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For sediment cores, the surface of the core must be covered with a thin plastic film (Fig Next1, Ultralene, 0.16 mil/4 µ thick, GLAD® wrap is too thick and will interfere with measurements). Cover the area of measurement and about 4-5 cm on each side, so a 10 cm piece of Ultralene would be appropriate. This is to protect the device nose from becoming dirty from the core. If making several measurements in an area, the entire area can be covered. If the entire core section will be measured ('high' resolution measurements), cover the entire core section. Important! Do not measure on sediment core sections without covering with film, however, do not waste Ultralene® to cover areas that will not be measured (it costs about $1 USD/meter). Tape the film on the sides of the liner and use a Kimwipe on the film to remove any trapped air bubbles under the film in the area of measurement. Cover the rest of the section in GLAD® Plastic Wrap so the instrument and holder does not get dirty. Make sure the top of the plastic is clean, dry, air-free and mud-free, especially the Ultralene®-covered locations. Important! Even a small amount of sediment on top of the thin film from a measurement will affect the next measurement of the core section half.
Figure Next1. Ultralene® polypropylene plastic covering the sediment surface.
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Preparing powdered samples
Discrete samples are dried, ground to powder, and loaded into a XRF sample cup. Powdered samples allow the analysis of a specific interval or feature on a section half. This process is more involved, time-consuming, and invasive (destructive) compared to the section half measurement. However, powdered samples can be run along with powdered standard reference materials and the data can therefore be reduced for quantitative elemental data. Powdering a sample also creates a homogeneous sample. If the powder is fully homogeneous and the sample cup is loaded to sufficient thickness (~1cm) and uniform powder density, quantitative error should be low.
Drying Samples
It is important to dry discrete samples prior to grinding them. Freeze-dry samples for 12 hours. For details on how to operate the Freeze Dryer refer to the X-Ray Diffraction (XRD) sample preparation
Grinding Samples
Once dry, samples are ground into a talc-like powder. Grinding is accomplished by three methods: agate mortar and pestle, SPEX Mixer/Mill®, or SPEX Shatterbox®. The specific grinding method used is dependent on sample hardness. For more details on grinding methods refer to the X-Ray Diffraction (XRD) Sample Preparation and ICP Hard Rock Prep User Guide.
Loading Samples into an XRF Sample Cup
To create a powdered XRF sample, assemble the following components shown in Figure
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2:
- Powdered & dried sample
- Scoopula
- XRF sample cups (32 mm Double Open Ended)
- SPEX Ultralene® thin film (0.16 mil; 4 µm thick) OR Polypropylene pre-cut circles (0.16 mil; 4 µm thick)
- Whatman Filter Paper Circles (32mm) or Parafilm M® film
- Foam plug
- Scalpel for trimming foam plug
Figure
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2. Mortar and pestle along with scoopula. XRF Sample Cup components denoted with red arrows A. Open-end Ring B. Cup C. Cap D. Ultralene® film box E. Whatman Filter Paper F. Foam plug inserts
1. A XRF Sample cup has three components: cup, ring, and cap. Take a piece of Ultralene® film or polypropylene pre-cut circle and stretch it over one end of the cup. Place the open ring over the film and cup and snap it firmly onto the cup. This will create a tight window on one end of the sample cup (Fig.
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3, step 1). Ultralene® is very thin and prone to ripping. Check for rips before and after sample powder is added.
2. Flip this unit upside down (film side down) and begin to load the sample into the cup. Remember that the powdered sample will be back loaded. An ideal depth of sample is ~1.5 cm or more, if possible, with the goal being ~1 cm of pressed material. The sample layer cannot be too thin, or X-ray penetration (and the results) will be inconsistent. Make sure the powder is evenly dispersed, maintaining a relatively flat, even surface.
3. Next place a barrier layer on top of the powder, either Whatman Filter Paper or Parafilm®. This creates a seal that prevents contamination and keeps powder secured in place. Take a piece of Whatman filter paper and put it on the powder or cut a square of parafilm, wrap it over the end of the foam plug and push it down inside the cup. Press down evenly until it is firmly on the powder.
4. Insert the foam plug (if not already inserted). Take care not to insert it too quickly and cause air displacement that might disturb the powder. Depending on how much sample has been loaded into the sample cup; a couple centimeters of the foam may need to be chopped off.
5. Once you have filled the unit properly, place another piece of Ultralene® film or a polypropylene pre-cut circle across the back of the sample cup and snap the closed cap on the cup. If you have over-filled the sample cup, this is the point where the film will break, so examine both sides of the cup after you snap the lid on. Tip: place the cap on most of the way as in step 5, but then flip the sample cup over and, holding only the edges, push the sample cup down into the cap until it snaps firmly in place. Holding the sample cup toward the edges allows the film covered surface of the sediment to bulge out as seen in step 6.
6. It is important to create some outward "bulging" of the film so that the powder stays well-packed and stationary. Cracks, gaps, tears in the film or inconsistent filling of the powder will create inconsistent results. Be careful, however, not to pack too tightly or the Ultralene® film will break and you will have to start over.
Your finished product should look like the cup in Figure
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3, step 6.
7. Put a sample label onto the cup. Remove excess Ultralene® to help the label stick. The powdered sample is now ready for analysis.
Figure
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3: Sample preparation steps for powdered pXRF sample. Note the slight bulge of the sample when correctly filled.
Do not forget to remove the sample from the pXRF sample cup after analysis. A 3D-printed tools exist to help disassemble the sample cup. Put powder back into it's original container or put it in a labeled jar (shipboard residue). Wash and clean the pXRF sample cup components before reusing.
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Power on the instrument by pressing and holding the button above the device screen for a second or so (Figure 1Fig. 4); release the button when it lights up green. The lights under the rail will flash orange and red and there will be some motorized noises. An initialization screen will appear showing the start up progress.
Figure 14. Power button (Left, arrow) and ports, A) Remote port, for connection to optional accessories, B) Power port, C) USB-A port with storage device installed, D) USB Mini-B port, for connection to a computer or laptop.
Click on Bruker RemoteCtrl shortcut on the desktop (Figure 2Fig. 5). This program simply mirrors the device screen. You will use it to control the device from the computer while measuring your samples.
Figure 25. Bruker RemoteCtrl program shortcut
Go to File 
Connect. A window will appear that will show the device serial number, 900G7838. Select it and click Ok (Figure 3Fig. 6). It may take up to 10 seconds or so to connect, then the current device screen will be displayed.
Figure 36. Connecting the device to the computer.
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After the device has initialized, a login window will appear (Figure 4Fig. 7). The User login is 12345.
Figure 47. Login screen in Bruker Remote Control
A radiation warning will appear on the screen, press and release the trigger to acknowledge this message. Next, a pop up message will appear that tells you the current configuration; click OK (Figure 5Fig. 8).
Figure 58. Configuration window when initializing the device.
The main device screen (Fig. 9, Left) contains a large box at the top displaying the status of the X-ray tube. The device will say Not Armed when the X-ray is not armed and the device will say Ready to Test when the X-ray is armed. The X-ray will be disarmed if any of the blue buttons on the screen are selected. The device will not be armed until a sample is placed in front of the measurement window or the device is placed against sample material. If the proximity sensor is disabled, the X-ray will still be armed if a sample is removedthe instrument is on this screen (Fig. 9, Right). Remember the trigger is active! Be aware of where the device is pointed if the proximity sensor is disabled!
Figure 69. The Tracer's main screen display. Left: X-ray is not armed. Right: X-ray is armed and ready to measure.
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Some application settings, such as beam scan duration, can be adjusted by selecting 
on the main display screen. Three settings can be adjusted (Fig. 110):
- Duration: This screen will display the number of phases used by the current application. The time in seconds spent on each phase can be adjusted or set to unlimited (ending when the trigger is released). Note: The longer the scan time, the greater the accuracy and precision and the lower the error. For geological samples, 1 minute per phase or longer is not uncommon, but not required.
- First Result/Test: This is the number of seconds before results will be shown on the display once a measurement has been triggered.
- Trigger Active: The trigger can be set to ‘Auto’ or ‘Manual’ by selecting this button.
- Auto: The measurement proceeds by pressing and releasing the trigger. Preferred.
- Manual: The trigger must be pressed for the duration of the measurement. If the trigger is released at any time during the measurement, measuring will stop.
Figure 110. Settings display screen. User will only see the top box. Supervisor will see the screen as is.
Select ‘Ok’ Select ‘Ok’ when finished adjusting or 'Cancel' to return to the previous screen.
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On the main display, click the ‘Edit Info’ button in the middle of the bottom row of buttons. This screen (Figure 4Fig. 11) is where the sample information is entered. All fields in the right column are editable by double clicking and should be reviewed and changed for each sample:
- Sample Type:
- Standard – a powdered standard in a sample cup
- SHLF – a measurement taken directly on a section half or of a piece from a section half
- Sample – a powdered sample in a sample cupcup
- Expedition: The current expedition
- Example: 397
- Site & Hole: The site and hole the sample was taken from
- Example: U1586A
- Core/Section: The core number with letter indicating the core type and the section in that core that is being measured or that the sample was taken from. If measuring a standard, enter the standard name.
- Sample example: 1H/6 or 32X/1
- Standard example: BCR 2 or BHVO 2
- TextID: The unique sample number for every sample. This is found on the lower right corner of the typical sample label, example: SHLF11754181. If measuring a standard, use the information from the appropriate QAQC label provided. If a standard does not have a QAQC label, leave this field blank. Note: If the device is connected to the laptop and using Bruker RemoteCtrl software, attach and use the barcode scanner to enter the TextID by scanning the QR code on the section half or sample label.
- Example: SHLF11744181
- Top Offset (cm):
- For a section half or piece from a section half, this is the distance in cm from the top of the core section, example: 34 or 101.5 (Do not put a range!).
- For powdered samples and standards, use 0.
- Comment: Use this to provide any additional information, such as a physical description for reference or to indicate a replicate measurement.
Figure 511. The Edit Info display screen.
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Remember to fill out the Log Sheet as you are editing the sample information. For the current version of the log sheet, do not worry about the Run#, this will be automatically assigned (refered to in the results data as 'File #') and you can fill that in after the measurement starts. It is important to fill in the Time (in UTC) as this will help the X-Ray technician match up the sample with the measurement and correct any errors, if any, before uploading the data. The most important information is the sample TextID and the Offset (if from a SHLF) as these are unique values needed to upload the data to LIMS.
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A beep will sound when the device has finished measuring and the device can be moved away from the sample or repositioned for the next measurement. At this point, the previous measurement’s data has been stored and added to the results file.
Downloading the Data
The Tracer updates the ‘Data’ folder after each new measurement with an associated .pdz file and also adds the data to the appropriate application .tsv file and .csv ‘Results’ file. Highlight the files you want to download and then select the ‘Download’ option in the toolbar of the program window. A smaller window will appear and here you can select the location you wish to download the files to. Download all data files (.tsv, .csv, and .pdz) to C:\DATA\IN. The .tsv and .csv files will have all measurements that have been taken since the most recent internal memory clean-up, which will typically be done after each site or more frequently depending on the number of measurements executed. After further measurements, downloading again will add only the new measurements, but will replace the .tsv and .csv files with updated versions that will include the new measurements.
Downloading the Data
To export the results, connect the device to the computer if not already connected. Also, log into the OES 
using your personal credentials.
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To download these results, connect the device to the computer, if not already connected, and log into the OES using your personal credentials.
Open the Bruker Instrument Tools 
found on the desktop. Go to Device,then Connect and select 900G7838. Click Connect(Fig. 12 and 13).
Figure 12. Menu bar of Bruker Instrument Tools.
Figure 13. Connection window of Bruker Instrument Tools.
After connection, a file tree will appear on the left side of the program window (Fig. 14). Select the folder ‘Bruker’ and double click to open it. Then select the ‘Data’ folder and double click to open.
Figure 14. Left, File tree for the Tracer 5 in Bruker Instrument Tools. Right, Inside the 'Bruker' folder.
Inside the Data folder is:
- A .pdz file (spectra files) for each measurement
- A .tsv file for each application used (i.e. GeoExploration.tsv)
- A .csv results file named Results.csv
If a USB stick is installed, the data is automatically written to the 'Data' folder on the USB. The Tracer is also set up to save each data measurement to the internal memory as a back up in case the USB stick should fail. The Tracer automatically updates the ‘Data’ folders in the Bruker and USB folders after each new measurement with an associated .pdz file and also adds the data to the appropriate application .tsv file and .csv ‘Results’ file.
Highlight all the files and then select the ‘Download’ option in the toolbar of the program window (Fig. 15, Box). A smaller window will appear and here you can select the location you wish to download the files to. Download all data files (.tsv, .csv, and .pdz) to C:\DATA\IN (Fig. 15, Arrow). The .tsv and .csv files will have all measurements that have been taken since the last internal
Figure 6. Menu bar of Bruker Instrument Tools.
Figure 7. Connection window of Bruker Instrument Tools.
After connection, a file tree will appear on the left side of the program window (Fig. NN). Select the folder ‘Bruker’ and double click to open it. Then select the ‘Data’ folder and double click to open.
Figure NN. File tree for the Tracer 5 in Bruker Instrument Tools.
Inside the Data folder is:
- A .pdz file (spectra files) for each measurement
- A .tsv file for each application used (i.e. GeoExploration.tsv)
- A .csv results file named Results.csv
If a USB stick is installed, the data is automatically written to the 'Data' folder on the USB. The Tracer is also set up to save each data measurement to the internal memory as a back up in case the USB stick should fail. The Tracer automatically updates the ‘Data’ folders in the Bruker and USB folders after each new measurement with an associated .pdz file and also adds the data to the appropriate application .tsv file and .csv ‘Results’ file.
Highlight all the files and then select the ‘Download’ option in the toolbar of the program window (Fig. LOL, Box). A smaller window will appear and here you can select the location you wish to download the files to. Download all data files (.tsv, .csv, and .pdz) to C:\DATA\IN (Fig. LOL, Arrow). The .tsv and .csv files will have all measurements that have been taken since the last internal memory clean-up, which will typically be done after each site or more frequently depending on the number of measurements executed. The data can be copied from this folder for data processing.
Figure LOL15. Downloading data with Bruker Instrument Tools. The box Box indicates the download button. The arrow Arrow indicates the location to save the data to.
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Once you find the folder, select All Files from the drop down menu at the bottom right (Fig. 8, Box). Then select the GeoExploration.tsv file and click Import. (Fig. 816).
Figure 816. Importing data from the .tsv files into Excel. The red box indicates where to select 'All Files'.
A window will open showing you a preview of the file. Select 'Tab' from the 'Delimiter' drop down menu options, if it is not already selected. Click Load. (Fig. 917)
Figure 917. Data Preview in Excel of the .tsv file. The red box indicates the correct 'Tab' should be selected as the delimiter.
The data will be imported to Excel in a more useable format(Fig. 1018). The columns with the sample information will be the last columns to the right.
Figure 1018. Exported file from pXRF device.
This file can then be saved in Uservol (when logged into the OES) to access for data processing. The file may contain repeat data from an earlier download, simply delete the rows of unwanted data.
Uploading data to LIMS
!!! Clearing data from the internal memory and USB!!!
Note: The internal memory of the device is only 512MB (~1200 scans)! Therefore, the internal memory needs to be cleaned up several times an expedition to prevent locking up the device’s onboard computer. The X-ray technician will take care of this, but keep this in mind if you are performing a lot of measurements!
To clear the internal memory of the device, from the main display screen select 
, then 
. Select the 'Delete' option along the top (Fig. 11, Green Box). To keep the run numbers consecutive through the expedition, deselect the 'Reset Assay filename counter' option (Fig. 11, Purple Box). If it is the end of the expedition, leave this option selected and the run number (the same as the file number), will revert back to '1'. Then select 
.
Open MegaUploadatron2 (MUT2) on the laptop desktop.
If the File #s have been reset, there will be identically numbered .pdz files within the expedition dataset. MUT2 will not be able to handle this. After uploading, move the data files into a folder within C:\Data\IN named for the date of upload so that MUT2 will not be confused if there are repeating file names.
!!! Clearing data from the internal memory and USB!!!
Note: The internal memory of the device is only 512MB (~1200 scans)! Therefore, the internal memory needs to be cleaned up several times an expedition to prevent locking up the device’s onboard computer. The X-ray technician will take care of this, but keep this in mind if you are performing a lot of measurements! The data should be copied from the C:\Data\IN folder to S:\data1\24.2 Chemistry pXRF before proceeding.
Do not perform this action until the data to be deleted has been copied to 'data1' AND uploaded to LIMS!
To clear the internal memory of the device, from the main display screen select , then . Select the 'Delete' option along the top (Fig. 19, Green Box). To keep the run numbers consecutive through the expedition, deselect the 'Reset Assay filename counter' option (Fig. 19, Purple Box). At the end of the expedition, leave this option selected and the run number (the same as the file number), will revert back to '1'. Then select .
Figure 19. Backup Data screen. Green box, the Delete option. Purple box, option to select/deselect if you want to reset the run number back to 1.
The files can also be deleted in Bruker Instrument Tools using the Supervisor log in. In the program menu bar, select 'Tools' and 'Login' (Fig. 20). A smaller log in window will appear. The password is root123 and select 'OK' (Fig. 21).
Figure 20. Bruker Instrument Tools Login from the Tools menu.
Figure 21. The Login window for supervisor access in Bruker Instrument Tools.
In both the 'Bruker' and 'Archive' folder are 'Data' folders (Fig. 14) which can be accessed by double clicking the folder. Once inside the folder, highlight all the files, right click with the mouse and select 'Delete' (Fig. 22).
Figure 11. Backup Data screen. Green box, the Delete option. Purple box, option to select/deselect if you want to reset the run number back to 1.
Additionally, it is important to keep the number of files in the Data folder of the USB low as well. This should also be done each time the internal memory is cleared. With the device connected to the laptop, open Bruker Instrument Tools and connect to the Tracer. The safest way to do this is to remove the USB from the Tracer and plug it into a USB port on the laptop. Navigate to the 'Data' folder and remove or delete all files inside the folder, but leave the 'Data' folder in place. Return the USB to the Tracer's USB-A port.
Setting Date & Time
Note: If the device is powered off for a significant period of time, it is possible for the internal battery to discharge. The only affect of this will be that the date and time are reset. If the device has not been used for an expedition, check that the date and time are correct before proceeding to measurements. This can only be done in the Supervisor log in.
To set the time, select 
on the main display screen. Then select 
and then select Date/Time from the available list. A stylus or fine pointed tool (non-metal, such as a wooden applicator stick) is helpful to access the small buttons involved in setting the date and time.
In the screen that displays (Fig. XX20), change the date by selecting on year, month and the numerical day. The time can be changed by using the selecting the hour, minute, second and AM/PM and using the small arrows to the right of the box to adjust the number. Please set the device to UTC time (NOT the same as ship operation time). If unsure what UTC time is, check the time on the nearest lab computer.
Once the correct date and time is shown (as close as possible), select ‘Apply’ and then ‘OK’ to exit the screen.
Figure XX. The date and time setup screen.
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the box to adjust the number. Please set the device to UTC time (NOT the same as ship operation time). If unsure what UTC time is, check the time on the nearest lab computer.
Once the correct date and time is shown (as close as possible), select ‘Apply’ and then ‘OK’ to exit the screen.
Figure 20. The date and time setup screen.
Disconnecting and Closing Programs
When finished with a measuring session, navigate back to the main screen (Fig. 9) and select 
. If connected to the laptop and use Bruker RemoteCtrl, select 'File' in the toolbar (Fig. 6) of this program and then 'Disconnect'.
If Bruker Instrument Tools was in use, select 'Device' in the toolbar (Fig. 12) of this program and then 'Disconnect'.
The Tracer can now be powered off by pressing and holding the power button (Fig 4, Left, Arrow) for a few seconds until the screen goes dark.
Appendix
Application Calibration Information
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