- 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
3. 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
4. Go to File 
Connect. A window will appear that will show the device number Ex. 900G7838. Select it and click Ok (Figure 3).
Figure 3. Connecting the device to the computer.
5. 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
6. 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.
7. When the device is connected, your screen should look like Figure 6. The device will say Not Armed when the x-ray is not active 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
Exporting Data
- Click on
in the bottom left of the main screen. After you click on Utilities the following window will appear on the screen (Figure 7).
Figure 7. Utilities Window.
2. Click on Backup Data.
Then make sure Copy is selected.
IMPORTANT: Never select Move as that will move the data from the internal memory into the computer, therefore deleting it from the device.
3. Save to Archive instead of USB by changing the following (Figure 8).
4. Click the blue down arrow and change the selected file from \USB to \ARCHIVE
Your Data File Destination Location should look like Figure 8.
Data File Destination Location: \ARCHIVE\Data\Backup-dd-mm-yyyy
Figure 8. Backup Data.
5. After you have selected the file destination folder click on 
6. Close Bruker RemoteCtrl.
Bruker Instrument Tools
After you backup the data go to Bruker Instrument Tools icon in the computer's initial window (Figure 9).
Figure 9. Bruker Instrument Tools program
Figure 10. Connect the device to Bruker Instrument Tools.
- Go to Device Connect Select 900G7838 and click Connect (Figure 10 & Figure 11).
Figure 11. Connect window.
2. After you are connected in Bruker instrument tools on the left side of the screen you will see a folder that says ARCHIVE
3. Open the ARCHIVE folder and you will see a screen like figure 12.
Figure 12. Archive folder
4. Go to Data Open the most recent backup (Figure 13).
Figure 13. Data folder
5. Select the file called GeoExploration.tsv (Figure 14)
Figure 14. GeoExploration file inside the backup folder.
6. Copy the GeoExploration.tsv file by right-clicking the file name and selecting copy from the dropdown menu.
7. Without exiting the program find the folder you want to place the data in the bottom window (Figure 15).
\\CLEAVELAND\VOL4\ scratch BCV
8. After you find the folder right-click the selected folder and select Paste from the dropdown menu.
Figure 15. Copy GeoExploration file and paste in to a folder in Windows(C:/)
Opening the file in Excel
- Open Excel.
- Open a new workbook and go to the Data tab and select
(Figure 16).
Figure 16. Excel Data window → Select From Text in the left.
You will be prompted to your computer saved folders and you can select the folder where you saved the GeoExploration.tsv file.
3. Once you find the folder select All Files in the bottom right (Figure 17).
4. Then select the GeoExploration.tsv file and click Import. (Figure 17).
Figure 17. Finding the GeoExploration file
5. A window will open showing you a preview of the file and you have to click Load. (Figure 18)
Figure 18. Data Preview
6. Click load and the data will be exported to excel and should look like Figure 19.
Figure 19. Exported file from pXRF gun.
7. Go to Uservol K_Inorganic_Geochemistry pXRF 393 Raw Data (Figure 20).
8. Open the most recent data and check the latest sample taken under File # EX. last file # was 209.
9. Go back to your new exported data file and delete all the samples before that last File # EX. total file number is from 1 to 309. Then delete 1 to 209. Only save sample 210 to 309.
Figure 20. Save the data to Uservol under the following folders.
10. Save the data in the format mm-dd-yyyy (month-day-year)
...
| Table of Contents |
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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
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 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. The beam coverage is about 8 mm2 and the ideal thickness of a sample should be ~1 cm or more.
For sediment cores, the surface of the core must be covered with a thin plastic film (Fig 1, 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 1. Ultralene® polypropylene plastic covering the sediment surface.
For hard rock cores, following the procedure at the onshore XRF laboratory in College Station (Texas), no film is put on hard rock sections. The surface is cleaned with DI and Kimwipe. When dried, the core surface is brushed to remove any remaining dust/contaminating particles. The pXRF device is then placed on top of the hard rock core section for measurement.
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 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 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. 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 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 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.
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
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.
If the Tracer has not been used in a while, check that the date and time are correct by going to 
, then 
, and select Date/Time.
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 (Fig. 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 4. 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 (Fig. 5). This program simply mirrors the device screen. You will use it to control the device from the computer while measuring your samples.
Figure 5. 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 (Fig. 6). It may take up to 10 seconds or so to connect, then the current device screen will be displayed.
Figure 6. Connecting the device to the computer.
Login
After the device has initialized, a login window will appear (Fig. 7). The User login is 12345.
Figure 7. 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 (Fig. 8).
Figure 8. 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 be armed the 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 9. 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. 10):
- 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 10. Settings display screen. User will only see the top box. Supervisor will see the screen as is.
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 (Fig. 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 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, 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.
Note: If any of the Field Names are changed using the 'Configure' button, this will impact the upload of the data! If changes are made, notify a developer of these changes so they can make the same changes in the upload code for 'Handheld X-Ray Fluorescence Analysis'!
Figure 11. 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 (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.
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.
Quality Assurance/Quality Control
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 'Results.csv' file. The element results are all reported in % Weight in both the '.tsv' and '.csv'.
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 'Results.csv' 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 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 15. Downloading data with Bruker Instrument Tools. Box indicates the download button. 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. 16).
Figure 16. 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. 17)
Figure 17. 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. 18). The columns with the sample information will be the last columns to the right.
Figure 18. 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
Open MegaUploadatron2 (MUT2) on the laptop desktop. MUT2 will look for certain files or file types in C:\DATA\IN, make sure all data is placed in this folder. For the pXRF results, MUT2 will look for a .tsv file and use the date and time of each sample to determine if new samples need uploading. To upload a sample, MUT2 will also require an associated .pdz file (that matches the File #). The 'Results.csv' will be uploaded with each sample if present as well. MUT2 will indicate with a green check if all associated files are as it expects and that the data is ready for upload based on this criteria (Fig 19). If the 'GeoExploration.tsv' file has a purple question mark for the status, it may be because the files it is looking for are not present (the associated .pdz files) within the DATA\IN folder. The 'Misc' column indicates there are new measurements that have not been uploaded. Check the box for the file to be uploaded. Multiple .tsv files can be uploaded at the same time as long as they do not include identical sample measurements and/or identical .pdz file names. Select 'Upload' in the bottom right corner.
Figure 19. MUT2 file list indicating the status of analysis files and if any new items need to be uploaded.
Once 'Upload' is selected, a Pre-upload Form will appear (Fig. 20). Each line is an individual sample measurement. Individual lines can be checked or unchecked, depending on whether this data should be uploaded (Fig. 20, Left). All sample data should be uploaded. To the far right of the pre-upload form is the sample information entered before the measurement (Fig 20, Right)
Figure 20. The pre-upload form used to correct any incorrect information in the editable information before upload. Left, red box indicates where individual lines can be checked or unchecked to indicate if they should be uploaded or not. Right, red box indicates the editable columns.
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.
On the laptop, MUT2 will already be configured for use. However, if something is not working, there are a few things to check. If files are not listed, check the upload directory. Under 'Options' in the program menu bar, select 'Set Upload Directories...' (Fig 21) and the DATA\IN folder should be listed (Fig 22). In this window, the bottom portion also allows you to nominate files to not display in MUT2, even when they are required for upload. Because each measurement creates an individual .pdz file, this becomes a lot of files for MUT2 to keep checking every 5 seconds and causes problems.
Figure 21. The Options menu.
Figure 22. The list of directories to direct MUT2 to upload from. The bottom portion allows the nomination of files to not display in file list.
NOTE: (Figure 22) Applying the items in bottom "Items for MUT to ignore" pane only changes the display. The additional files will still be uploaded, but only the TSV will show in the processing window. The configuration declutters the MUT upload list.
When MUT presents a "purple question mark", it indicates a file that MUT doesn't how to handle. By adding *.pdz and Results.csv to the MUT ignore list, MUT will no longer present them, nor attempt the processing it normally does for files that it does recognize.
Under 'Set active analyses...', be sure that the 'Handheld X-Ray Fluorescence Analysis' is set as the 'Active Analyses' (Fig. 23).
Figure 23. Setting the active analyses for MUT2 on the pXRF laptop.
To examine the settings of the analysis, click once on 'Handheld X-Ray Fluorescence Analysis' and then select the settings icon 
that appears. A window will appear below this icon detailing the parameters the analysis is looking for (Fig. 24). If any changes need to be made to file types or editable fields, this can be adjusted here. The analysis parameter 'FirstElementName' should change when the 'Application' for which an upload is being conducted is changed. The 'MgO' shown here supports the GeoExploration application (and it eponymous TSV file).
Figure 24. Settings parameters of the 'Handheld X-Ray Fluorescence Analysis' as they should be set.
Regarding the 'AddFiles' setting. This field accepts full file names. It does not accept wildcards or a bare undotted extension--for example supply "csv" will have no effect unless the file is actually named that.
Options for 'FirstElementName'.
- The 'MgO' search string is associated with the GeoExploration application. This is the most often used configuration of the Bruker device in the IODP environment.
- At this time MUT supports only one 'Application' at a time. Switching applications requires changing the search string to accommodate processing for a different application.
- Note that vendor application defaults cause the TSV file to carry the same name as the 'Application'.
- The search string is simply an aid for the software to find the first column of data to be prepared for transfer to LIMS. The software assumes all subsequent columns carry content for LIMS. While this has been tested for the output of the GeoExploration application, it has not been vetted for all the applications that the Bruker device supports.
| First Element Name (search string) | Application |
|---|---|
| MgO | GeoExploration Limestone |
| Al | Precious Metals 2 |
| Na | Mudrock |
If the application of interest is not listed here, conduct a test so that a TSV file is generated for the application. Open that file with a text editor. Look for the element or simple compound that identifies the first column of data. That will become the search string that MUT requires to conduct its processing for that 'Application'.
pXRF Log sheet Uploading
According to new policy the procedures for documenting log sheets for pXRF have changed and the changes are as follows:
- Log sheets for the pXRF will be scanned and put into data1 after every expedition
- The physical copy of the log sheets does not need to be sent back to College Station anymore it can be disposed off after they are scanned into data1
!!! 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!
There are 2 ways to clear data files from the device. The first way to clear the internal memory of the device is to select 
from the main display screen, then 
. Select the 'Delete' option along the top (Fig. 25, Green Box). To keep the run numbers consecutive through the expedition, deselect the 'Reset Assay filename counter' option (Fig. 25, 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 25. 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 second way to clear data files from the device is by using Bruker Instrument Tools and logging in as the Supervisor. In the program menu bar, select 'Tools' and 'Login' (Fig. 26). A smaller log in window will appear. The password is root123 and select 'OK' (Fig. 27).
Figure 26. Bruker Instrument Tools Login from the Tools menu.
Figure 27. The Login window for supervisor access in Bruker Instrument Tools.
In the 'Bruker' folder, there is the 'Data' folder (Fig. 14), which can be accessed by double clicking. Once inside the 'Data' folder, highlight all the files, right click with the mouse and select 'Delete' (Fig. 28). With this method, the 'File #' (Run #) is not reset.
Figure 28. Deleting files using Bruker Instrument Tools Supevisor login.
With both methods, to completely remove the files from the device, power the device off and back on again. This will clear the 'Temp' and 'Recycled' folders of any copies of the data.
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. 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. 29), 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 29. 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
GeoExploration/GeoMining
Limestone
Precious Metals 2
Mudrock 2 Air
Mudrock 2 He
Credits: J. Riekenberg and B. Cervera
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" |
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