...
- Laptop (IL-53409-XRF)
- Bruker RemoteCTRL (mirrors device screen)
- Bruker Instrument Tools (data management)
- Artax Spectra (for data processing)
- Barcode scanner to read sample labels
- All-in-one Filehub
Safety & General Precautions
The pXRF should be set up in a location that is out of the way with minimal people working nearby, but that is also easily accessible with sufficient space to scan section halves. This should be done without disrupting other workstations or without danger of dropping or mishandling section halves or core material. Typical locations have been the Downhole Lab bench, Paleo Lab bench or Correlators' station, if they are not sailing. Consult with the scientists, co-chiefs, and Lab Officer/Assistant Lab Officers for a preferred location for each expedition. Once set up and it has been established which scientists will be trained to use the device (usually two scientists per shift), a dosimeter ring will be issued to each person that will be operating the device and the training technician. Each dosimeter ring has a unique ID and is assigned to a specific person. These dosimeter rings are checked out from the Laboratory Officer.
Use the Bruker Tracer 5 pXRF Safety Presentation PowerPoint found on the desktop of pXRF laptop and the pXRF Safety Information guide on the pXRF Laboratory Manuals page to inform the operating scientists of all safety measures and procedures for the device. Also provide a demonstration of the operation of the device. Make sure to provide the pXRF Safety Information guide and the Bruker Tracer 5 pXRF Quick Start guide for their reference
Sample Preparation
Preparing section halves
Preparing powdered samples
Sample Measurement Set Up
Shielded Holder for section halves
Desktop Stand
Benchtop Chamber
Instrument Set Up
Begin by installing a fully charged battery or powering the device using an AC power adaptor. Note: The batteries cannot be 'hot swapped'. If a battery is running low, either shut off the Tracer, switch batteries and power it back on again, or plug the AC power in, change the battery, and then unplug the device again. No loss of data will occur when the device is powered off.
The Tracer 5 can be operated alone or connected to a laptop. Using Bruker RemoteCTRL 
, the device screen is mirrored on the laptop. They type of sample you are measuring or your chosen measurement set up.
Computer connection
Login to the computer using the login information on top of the computer keyboard.
First, turn on the instrument. To do this press the button on top of the device screen and hold it for a few seconds (Figure 1).
Figure 1. Bruker pXRF Handheld instrument
Click on Bruker RemoteCtrl in the computer screen (Figure 2). You will use this program to control the device from the computer while measuring your samples.
Figure 2. Bruker Remote Ctrl program
Go to File 
Connect. A window will appear that will show the device serial number, 900G7838. Select it and click Ok (Figure 3).
Figure 3. Connecting the device to the computer.
A login window will appear on the screen, login using the info on top of the computer keyboard (Figure 4).
Figure 4. Login screen in Bruker Remote Control
A pop up message will appear after logging in that tells you the gun's configuration just click OK (Figure 5).
Figure 5. Configuration window when initializing the device.
When the device is connected, your screen should look like Figure 6. 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 active.
Figure 6. pXRF initial screen. Left: X-ray is not active. Right: X-ray is active
Application and Settings
The current application can be changed by selecting 
, choosing a different application type and selecting ‘OK’. This device has 5 applications installed (See Appendix for details). The best application for our purposes is GeoExploration. Each application has different scanning parameters which preferentially pick up some elements better than others. The device will keep the chosen application until manually changed.
Some application settings, such as beam scan duration, can be adjusted by selecting 
on the main display screen. Three settings can be adjusted (Fig. 1):
- 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 1. Settings display screen.
Select ‘Ok’ when finished adjusting or 'Cancel' to return to the previous screen.
Making a Measurement
Edit Sample Information
On the main display, click the ‘Edit Info’ button in the middle of the bottom row of buttons. This screen (Figure 4) 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 cup
- 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, 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 5. The Edit Info display screen.
Select 'OK' in the lower left corner of the screen. The display will return to the main display screen.
Once a measurement is complete, returning to the 'Edit Info' screen will advance the run number in preparation for the next measurement.
Execute a Scan
There are 2 ways to initiate a scan:
If the device is connected to the laptop 
select ‘Trigger Pull (F6)’ along the top of the RemoteCtrl program window or press F6. The measurement will begin and continue until finished. Note: If the device is moved away from the sample, the measurement will stop!
If you are not connected the laptop press the device to the sample, the proximity sensor will detect a sample and the device will be armed for measurement. Press and release the trigger. The measurement will begin and continue until finished. Note: If the device is moved away from the sample, the measurement will stop!
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.
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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Laboratory Supplies
- pXRF plastic sample cups (32mm double open ended, ring and cap)
- SPEX Ultralene thin film for XRF or polypropylene film circles (0.16mil, 4µ)
- Whatman filter circles (24mm, grade 540)
- Foam plugs (24mm)
- Spatula or scooping tool
- Powdering equipment (depending on sample hardness)
- Agate mortar and pestle
- Mixer mill with alumina ceramic grinding cannisters
- SPEX Shatterbox with tungsten carbide grinding vessels
- X-press, hydraulic
Safety & General Precautions
The pXRF should be set up in a location that is out of the way with minimal people working nearby, but that is also easily accessible with sufficient space to scan section halves. This should be done without disrupting other workstations or without danger of dropping or mishandling section halves or core material. Typical locations have been the Downhole Lab bench, Paleo Lab bench or Correlators' station, if they are not sailing. Consult with the scientists, co-chiefs, and Lab Officer/Assistant Lab Officers for a preferred location for each expedition. Once set up and it has been established which scientists will be trained to use the device (usually two scientists per shift), a dosimeter ring will be issued to each person that will be operating the device and the training technician. Each dosimeter ring has a unique ID and is assigned to a specific person. These dosimeter rings are checked out from the Laboratory Officer.
Use the Bruker Tracer 5 pXRF Safety Presentation PowerPoint found on the desktop of pXRF laptop and the pXRF Safety Information guide on the pXRF Laboratory Manuals page to inform the operating scientists of all safety measures and procedures for the device. Also provide a demonstration of the operation of the device. Make sure to provide the pXRF Safety Information guide and the Bruker Tracer 5 pXRF Quick Start guide for their reference
Sample Measurement Set Up
Shielded Holder for section halves - the Tracer must be picked up and moved, do not slide the nose of the device along the core surface!
Desktop Stand
Benchtop Chamber
Sample Preparation
Preparing section halves
If measurements are taken on a section half, of sediment or hard rock, some steps must be taken to protect the device measurement window from puncture or sediment contamination.
For sediment cores, the surface of the core must be covered with a thin plastic film (Fig Next, 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.
Figure Next. Ultralene polypropylene plastic covering the sediment surface.
For hard rock cores, place a layer of Ultralene over the nose of the device. This can be taped in place on each side of the device nose and adding an extra layer over the measurement window.
Preparing powdered samples
Instrument Set Up
Begin by installing a fully charged battery or powering the device using an AC power adaptor. Note: The batteries cannot be 'hot swapped'. If a battery is running low, either shut off the Tracer, switch batteries and power it back on again, or plug the AC power in, change the battery, and then unplug the device again. No loss of data will occur when the device is powered off.
The Tracer 5 can be operated alone or connected to a laptop. Using Bruker RemoteCTRL , the device screen is mirrored on the laptop. This will be necessary if using the benchtop chamber or the desktop stand.
If using the device alone, skip ahead to 'Login'.
Computer connection
Login to the computer using the login information on top of the computer keyboard.
Username: daq
Password: daq
Power on the instrument by pressing and holding the button above the device screen for a second or so (Figure 1); 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 1. 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 2). This program simply mirrors the device screen. You will use it to control the device from the computer while measuring your samples.
Figure 2. 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 3). It may take up to 10 seconds or so to connect, then the current device screen will be displayed.
Figure 3. Connecting the device to the computer.
Login
After the device has initialized, a login window will appear (Figure 4). The User login is 12345.
Figure 4. 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 5).
Figure 5. Configuration window when initializing the device.
The main device screen 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 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 removed. Remember the trigger is active! Be aware of where the device is pointed if the proximity sensor is disabled!
Figure 6. The Tracer's main screen display. Left: X-ray is not armed. Right: X-ray is armed and ready to measure.
Application and Settings
The current application can be changed by selecting , choosing a different application type and selecting ‘OK’. This device has 5 applications installed (See Appendix for details). The best application for our purposes is GeoExploration. Each application has different scanning parameters which preferentially pick up some elements better than others. The device will keep the chosen application until manually changed.
Some application settings, such as beam scan duration, can be adjusted by selecting on the main display screen. Three settings can be adjusted (Fig. 1):
- 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 1. Settings display screen.
Select ‘Ok’ when finished adjusting or 'Cancel' to return to the previous screen.
Making a Measurement
Edit Sample Information
On the main display, click the ‘Edit Info’ button in the middle of the bottom row of buttons. This screen (Figure 4) 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 cup
- 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, 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 5. The Edit Info display screen.
Select 'OK' in the lower left corner of the screen. The display will return to the main display screen.
Once a measurement is complete, returning to the 'Edit Info' screen will advance the run number in preparation for the next measurement.
Fill out the Log Sheet
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 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.
Execute a Scan
There are 2 ways to initiate a scan:
If the device is connected to the laptop select ‘Trigger Pull (F6)’ along the top of the RemoteCtrl program window or press F6. The measurement will begin and continue until finished. Note: If the device is moved away from the sample, the measurement will stop!
If you are not connected the laptop press the device to the sample, the proximity sensor will detect a sample and the device will be armed for measurement. Press and release the trigger. The measurement will begin and continue until finished. Note: If the device is moved away from the sample, the measurement will stop!
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.
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.
Open the Bruker Instrument Tools 
found on the desktop. Go to Device,then Connect and select 900G7838. Click Connect(Fig. 6 and 7).
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 LOL. Downloading data with Bruker Instrument Tools. The box indicates the download button. The arrow indicates the location to save the data to.
Note: If a set of data is downloaded, then more measurements are created, and then another download is performed to the same file location before the internal memory is cleared, the new .pdz files will be added and a new version of the .tsv and Results.csv will replace the previous version. No data will be overwritten or lost!
Opening the .tsv file in Excel
The .csv file is not set up well for further data processing, however, the .tsv file can be opened in Excel in a more user-friendly set up.
Open a new workbook and go to the Data tab and select 
.
You will be prompted to navigate to the folder containing the GeoExploration.tsv file.
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. 8).
Figure 8. 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. 9)
Figure 9. 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. 10). The columns with the sample information will be the last columns to the right.
Figure 10. 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 
.
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.
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 LOL. Downloading data with Bruker Instrument Tools. The box indicates the download button. The arrow indicates the location to save the data to.
Opening the .tsv file in Excel
The .csv file is not set up well for further data processing, however, the .tsv file can be opened in Excel in a more user-friendly set up.
Open a new workbook and go to the Data tab and select .
You will be prompted to navigate to the folder containing the GeoExploration.tsv file.
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. 8).
Figure 8. 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. 9)
Figure 9. Data Preview in Excel of the .tsv file. The red box indicates the correct 'Tab' should be selected as the delimiter.
...
Figure 10. 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.
!!! Clearing the internal memory !!!
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. Additionally, it is important to keep the number of files in the Data folder of the USB low as well. The X-ray technician will take care of this, but keep this in mind if you are performing a lot of measurements!
With the device connected to the laptop, open Bruker Instrument Tools and connect to the Tracer.
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.
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.
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