path.  This file path will be where the data is placed when SAVE is selected. Name the file appropriately – for example: 341_U1234A (Expedition_Site/Hole).  Save to the folder C:\JR6Data\IN.
3. Click New Specimen in the bottom left corner of the window (Figure 10).  This will prompt the New Specimen dialogue box to open (Figure 11).
4. Use the barcode scanner to enter the name of the sample in the Name field (sample names are truncated to 9 characters in the .jr6 file).  IODP convention is to use the Text ID of a sample as the name. 
   1. Data will upload if the name is a valid Text ID. User may manually enter the sample name if the barcode scanner is unavailable.
5. Enter the Treatment information for the cube (NRM, AFD, TD, etc.)
6. Enter the Orientation information. 
   1. For Japanese cubes and hard rock cubes prepared following option 1 from the Preparing the Sample section, enter Azimuth = 0 and Dip = 90. This will make the correction for the coordinate system discrepancy and report the data in the IODP reference frame under “geographic coordinates” in the data files.
   2.  For hard rock cubes prepared following option 2 of the Preparing the Sample section, leave the orientation fields blank.
7. Select OK in the dialogue box.  The main window will now display the updated sample information (Azimuth, Dip, Name, and Treatment) (Figure 10).Select Start at the bottom of the window (Figure 10).
   1. During a measurement, the Stop bar at the bottom of the window or the space bar will stop a measurement immediately.  Use these options if the sample comes loose in the holder.
   2. During measurements, the status of the instrument is displayed in the lower left-hand corner.
8. When the run is completed, click Save in the right hand bottom corner (Figure 10) in order to save the run and continue to the next specimen, or click Start to redo the run.
   1. The file will be saved to the path set by the user.  If no path has been set, the Rema6 software will prompt the user for a path.
   2. b.     Three files will be written: .csv, .jr6, and .txt.  These three files are necessary for data upload to LIMS.  The .csv file is an IODP specific format.  For further information on file formats and uploading see Appendix B or the JR6 Uploader Guide.

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Figure 10: Main screen after sample has been run.

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Figure 11: New Specimen dialog box.

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IODP provides two options for processing JR-6A data: Remasoft 3.0 software and Puffin plot.  To use Remasoft 3.0, export specimen files from the Rema6 main window.  To use Puffin plot to process the data, download the .csv file from LIMS.  An Excel macro (JR6toPuffinPlot) has been added to the JR6 PC and MAC workstation.  This macro will format the LORE download file into a simple file for use within PuffinPlot.  See the Quick Start Guide to using Puffin Plot for further details.

Appendix

A.1 Holder Correction

The Rema6 program has experienced errors during holder correction. Figure A.1 displays very briefly in the middle of the correction routine, displaying an E9 overflow in the bottom of the window. Following this, the program states that it has done a successful holder correction, even though it has not gone through all three positions yet.  The new holder values cells may be empty.

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Figure A.1: E9 OVERFLOW Error.

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Once the error has occurred, the holder correction measurement must be redone. Make sure the holder is clean and attempt to remeasure the holder.  One remedy used during Exp. 345 is to take off the shield and run the holder correction. Agico suggests cleaning the optical system rotation screen (see directions in the JR6 screen cleaning files saved in IODP_Share\IODP_Technical_Manual\PaleoMag/Current/JR-6.

A.2 Orientation and varying coordinate systems

The JR-6A coordinate system is different from the IODP coordinate system (from Exp. 342 “Methods”):

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Figure A.2: Coordinate systems (Source: Exp. 342 Methods).

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A.3 Specifications

Specifications

(Source: ascscientific.com)

B.1 Uploading JR6 data

The current REMA6 version (6.2.06) has been modified for IODP use.  REMA6 will output three file types: .csv, .jr6, and .txt.  These three files are necessary for data upload to the LIMS database. The .txt file and .jr6 files are standard REMA6 outputs. 

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