Earth and Planetary Sciences
Micro X-ray Fluorescence Laboratory

Procedures for Using the Edax Orbis Micro X-ray Fluorescence Spectrometer

Paul Carpenter, Earth and Planetary Sciences, Washington University

Contacts: Paul Carpenter Dr. Brad Jolliff

These procedures are your initial and annual Orbis training
You are required to use them during your μXRF session as the standard operating procedure

****** Sorry, this instrument has an inoperative detector and is not available as of fall 2020 *****

Contents

General Information

1. General Information Section
1. Micro X-ray Fluorescence Overview
2. Micro X-ray Fluorescence Details
3. Examples of Orbis EDSXRF Spectra
4. How Conventional XRF Differs from Micro X-ray Fluorescence
5. Bragg X-ray Diffraction
2. Orbis μXRF Vision Manuals, Short Course Documents, and XRF/μXRF References
3. XRF Utility Programs

Orbis Use Policy and User Training

1. Policy and User Training Procedures for Orbis μXRF
2. Orbis Instrument Usage Fees
3. Contact Information and Mailing Address
4. How to Reserve Time on the Orbis μXRF
5. User Acknowledgement Information for Published Papers

μXRF Orbis Vision Computer and Software

1. μXRF Lab Computer
2. About the Orbis Vision Software

Sample Preparation and Sample Holders

1. Sample preparation
2. Sample holders for the Orbis

Setting Up the Orbis for a Routine EDSXRF Run

1. Setting Up a Run on the Orbis
2. About the Orbis Hardware and Software
3. Orbis Computer Setup
4. Orbis Sample Exchange
5. Setting the X-ray Tube High Voltage and Current
6. Orbis Vision Program Controls

Orbis Procedures for EDS acquisition, table, pattern, linescan, and mapping procedures

7. Acquiring EDS spectra
8. Acquiring point data using the stage table
9. Acquiring point data using the pattern table
10. Acquiring point data using the stage and pattern table
11. Acquiring linescan data using the stage table
12. Acquiring stage maps
13. Using Primary Beam Filters
14. End of Run -- Procedure to Put Orbis in Standby Mode

Miscellaneous Topics

1. Orbis EDS Energy Calibration

Orbis Emergency Procedures

1. Orbis Emergency Procedures

Orbis Startup and Shutdown (authorized users only)

1. Orbis Reboot Procedure
2. Orbis Instrument Cold Startup
3. Orbis Instrument Full Shutdown

Appendix

1. Sample Preparation
2. Sample holders for the Orbis
3. Laboratory Safety Document (Appendix 4 of Blue Book)

Misc Materials

Setting Up a Run on the Orbis

About the Orbis Hardware and Software

Hardware

There are two main parts to the Orbis μXRF hardware. The first is the large beige box with "Orbis PC" on it (as pictured above) that contains the following hardware components:

1. Rh x-ray tube and high voltage supply with software selected high voltage and microamp tube current.
2. Beam shutter and software selectable primary beam filters.
3. Silicon-drift energy-dispersive spectrometer (SDD-EDS) and pulse processing electronics with software selected time constants.
4. Infrared sample proximity crash-detection system which is intended to keep you from running your sample into the capillary/aperture and SDD-EDS components.
5. Automated XYZ stage for point, linescan, and xy mapping modes.
6. A vacuum pump used to evacuate the μXRF sample chamber.
7. X-ray safety and vacuum interlock system which closes the x-ray shutter if the chamber is opened and also prevents the chamber from being opened when the system is under vacuum.

The second is the HP computer system that controls the Orbis PC and is used for the following:

1. Establish communication with the Orbis μXRF using the Orbis Notifier, which starts after the HP PC is booted and confirms or flags communication with the Orbis PC.
2. Communicates with the Orbis μXRF to control the x-ray tube, beam shutter and filter selection, pulse processing electronics, low and high magnification digital cameras, XYZ automated stage, and vacuum pump.
3. Run the Edax Vision and other software to acquire spectral data and perform automated analysis procedures.

You must be careful when dealing with the hardware components of the Orbis. No loose samples, powders, or liquids are to be put into the instrument without using the correct sample mounting procedures. Any sample that is tall and has a high aspect ratio can potentially cause damage by hitting the collimator assembly, so you must pay attention to the sample positioning requirements.

Software

The Orbis PC must be turned on first and completely booted up before the Orbis PC can be turned on. The Orbis Inspector has to launch and communicate with the Orbis PC hardware or there will be problems.

Orbis Computer Setup

These are the step-by-step procedures for setting up the Orbis. It is in part from Chapter 4 in the Orbis Users Manual.

Confirm that the Orbis μXRF PC is ready

1. Confirm that the green power light is illuminated on the front of the Orbis PC as indicated below.
   The Orbis PC is almost always turned on and is left in that condition when not being used. This is indicated by the green power light on the unit. If the green power light is not turned on, you will need to go through the cold startup procedures.



Confirming that the HP computer is set up for use

2. Confirm that the HP computer is booted up and you are logged in using the xrf account. If not, start the computer, wait for the login screen, and log in to the account as listed in the hard copy of instructions in the lab.
3. Enter your user information in the User Excel sheet:
1. Launch the Orbis Usage Excel spreadsheet by double-clicking on the shortcut on the desktop.
2. In the Excel spreadsheet enter:
   1. Date
   2. First and last name
   3. Email address
   4. Advisors last name
   5. 1st 4 digits of department charge code (NOT campus box number)
   6. User code (eps=Earth Planetary Sci, wu=all other Wash Univ departments, ext=other university, comm=commercial).
4. The Orbis Notifier will automatically launch and establish communications with the Orbis PC; you will see the window come up about 1 minute after you log in.
5. Confirm that the Orbis Notifier has no indicated problems. To view the Orbis Notifier, double click on the notifier icon in the task bar at the lower right of the computer desktop. Here the notifier display indicates all communications with the Orbis PC have been established (on the left side) but the x-ray high voltage is turned off:



6. Turn on the X-ray power. On the Orbis PC, press the On button above "X-ray" to turn on the X-ray power.
   Important: Press the button for only 1 sec. and release; if you press and hold the button the Orbis PC will interpret as an on-then-off sequence and if you get the circuit confused you will have to reboot the Orbis PC.
7. Confirm that the X-ray lights are illuminated both on the front of the Orbis PC and on the pole at the rear quarter of the Orbis PC enclosure. Here is the front panel with the X-ray high voltage turned on:



8. Note that the Open button above "Shutter" on the front panel is an indicator light only. The shutter is controlled from software only.
9. If you open the chamber while the shutter is open, the safety interlock system will close the shutter automatically.

Vision Startup

10. Now launch the Vision software by double clicking on the Orbis Vision icon on the desktop. Vision will work through communications with the Orbis PC during launch and the progress is shown on the blue speedometer display as Vision works through the individual hardware communications sequences (I/O, stage, camera, etc.).
11. If the Orbis PC was turned off, then the stage will need to be recalibrated because the Vision program will not have the XYZ coordinates of the current stage position. The startup routine will tell you what to do, but there are also instructions for recalibrating the stage at any time.
12. If there are communication problems and (for example) the Spellman hangs, you will need to go through a full reboot procedure (see reboot instructions from the table of contents).





Stage Recalibration Procedure (if required)

13. If the stage needs to be recalibrated, follow these directions to do so.
1. Select the menu Setup - Stage to open the Orbis Vision Stage Setup window:



2. If there is a sample in the Orbis PC, you must remove it. It is easiest to remove the plexiglass stage assembly from the Orbis.
3. Do not change any values, all you need to do is click Recalibrate.
4. The stage will now drive to the X, Y, and Z limits to establish the calibration.
5. The clunking noise you hear is the stage driving full range to the limits, and is normal.
6. When finished the stage should be operable.
7. The Vision XYZ display tends to have a stale value for some of the XYZ axis positions (in particular the slider will not be in agreement with the actual position), but when you move the stage using the slider controls it will update properly.
14. Assuming that Vision launches, you should have this window with an indication that the high voltage is turned on (here the high voltage was turned off):.



15. Note that the vacuum control, pulse processing time constant, and shutter/filter control are all accessed from pull down menus along the upper part of the Vision display window.

Sample Exchange

Sample Exchange summary
The Orbis PC needs to have the X-ray shutter closed, be vented to air, and have the stage moved down to minimum Z-axis position for sample exchange. Note that the X-ray tube can be left at high voltage and current settings during a run, you do not need to ramp down the X-ray tube to perform a sample change.

To change samples do the following:

1. Close the x-ray beam shutter using the pull down menu at the upper right of the Vision window: select Closed.
2. Click on the Unload button on the Vision Instrument Console area (upper right Vision window).
3. This will automatically vent the chamber if it was under vacuum and will also lower the stage to Z=0 mm and X = Y = 50 mm.
4. Wait for the chamber to fully vent.
5. Open the chamber by rotating the black handles to the vertical position:



6. While wearing gloves, gently unscrew the plexiglass stage insert and carefully remove from the Orbis PC chamber.
7. Change samples. Here is what the plexiglass holder and typical sample substrates and samples look like:



8. You should try to put samples in the center of the plexiglass insert so that if a montage is required you will be able to acquire the full montage.
9. All samples must be secured using appropriate tape, and no loose powders etc.!.
10. Reinsert the plexiglass stage assembly into the Orbis PC and gently tighten the screw.
11. Close the door to the sample chamber and rotate the handles to horizontal:



12. Use Reload only if the new sample has the same aspect ratio or z-thickness as the previous sample.
    Otherwise, incrementally raise the z-axis to locate the sample using the low magnification camera.
13. If using vacuum mode: Select menu Setup - Orbis Controls, then use the Vacuum pull down menu to switch from Air to Vacuum.
14. The Orbis Controls window should be set to monitor so you can see the vacuum pump down. There is a pop-up alert that will keep you from doing anything until the instrument reaches almost 0.5 Torr:



15. Wait for the vacuum level to reach 0.5 Torr at which point the Vacuum color code changes to light green.
16. You are now ready to continue setting up for a run, or continue working if you have just done a sample change during a run.

Setting the X-ray Tube High Voltage and Current

Important information about the X-ray tube and how it is set on the Orbis PC system

The X-ray tube on the Orbis is controlled manually: the power is turned on and off using the X-ray pushbutton on the Orbis PC, but the actions of ramping the tube up to analytical conditions for work, and ramping down after you are done, are both done manually using the Vision software. Vision is currently set to ramp the tube down to 15 kV and 20 μA after 30 minutes of inactivity, but it does not turn off the tube power, you have to do that yourself and in person.

It is your responsibility to turn the high voltage off when you are done with any work on the Orbis, especially when acquiring long map runs. We do not leave the X-ray tube turned on when the instrument is not being used.

X-ray tube ramp up procedure

Normal conditions for analysis on our Orbis depend on the material being studies. Typical settings are 30 kV and 400 μA to start with, but you will adjust the μA tube current setting to avoid high deadtime on the EDS detector. With the Orbis system you can change kV and μA values essentially simultaneously.

To ramp up the X-ray tube:

1. Confirm that the X-ray high voltage is on: the X-ray light on the Orbis PC is illuminated, and the Vision program window will show X-rays On in the upper right colored text box.
2. Enter the desired high voltage in the kV field of the Vision Instrument Console window. After entering the value, you must press Enter or Return key (this is a text entry) or the value will not be enforced.
3. Enter the desired tube current in the μA field. Again, press Enter or Return.
4. The software will autmatically ramp the tube kV and μA up to the desired values.
   It is a good idea to not do anything else until the tube conditions have finished being set.

X-ray tube ramp down procedure

To ramp down the X-ray tube to 15kV and 20 μA:

1. Enter the high voltage value of 15 kV in the kV field of the Vision Instrument Console window. After entering the value, you must press Enter or Return key (this is a text entry) or the value will not be enforced.
2. Enter the tube current value of 20 μA in the μA field. Again, press Enter or Return.
3. The software will autmatically ramp the tube kV and μA down to the desired values.
   It is a good idea to not do anything else until the tube conditions have finished being set.

Orbis Vision Program Controls

Vision Controls Images

Vision toolbar top row:

1. Stopwatch icon is start/stop EDS acquire.
2. Paint roller icon is clear display, can use to restart EDS acquire by clicking before preset is reached.
3. "A" pulldown menu is A-B memory select, overlay, and switch.

1. Vacuum/Air pulldown menu.
2. Amptime time constant pulldown menu.
3. Shutter-Filter X-ray beam shutter and primary filter selection pulldown menu.

Acquiring EDS Spectra using Vision

Acquiring EDS Spectra using Vision

The following section covers how to collect EDS spectra and perform identification. It assumes you have already turned the Orbis PC on, launched Vision, performed a sample exchange, and ramped the X-ray tube up to operating conditions.

You will first locate the sample and position the z-axis so that the sample is in optical focus. The polycapillary X-ray optic has a narrow depth of focus for X-rays and you will use the high magnification camera to set this focus.

1. The Orbis has two color video cameras:
1. Low Magnification (~10x) oblique angle camera that is used to locate the sample.
2. High Magnification (70x with an additional 1x-3x digital zoom for Orbis PC) that is used to set the z-axis focus of the sample. When the sample is in focus from the High Magnification camera view, the sample distance is set correctly.
2. Start with the Low Magnification camera. Using the X and Y stage controls, locate the sample. Starting with the sample below the focus point, use the Z stage control on the u-Probe control panel to slowly raise the stage until the sample is in approximate focus. Since the Low Magnification camera looks at an angle on the sample, you may need to use the X and Y controls to bring the sample back into view. You will click on the tape portion of the XYZ slider controls for this coarse movement.
3. If you have trouble finding the focus position, try turning on the laser. If the laser spot is south of the red beam circle the sample is below focus, and if it is north of the beam circle the sample is above focus. Alternatively, move to an area with surface features you can use to focus on.
4. Switch to the High Magnification camera. Adjust the Z-axis to bring the sample into focus. You will click on the arrows of the XYZ slider controls for this fine movement.
5. At this point, we are focused in high magnification.
6. If you are doing general qualitative analysis, you can now adjust the X-ray tube to get optimal throughput of EDS counting. If you are going to do quantitative analysis you must use a common setting for all data collected and processed.
1. Open the beam shutter.
2. If necessary, clear the X-ray spectrum using the paint roller icon.
3. Click on the Preset button to set the livetime acquisition count time, 30-100 sec is typical.
4. Select an appropriate time constant for measurement: For qualitative and quantitative analysis use the 3.2 or 6.4 μsec settings (typically 6.4 μsec is used), for mapping setup use the short time constants (0.5-1.6 μsec, typically 0.8 is used).
5. Start an acquisition by clicking on the stopwatch icon.
6. Observe the deadtime value on the bottom bar of the Vision window. The optimum deadtime is in the 30-50% range. If you are using a primary beam filter you will likely have a lower deadtime due to significant absorption within the filter material.
7. Adjust the X-ray tube μA current value to raise or lower the count rate and therefore the deadtime.
8. Try to avoid deadtime values of more than 50% and pay attention to different sample chemistry as you work. Different samples will result in variable pulse processing demands and resulting deadtime values.
7. About live imaging and EDS spectral acquisition:
1. Because the high magnification camera is on the turret, you can only acquire a live image when you are not acquiring an EDS spectrum.
2. If you are in high magnification and you start an EDS acquisition, the image will freeze and stay thay way until you either restart the high mag. video by clicking on the red camera on/off icon, or switch to the low mag. camera.
3. You can click on the frozen image to move the stage if the Get feature icon has been clicked and is beige in color, but the image is static and the green cross hair is your only indication of where you are on the sample.
4. If you stay in the low mag. imaging mode, you can always have a live image while you repeatedly acquire EDS spectra on a sample. This works only if the sample is flat and as you move around you are close to optimum Z-axis focus position.

Peak Identification

8. To identify the peaks in the spectrum, click on ID from the menu to invoke the Peak Identification control panel on the right side of the Vision window, or click the shortcut icon in the upper right side of the window:
   1. From the Peak ID control panel, click on Clear All and then Auto for an automatic peak identification.
   2. If there are more elements that need to be identified, use the Z+ and Z- buttons to scroll up and down the periodic chart.
   3. Click on Add when the elemental marker lines coincide with the center of spectrum peaks. The software can label/identify peaks up to 97 – Berkelium(L). To change X-ray series labels that are added into the list and on the spectrum, type the element and series letter (K, L, or M) in the top text window of the ID control panel and press the enter key.
   4. To add markers for both K and L-family lines (for the Rh K and L families for example), click on the Z+ button to get to element Rh, then click on add (for RhK for example) then enter RhL in the text field and click on Add again. Only one element marker can be active and it signifies that element line is to be used for analysis. Right click on the element in the list to disable that element for analysis, and it will put a "-x" next to the element to indicate that a marker symbol is on the spectrum but that line will not be used for analysis.
   5. Important: there is a maximum of 24 elements that can be identified by markers at any one time; elements with -x are not counted in this total number.

   Standardless FP Quantitative Analysis

   The total number of elements that can be analyzed by standardless (aka No-Standards) Fundamental Parameters (FP) is 24, which is the maximum number of elements that can be identified in a spectrum. That ID list is used as the input into the FP analysis. The FP quantitative analysis is very easy to run and gives an instant answer. Remember that FP quant works well for some matrices but not for others, so it is always important to analyze a standard for comparison. In general FP works best for metals and energetic X-rays, and apparently not that well for low energy elements such as Na and Mg K-α.

9. To perform quantitative analysis on the spectrum:
1. Switch to the Vision Quantify window by clicking on the quantitative analysis icon on the Vision toolbar (the one that has FeCr).





2. Make sure that intensities are set to Net so that background correction will be performed on the spectrum.
3. Click on the Options button to open the Vision Quantitative Options window.



4. If your sample is a non-oxygen sample (i.e., metals or other materials), set the Sample radio button to Element, or if it contains oxygen which needs to be calculated by stoichiometry, set the radio button to Oxide.
5. From the Quant Mode pull down menu select FP no standards if it is not selected. Click on Ok to exit this window.
6. Click on Concentrations on the Quantify window (or the Conc Vision menu).
   This will perform a background fit, peak deconvolution, and a No-Standards FP concentration calculation.
7. The results are shown in the Orbis Vision Results table.
8. For oxygen-containing materials, check the oxide formula in the listing, and if it is not correct, you will need to edit the oxide factor.
9. To save the analysis you can highlight the data you want to copy, then click on copy, and finally paste into an Excel spreadsheet to save in your folder.
10. If you click on the Save menu from this window, the data will be pasted to a common Excel file [in the edax32 directory on drive C]

Saving, Copying, and Exporting the EDS Spectrum

10. The Orbis spectral data can be saved in several ways:
1. To save a .spc Edax spectrum file, use the File menu to Save As and name the spectrum and save it to your work folder. This file is not in a text format and can only be opened using Edax software. This is the default format and is needed for any further quantitative analysis.
2. To get a screen capture of the spectrum as displayed including element ID markers, use the Windows snipping tool.
3. To export the spectrum data as an EMSA format text file, use the File Save As menus selection, but save the file as type .msa and the data will be saved in the EMSA format. The EMSA-format is a text file that can be opened using DTSA-II for display. The EMSA file format is not straight column format but can be parsed using a script.

Orbis Procedures Stage Table Acquisition

Orbis Multipoint Analysis Using the Stage Table

You should have your sample in the Orbis and all X-ray parameters set, sample preset count time, etc. all set before running a stage table for points analysis.

Setting points using the stage table

1. Click on the Stage button in the u-Probe control panel, this will display the stage location table.
2. Enable the clickable stage format by clicking on the + icon on the lower right. It should be beige in color and that will move the stage to the clicked position on the live camera window.
3. Use either low or high magnification to locate the point you wish to digitize.
4. Click on the Save Point button to save analysis locations to this table.
5. You can enter a label for each point in the text field. You need to press the Enter key to copy the label to each point in the stage table. It is helpful to copy the text label for pasting when you set a new point because that clears the existing text string from the current point.
6. Click on the Ok button when done setting points.

Running the stage table using Automated Analysis

1. Open the Preset window at the lower corner of the u-Probe Control Panel, and set the acquisition time (per point). The acquisition time can also be set in the Setup window.
2. Click on the Setup button. Choose between Live X-ray, Save spectra, and Concentrations Calc.
3. You can also turn on a display window of the quantification results acquired in the auto collection by selecting the "Automation Setup – Display Quant%" checkbox.
4. Input the desired filename for the first spectrum e.g. "BasicTest1", you may need to use the Filename button to specify this. Click on OK. The spectral files will be incremented as BasicTest1.spc, BasicTest2.spc, ..., and each spectrum label will be “Analysis Pt# / Total # pts” plus the 16 character label entered in the stage table.
5. Additional options can be utilized to minimize tube power when the run is complete, to perform an auto dead time micro-amp adjustment at each point, to auto-focus at each point, or to collect a matrix scan at each location (in which the number and separation of the points in the X and Y are user defined).
6. Click OK to exit the window.
7. Click on Auto, and View Parameters, take note that the estimated runtime in the automation section has a time specified, otherwise it will display N/A for the Est.Time, and the Autorun will not execute.
8. To begin the auto run, click on the Auto menu item, then Start Auto begins the Automated run. If enabled, an audible tone will be generated at the conclusion of the Auto run, to inform you that the analysis has completed.

During the analysis, you can watch the stage being moved to each of the stage locations that you have defined. The time remaining for the analysis will be displayed in the status display area at the top center of the ORBIS VISION application window. At the conclusion of the analysis you can view the summary data generated by clicking on Auto and Summary…, and selecting the newly collected filename [ *.SMY ]. The results table will be read in and displayed. You can use the Copy function to export the data to the Clipboard and then to paste it into Microsoft Excel.

To view the quantitative summary results graphically in ORBIS VISION, click on “Graph” from the results summary dialog.

Orbis Procedures Pattern Table Acquisition

Orbis Multipoint Analysis Using the Pattern Table

The Pattern Table procedure allows you to acquire data in a specified pattern of points centered at specific xyz locations set using the stage table. Using the stage table allows you to save stage analysis coordinates in X, Y and Z. So, you can adjust the Z with the stage table. The pattern table saves coordinates with respect to a single video frame. Therefore, there is no control of the Z position with the pattern table. The general use of the pattern table is when you want to repeat the same pattern of analysis within a given video frame. You can move to different places on a sample and do an analysis based on a specific pattern. Or you can save different stage coordinates using the stage table and execute different patterns at each stage position.

You should have your sample in the Orbis and all X-ray parameters set, sample preset count time, etc. all set before running a stage table for points analysis.

How to set up pattern table acquisition

1. Open the Preset window at the lower corner of the u-Probe Control Panel, and set the acquisition time (per point). The acquisition time can also be set in the Setup window.
2. Click on the Start button to start the spectrum analysis. Identify the peaks in the spectrum by using the Peak ID function. It is very important to identify all the elements that you may expect for the automated analysis.
3. You can define locations via Low or High Magnification mode, but you cannot mix the 2 magnifications in the same table.
4. Move the stage to the location where you want to digitize a position.
5. Click on Pattern-Table from the main menu to display the table.
6. Click on the video image to select the points to analyze and then on the “Save Location” button to save analysis locations to this table.
7. After setting the points, save the pattern table in a *.loc file if you want to use this pattern in the future.
8. Click on the “OK” button when you are finished with the pattern table.

Running the stage/pattern table using Automated Analysis

1. Open the Preset window at the lower corner of the u-Probe Control Panel, and set the acquisition time (per point). The acquisition time can also be set in the Setup window.
2. Click on the Setup button. Choose between Live X-ray, Save spectra, and Concentrations Calc.
3. You can also turn on a display window of the quantification results acquired in the auto collection by selecting the "Automation Setup – Display Quant%" checkbox.
4. Input the desired filename for the first spectrum e.g. "BasicTest1", you may need to use the Filename button to specify this. Click on OK. The spectral files will be incremented as BasicTest1.spc, BasicTest2.spc, ..., and each spectrum label will be “Analysis Pt# / Total # pts” plus the 16 character label entered in the stage table.
5. Additional options can be utilized to minimize tube power when the run is complete, to perform an auto dead time micro-amp adjustment at each point, to auto-focus at each point, or to collect a matrix scan at each location (in which the number and separation of the points in the X and Y are user defined).
6. Click OK to exit the window.
7. Click on Auto, and View Parameters, take note that the estimated runtime in the automation section has a time specified, otherwise it will display N/A for the Est.Time, and the Autorun will not execute.
8. To begin the auto run, click on the Auto menu item, then Start Auto begins the Automated run.
9. The time remaining for analysis will be displayed in the status display area at the top center of the Orbis Vision application window.
10. If enabled, an audible tone will be generated at the conclusion of the Auto run, to inform you that the analysis has completed.

At the conclusion of the analysis you can view the summary data generated by clicking on Auto and Summary…, and selecting the newly collected filename [ *.SMY ]. The results table will be read in and displayed. You can use the Copy function to export the data to the Clipboard and then to paste it into Microsoft Excel. Also, at the end of the analysis the stage should move back to the locations it was at before the analysis started. To view the quantitative results graphically in ORBIS VISION, click on “Graph” from the results summary dialog.

Using Stage Table and Pattern Automated Analysis

Automated Analysis Using Stage and Pattern Tables

The basic concept for performing Stage & Pattern automation, is that all pattern locations are stored in pattern location files *.loc. These pattern files (*.loc) are spatial XY patterns that you can use repeatedly for an analysis template on sample positions. The utility of the pattern files is to avoid having to explicitly digitize the sample positions of a pattern, such as a 2 by 2 array of points. The utility of the pattern approach is therefore to allow replicate sampling centered around digitized XYZ locations in a stage table file.

The pattern files must be saved in the directory where you will ultimately save spectral data.

There are 3 possible ways to save stage coordinates:

• Point: Single XYZ stage locations.
• Line: Equidistant multi-point line segment defined by a start and end position. (The default number of intermediate points is 5, but it can be edited in the stage table).
• Matrix: Equidistant multi-point grid of points defined by the diagonal XYZ locations of the corners of the matrix array. (The default size is 2 x 2 but it can be edited in the stage table).

Here is an example of the steps needed to collect data from 2 different stage locations.

1. Define the elements in the spectrum, EDS preset, and Auto output options for collection, and or processing.
2. Move the stage to the first location you wish to analyze and save this point in the stage table.
3. If a pattern of analysis points is to be collected around this first point:
1. Type the pattern table name into the column marked “Pattern” for this point.
2. The pattern table name is the prefix of the *.loc file. For example, if the pattern filename is Square.loc, type “Square” in the appropriate stage table label column. (Remember, the pattern table files must be saved in the directory where the spectral data will be saved.)
3. If a pattern has not been saved, close the stage table and open the pattern table dialog box. Create the pattern you want to analyze within this video frame as described in the previous section. Save this pattern table into the directory where you plan to save collected spectra. Close the pattern table dialog box and open the stage table dialog. Type the name of the pattern table just created in the appropriate row.)
4. Repeat these steps to set stage and pattern points as needed. Note that it is not necessary to execute a pattern at each and every stage location.
5. From the Auto Setup Dialog box, check off the appropriate actions to take place during the Auto run, set the time of data acquisition and enter the filename of the first file.
6. Start the auto run from AUTORUN button in the lower right corner of the ORBIS VISION window's u-Probe Control Panel or from the main menu item, AUTO ==> START.
7. During this process, you will see the stage moving, spectrum collected and then processed. The time remaining for the analysis will be displayed in the status display area at the top center of the ORBIS VISION application window.
8. As with the pattern Auto run, all results data is saved to a *.SMY file and a *.CSV file.

Orbis Procedures Acquiring Linescans

How to Acquire a Linescan

1. Collect a spectrum and identify all elements.
2. Set the menu Video mode to Line. Click and drag on the image, you should see a line displayed. Note : If the image is live, you must first freeze the video image, otherwise the green line will disappear as soon as you stop drawing. This will be the location where the x-ray data will be acquired from. You can collect Linescan data in either high or low magnification.
3. There are two alternative ways to set the Linescan distance:
1. In u-Probe Control, open the “Stage” icon, located at the bottom of the panel. From the stage table, you can select “Get Location From Stage Location” in the upper left corner, and using the “Line” mode, select the starting point, and then clicking the Set Start Loca button. Then, move to the ending location, and click the same button which reads Set End Location.
2. The second way is to use the montage:
1. In the u-Probe Control panel, click the montage icon.
2. By collecting a montage, and selecting “Set LScan Area” from the dropdown menu in the right side, you can then draw your own line. This works in both low or high magnification.
4. Under the Auto menu, click on Linescan…, and then click on “Read Scan Location.” If the montage or stage table was used to set the linescan, check off the “Use StgTable Pos#1” box. Then set the dwell time to 500 msecs; set the number of points on the line; choose whether a live display is desired, and then select the type of Linescan: ROI , Net or WT%.
• ROI: This is the sum of all the counts within the energy range defined for each element. This is known as “Gross” intensity. This is the simplest choice.
• NET: This fits a spectrum background and peak deconvolution to each spectrum. The peak deconvoluted for each defined element is used to calculate the “Net” intensity.
• WT% : Similar to NET, but then processes the Net intensities with the last quantitative model used. This can be No-Standards or Standards.
5. Click on “Start” , you should see a blue line drawn on the image and a red crosshair moving across the line and the LScan data being drawn at the bottom of this dialog.
6. When the acquisition is complete you can click on the “Display” button, and this will display the collected data in a flexible format. It is possible to superimpose this data on the image, via the VideoOvly menu item.
7. The linescan data is saved to disk automatically at the conclusion of the acquisition, with the filename listed at the top of the Linescan collection window.

How to Read a stored LineScan from a file:
Under the Auto menu, click on Linescan…, and then Open, select the filename “C:\Vision\Usr\Vision.Lsc” . This will read in the example LineScan file. Click on the Display button, and the LineScan data will be displayed on a standalone work area that can moved and resized. Click on Video- Horizontal ( or Vertical ) to transfer the LineScan data to the main video image. Click on Print to choose between the 3 different modes in which you can output the Linescan data to the system printer.

Orbis Procedures Stage Map Acquisition

About Orbis Stage Mapping

Our Orbis is equipped with a 30 μm polycapillary optic as well as a 1 mm and 2 mm collimator optic which are software selectable. You will likely use the 30 μm polycapillary optic for stage mapping. The Orbis PC has a high speed SDD EDS detector and so is capable of a high X-ray count rate. For mapping applications you should use a relatively high tube current μA setting as well as a short time constant in order to provided the highest count rate and throughput. The stage movement is a step procedure with a fairly high time overhead per point, so actual map acquisition times can be quite long compared to the electron micoprobe. The time requirements will drive you to select a map with a coarse step size if you are acquiring over a large sample area.

Important notes

1. The sample for mapping should be loaded into the center of the stage holder. If you use a large montage to acquire the location image, it is likely that the montage routine will run up against a stage limit during the montage acquisition. This may cause the stage to move and disrupt the montage map acqusition. Secondly, if more than one sample is in the Orbis and they have different Z-axis aspect ratios (i.e., sample height), it is possible that the taller sample can trip the infrared crash sensor during the mapping run and this will cause the stage to drive 5 mm lower in Z and the rest of the map will not have usable data. So mapping should be conducted on samples of similar Z height and if possible centered on the stage holder.
2. Each Orbis stage map will produce a spectrum image data cube that is relatively large, on the order of several hundred Mb to several Gb in size. These files are kept on the microxrf computer for a time (and backed up) but it is your responsibility to copy all the data to an appropriate storage device for archival.

How to Acquire Element Stage Maps

You should have your sample in the Orbis and all X-ray parameters set, tube current, sample preset count time, etc. all set before running a stage map.

1. Collect a few spectra from the sample area of interest to identify the range of phases and elements that are present. Identify the elements in each and add them to the total list. Note that the mapping routine will generate .bmp maps for all elements in the identification list based on ROI mapping. You will also have a spectrum image datacube .spd file that has the full EDS spectrum at each stage pixel location, from which you can generate maps after the run. So it is not necessary to have every element identified before the map run, but is convenient to do so since the ROI maps capture much of the element variation in the sample.
2. Now define the map area using the montage method (most of our maps will be on large areas so the montage works best for this). Open the montage window by clicking on the montage icon.
3. The montage size is acquired using either low or high magnification camera and the size of the montage array. For example a 3x3 or 5x5 low mag montage will cover most of the stage holder, and a similar array at high magnification will cover a smaller area at high magnification. The low magnification camera has an inclined view of the sample and will therefore have spatial misorientation compared to the high magnification camera which has normal incidence to the sample.
4. After collecting the montage, you can save it. This is a good time to set up the folder for your maps to be saved to (do this using the Windows Explorer).
5. Now select from drop down menu in the right side of the montage window either “Set XMap Area” or “Set AnyXMap Area.”. You can then draw the desired area directly onto the montage image. The “XMap” option locks the area with a 5:4 aspect ratio, and the “AnyXMap” option allows a customized area to be selected. This has implications for the possible resolution formats for the map image: The XMap mode restricts you to 5:4 image formats but avoids aspect distortion of the sample, while the AnyXMap mode allows complete flexibility in selecting the resolution but will likely have aspect distortion unless the X and Y step size is set equal to the image resolution.
6. Click on Ok after setting the map area.
7. Now click on Auto & Spectrum Mapping… to open the Mapping window.
8. Important: Set an appropriate filename by clicking on the ... icon at the end of the file path. If you don't name the file it will name all files ABCD and you will have to then edit them individually.
9. Select a dwell time (i.e. 200 ms).
10. Select Clock Time or Live Time depending on the following. Clock time ignores variations in count rate and therefore EDS deadtime but gives a predictable run time for the map. Live Time counts for live time and therefore counts the same time regardless of deadtime/count rate variations during the map run. For quantitative mapping one should use the Live Time option, but for general mapping the Clock Time option is fine.
11. Set the pixel resolution for the map (i.e. 64x50) and note using the information button what this pixel resolution translates into in terms of beam coverage on the sample. For example, using a 30 μm polycapillary optic with a 100 μm step size, there will be undersampling of the sample (this is typical with Orbis mapping). For some applications one wants complete coverage or even oversampling of the sample, and this is established using the pixel resolution and information buttons to adjust the sampling parameters.
12. Select how the maps should be displayed (i.e. ROI, Net Intensity, or Wt%); normally we acquire ROI maps.
    Important: Using the Wt% mode will cause the map run time to be dramatically longer (i.e., a week vs. 20 hours) and is pointless unless an accurate calibration has been established for quantitative analysis.
13. Select 16-bit Spectral Data to be saved for further re-processing. If a long count time is used it is possible that the Vision software will require data to be saved in 32 bit format, but this will make the data cube much larger.
14. Set the kV range of the data to be either 20 kV or 30 kV unless you specifically have peaks that will be detected at high energies. This reduction in kV only reduces the number of channels in the EDS spectrum saved in the data cube.
15. The dialog box will tell you how much time the map will take.
    Important You will need to be present to turn off the X-ray tube at the conclusion of the map run, so don't set up a run that ends at a time when you will not be present.
16. To begin the map, click on START.
17. A preliminary scan will be acquired over the entire map area to establish the count rate for map scaling purposes.
18. If the Orbis goes off of the map area during this preliminary scan, then something is wrong and you should halt the map and set it up again.
19. A red cursor shows you roughly where the stage is during the map scan.
20. The maps are displayed (for the elements that were formally identified) as the data is acquired.
21. X-ray bitmap files are automatically created at the conclusion of the collection and the spectrum image datacube is written to the hard drive (it is actually prestored at the beginning and filled with data during the map run).

Displaying Acquired Maps

1. Click on the Open button in the “Standard Map” area on the control panel, and select 1 BMP filename to read in. All the maps names from that data series will be displayed in the filename list box close to the bottom of the view.
2. Select all the maps you wish to display, and click on the 1,4 or 16 button , to display them in that particular map view.
3. If the 16-bit spectral data option was selected in the setup, the maps can be opened with the spectral data through the “Spectrum Map”>”Open” section underneath the “Standard Map” section. Again, simply double-click one of the maps, and all of them will open.
4. By using the Data Mining option, the 16-bit spectral data for spectra can be read and displayed from each point within each map, and can also sum up and display spectra for lines and matrices within the maps (utilized by selecting “Line” or “Matrix” from the Video Pointer Mode). It also allows for the re-building of maps for elements that may have been missed. In the folder created for the map, there will be a TotalArea Spectrum and a MaxChannel Spectrum saved, which allows you to go back and search for missing elements.

Orbis Primary Filter Selection and Use

About Orbis Primary Beam Filters

Our Orbis is equipped with primary beam filters that are very useful for both qualitative and quantitative analysis. These filters are housed in a software controlled turret and the filter is placed between the Rh X-ray tube and the optic (30 μm polycapillary, 1 mm and 2 mm collimator). The available filters on the Orbis are selected using the Shutter-Filter pull down menu. Here is a summary of the filters, the K and L edge absorption energies and line energies for comparison, and possible applications (assuming sufficient concentration of the example elements):

Filter material and thickness	K edge, keV	Kα, keV	LIII edge, keV	Lα, keV	Example applications
Aluminum, 25 μm	1.599	1.487	---	---	Suppression of Rh L-family, diffraction peaks Analysis of S, Cl
Titanium, 25 μm	4.964	4.508	0.454	---	Improved Cr Mn Fe Co (K-lines)
Nickel, 25 μm	8.331	7.472	0.853	0.849	Improved Zn - As (K-lines), Re - Bi (L-lines)
Niobium, 127 μm	18.987	16.584	2.374	2.166	K-edge: improved Rh - Ag (K-lines), L-edge: S - K (K-lines), Th - U (M-lines?)
Rhodium, 100 μm	23.224	20.167	3.002	2.696	K-edge: improved Rh - Sn (K-lines), L-edge: K-Ca(?)
Aluminum, 250 μm	1.599	1.487	---	---	Improved K - Co (K-lines)

[ Orbis documentation indicates Nb filter for Rh - Cd, and Rh filter Ti - Zr, Pb, Bi. ]

The Rh X-ray tube has a tungsten filament which directs energetic electrons under the high voltage potential to impact the Rh cathode of the X-ray tube. The tube emits the characteristic X-ray lines for both the Rh K-family (Rh Kα and Kβ) and Rh L-family (Rh Lα, Lβ1, and other lines) and additionally continuum X-rays produced by deceleration of electrons by Rh atoms in the cathode. The tube spectrum consists of continuum and characteristic X-rays and both of these are used to excite characteristic X-rays from atoms in the sample you are studying. Characteristic X-rays in the sample are fluoresced by a combination of both characteristic and continuum X-rays from the tube. X-ray scattering from the sample is due to interaction of these tube X-rays with the electrons in the outer shells of the sample atoms. Scattering with no energy loss is called coherent scattering and plots at the characteristic energy of that X-ray on the EDS display. For example, the Rh Kα and Kβ coherent scatter peaks are observed on all samples at the peak energy for those characteristic lines. Scattering with a loss of energy is called incoherent or Compton scattering and plots at an X-ray energy below the characteristic lines for Rh. The incoherent scatter peaks have an intensity that is inversely related to the average atomic number Z-bar of the sample, and a FWHM energy resolution that is larger than the characteristic peak.

The sample XRF spectrum contains a significant number of continuum X-rays scattered from the tube source. This continuum is a high background component that reduces the sensitivity for minor and trace element detection. Crystalline grains in a sample also will diffract X-rays which produces peaks at various energies in the EDS spectrum having FWHM peak resolution that depends on the crystalline character of the sample (i.e., the d-spacing and degree of crystallinity affect the energy distribution of diffracted X-rays).

Primary beam filters are used to reduce the continuum X-ray intensity of the tube so that detection of minor and trace elements is improved. The filter can also be used to reduce or eliminate the presence of X-ray diffraction peaks in the spectrum. The following XRF spectra illustrate aspects of primary filter use.

This spectrum and the following were acquired on PMMA (polymethyl methacrylate) which contains only H, C, and O, so it has no peaks observed in an EDSXRF spectrum. The spectrum is essentially the scattered spectrum from the Rh X-ray tube and exhibits (from high energy to low energy) the Rh Kα and Kβ coherent scatter peaks, the incoherent scatter peaks for the same X-ray lines, a large broad peak of continuum X-rays, and the Rh L-family coherent scatter peaks. This spectrum is used to establish the X-ray tube distribution for the fundamental parameters (FP) correction algorithms.

The Aluminum 25 μm filter is a good all-purpose filter for improving detection of elements and reducing the intensity of diffraction peaks, without significant loss of counts across the spectrum. In particular it absorbs the Rh L-family and should be used for the analysis of Chlorine-bearing materials (and other X-rays with energies similar to Cl Kα).

The Titanium 25 μm filter is good for improved measurement of the K-lines of Cr - Co. This spectrum shows the absorption of continuum X-rays above the K-edge of Ti at 4.931 keV.

The Nickel 25 μm filter is good for improved measuremnt of the K-lines of Zn - As, and the L-lines of Re - Bi (assuming these elements are at suffient concentration to be detected by EDSXRF). The discontinuity at the Ni K-edge at 8.331 keV is well illustrated here.

The Niobium 127 μm filter is good for improved measurement of the K-lines of Rh - Ag (using Nb K-edge absorption) and the K-lines of S - K and M-lines of Th - U (using Nb L-edge absorption). In particular, if Rh is to be measured, you want to remove it from the primary tube spectrum and that is accomplshed using a Nb filter (here the Rh K-lines have been completely removed). You can see the Nb K-edge at 18.987 keV and the Nb L-edge at 2.374 keV.

The Rhodium 100 μm filter is good for improved measurement of the K-lines of Rh - Sn (using Rh K-edge and direct Rh excitation from the tube) and the K-lines of K - Ca (using Rh L-edge absorption [to be confirmed]. Note that a higher tube current is required due to heavy absorption at all energies when using the Rh filter. The Rh K-edge is at 23.224 keV and the Rh LIII edge is at 3.002 keV.

The Aluminum 250 μm filter is good for improved measurement of the K-lines of K - Co. Note by comparison to the spectrum acquired with the Al 25 μm filter the increased absorption of the continuum up to about 7 keV, hence the improved measurement of elements like Fe and Co.

For more information see Chapter 3 from the Orbis training document, "Orbis Setup and Hardware", 03 Setup and Hardware.

End of Run -- Procedure to Put Orbis in Standby Mode

When you are finished with work on the Orbis, use the following procedure to put the instrument into standby mode.

1. Use the X-ray tube ramp down procedure to put the tube at 15 kV and 20 uA.
2. Close the beam shutter.
3. If in vacuum mode, vent to air.
4. Lower the stage or use the unload button to move the stage to the exchange coordinates.
5. While wearing gloves, remove the plexiglass sample insert from the stage assembly.
6. Close the sample chamber.
7. Turn off the X-ray high voltage by pressing the button on the Orbis control panel.
8. Lower the LED light level on the Vision Instrument Console window.
9. Enter your usage in the Excel sheet.
10. Copy any important data. If you have acquired large spectrum data cube files, you may need to make your own copies for further processing.

Orbis Vision Software Summary

Edax Software Programs and Capabilities

The Orbis μXRF has a number of capabilities which are summarized in this instruction document but are discussed more completely in the Edax manuals. You should download these manuals and refer to the complete discussion in order to fully understand the capabilities (Edax Orbis Manuals).

1. Edax Notifier. The notifier is launched after you log in to the microxrf computer and monitors communication between the PC and the Orbis hardware. It runs continuously once established and needs no other input from you. You must wait about 1 minute for the Notifier to lauch before trying to start the Vision software. If Vision is started before Notifier completes the communication links, you may ultimately have to completely restart the computer and possibly the Orbis.
2. Edax Vision. The Vision program is used for all data collection on the Orbis, such as EDSXRF spectral acquisition, mapping, point and line based measurements, and data processing. It can also be used to reprocess and inspect EDS spectra previously acquired, and spectrum image data from a mapping run.
3. Combine (Comb32). The Combine program is run on previously collected EDS spectra from known standards in order to take element intensity and composition data, determine least-squares fits to the intensity data, and ultimately produce a calibration file that is used for quantitative EDSXRF analysis.
4. Edax Utility Software. This is a collection of programs used for basic presentation of data. See the Edax Utilities manual for more information.
1. EPIC Table (DKENGR32). Edax periodic table X-ray energy utility, used to show X-ray lines and energies for elements in the periodic table.
2. Spectral Utility. Utility program used to display and process EDS spectra and .bmp images acquired with the Edax software.
3. Screen capture (grab32). Screen capture utility that may be slightly better than the Windows snipping tool.
4. LiveSpcMap viewer. Utility that is designed to process Edax spectrum data cube .spd files.
5. SpecUtil. Spectrum utility to display single, multiple, and overlay EDSXRF spectra.

Miscellaneous Topics

Orbis Procedures EDS Energy Calibration

Energy Calibration on the Orbis

Energy-dispersive spectrometer systems have excellent long-term energy calibration, but if the system high voltage power supply has been turned on and off and/or other disruptions have taken place, it may be neceesary to recalibrate the processing electronics.

Several points to be made regarding energy calibration:

• Energy recalibration is not needed for routine identification of elements and normal work such as sample mapping. The greatest drift in calibration is typically about 10 eV, which can only be observed by comparing spectra. Elements will be properly identified regardless of this type of long-term drift.
• However, for quantatitive analysis you want to be sure that the energy calibration of the sample spectra and data collected on the standards are both at the same calibration.
• In particular, if an extended quantitative analysis run is to be performed it is a good idea to check the energy calibration and perform a recalibration before many measurements are to be acquired. You should not perform an energy calibration in the middle of a quantitative analysis run, either do it at the beginning or deal with the small drift and acquire all data under the same conditions.
• The main reason for doing energy recalibration is that the peak fitting routines and extracted peak intensities are dependent on the peak centroid and peak full width at half maximum (FWHM) energy resolution, and should be identical for the two sets of EDS data, namely the standardization and the measurements on the samples.
• Also note that the same time constant must be used for all data sets in quantitative analysis because the TC affects the peak resolution and therefore the extracted intensities.

Calibration Procedure

1. The energy calibration is made using the Aluminum Copper standard (marked CuAl). This material should be mounted (while wearing gloves) on one of the graphite substrates and placed in the Orbis. The Aluminum Kα peak is at 1.486 keV and Copper Kα peak is at 8.04 keV, and this energy separation is sufficient to establish the gain.
2. Turn on the X-ray source using the button on the Orbis front panel.
3. Using the Vision software, set the kV to 30 and current to 200 micro amps.
4. Make sure the 30 micron polycapillary optic is selected in the Setup X-ray menu. (This calibration is also good for the 1 mm and 2 mm collimators, so you don't have to perform a separate energy calibration for them.
5. Select Vacuum from the pull down menu on the Vision software and wait for the system to pump down to below 0.5 Torr (light green color on the Vision Vacuum button.
6. Locate the AlCu standard and set it to focus at low and then high camera magnification. Select a spot that is relatively free of scratches to be used for calibration measurements.
7. Acquire a spectrum to confirm that you are on the standard and have a good count rate.
8. There are 6 time constants on the DPP3 system with a SDD EDS detector from which to choose. The time constant values are used to trade off X-ray count rate vs. peak resolution:
1. 0.5 μsec, which has the highest throughput but lowest energy resolution and is used for mapping applications
2. 0.8 μsec, for mapping requiring slightly better resolution.
3. 1.6 μsec
4. 3.2 μsec, used for FP spectral collection on the PMMA block and is a setting with good throughput and energy resolution.
5. 6.4 μsec, which has good energy resolution and is used for quantitative analysis runs in our lab.
6. 12.8 μsec, which has the highest energy resolution but the lowest throughput.
9. Select the menu Setup – EDAM & Calibration, and the calibration window will be displayed. On this window in the Peak #1 Input box – will have the keV of the first peak (i.e. Al), and in the Peak #2 input box will have the keV of the second peak (i.e. Cu). Below this there is the full scale value to use for calibration, we will use 10000 counts full scale.
10. We want to calibrate all 6 time constants in an automated sequence where the Vision software sets the X-ray tube current to achieve the proper total count rate at each time constant setting.
11. Click on the AutoALL TC button to start the automatic calibration procedure. This will take about 15-30 minutes to complete.
12. When the automatic procedure is complete, click on the PrintALL TC button to print out the summary results of the calibration and place it in the Orbis calbration result folder in the drawer under the Orbis computer.
13. The calibration results are also copied to the Excel file CALIBRAT.CSV in the Windows directory of the C drive, which keeps a record of all calbrations performed on the system.
14. That is the end of the procedure for auto calibration of all time constants.
15. If only one time constant needs to be calibrated, then check the Time Constant that you want to use, and click on the Auto button to start the process. When auto calibration is running, the newly calculated values will be displayed in the output boxes (in blue). The bottom 2 output box's display the increment values of the gain and zero. Increment values must be less than 50 for auto calibration to complete successfully. Increment values are the difference in the Gain & Zero numbers since the last calibration iteration.
    Auto calibration completes when both of the defined peaks are within 1.5 electron volts (eV) of their reference values. If this condition is not met, one more iteration [ up to a maximum of 6 ] will be executed. If enabled, there is an audible tone generated at the completion of the auto calibration.

Orbis Emergency Procedures

About the Orbis system safety protection

The Orbis has built-in safety protection as follows:.

1. The X-ray source has a shutter that is automatically closed if the sample chamber door is opened. This provides positive protection from exposure to X-rays.
2. The shutter is also manually controlled by software using the Shutter-Filters pull down menu in the Vision program.
3. The shutter can only be opened using the Vision program, and only when the Orbis sample chamber door has been closed and locked (see the sample exchange procedure).

The Orbis Rh X-ray tube is a low power source with maximum output of 50 watts (compare this with a 3-5 kW conventional X-ray tube in X-ray diffraction and X-ray fluorescence systems). On the Orbis system this relatively low power output does not require water cooling to be used for routine operation of the X-ray tube.

Events requiring emergency stop

The following events require immediate action:

1. Electrical fire (burning smell, smoke, flame), arcing, etc.

If there is an emergency, do the following:

1. If the Orbis is under vacuum, immediately vent the instrument using the vacuum pull down menu.
2. Turn off the X-ray power using the X-ray push button on the front of the Orbis PC unit.
3. Turn off the Orbis power by pressing the Power button on the front of the Orbis PC unit.
4. Contact Paul Carpenter (Cell 314-602-9697, paulc@levee.wustl.edu)/ Jeff Catalano / Brad Jolliff immediately.
5. You will need communicate what happened verbally and also write an email summarizing the specific problem and what may have caused it to occur.

The Following Sections Are Orbis Procedures For Authorized Users Only

Orbis Reboot Procedure

Orbis Reboot Procedure

If communication has been interrupted between the Orbis PC and the HP PC computer, then it is necessary to perform a complete system reboot to enable communications again.

Please follow the Orbis Shutdown procedures to completely turn off the Orbis PC and HP PC computer, then use the Startup Procedure to turn the system back on again.

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Micro X-ray Fluorescence -- About the Technique

This section summarizes the technique of micro X-ray fluorescence (μXRF) and provides some links to further information, see also the reference list for more complete treatment.

Micro X-ray Fluorescence

1. Primary capabilities of μXRF:
   • Non-destructive analysis of inorganic materials for elements Na-U (nominally) with best sensitivity for energetic X-rays not normally analyzed by SEM/EPMA (e.g., Kα lines of Ga-Mo).
   • Rapid identification of major element chemistry by acquisition of energy-dispersive (EDS) X-ray spectrum.
   • Very good sensitivity for trace elements as no continuum X-rays are produced.
2. X-ray tube source: An X-ray tube source is used to generate characteristic X-rays that are collimated and/or focused into a narrow beam that is directed onto the surface of a sample. The incident X-rays fluoresce characteristic X-rays from the atoms of elements in the sample, which then travel out of the sample are are detected by an energy-dispersive detector (EDS).
3. Energy-dispersive spectrometer: The EDS detector can acquire X-rays from a wide range in energy and the data are presented as a &muXRF-EDS spectrum of X-ray energy on the x-axis and photon counts on the y-axis.
4. Qualitative Analysis:The X-ray spectrum from the sample is inspected for the presence and absence of elements; the list of elements and interpretation of relative concentration makes up qualitative analysis.
5. Quantitative Analysis: Quantitative analysis can be performed by acquiring EDS spectra on standards of known composition and processing of the standard intensity data to correct for X-ray absorption, secondary fluorescence, and background interferences. A least squares matrix method is used to establish a system of equations that relate concentration to measured intensity in a multielement matrix. Measurements on samples are made by acquiring EDS spectra and correcting the data to concentration units using this calibration matrix.
6. Automation System: In μXRF systems a motorized xy stage coupled with a digital camera system is used to locate regions of the sample for analysis. This automated measurement capability allows for:
1. Automated acquisition of digitized points on a sample. Individual EDS spectra and spot analyses are acquired. Typically a long count is used for spot analysis compared to linescan and mapping.
2. Linescan acquisition where two points are used to define a line segment across a feature boundary in the sample. Either relative intensity data or concentration data can be acquired and are plotted vs. distance in the linescan. Typically an intermediate count time is used for linescan acquisition.
3. Stage mapping allows for an xy area to be mapped using a digital matrix of points where an EDS spectrum is acquired at each point and the entire data set is saved as a hyperspectral data cube. This data cube is used to generate element maps, perform inspection of the map area including data mining, assembly of maximum pixel and total sample EDS spectra, and conversion to quantitative map data given enough computer time. Typically short times are used on a per-pixel basis for mapping.
7. Vacuum System Modes XRF systems are equipped with a rotary pump vacuum system. Light element analysis for Na-Si requires use of vacuum mode as X-rays of these energies are strongly absorbed by air molecules. An Ar Kα peak is also observed for samples analyzed at atmospheric pressure. A vacuum of less than 0.5 Torr is typically used for all measurements where light element detection and quantitative analysis is required.
8. Sample requirements and restrictions A significant advantage of μXRF is the ability to work with a diverse range of sample types. Sample capabilities and requirements are as follows:
1. Samples do not need to be electrically conductive or carbon coated as is the case for SEM or EPMA analysis.
2. Best results are obtained on samples that are flat and polished to approximately 1 micron final polish. This minimizes topographic effects on differential X-ray absorption.
3. Large area samples, up to 10 cm on a side can in principle be accomodated in the sample chamber.
4. In principle, materials which are vacuum sensitive such as hydrous phases can be analyzed under atmospheric pressure.
5. Powders must be compressed to a small pellet having a smooth flat surface for analysis, and may require the use of X-ray transparent film and isolation from the sample chamber if vacuum mode is to be used.

Micro X-ray Fluorescence -- Details

1. An X-ray source is used to provide X-rays in a collimated or focused beam that is directed normal to the surface of a sample. On the Orbis μXRF this source is a Rh X-ray tube with 1 kW power and can operate at up to 50 kV and 1000 μA.
2. The X-ray beam diameter is determined by selection from three different optics on the Orbis:
   1. A nominally 30 μm beam is produced by the polycapillary optic (the actual beam diameter is a function of the X-ray energy portion of the continuous tube spectrum).
   2. A 1 mm or 2 mm diameter beam is produced by the 1 mm or 2 mm brass collimator optics, respectively. There is attenuation of the low energy portion of the tube spectrum with these optics, but no effect on the high energy portion of the spectrum.
3. The X-ray beam interacts with atoms in the sample in several important ways. The tube spectrum photons can:
1. Eject inner-shell electrons from sample atoms and produce characteristic X-rays that identify that element and from the emitted X-ray intensity can be used for quanitative analysis. This process is X-ray fluorescence.
2. Scatter from atoms in the sample by interacting with valence shell electrons in a coherent manner where no energy is lost. This is primarily seen in coherent scatter of the Rh Kα and Kβ X-ray lines.
3. Scatter from atoms in the sample by also interacting with valence shell electrons in an incoherent manner where an electron is ejected as a photoelectron and energy is lost in the process. This produces an X-ray peak at a lower energy than the characteristic peak in the X-ray spectrum. These peaks must be correctly identified as scatter peaks.
4. Be diffracted by the lattice planes of a crystalline material so that the incident photons are re-emitted from the sample at an energy determined by Bragg's law for diffraction (both the d-spacing of the diffracting plane and the energy of the diffracted photons are required to calculate the diffracted energy in the spectrum).
4. While the beam diameter using the polycapillary optic is nominally 30 μm, the depth production of X-rays can be quite large and is a function of the return depth of fluoresced X-rays. Low energy X-rays such as Si Kα are emitted from the surface microns whereas high energy X-rays such as Sr Kα can be emitted from approximately 1 cm depth in the sample. Samples place directly on the plexiglass stage assembly will also produce a large scattering hump in the spectrum due to beam interaction with the plexiglass after transiting the sample.
5. EDSXRF spectra exhibit a number of spectral artifacts that can be confusing. Here is a list:
1. Sum peaks: The Orbis silicon-drift EDS detection system has a high speed X-ray pulse processing system that allows high throughput. Several time constants are available which are used for high throughput mapping mode (short time constant) vs. low throughput quantitative analysis mode (long time constant). Especially when using the long time constant one observes sum peaks where two or more photons arrive within the resolving time of the counting system and are counted as an X-ray with the sum of the photon energies. Comparison of the KLM marker lines is necessary to avoid mis-identification of elements.
2. Escape peaks: Any photon which can generate a Si Kα X-ray in the SDDEDS detector element (which is made of Si) will exhibit an escape peak that is 1.74 kV below the main peak on the EDS spectrum.
3. Scattering peaks: The Rh Kα and Kβ peaks show coherent and incoherent scattering peaks at the high energy portion of the EDS spectrum. You will also observe incoherent scattering peaks at lower energies that are related to the Rh K-lines.
4. Diffraction peaks: Crystalline materials may diffract the primary X-ray beam and will produce diffraction peaks in the EDS spectrum. Use appropriate primary beam filters to identify and reduce the intensity of diffraction peaks.

Energy-dispersive spectra acquired on Orbis μXRF

Here are EDS spectra acquired on our Orbis μXRF which illustrate important spectral features and artifacts.

Orbis X-ray Tube Spectrum

1. Fundamental parameters spectrum acquired at 40 kV on "wax" sample of polymethyl methacrylate PMMA.
   This set of spectra on PMMA illustrates EDSXRF artifacts. The PMMA contains only C, H, and O, which do not produce X-rays that can be measured with this system. The entire X-ray spectrum observed in these spectra is essentially the Rh X-ray tube spectrum as scattered off of the PMMA sample and then detected by the SDD EDS detector. The Rh tube spectrum consists of the characteristic X-rays for the Rh K-family and L-family superimposed on continuum X-rays all produced in the X-ray tube.
1. The spectrum on left was acquired using the polycapillary optic which collects low energy X-rays with better efficiency compared to high energy X-rays. Note the higher intensity of the Rh L-family lines compared to the Rh K-lines and higher continuum "hump" in the spectrum.
2. The spectrum on right was acquired using the 1 mm collimator optic which collects high energy X-rays more efficiently compared to low energy X-rays. Note the higher intensity of the Rh K-family lines compared to the Rh L-family lines.




Note the following features:
1. Coherent scatter peaks for Rh Kα and Rh Kβ. These peaks are the coherently scattered X-ray lines of the characteristic X-rays for Rh Kα and Rh Kβ at the characteristic peak energies for Rh Kα and Rh Kβ originating from the Rh X-ray tube source. These X-rays are scattered with no energy loss by electrons in the PMMA.
2. Incoherent scatter peaks for Rh Kα and Rh Kβ. These peaks are the incoherently scattered X-ray lines of the characteristic X-rays for Rh Kα and Rh Kβ and are observed at a lower energy than the marker lines for those X-rays. The intensity of the incoherent scatter peaks is inversely proportional to the average atomic number Z-bar of the sample (highest intensity on a low Z-bar material like PMMA, lowest intensity on high Z materials).
3. Coherent scatter peaks for Rh L-family X-ray lines. The coherent scatter peaks for the Rh L-family plot at the energy of the Rh L-family X-ray lines. That is, the sample appears to contain Rh but it is a coherent scatter artifact from the tube source.
4. Escape peaks. Any X-ray having energy greater than the excitation energy of the Si detector crystal can fluoresce a Si Kα X-ray which then exits or escapes from the Si detector and does not generate electron-hole pairs in the process. This loss of X-ray energy results in those X-rays plotting at 1.74 keV below the X-ray line which fluoresced the Si Kα X-ray. These are called escape peaks and can be seen 1.74 keV below the Rh Kα and Rh Lα peak energies in the spectra.
   It is important to correctly identify escape peaks and to not assign them to other elements thought to be in the sample. Remember to confirm the presence of an element by observing multiple family lines (e.g., if a Kα peak then there should be a Kβ peak at the correct relative intensity of 10:1.

Example Spectra from Various Materials -- Major Elements

Here are examples from materials with an emphasis on major element detection and sensitivity. Unless otherwise noted, all spectra were acquired using the 30 μm polycapillary optic which is very good for light element sensitivity. The Orbis can be used to very quickly identify the element inventory when the concentration is above the trace element level.

Example Spectra from Various Materials -- Minor and Trace Elements

Corning 95IRX trace element glass
Here are examples of trace element glasses. The first is Corning 95-IRX, which is a Mg-Ca-Al-Si borosilicate glass doped with approximately 0.75 wt% as oxide of Ni, Zn, Rb, Sr, Y, Zr, Pb, and U, and is used a primary and secondary EPMA standard and for the same purpose on the Orbis. Glass 95IRX also contains low Fe and K that were present in the bulk materials used to batch the glass.

NIST SRM 610 trace element glass
The second example is NIST SRM 610 trace element glass, which contains approximately 500 ppm concentration of ~ 60 elements in a Na-Al silicate glass.

Brazil Monazite Sample
Monazite is nominally (REE)PO₄ with LREE > HREE. Two Orbis spectra are compared, first a spectrum using no primary beam filter, and a second spectrum using the 250 μm Al filter. The 250 μm Al filter reduces intensity of the tube continuum and improves the detection of the L-lines for Th and Y.

Differences between Conventional XRF and μXRF

How μXRF Differs from Conventional XRF

It is important to understand the difference between μXRF and conventional XRF:

1. Conventional XRF
1. Conventional XRF is a bulk analytical technique where a sample (typically a bulk rock sample) is ground to a fine powder and either mixed with a flux and melted to form a glass disc, or pressed in a binder to form a "biscuit".
2. The sample size is several hundred mg to ~ 1g; modern methods include use of smaller glass bead sample aliquots.
3. The fusion disc method is used to eliminate particle effects that cause differential X-ray absorption and to homogenize the sample for measurement. This reduces the dependence on the number of standards as they are all converted to a glassy state.
4. A conventional high power X-ray tube is used and approximately 1-inch area is analyzed.
5. Both wavelength-dispersive (WDS) and EDS systems exist and it is generally acknowledged that WDS is superior for trace element measurement and resolution of peak interferences in multielement samples, while EDS is very good in general and allows rapid acquisition of data.
6. Quantitative analysis is well established because relatively few issues arise from sampling considerations.
2. μXRF
1. In μXRF the sample is analyzed "as is" because the method is used to analyze small volumes of material, so it is a microanalytical rather than bulk technique. The sample is not required to be ground to a powder.
2. A glass is not required although in principle μXRF could be used for analysis of small glass volumes from bulk powders.
3. A lower power X-ray tube is used in order to allow the tube source to be compact; air-ccoling is used rather than water cooling of the tube.
4. The advantage of μXRF is the acquisition of spot, linescan, and map data on materials that have some type of compositional variation. This advantage must be balanced against complications due to sampling of multiple phases from deep within a sample and the problem of correcting for differential X-ray absorption, fluorescence and scattering in these materials (there is no current correction for this).
5. A significant advantage of μXRF includes the ability to analyze materials with minimal or no sample preparation which would be required for conventional XRF, SEM, and EPMA.

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Bragg X-ray Diffraction

Bragg X-ray Diffraction

This section covers X-ray diffraction with respect to powder XRD, but the material is truncated relative to the full discussion used for powder XRD and phase identification. It is relevant to μXRF because crystalline materials can diffract the X-ray beam and produce diffraction peaks in the EDSXRF spectra.

1. Crystalline solids are structurally composed of periodic arrays of atoms that have differential X-ray scattering probability.
2. When placed in an X-ray diffractometer and exposed to monochromatic X-rays, the X-rays are diffracted according to Bragg's law:
   n * λ = 2 * d * sin(θ)
   n is the order of diffraction
   λ is the wavelength of X-rays (on our instrument it is Cu Kα, units are in Angstroms)
   d is the interplanar spacing between layers in the crystalline structure, units also in Angstroms
   θ is the angle of the diffracting X-rays to the layers of atoms which cause the constructive interference of the X-rays



3. The interpretation of Bragg's law is that whenever the path length of diffracted X-rays is equal to twice the d-spacing of the layer of atoms (multiplied by the sine of the diffraction angle), then constructive wave interference occurs and a diffraction peak is observed. In the figure below, the distance AB is d*sin(θ) and for constructive interference the X-rays have a path length of AB + BC which is 2*d*sin(θ).



4. Here is a web link to a java applet that allows you to visualize how changes in the Bragg equation are seen graphically. Note that for a constant wavelength there is a unique set of d-spacing and diffraction angle θ that results in diffraction. Use the Details button to see the relationships. You may need to modify your Java security settings to get the app to run.
Java Applet
5. In powder X-ray diffraction, a randomly oriented, finely ground powder (~ 10 microns) is required for analysis. The powder can be in the simplest case a single crystalline phase (e.g., quartz), or a mixture of phases (e.g., quartz, calcite, dolomite). As the number of phases or diffraction peaks increases it becomes more difficult to identify all phases.
6. Below is an X-ray powder diffraction plot collected on halite (NaCl) using a Cu Kα X-ray tube source. The data are collected by progressively increasing the angle between the sample and both the X-ray source and detector (which are at the same angle to the sample for a θ-θ instrument) and counting the detector at each angle. For this sample the diffractometer was driven from about 17.5 to 60 degrees 2θ. The peaks on the diffraction plot show the angles where Bragg's law is satisfied, i.e., the angles where n*λ = 2*d*sin(θ) for the NaCl structure. The regions of background scattering in between the peaks are angles for which n*λ does not equal 2*d*sin(θ). Note that the diffraction peaks are related to fundamental atomic planes in the NaCl lattice and that the plane with largest d-spacing is diffracted at the lowest angle while those planes with smaller d-spacing are diffracted at higher angles. Also, the d-spacing for the (222) reflection is half of that for the (111) reflection thus indicating the relationship between Miller indices of a plane and the d-spacing for that plane.

Example Orbis Spectrum With X-ray Diffraction Peaks

When EDSXRF spectra are acquired on large crystalline samples, it is likely that X-ray diffraction peaks will be observed in addition to the X-ray fluorescence peaks (and other artifacts such as sum, escape, and scatter peaks). It is important to recognize these features to avoid mistakes in element identification.

The figure below shows EDSXRF spectra collected on a large natural crystal of corundum (Al₂O₃) which contains in addition to Al as a major element the chromophores Cr and Fe which are both in the 3+ state. There are also small peaks due to inclusions of silicate minerals. Three spectra were acquired and the sample was rotated 90 degrees for each, so the sample orientation is 0, 90, and 180 degree rotation. Note that each spectrum contains diffraction peaks that change in energy and intensity as a function of sample rotation.

Some of the peaks at the energies for Ti, Cr, and in the range 7-12 keV are diffraction peaks. The X-ray wavelength(s) that are diffracted include the Rh Kα and Kβ peaks (coherent and incoherent to some extent) and the d-spacing and diffraction angle to the diffracting planes is that which satisfies the Bragg equation. The Vision software has a utility which takes up to 5 spectra acquired at different orientations and subtracts the peaks that occur in only one of the spectra. This has been used to obtain the final spectrum below which confirms that Cr and Fe are present.

In general, one should inspect the spectrum and identify all family lines to ensure a correct identification of an element. If a Kα line is present then there must also be a Kβ line. The X-ray diffraction peaks also typically have a larger FWHM peak resolution resulting from a range of X-ray wavelengths being diffracted and/or a variation in the crystal diffraction planes that have caused the diffraction to occur.

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Orbis μXRF Manuals, Short Course Documents, and References/Links for XRF and μXRF

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Edax Orbis Vision Manual and Utility Manuals

These links are to the manuals for the Vision software which is used to acquire data on the Orbis μXRF, and for the XRF Combine software that is used to generate calibration data for quantitative analysis; there is also a document for the Edax utilities.

1. Orbis Vision manual
2. XRF Combine manual
3. Edax Utilities manual

Edax Orbis User Course on μXRF Analysis

These are the presentations from the Edax user course on μXRF and the Orbis spectrometer. They are available from Edax for our use. These materials cover the instrument, EDS XRF, sample preparation, spectral features and artifacts, and applications.

1. 01 Hazardous Sample Handling
2. 02 Properties and Production of X-rays
3. 03 Setup and Hardware
4. 04 Spectral Artifacts and Other Issues
5. 05 Sample Considerations
6. 06 Mapping and Linescan
7. 07 XRF Combine User Manual
8. 08 Applications

References for X-ray Fluorescence and μXRF

There are general references to XRF in general and μXRF in particular. For μXRF you will be interested in energy-dispersive X-ray fluorescence in preference to wavelength-dispersive XRF. In so-called conventional XRF of earth materials one typically uses glass fusion discs for analysis and that approach is not used in μXRF as we analyze materials as-is. These references are listed by date of publication.

Books and E-books

1. X-ray Fluorecence Spectrometry
   Ron Jenkins. 2nd ed. ; New York : Wiley, 1999.
2. Quantitative X-ray Spectrometry
   Ron Jenkins, R.W. Gould, and D. Gedcke, Second edition, 1995. This is an excellent text on XRF, EDSXRF, and quantitative analysis. WUSTL library has the first edition.
3. A practical guide for the preparation of specimens for x-ray fluorescence and x-ray diffraction analysis
   Edited by Victor E. Buhrke, Ron Jenkins, Deane K. Smith. New York : Wiley-VCH, c1998.
4. Handbook of X-Ray Spectrometry
   Edited by René E . Van Grieken and Andrzej A . Markowicz, CRC Press 2001. WUSTL library has electronic access to this book and you can download the chapters.
5. X-ray Fluorescence Spectrometry and Related Techniques : An Introduction (2013).
   E. Marqui and R. van Grieken. E-book.

Journals

The journals X-ray Spectrometry and Powder Diffraction have papers covering both X-ray fluorescence spectrometry and μXRF. Many other journal papers can be found with applications of μXRF to various fields.

Links for X-ray Fluorescence

Here are links to information about X-ray fluorescence and related topics.

1. Wikipedia articles:
1. X-ray fluorescence
2. Micro X-ray fluorescence
2. Links to websites with good discussion of X-ray fluorescence:
1. Edax Orbis web site
2. Palmer presentation "Introduction to Energy-Dispersive X-ray Fluorescence (XRF) -- An Analytical Chemistry Perspective
3. Basic XRF powerpoint presentation from www.learnxrf.com

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XRF Utility Programs

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The following programs are useful for processing data sets obtained on the Orbis μXRF.

NIST Lispix Program

The NIST Lispix program is primarily used for processing of X-ray and imaging data sets acquired by electron-beam instruments. It is also used for processing of spectrum image data cubes and has routines that can open the .spd data cube saved by the Edax Vision software. There is documentation and tutorial help on the Lispix web site:

http://www.nist.gov/lispix/

NIH ImageJ

NIH ImageJ is a Java program that can be used for various image processing procedures applicable to X-ray maps. For example, one can perform histogram expansion, merging of grayscale images to RGB composite images, create ImageJ stacks (which can also be saved as animated .gif images), and other actions. The program is available from the NIH ImageJ web site:

http://imagej.nih.gov/ij/

ENVI

We have used the ENVI software to open the Edax Vision .spd data cube. This software is licensed for use in the Jolliff research group.

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Policy and Training Procedures for Orbis μXRF System

Policy Statement for Use of Orbis μXRF System

The Earth and Planetary Science Orbis μXRF System is made available to selected members of the EPS department, Washington University, other non-profit organizations, and commercial clients. Users are permitted to use the instrument subject to the following requirements:

1. Mandatory user training conducted by EPS staff.
2. Demonstrated ability to follow laboratory procedures including final check-out.
3. Maintain a current entry in the EHS blue book in room 152 XRD lab. You are not authorized to use the lab for any purpose unless you have a valid EHS safety certification as required by EHS prodecures (your printed name, signature, and date of EHS training). See below for how to access the WUSTL compliance page.
4. The procedures on this web page are your annual lab-specific user training and you are therefore required as part of your annual EHS training to use them during your session.
5. Users who do not follow procedures in the on-line manual, cause problems regarding necessary care during use of the instrument, software procedures, and lab cleanliness will have their check-out revoked.

Orbis μXRF Training

Please note that users are trained approximately once a month in group sessions only. Be prepared to spend approximately 3 hours in these training sessions and come prepared to use the software by reviewing the procedures in this web document including the Orbis pdf manuals. You will be asked to demonstrate your knowledge of these procedures and your ability to follow them during and after the training session. If you do not demonstrate adequate knowledge you will not be able to use the instrument.

Each research group has a "main user" that is the person responsible for helping new users by running samples during the period between training sessions. Contact Paul Carpenter to be added to the list for the next training session. You cannot be trained by another user but they can run samples for you.

WUSTL EHS Safety Training and Verification From Compliance Web Page

If you have not taken the laboratory safety EHS training, go to the EHS lab safety training course.

To obtain proof of your EHS on-line training, you can access your electronic information on the WUSTL web site in order to determine when your most recent EHS on-line training was conducted:

1. Go to the WUSTL compliance web site: http://complianceprofile.wustl.edu
2. Click on the Compliance Profile link.
3. Log in to WUSTL connect using your user and password. This will take you to the AIS system.
4. You may need to answer one or more questions related to compliance and training.
5. Click on the My Compliance Profile menu, Show Requirements (or the system will take you to your page).
6. This will show you a page with Compliance Requirements Completed. There may be an initial one time EHS training entry, but you need to have the annual refresher EHS training. Training entries have the date listed.
7. If the EHS date is more than one year old, you are not in compliance and you need to take your annual EHS training.
8. You need to enter the date of your EHS certification from this page in the μXRF lab blue book.
   You do not need to bring a printed copy with you. EHS can verify your training online.

Laboratory Operating Hours

The Orbis μXRF lab is available for use during normal weekdays from approximately 9am-5pm. It is also necessary for Paul Carpenter or a designated person to be available for supervision of your time in the lab. The lab is closed on weekends and holidays.

The building and hall require electronic key card access so that lab is not available on nights and weekends except to EPS personnel. Please remember this when scheduling time on the calendar. The Orbis μXRF laboratory is kept locked because it is an environment where ionizing radiation is used. For routine users a key can be obtained for entry into the lab. Please use one key for your research group (let Carpenter know if you are a user in a new group that does not have a key).

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Fee Schedule for use of the Orbis Micro X-ray Fluorescence System

• All instrument fees are on a per hour usage basis.
• Instrument time is determined from high voltage tube time.
• There is a nominal one hour operator charge for each user that is trained.
• Operator time is charged thereafter as determined by Carpenter.
• Material fees are chaged for:
  • Use of laboratory Si zero background MTI holder, charged on a per session basis. Replacement cost is assessed if the holder is broken or removed from the lab.
  • Other costs such as Fedex, parking, etc.

User Group	Instrument Rate	Operator	Material use fee
Earth and Planetary Science Department	$20	$20	$15
Washington University (non-EPS)	$25	$25	$15
Other Universities and Non-profit Organizations	$30	$30	$15
Commercial Users	$85	$85	$15

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Contact Information, Location and Mailing Address

The Micro X-ray Fluorescence Lab is located here:
Scott Rudolph Hall, Earth and Planetary Sciences, Room 153 (accessed through Room 152)

Here is the Official Washington University Hilltop Campus map (PDF) (note: North is NOT up). Scott Rudolph Hall is building number 33 at coordinates J-K, 7-8.

Here is the mailing address if you are sending samples:

Paul Carpenter
Department of Earth and Planetary Sciences, CB1169, Room 110
Washington University
1 Brookings Drive
St. Louis, MO. 63130-4899

Phone: (314) 935-5471
Fax: (314) 935-7361

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Orbis Acknowledgement for Published Papers

The Orbis μXRF was purchased by Dr. Brad Jolliff and is supported by user fees. Please include the following information in the acknowledgements section of published papers that use data acquired on this system. You can use the following statement:

The Edax Orbis μXRF in Earth and Planetary Sciences at Washington University in St. Louis is supported by user fees.

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Appendix Materials for Orbis

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Laboratory Safety Document -- Appendix 4 of Blue Book

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X-ray Diffractometer and Micro X-ray Fluorescence Labs (Rudolph Rooms 152-153)

Use: In this lab, we work with instruments that generates X-rays. Exposure to X-rays is harmful to you even though you can not see them or necessarily feel their effects. Our instrument has an annual radiation survey and the results are in the laboratory blue book for the current and past year surveys. The sheilding and safety interlock system permit us to work without the requirement of dosimetry badges. During normal operation, you will not be exposed to harmful levels of radiation.

It is important for you to follow the standard operating procedure and placards on the instrument during sample exchange. Failure to do so will result in you being banned from the laboratory.

As with any radiation source, you should limit exposure time and maximize shielding and distance from the X-ray source. Note that the exposure limits during pregnancy and for minors are much lower than for routine workers. It is therefore not recommended to use any x-ray source during pregnancy or to bring children into the lab. For information concerning typical exposure levels see http://www.new.ans.org/pi/resources/dosechart/

The main concerns for safety in this lab lie with sample preparation and with cleaning (see below). For sample prep, we work mainly with powders. Most of the powders used in this lab are harmless. If your samples are harmful, you need to take appropriate precautions in handling them to prevent contamination of the lab, bench tops, and instrument. Acetone and Ethanol are present in the lab for after-analysis clean-up. The instructions here are meant to supplement the University’s Chemical Hygiene and Safety Training. After this instruction, please sign the Bluebook for the Lab indicating that you have received the annual Lab training.

OSHA requires every laboratory to have laboratory-specific training and documentation.

1. Use of Volatile Organic Chemicals, Corrosives, Flammable Materials, Epoxies, and Toxins
1. Use these chemicals only in the chemical fume hood.
2. Wear appropriate eye protection, foot protection, lab coat, and gloves.
   Long pants and closed-toe shoes are required; sandles are not permitted (this lab has the potential for exposure to broken glass and high-voltage sources are prsent).
3. Store segregated by hazard class and label as Flammable, Corrosive, or Oxidizer.
4. Clean up solvent spills using a towel or other absorbent.


2. Working with Powders
1. If your samples are harmful (e.g. if your samples contain Arsenic, Barium, Chromium, Lead, Mercury, Nickel, Osmium, Selenium or Silver), you need to take appropriate precautions in handling them to avoid contaminating the lab or bench tops.
2. If you use the mortar and pestle with your samples, clean it completely using the St. Peter’s sandstone to remove any staining.
3. If you spill, there is a spill kit in the prep lab, if needed.
4. Dispose of waste properly (i.e. put in plastic baggy and remove as hazardous waste through Environmental Health and Safety).


3. Labelling Powders
1. If you leave your samples in the lab for any period of time, they must be labeled properly.
1. The label must have your name, the date, and what the sample is composed of.
2. If the sample is harmful, it should be in a secondary container that you will supply.


4. Proper Disposal of Sharps and Broken Glass
1. Discard razor blades in Sharps container.
2. Discard broken glass in broken glass box.


5. Use of the Chemical Fume Hood (room 153)
1. The fume hood should not be used as a storage area for chemicals or equipment.
2. All containers must be capped when not in use. Evaporation of chemicals is prohibited.
3. Work at least 6" inside the hood with a hood sash opening of approximately 14 inches.


6. Use of Carcinogens
1. Carcinogens are not permitted in this lab during normal procedures and carcinogen training is not routinely provided.
2. If your samples contain carcinogens, please notify lab personnel.


7. Consumption of Food and Beverage
1. Consumption of food and beverage is not permitted in the sample prep lab (153).
2. Beverages may be consumed in the main XRD lab (room 152) as long as the beverage is not set on the XRD console or near computer equipment.


8. The lab is equipped with an eye wash and 2 showers should you need them
1. Flush your eyes for as long as you can stand it.
2. Contact your supervisor or a health and safety officer to report the incident and to receive further instructions.


9. Fire extinguishers
1. The lab (152) is equipped with a fire extinguisher.
2. Familiarize yourself with its location and use.


10. If you think of something that has been left off this list, please report it to the laboratory manager so that it can be incorporated in the next version of this training.

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Document last updated on by Paul Carpenter

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