Introduction

The Bruker Tracer 5 is a fully portable analyzer based on energy dispersive X-ray fluorescence (EDXRF) technology. When X-ray radiation from the handheld XRF instruments' X-ray tube (source) excites the atoms in a sample, the atoms release low-energy fluorescent X-rays detected by device's detector. The energy level of each fluorescent X-ray is characteristic of the element excited. As a result, one can tell what elements are present based on the emitted energy patterns of the X-rays. The Bruker Tracer 5 portable XRF (pXRF) allows for elemental measurements on section halves, discrete samples and prepared powder mounts. It is standard for the onboard technician to train one or more scientists in pXRF operation and sample prep. The scientists are then responsible for the work flow during the expedition.

Before you begin: The instrument generates X-rays and should only be operated by users trained in radiation safety. Do not expose any part of your body to X-rays!

Theory of Operation

X-ray fluorescence is the production of X-rays in the electron orbits. The handheld XRF functions by bombarding the atoms of the target sample with X-rays. Some of the photons collide with K (and L) shell electrons of the sample, dislodging them from their orbits. This leaves a vacant space in the K (L) shell, which is immediately filled by an electron from the L, M, or N (M or N) shell. This is accompanied by a decrease in the atom's energy, and an X-ray photon is emitted with energy equal to this decrease. Since the energy change is uniquely defined for atoms of a given element, it is possible to predict definite frequencies for the emitted X-rays. This means that when electrons are dislodged from atoms, the emitted X-rays are always identical. These X-rays are analyzed with an X-ray detector and the quantity of K shell and/or L shell X-rays detected will be proportional to the number of atoms of the particular element or elements present in the sample.

Instrument and Accessories

Instrument

Bruker Tracer 5 portable XRF (pXRF) with 5 application calibrations (and associated reference check samples):
- GeoExploration (CS-M2, Geo/Soil sample)
- Limestone (Limestone square)
- Mudrock (Air) (Mudrock square)
- Mudrock (He) (Mudrock square)
- Precious Metals 2 (Silver disk)
Color touch screen
AC power adaptor
3 Lithium ion batteries and battery charger
3mm and 8mm collimators
Filters for Cu, 200µm/Ti, 25µm/Al, 300µm (black) and Al, 76µm (orange)
Prolene exam windows
Holding stand (IODP 3D Printed)

Accessories

Desktop stand
Benchtop stand
Small stage with leaded cup shield
Shielded holder for section half measurements (IODP 3D Printed)
Section half holders with ruler bracket
Background plate
Small scissor platform
Remote trigger cable
Thermometer/Clock/Humidity Monitor

Computer & Software

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.

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.

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.

!!! 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!

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.

In the screen that displays (Fig. XX), 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.

Appendix

Application Calibration Information

GeoExploration/GeoMining

Limestone

Precious Metals 2

Mudrock 2 Air

Mudrock 2 He

LIMS Component Table

PLACEHOLDER until the new PXRF components and data structure is defined
ANALYSIS	TABLE	NAME	ABOUT TEXT
PXRF	SAMPLE	Exp	Exp: expedition number
PXRF	SAMPLE	Site	Site: site number
PXRF	SAMPLE	Hole	Hole: hole number
PXRF	SAMPLE	Core	Core: core number
PXRF	SAMPLE	Type	Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X).
PXRF	SAMPLE	Sect	Sect: section number
PXRF	SAMPLE	A/W	A/W: archive (A) or working (W) section half.
PXRF	SAMPLE	text_id	Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples.
PXRF	SAMPLE	sample_number	Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table.
PXRF	SAMPLE	label_id	Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples.
PXRF	SAMPLE	sample_name	Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter.
PXRF	SAMPLE	x_sample_state	Sample state: Single-character identifier always set to "W" for samples; standards can vary.
PXRF	SAMPLE	x_project	Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises
PXRF	SAMPLE	x_capt_loc	Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2
PXRF	SAMPLE	location	Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2
PXRF	SAMPLE	x_sampling_tool	Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula)
PXRF	SAMPLE	changed_by	Changed by: username of account used to make a change to a sample record
PXRF	SAMPLE	changed_on	Changed on: date/time stamp for change made to a sample record
PXRF	SAMPLE	sample_type	Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ)
PXRF	SAMPLE	x_offset	Offset (m): top offset of sample from top of parent sample, expressed in meters.
PXRF	SAMPLE	x_offset_cm	Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm)
PXRF	SAMPLE	x_bottom_offset_cm	Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm)
PXRF	SAMPLE	x_diameter	Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master
PXRF	SAMPLE	x_orig_len	Original length (m): field for the original length of a sample; not always (or reliably) populated
PXRF	SAMPLE	x_length	Length (m): field for the length of a sample [as entered upon creation]
PXRF	SAMPLE	x_length_cm	Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm).
PXRF	SAMPLE	status	Status: single-character code for the current status of a sample (e.g., active, canceled)
PXRF	SAMPLE	old_status	Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample
PXRF	SAMPLE	original_sample	Original sample: field tying a sample below the CORE level to its parent HOLE sample
PXRF	SAMPLE	parent_sample	Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR)
PXRF	SAMPLE	standard	Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T)
PXRF	SAMPLE	login_by	Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created])
PXRF	SAMPLE	login_date	Login date: creation date of the sample
PXRF	SAMPLE	legacy	Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition
PXRF	TEST	test changed_on	TEST changed on: date/time stamp for a change to a test record.
PXRF	TEST	test status	TEST status: single-character code for the current status of a test (e.g., active, in process, canceled)
PXRF	TEST	test old_status	TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test
PXRF	TEST	test test_number	TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table.
PXRF	TEST	test date_received	TEST date received: date/time stamp for the creation of the test record.
PXRF	TEST	test instrument	TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input)
PXRF	TEST	test analysis	TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table)
PXRF	TEST	test x_project	TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises
PXRF	TEST	test sample_number	TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table
PXRF	TEST	Top depth CSF-A (m)	Top depth CSF-A (m): position of observation expressed relative to the top of the hole.
PXRF	TEST	Bottom depth CSF-A (m)	Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole.
PXRF	TEST	Top depth CSF-B (m)	Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user.
PXRF	TEST	Bottom depth CSF-B (m)	Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user.
PXRF	RESULT	datetime	RESULT datetime: date/time stamp for each run
PXRF	RESULT	mode	RESULT mode: the calibration selected for the run (e.g., Geochem, Mudrock)
PXRF	RESULT	run_number	RESULT run number: serial number of the run (incremented by the instrument for each sample)
PXRF	SAMPLE	sample_name	SAMPLE sample name: repeated display of the sample label ID from the SAMPLE table
PXRF	RESULT	reading	RESULT reading number: human-input run number for each sample
PXRF	RESULT	run_spm_asman_id	RESULT spectrum file ASMAN_ID: serial number of the ASMAN link for the spectral raw data (.SPM) file
PXRF	RESULT	run_spm_filename	RESULT spectrum filename: file name for the spectral raw data (.SPM) file
PXRF	RESULT	run_main_asman_id	RESULT main report ASMAN_ID: serial number of the ASMAN link for the reduced data table (.CSV) file
PXRF	RESULT	run_main_filename	RESULT main report filename: file name for the reduced data table (.CSV) file
PXRF	RESULT	offset (cm)	RESULT offset (cm): position of the observation made, measured relative to the top of a section half.
PXRF	RESULT	result comments	RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments"

Bruker Tracer 5 pXRF (In Progress)