Outline of Typical EPMA Setup

Washington University EPSC Electron Microprobe Laboratory

Paul Carpenter
Version 1.0


Document Contents


    1. Preparing for an EPMA Run
    2. Setting Up a Probe for EPMA Run
    3. Launching Probe for EPMA
    4. Starting a New Run
    5. Adding Standards to Run
    6. Acquire Window
    7. Creating a New Sample
    8. Adding Elements to the Sample -- Elements/Cations
    9. Analytical Conditions
    10. Combined Conditions
    11. PHA Settings
    12. Peak/Scan Options
    13. Count Times
    14. About Analysis Options
    15. Acquisition Options Window
    16. Analysis Options Window
    17. Special Options Window
    18. Automate Window
    19. Confirming Standard Positions
    20. Peak Spectrometers
    21. Primary Calibration: Acquiring Standard Samples
    22. Analyze Window
    23. Evaluating the Standardization: Analyze
    24. Automated Analysis
    25. About the Position Database
    26. Sample Setups
    27. Generating Sample Setups
    28. Using Sample Setups
    29. Standard Assignment
    30. Peak Interference Setup
    31. TDI Time Dependent Intensity Evaluation
    32. Blank Assignment
    33. MAN Mean Atomic Number Background Setup
    34. Output of Data from PFE Analytical Run


    Preparing for EPMA Run


    Sample Preparation, Documentation, and Quantitative Analysis Plan

    1. Mounting and Polishing of Bulk Samples

      1. Samples mounted / cast in appropriate holders to fit constraints of microprobe stage assembly. This can be perfomed by commercial thin section laboratories.
      2. Samples polished progressively to 0.25 μm final polish and cleaned of residual polishing material and oil.
      3. Samples trimmed of excess epoxy to fit top referencing microprobe sample holders.
      4. Samples placed in evacuated bell jar to outgas, followed by cleaning (as necessary).
      5. All subsequent handling to be performed wearing gloves, no fingerprints on samples.

    2. Sample Photography and Documentation

      1. If detailed EPMA is to be performed, a locator master image is required. This can be a relatively low magnification digital camera image for basic work, but a photomosaic is required for high magnification analysis.
      2. In the EPMA samples are viewed using reflected light, secondary-electron, and backscattered-electron imaging. Transmitted light is typically not used so transmitted light images are of secondary value to reflected light images.
      3. Reflected light or BSE photomosaics are ideal and should be prepared and organized in Photoshop.
      4. A stage-registered image is used by PFE and requires an image (jpg, bmp) with less than 2k by 2k resolution. This requires a downsampling of large format images for the microprobe session. Please prepare the downsampled final locator images, with appropriate resolution, grouped together in a folder, prior to the session.

    3. Carbon Coating of Samples

      1. Samples must be carbon-coated before microprobe analysis. Please do this before the day of the session.
      2. If samples are not clean, contain residual oil, have fingerprints, they must be cleaned before coating. All coating work is performed wearing gloves.
      3. The target thickness of carbon is ~ 22 nm. This corresponds to red-blue on polished brass reference target used in the carbon evaporator.
      4. Follow specific carbon coating instructions in lab.
      5. Coated samples should be stored in dehumidifier cabinet or evacuated bell jar, as necessary.

    4. Prioritized Plan for EPMA Session

      1. The electron microprobe is typically used for SEi and BEI imaging, X-ray mapping, and quantative microanalysis. You need to determine the exact focus of research, the priority of tasks, and the time required vs. time available on the instrument.
      2. This requires a logistical plan for efficient use of the microprobe.
      3. Efficient use of the instrument requires flexibility in your schedule. When the instrument has been setup and made available, you should be prepared to work extended hours to finish your work. Please do not assume that your work can spill over into subsequent days.
      4. If no photomosaic images exist and are necessary for detailed work, this should be done first.
      5. Quantitative analysis requires significant setup (typically 2 hours or more) and should be performed all in one run if at all possible. These runs include manually acquired points and segue to automated analysis for overnight runs.
      6. X-ray mapping runs are typically performed during overnight hours and also require significant setup time.

    5. Quantative Electron-probe Analysis

      1. EPMA is excellent for "routine" analysis of polished bulk samples at points that are approximately 1-10 μm in size.
      2. A complete analysis of cations, with oxygen calculated by stoichiometry, is routinely obtained.
      3. EPMA requires relatively short X-ray counting times for major elements (~10-100 wt%), longer times for minor elements (~1-10 wt%), and significantly longer times for trace elements (<1 wt%) . This contstraint, coupled with logistical sequencing of all elements for a complete analysis, is the limiting factor for quantitative EPMA.
      4. An organized list with realistic element inventory, should be identified prior to the microprobe session. See the section on a typical EPMA setup.


    Setting Up a Probe for EPMA Run


    Selection of Standards

    1. The PFE Standard Program

      1. Use the PFE Standard program to find and inspect standards in the standard.mdb database.
      2. Identify the primary standards to be used in the run. These primary standards will be used for WDS spectrometer peaking and for X-ray intensity measurement.
      3. In practice, a core set of simple end-member oxide, silicate, and metal standards is used for primary calibration. For example, for Mg a synthetic forsterite is used.
      4. Identify appropriate secondary standards to be included in the run, that is, standards that are not used for primary calibration but are included in the standard inventory for the purposes of cross-checking the primary calibration. An example is Kakanui Hornblende, which contains a number of elements at a sufficient concentration to be analyzed routinely as a quick check of the calibration.
      5. If the compositions of all standards have not been entered into the standard.mdb file, it should be done prior to the run if possible.
      6. Use the List Standard Names utility to list all standards in the database.
      7. Use the Find utility to list standards in increasing concentration of an element.
      8. See the documentation for Standard for more information.

    Mounting of Standards and Samples, and Generation of Stage Block Image

    1. Mounting of Standards

      1. Standards used in routine EPMA runs are semi-permanently mounted in the stage block assembly. If additional standards are required, the mounts need to be selected and put in the default position in the stage block for that mount. Familiarize yourself with the locations of the standards to be used in the run.
      2. If digital location maps have not been made for all standard blocks to be used, this should be done prior to the run.
      3. Refer to the documentation for standard mounts to identify these standards and their location on the mounts.

    2. Mounting of Samples

      1. Samples should be mounted in the holders and securely fixed using the allen screws.
      2. Important: The samples should be mounted in the same orientation as the photomosaic image map in order to minimize the rotational correction that must be made when using Picturesnap.
      3. Use small pieces of copper tape to ensure electrical ground for the samples. (Other labs may use a different procedure but we do not use carbon paint or other carbon compounds in our oil-free vacuum system).
      4. Make sure that the samples are not tilted and that the z-axis position of the sample will be reached. Remember that the microprobe has an ~ 3 mm range on Z, so tall samples are problematic.

    3. Generating the Stage Block Image

      1. A master image of the stage block is very helpful in locating major features during the microprobe run.
      2. A flat-bed scanner can be used to digitize the entire stage block, or a digital camera image can be used.
      3. This master locator image will need to be saved as a jpg or bmp file, and converted to a maximum resolution of 2k by 2k for use in Picturesnap.

    Sample Exchange

    1. Sample Exchange

      1. Perform the sample exchange procedure to place the stage block in the microprobe.
      2. Drive the stage to a standard position to confirm the block is in the correct xy position.

    Filament Saturation, Column Alignment, Probe Current Selection, and Focus/Stigmation

    1. Filament Saturation

      1. Perform the filament saturation procedure as necessary to set the filament to saturation. If this is being done initially you should let the filament stabilize prior to standardization.

    2. Column Alignment

      1. Perform the column alignment procedure as necessary. Typically this utilizes an existing gun shift setting and at most requires a small change in the gun tilt adjustment.
      2. Use a cathodoluminescent material such as benitoite to verify that the column is aligned.
      3. Set the gun shift. This can be done by varying the coarse condenser lens and confirming concentric expansion of the beam diameter on this CL material. If the beam moves laterally while the coarse lens is adjusted, then the gun shift is not set correctly.
      4. Set the gun tilt. This can be done by inserting the faraday cup and setting the tilt control to obtain maximum probe current on the faraday cup.

    3. Probe Current Selection

      1. Set the probe current to the desired value for the initial setup for the run.

    4. Focus and Stigmation of the Electron Beam

      1. Set the microprobe up in imaging mode using SEI imaging and TV rate raster over a reduced scan area.
      2. Drive the stage to a feature that has sharp boundaries in both the x and y direction.
      3. Make sure the sample is at the correct Z-axis position by moving the sample until it is sharply focused using the optical microscope.
      4. Adjust the focus and stigmation until the sample is sharply focused with no diagonal stretching of the image or lateral movement as you go through the focus point.

    5. Centering the Electron Beam

      1. Use a cathodoluminescent material like benitoite.
      2. Set the microprobe to spot mode.
      3. Use the image shift control to move the spot to the optical microscope cross-hair. This will ensure that the beam is at the cross-hair for quantitative analysis.


    Starting Probe for EPMA Software


    1. Launch Probe for EPMA (PFE) and connect to microprobe

      1. Launch PFE.
      2. Connect to microprobe. If error check communications.

    Start a New Run

    1. Start New Run and Enter User Information

      1. Start new run. File New.
      2. Set file location using consistent file structure.
        Example: User Data\Lastname\Lastname date\Lastname date.mdb
      3. Enter User, Title, Department, Acct number, Group, Description.
      4. Use Acquire, Analyze, and Automate buttons to open these windows.

    Add Standards to Run and Verify Standard Positions Exist

    1. Add Standards to Run, Enter Standard Data if Necessary, Verify Standard Positions Exist

      1. Add Standards to Run. Standards--Add/Remove Standards To/From Run.
      2. Note: if you will be using New Sample -- File load you can have the standards automatically loaded using that procedure.

    2. Enter Standard Data if Necessary

      1. If standard is missing, use Standards--Standard database to launch Standard.exe.
      2. Enter new standard number and composition.
      3. If a new standard was entered then need to digitize position.

    3. Verify Standard Positions Exist

      1. Automate window, select Standards radio button to view standard position list.
      2. If positions need to be loaded from .pos file, load standard positions using Import button.
      3. Automate window, click Select Standards. Verify that all standards have a digitized position.
      4. If standard(s) missing from list, digitize using Automate--Digitize button.

    Acquire Window

    The Acquire window is used to set up samples, enter analytical parameters, and perform analysis in real time

      Sample Parameter Entry Buttons
    1. New Sample Declare new sample and load element data from element, sample, or file locations.
    2. Elements/Cations Enter new or edit existing element properties for measured and specified elements.
    3. Analytical Conditions Set or change analytical conditions in real time mode (conditions enforced on exit).
    4. Combined Conditions Set analytical conditions on per-element basis. Change measurement order.
    5. PHA Edit PHA properties and perform bias, gain, and PHA scans on a per-element basis. Uses current xyz position for measurements.
    6. Peak/Scan Options Edit offsets for off-peak backgrounds, wavescans, and peaking parameters on a per-element basis. Enable ROM scanning acquisition mode.
    7. Count Times Edit count times on a per-element basis for measurement of standard, unknown, or wavescan samples.
    8. Locate Display xyz coordinates of unknown samples acquired in current run. Coordinates are saved with each analysis from either realtime or automated analysis mode.
    9. Move Manual command movement of stage and WDS spectrometers, element and crystal selection. Clearing process flags and device reset.
    10. Acquisition Options Measurement options such as element measurement order, MAN on/off flags, etc. on both per-element and per-sample basis. See discussion of Acquisition Options window.
    11. Special Options Normal vs. TDI data collection switch, on a continuous and per-sample basis. See discussion of Special Options window.
    12. Rate Meter Simple rate meter display for spectrometers at current position on current xyz location.
    13. Stage Stage window for point and click movement of stage, display of static stage map images.
    14. Imaging PFE digital image mode for collection of BSE, SEI, and AUX images.
    15. Peaking Options WDS spectrometer peaking using current xyz location. Selection of elements to peak, peaking options, bias/gain/PHA coupled scans.


    16. Buttons Which Initiate Formal Sample Measurement
    17. Start Peaking Initiate peaking using parameters and element selection established with Peaking Options button. Uses current xyz location.
    18. Start Standard or Unknown Acquisition Initiate an analysis in real time mode using current sample parameters. If standard sample has been selected (via New Sample), drives to standard position and performs an analysis. If unknown sample has been selected (via New Sample), performs analysis on current xyz location. Repeated clicking of this button adds additional data rows to current sample.
    19. Start Wavescan Initiates collection of a wavescan sample using current sample parameters and uses current xyz location. Must have sample of type wavescan selected (via New Sample). Acquires step scan unless ROM scan mode enabled in Peak/Scan Options.


    20. Information and Progress Display
    21. Spectrometer and Stage Display Display of current spectrometer and stage positions.
    22. Spectrometer-Element Measurement Sequence Displays spectrometer-crystal information and current measurement action (peak, high background, low background) and number of x-ray counts collected. Also shows incremental measurement during TDI data collection.
    23. Faraday Displays faraday cup current after measurement.
    24. Current Sample Displays name of current sample. If asterisk * appears, the sample does not yet contain data and further changes to sample measurement parameters can be made. If sample contains data, only limited changes can be made to these parameters.
    25. Data rows and Good data rows Number of rows of data collected for this sample, and (if any rows have been disable from Analyze window, remaining number of good data rows.
    26. Progress/Beam Deflection Shows vertical yellow progress bar (starts at bottom, finishes at top) and stylized display of element sequencing on each spectrometer with time scaling. Also used for beam deflection display.
    27. Other parameters Display of Magnification, Beam analysis mode, Accelerating voltage, Probe current, and Beam Size (um) for current sample.

    Create New Sample

    1. Create New Sample

      1. Click on Acquire--New Sample.
      2. Important: New sample should always be of type unknown, except for following situations.
        Use sample of type standard when manually calibrating standards from Acquire window.
        Use sample of type wavescan when manually acquiring wavescan sample from Acquire window.
      3. Enter name of initial sample. Suggest "Initial master list".
      4. If entering elements manually (i.e., using Acquire:Elements/Cations) then skip next choices.

    2. Enter elements from Element Setup (option 1)

      1. Elements can be recalled from element database one-by-one to assemble the full list. Click Load Element Setup.
      2. Enter element symbol and browse database for previously saved elements.
      3. Remember, element setups are saved on a per-element basis preferably from a standard.

    3. Enter Sample Setup (option 2)

      1. Sample setups from current run can be selected and loaded (Current run only, must be set up in current run to appear in list). Click Load Sample Setup.
      2. Select sample setup from this run. This selects entire sample element list and all associated settings (probe current, background offsets, etc.).

    4. Enter File Setup (option 3)

      1. Sample setups and associated standards can be loaded from a preexisting run. Click Load File Setup.
      2. Browse to preexisting .mdb file, browse to appropriate sample and select. Suggest loading master list, then repeak spectrometers, then re-generate sample setups (vs. loading individual sample setups which will require repeaking and editing of peak positions).
      3. Two choices for loading of standards: "Yes" will load assigned standards and standard intensities, "No" will load standards into run but not the intensities.

    Enter Elements for Sample Using Acquire--Elements/Cations

    1. Acquire--Elements/Cations

      1. Click on Acquire--Elements/Cations. This opens Element Properties window
      2. Click on empty row to open Element Properties window, repeat this for all elements in sample.
      3. Other options:
        Load Element Setup: Load elements from Element database.
        Load Sample Setup: Load sample from current run from saved Sample Setups.
        Add/Remove Standards from Run: Modify or add to list of standards declared in run.

    2. Enter element symbol, X-ray line, and Cations/Oxygens

      1. Symbol: Enter element symbol or use drop-down list. Suggest "Ca" instead of "ca" for output formatting.
      2. X-ray line: Default X-ray line is selected based on elements.dat configuration file.
        Oxygen by stoichiometry is a specified element and uses a blank X-ray field at bottom of menu.
        Other specified elements (fixed wt%, stoich to other elements, etc. can also be added now).
        X-ray line selection issues: low overvoltage and/or incorrect line due to interferences or high absorption.
      3. Valence: Default valence via cations and oxygens in oxide formula is derived from elements.dat configuration file. Normally do not need to change.

    3. Disable Acquisition and Disable Quant Switches

      1. Disable Acquisition: used to modify the master element list so that a subset of elements are actually acquired for a given sample or sample setup.
        Suggestion: Set master list for all elements anticipated in probe session, peak and calibrated standards, then use DA to disable the elements which should not be acquired on a set of samples. Then reenable them as necessary.
      2. Disable Quant: used to disable the quantitative analysis of a measured element. Example of use is to disable multiple instances of an element when doing multiple spectrometer analysis so that individual element concentration can be inspected (see also Analysis Options--Use Aggregate Intensities). Second use is to disable an element that is known to be a "contaminant" in analyzed volume in order to obtain an element-free analysis (note this is strictly not correct).
      3. Note: If using multiple spectrometers for initial setup, then disabling elements on samples, must use both DA and DQ for the element you are turning off.

    4. Enter background type

      1. Conventional movement to off-peak position vs. Mean Atomic Number background correction.
      2. Off-peak requires no further setup other than correct offset.
      3. MAN requires calibration of MAN vs. Z or read-in from file setup. See also switches in Acquire--Acquisition Options.

    5. Enter Spectrometer and Diffracting Crystal, Inspect On-peak peak position and Off-peak background offsets

      1. Spectrometer: Select spectrometer number.
      2. Crystal: Default crystal is selected, if possible, from elements.dat config file compared to crystal inventory on spectrometer. If incorrect crystal is selected then red error is listed for out of range position. Further discussion of crystal selection based on resolution vs. intensity.
      3. Peak position: Important: Initial peak position is theoretical value and will be updated after successful spectrometer peaking. Note that if element is edited to change spectrometer or crystal the theoretical value will be reloaded.
      4. Background offset: Default X-ray line is selected based on elements.dat configuration file.
        Important: The default offsets are calculated from position-dependent function and are only approximately correct.
        Correct background offsets must be determined from a combination of wavescans on standards, samples of similar chemistry, and/or full-range wavescans acquired on pure elements/oxides, etc.
        Do not use default background offsets unless they have been approved!
        Suggestion: Edit background offset to consistent decimal place to indicate inspection and approval, also compare with accepted typical offsets.

    6. Enter PHA Baseline, Window, Gain, and Bias Settings

      1. Preferred setup is to use consistent baseline and window settings. Each detector/crystal combination requires calibrated values for gain and bias as follows:
        JEOL microprobes use discrete gain values (typically 16x, 32x, 64x, or 128x) with specific bias values determined on a per element basis. SCA scan range is from 0-10 volts with bias adjusted for 4 volt PHA pulse. Baseline of 0.5 volt and integral window of 9.5 volt are typical but superceded as needed for light element measurement or escape peaks, for example.
        CAMECA microprobes use a constant bias value and specific gain values determined on a per element basis. SCA scan range is 0-5 volts with gain adjusted for ~2 volt PHA pulse. Baseline of 0.X volt and integral window of ~4.X volt are typical but superceded as outlined above.
      2. If emppha.dat file is properly calibrated and enabled in probewin.ini file, then Calibrated PHA button is enabled. This button will calculate:
        Calibrated bias for approved gain setting on JEOL microprobe.
        Calibrated gain for approved bias setting on CAMECA microprobe.
        Select appropriate gain on JEOL or bias on CAMECA, then click Calibrated PHA button. If green value is displayed then calibrated value is being used. Otherwise enter appropriate value in text field.
      3. If differential mode is required, select Use Differential PHA mode (not typical).

    7. Integrated Intensity Scan Settings

      1. Enable integrated intensity scan using checkbox (not typical, used for light element measurement).
      2. Enter initial step size, minimum step size, and area peak factor APF.

    8. Off-peak Correction Type

      1. Linear: Default off-peak correction type is linear. This uses a linear fit (of form y = mx + b) to the high and low background offsets to calculate the background intensity at the peak position.
      2. Average: uses average value of the two background measurements, whereas high and low only use only those single measurements.
      3. Exponential: uses exponential calculated value based on two measured background values from high and low positions
      4. Polynomial: uses polynomial calculated value based on two measured background values from high and low positions. Typically this option is evaluated using a wavescan sample and background modeling that is accessed from the Plot window. The position and coefficient values are assigned to samples from the modeling window.

    Analytical Conditions

    1. Analytical Conditions from Acquire--Analytical Conditions

      1. Click Acquire--Analytical Conditions. This opens the window and populates the text fields with default values loaded from probewin.ini. The Analytical Conditions are set on a per-sample basis, meaning that each sample may have unique conditions used for analysis (see Automate: Digitized Conditions mode for comparison).
        Note: if instrument does not have automated control of item (e.g., probe diameter) then item is grayed out.
        Important: Conditions set in Acquire--Analytical Conditions window are enforced upon exit from window when Ok button is clicked. Inspect status bar of log window for progress of conditions being set. For analytical conditions to be set on a per-sample basis for automated analysis, use Automate window with mode set to Digitized Conditions.

    2. Enter Analytical Conditions

      1. Read Conditions: can read conditions from instrument, however, typical use is to enter desired values in text fields which are enforced upon exit from window.
      2. Accelerating voltage: Typically left to default value but can request new kV as necessary.
      3. Probe current: Value in nA, set as necessary.
      4. Probe diameter: Value in μm, set as necessary.
        Suggestion, use defocused beam initially for standardization, then set as necessary for analysis of samples. If using defocused beam, set right before acquiring standard samples so you do not have to set diameter to zero for imaging during the confirmation step.
      5. Default aperture: If probewin.ini flag is set, can have specific probe current calibration data for up to 2 apertures for use in automated setting of probe current. This value is the aperture setting number which may refer to any actual aperture on the instrument.

    3. Select Beam Mode and Magnification

      1. Read Beam/Mag: Can read current values for magnification and (on JEOL) x and y shift.
      2. Analog Spot: Use Analog Spot for non-rastering spot mode. The probe scan should be on and Analytical Magnification is magnification value used with instrument in spot mode to allow control of x and y shift (for JEOL microprobes).
      3. Analog Scan: Use Analog Scan mode for rastering of electron beam during analysis. Analytical Magnification is magnification used to set the dimension of rastering area. Probe scan is on to allow x and y shift (for JEOL microprobes).
      4. Magnification: value of magnification used at end of analysis, should set to typical working value for selection of next analysis point or inspection of sample.
      5. Imaging magnification: default magnification used for PFE digital image acquisition.
      6. Read column conditions: reads the current values of the magnification, and x and y shift values (on JEOL microprobe) for inspection.

    4. Select Column Conditions

      1. Column conditions: Complete snapshot of column conditions can be read, saved, or loaded for customization of column setup. The settings are significantly expanded compared to the JEOL column conditions.
      2. Pre-acquire and Post-acquire strings: for JEOL 8900 only, text string to be sent to SC board prior to analysis (e.g., MG 400 to set magnification to 400) and after analysis. See JEOL EOS documentation.

    Combined Conditions

    1. Set Combined Conditions from Acquire--Combined Conditions

      1. Click Acquire--Combined Conditions. This allows analytical conditions to be set on a per-element basis rather than a per-sample basis as used in Analytical Conditions. This mode is not routinely used and would apply to trace element analysis, for example.
        Note: if instrument does not have automated control of item (e.g., probe diameter) then item is grayed out.
      2. Set parameters as in Analytical Conditions window, but on a per-element basis.

    PHA -- Pulse Height Analysis Settings

    1. Proper measurement sequence

      1. Note that bias or gain and PHA scans should be acquired when the spectrometer is on the peak for the given element. The setup sequence should therefore be:
      2. Confirm standard positions to have valid xyz coordinates for standard.
      3. Peak spectrometers to have correct peak position for elements.
      4. Perform primary calibration (i.e., acquire standard sample)s.
      5. Note that bias or gain scans can be coupled with the automated peaking procedure, so that peaking precedes acquisition of a bias or gain scan, which can all be reviewed from the Run menu.

    2. Edit PHA Settings from Acquire--PHA

      1. Click Acquire--PHA. This opens Pulse Height Analysis (PHA) window. Click on element row to open PHA Properties window.
      2. It is necessary to use a standard with sufficient concentration of the element for PHA scanning, if not positioned, this needs to be done first.
      3. The spectrometer needs to be on the X-ray peak for this element and this can be done using the Move On Peak button.
      4. All PHA scans should be performed at a moderate count rate to avoid gain shift behavior. Suggestion is ~ 20kcps.
      5. All scans (bias, gain, PHA) are added to the current run and can be viewed using the Run: Display and Export Scans menu selection, or the PHA--Display and Export Scans button.

    3. Acquiring a Bias Scan (JEOL)

      1. If spectrometer for this element is not on the peak, drive to peak using Move On Peak button.
      2. Edit Bias Low and Bias High limits for bias scan in Bias and Gain Scan Range section.
      3. For JEOL you should use a 4 volt baseline with a 0.1 volt window for a bias scan. These are set in Bias/Gain Scan Window.
      4. Edit Count Time (seconds) and Intervals as needed for bias scan.
      5. Start the bias scan by clicking on Acquire and Graph Bias Scan Distribution.
      6. When the scan is finished, read the bias value from the graph and edit the bias field for this element, if necessary.

    4. Acquiring a Gain Scan (CAMECA)

      1. If spectrometer for this element is not on the peak, drive to peak using Move On Peak button.
      2. Edit Gain Low and Gain High limits for gain scan in Bias and Gain Scan Range section.
      3. For CAMECA you should use a ~2 volt baseline with a 0.1 volt window for a gain scan. These are set in Bias/Gain Scan Window.
      4. Edit Count Time (seconds) and Intervals as needed for gain scan.
      5. Start the gain scan by clicking on Acquire and Graph Gain Scan Distribution.
      6. When the scan is finished, read the gain value from the graph and edit the gain field for this element, if necessary.

    5. Acquiring a PHA Scan (Both Instruments)

      1. A PHA scan is used to confirm that the bias/gain setting and the baseline are set properly.
      2. If spectrometer for this element is not on the peak, drive to peak using Move On Peak button.
      3. The Gain and Bias settings in the PHA Properties section are used, make sure they are correct.
      4. In the Scan PHA Distribution section, edit Count Time (seconds) and Intervals as needed for PHA scan.
      5. Start the PHA scan by clicking on Acquire and Graph PHA Distribution.
      6. When the scan is finished, inspect the graph and make sure the baseline and window are appropriate for this element, and edit the fields in the PHA Properties section if necessary.
      7. JEOL: Bias is set to place PHA pulse at ~4 volts. Baseline is ~0.5 volts and integral mode is used with ~ 9.5 volt window.
      8. CAMECA: Gain is set to place PHA pulse at ~2 volts. Baseline is ~0.X volts and integral mode is used with ~4.X volt window.

    6. Control buttons

      1. Get PHA: will retrieve PHA settings from the instrument.
      2. Set PHA: will send the current (edited) values to the instrument; this is also done on exit from the PHA Properties window.
      3. Move On Peak: will drive to the peak position for this element to set up for PHA measurements.

    7. Enter PHA Properties

      1. These are typically determined from Bias/Gain and PHA scans, then edited.
      2. Edit Baseline, Window, Gain, and Bias as necessary.
      3. Click on Calculate Empirical PHA to use emppha.dat calibration to calculate PHA parameters using calibration data that you generated.

    Setting Peak / Scan Options

    1. Acquire--Peak/Scan Options

      1. Click Acquire--Peak/Scan Options. This opens Peak and Scan window.
      2. The Peak and Scan window shows all elements in the sample; the Display radio buttons can be used to display the On/Off Peaks, Wavescan limits, etc. in this view. The spectrometer offsets value shows the difference between theoretical and actual peak positions for calibrated elements.
      3. The Use ROM Based Spectrometer Scanning checkbox allows faster (continuous) wavelength scanning when selected. This applies to acquisition of a wavescan sample.
      4. Incremental movement of the stage during peaking or wavescan acquisition is enabled with checkboxes and the increment is set in the text fields as necessary. If these are selected, make sure that sufficient area of the standard or sample is available for use during incremental movement (i.e., avoid epoxy, etc.).

    2. Editing Peak/Scan Properties

      1. Click on element row to open Peak and Scan Properties window.
      2. This window allows you to edit:
        Peak and background offsets that are used by default on standards and samples for an element
        Wavescan limits for a wavescan sample using this element
        Peaking parameters that are used when peaking this element.
      3. It is assumed that a wavescan range exceeds the offsets used for background measurement, so that a wavescan acquisition can be used to evaluate the background offsets.
      4. Adjustments to these parameters will be used on the current sample and retained until changed in subsequent samples.

    3. Editing Peak and Background Positions

      1. Edit On Peak, Hi Off Peak, and Low Off Peak values if necessary. These are the same values displayed in the Elements/Cations window during initial element setup.

    4. Editing Wavescan Limits

      1. Wavescan limits are used for a sample of type wavescan. A wavescan can be used for the following purposes:
        Evaluating background offsets using a wavescan that is centered around a peak (typical range is about 10 mm on a JEOL)
        Evaluating the wavelength scan structure of a spectrometer using a full-range wavelength scan
        Determining the presence or absence of elements in a material using a short range wavelength scan coupled with an extended count time.
      2. For conventional wavescans edit the Wavescan Hi Limit and Wavescan Low Limit as necessary. Edit the Wavescan Points so that proper sampling of the spectrometer step size is being used.
      3. For a full-range wavelength scan:
        Click on Set Wavescan Full Range
        Use Absolute Position radio button in Display Positions section to view absolute range
        Adjust range as necessary, then adjust Wavescan Points for proper sampling of wavelength step size.

    5. Editing Peakscan Limits

      1. The peakscan limits can be edited, but typically the default values are used for ROM peaking.
      2. The Peakscan Hi Limit and Peakscan Low Limit values nominally set the range of scanning for both ROM and Manual peaking.
      3. The Peakscan Points setting determines the number of steps in the peaking scan.

    6. Peaking Parameters

      1. Peaking Start Size and Peaking Stop Size are used in the built-in PFE routines.
      2. Minimum P/B tests for a valid peak prior to the peaking routine. If the P/B test fails the peaking procedure is ended.
      3. Minimum Peak Counts (cps) sets the minimum X-ray intensity that is valid for a peaking attempt, and if insufficient the peaking routine is also terminated.
      4. Maximum Peaking Attempts is used only by the built-in PFE routines.

    Setting Count Times

    1. Acquire--Count Times

      1. Click Acquire--Count Times. This opens the Count Times window.
      2. Count Times are displayed for all elements in the upper section.
      3. A time-budget graphic is shown in the lower section, which indicates the sequencing and timing of element measurement on each spectrometer. Adjustments to the count times will be reflected in this graphic.
      4. Beam averages and nominal beam are superceded on JEOL and CAMECA instruments where the probe current is measured after each sample and beam averages is set in probewin.ini.

    2. Editing Count Times

      1. The count times for an element can be edited by clicking on the row for that element, which opens the Count Time Properties window.
        Important: If you select the top row and drag, you can edit all elements simultaneously from the properties window that is opened.
      2. The On-Peak, Hi-Peak, and Lo-Peak Times allow assignment of counting on a per-element basis. These times default to probewin.ini values.
        Note that for major element concentrations where P/B is high, it is acceptable to count the backgrounds less than half of the peak count time. However, for minor and trace element concentrations it is necessary to count the peak and backgrounds the same total time.
      3. The Wavescan Time is the time per point for a normal wavescan acquisition where the spectrometer is stepped, then counted, etc. This is a high overhead process so for slow wavescans this mode should be used, but for fast wavescans the ROM Based Spectrometer Scanning checkbox in the Peak/Scan Options window should be selected.
      4. Peaking time is used for manual peaking. Peaking time divided by 4 is used for ROM peaking.
        Important: Do not change the peaking time to a value such that (value/4) is an uneven number as this can cause problems with the ROM peaking call on the instrument.
      5. The Quickscan Time is used for quick wavescan acquisitions (set in the Acquire--Special Options window).
      6. For samples of type standard and unknown, all fields are enabled except the Wavescan Time. Conversely, for a sample of type wavescan only the Wavescan Time is enabled.

    3. Statistics Based Counting

      1. For some instruments counting can be made using a count basis rather than time basis.

    4. Unknown Count Time Factor

      1. The count times set in the time properties section apply to samples of type standard and unknown. That is, by default or until changed by the user, the peak and background count times are identical for standards and samples.
      2. The Unknown Count Time Factor is used to scale the counting time for unknowns relative to the nominal count times entered in the Count Time Properties fields.
        A factor of 2 results in this element being counted a total of 2x the nominal value for peak and backgrounds, a factor of 5 results in a total of 5x count time increase, etc.
        These count time factors are assigned on a per-element basis and allow for adjustable count times for samples with, for example, some elements disabled for a customized element list derived from the master list.
      3. This factor is also used by the Alternating On and Off peak acquisition mode.



    About Analysis Options


    About Analysis Options

    There are three locations where options are set that affect all samples or are assigned on a per-sample basis.

  1. Analytical Menu -- Analysis Options

    1. Analytical Menu -- Analysis Options opens the Analysis Options window.
      These global switches are used to engage a correction, to demonstrate the degree of difference in using vs. not using a correction, and for purposes of debugging problem data.
      This window has global on/off switches which are used to turn processing features on and off. These settings are for processing of data, not measurement parameters. See toolhelp and help menu for more information).
    2. Quantitative Acquisitions Options. Global switches for deadtime correction, and time-corrected drift correction for probe current and standard intensities. If dramatic changes in standard intensities exist (loading old standards into run and acquiring samples, then restandardizing) then a large drift correction may be applied. Turn off, run Analyze and compare results.
    3. Quantitative Analysis Options. Global switches to turn on and off Interference Correction, Time Dependent Intensity correction, Absorption correciton of MAN intensities, Particle correction, Same peak and PHA settings unknown vs. standard, Zero point in calibration curve, Conductive coating correction, and Fast Quantitative Analysis correction mode.
    4. MAC (mass absorption coefficient) and APF (area peak factor) Options. Global switches for use of Empirical MAC values, and Empirical APF Values.
    5. Calculation Options. Global switches for Aggregate Intensity correction (combining multiple spectrometer measurements to single k-ratio), Blank Calibration, Force negaive k-ratios to zero, Calculate electron/x-ray ranges, Oxygen-halogen correction, Nth-point background on/off, Count overwrite to data, Force negative interference corrections to zero, Chemical age calculations, and Savitsky-Golay smoting for integrated intensities.
    6. Formatting Options. Automatic formating for number of significant digits, Detailed printout mode, Print analyzed and specified elements on single line, Display count intensities un-normalized to time, and Print Additional MAN Parameters.
    7. Output Options. Display charge balance calculation, Element output order for specific Output menu modes.

  2. Acquire Window -- Acquisition Options

    1. Acquire Window -- Acquisition Options opens the Acquisition Options window.
      These switches and settings are used to set measurement parameters using during the acquisition of data for a sample. They are set on a per-sample basis and can be set and assigned to sample setups.
      See following section, toolhelp and help menu for more information.

  3. Acquire Window -- Special Options

    1. Acquire Window -- Special Options opens the Special Options window.
      These settings control normal vs. TDI (time-dependent intensity) modes for the measurement of data on a sample (and standard if desired). These settings are on a per-sample basis, and can be set and assigned to sample setups.
      See following section, toolhelp and help menu for more information.


    Acquisition Options Window



    1. Acquire--Acquisition Options

      1. Click Acquire--Acquisition Options. This opens the Acquisition Options window.
      2. Acquisition Options properties are displayed for all elements in the upper section.


    2. Editing Acquisition Properties

      1. Click on the row of an element to open the Acquisition Properties window for that element. This window is used for several purposes.
      2. The order of measurement for this element is set using Spectrometer Order Number, where 1 is the first element to be measured. If a user-defined order should be used as when using TDI, the Acquisition Order should be set to User Defined Order Number.
        Important: If using the TDI correction, the first element on each spectrometer will be measured incrementally for the TDI correction. Be aware that if elements are disabled, you must check the order sequencing so that a valid TDI is being made (i.e., resequence the element list so an enabled element exists for the first sequence).
      3. On-off switches for the MAN background measurement type allow the background treatment to be set here and customized for samples vs. standards. This capability extends the setting made in Elements/Cations where the background measurement type of Off-peak vs. MAN would apply to all sample types.
      4. The capability to peak the spectrometer for a given element when analyzing samples is set using the Peaking on Acquisition checkbox. The spectrometer will be peaked on the first analysis of a sample (i.e., first digitized point of an automated sample with multiple points per sample).

    3. Acquisition Order

      1. The Acquisition Order radio button allows the choice of element sequencing on a spectrometer. One should use Descending Angstroms in general, and User Defined Order Number to set the beam-sensitive elements to be measured first for TDI correction.

    4. Miscellaneous Options

      1. The Miscellaneous Options are generally self-explanatory. Suggested settings are listed here.
      2. Return to On Peaks After Acquisition should be enabled, as this allows monitoring of X-ray intensity prior to analysis.
      3. Blank Beam After Acquisition should be enabled to prevent damage to samples and unwanted contamination of the column during long beam irradiation of materials.
      4. Both Measure Beam On... and Measure Absorbed Current should be enabled in order to properly correct for probe current drift for each analysis and to monitor current instability on the sample via the absorbed current reading.
      5. Use Automatic Analysis After Acquisition should not be enabled until all standard samples have been acquired. This is because a ZAF correction cannot be performed until all the standard intensities have been acquired. Prior to analyzing samples, Automatic Analysis can be enabled, which will automatically perform the ZAF correction at the conclusion of spectrometer counting.
      6. Use Automated PHA Control should be enabled for instruments that allow that function as calibrated bias and/or gain settings should be used to place all pulses at a consistent voltage.
      7. Use Alternating On and Off Peak Acquire should only be enabled for the specialized capabilities of low-level concentration measurement.
      8. Load Standard Data From File Setup, when enabled, loads the list of standards and their most recent calibration intensitities from another PFE run when the File Setup function is being used.
      9. Do Not Display Standard Images controls display of image XXXX_standard.bmp image, if present, during digitization of a standard.
      10. Use Last Unknown As Wavescan Setup allows the element inventory of the last sample of type unknown to be used as the template for a new wavescan sample (this is desirable and eliminates the need to completely set up an element list again for a sample of type wavescan).
      11. Use Unknown Count Time for Interf. Standard allows use of the count time assigned to the given element to be used for measurement on the interference standard (as opposed to the default count time for measurement on the standard). Use a longer count time for the unknown element to improve counting statistics for the interference correction.

    5. Automatic Analysis and Excel Export Options

      1. PFE does not automatically run the ZAF/PRZ correction at the end of each sample measurement. This is because during standard sample acquisition the correction cannot be run until all x-ray intensity measurements on all standards have been acquired.
      2. To automatically run the correction at the end of each unknown sample measurement, select Use Automatic Analysis After Acquisition.
      3. Select appropriate Excel output format. Must have opened link to Excel from Output Menu (Open Link to Excel ...).


    6. Automated Standard Acquisition

      1. Use Only Digitized Standard Positions will limit the number of points acquired in the Automate window for acquisition of standard points. For example, if 5 points are set for number of standard points in the Automate window and only 2 have been explicitly digitized, only those two points will be acquired. This is to limit generation of virtual standard points. It is always recommended to use explicit standard points rather than relying on generation of virtual points that may fall on cracks or epoxy.

    7. Spectrometer Motion

      1. Use Synchronous vs. Asynchronous acquisition: synchronous mode forces all spectrometers to start in sequence and should be used for TDI measurement so that all spectrometers start at the same time-zero point. However, this will also force all spectrometers to wait for completion of the current element on all spectrometers before continuing. Asynchronous acquisition will allow all elements to be measured independent of coordinated sequencing on the other spectrometers.

    8. Automation Email Reporting

      1. Sends email message upon detection of error condition. Note: requires SMPT to be set up on the PC and will not work otherwise.

    9. Stage/Spectrometer Backlash

      1. Global switches for software-controlled backlash correction. For most microprobe setups we are using the hardware-controlled backlash settings so these radio buttons will normally be grayed out.

    10. Autofocus Options

      1. Autofocus threshold sets the brightness threshold for data to be used in the autofocus fit of brightness vs. z-axis sample position. This value can be used to eliminate noisy data from the autofocus profile. Also check the hardware settings (JEOL 8X00 check CAF hardware settings).

    11. N-th Point Background Options

      1. Global switch for turning the N-th point background measurement on and off.
      2. The settings for N-th point are on a per-element basis and are set in the Acquisition Properties window for each element, accessed from the Analysis Options window (i.e., this window).
      3. Can also use a specific element intensity variation to trigger measurement of a new background value.
      4. See also the MAN background measurement method.


    Special Options Window


    Special Options


    1. The Special Options window is used to turn on and off the normal vs. Time Dependent Intensity acquisition of data.
    2. When Normal Acquisition is selected, no TDI is performed and all analyses are acquired without any special treatment; no incremental counting is performed. This mode once selected, commences with the next analysis or is assigned to the current sample or sample setup.
    3. Self Calibration TDI Acquisition performs an incremental measurement on the first element of each spectrometer only and acquires the data incrementally on the sample or standard using the number of TDI intervals. Use Acquire -- Analysis Options to set the measurement order using User Specified Order to arrange the element measurement in the proper sequence. Planning is required so that you do not have, for example, Na and Si on the same spectrometer as they should be on different spectrometers for TDI correction. The on-peak count time is divided into the number of intervals specified and incremental counts are made on the sample or standard.
    4. For TDI correction on standards, the Acquire TDI Data on Standard Samples checkbox must be selected.
    5. Assigned Calibration TDI Acquisition uses the TDI behavior on a specific sample to perform the TDI correction on all samples. This requires that the TDI behavior on a set of materials is identical, which is typically not the case.
    6. Quick Wavescan Acquisition is not for Normal vs. TDI acquisition. It is for the acquisition of very rapid wavescan samples using a percentage slew speed for the wavescan. This mode is not recommended, please use rom scan mode for wavescan samples.


    Automate Window


    Also see discussion on Automated Analysis

    Confirming Standard Positions

    1. Ensure that all necessary standards have been added to the run via the Standard Menu.
    2. Secondly, ensure that all standards in the run have position entries in the Automate position list. Set the list to show Standards by selecting the Standards radio button.
    3. Click Select Standards to highlight all standards that are both in the run and which have positions in the Automate window.
    4. If standards need to be digitized use: (Automate -- Digitize, Standard, select standard from list, drive to position, use Single Point to set default position).
    5. Automatation Actions: check Confirm Standard Positions. Recommend not having any other AAs selected for initial sweep of standard positions.
    6. Click Run Selected Samples yellow bar and cycle through all standards to set their position for subsequent measurement.

    Peak Spectrometers

    1. Ensure that all necessary standards have been added to the run via the Standard Menu.
    2. Confirm that standard assignments are as intended using Analyze -- Standard Assignments, this is done using the initial unknown sample for a new run. The assigned standard for an element is used by default for both spectrometer peaking and primary calibration (acquire standard samples). If there is a peak shift anticipated for an element (e.g., light elements) then an appropriate standard should be used for both peaking and calibration.
    3. Secondly, ensure that all standards in the run have position entries in the Automate position list. Set the list to show Standards by selecting the Standards radio button.
    4. Click Select Standards to highlight all standards that are both in the run and which have positions in the Automate window.
    5. Check the Peak Spectrometers checkbox. Suggest no other checkboxes are selected in case peaking fails and needs to be repeated.
    6. Click the Peaking button. If all elements are not selected in the list, select all or the ones that need to be peaked.
    7. Peaking parameters are a function of analytical requirements. The following guide is useful based on experience:
      Peak Center Method: Use ROM Based for standards with sufficient count rate to use a ROM peaking scan.
      Use Manual scan mode for elements/standards with a low count rate (light elements, minor elements in standards).
      ROM Peaking Type: Suggest Highest Intensity (note that a smoothing operation is performed that is not seen in livetime peaking display but can be duplicated in Run Menu -- Display Peaking Scans).
      However, other peaking types can be used and are simply treatment of the acquired ROM peaking data.
      Peak Center Options:
      For automated bias/gain and/or PHA scanning: Acquire Automated PHA Scan After Peaking and (typically) either Acquire PHA Bias scan or Acquire PHA Gain scan. These ensure proper PHA scan which can be performed later.
      For manual peak scanning, suggest Display Spectrometer Pre-Scan for Confirmation, this dialog will allow selection of the peak position by use of a slider and peak marker. The post-scan confirmation is typically redundant but may be used if desired.
    8. Click Run Selected Samples yellow bar and cycle through all standards which will use them for spectrometer peaking.
    9. After spectrometer peaking completes, use the Run menu -- Display Fit and Export Spectrometer Peaking Scans to inspect each scan performed. All peaking profiles, bias or gain scans, and PHA scans should appear here and are stored in the run .mdb file.
    10. For ROM scans using the Highest Intensity option, remember to select that same option with smoothing checkbox enabled. This is necessary to duplicate the same data as used for the centroid determination.
    11. Note that the mouse can be used to determine the peak position by inspection in this display mode. If you are not satisfied with the centroid determined by the software, determine the centroid yourself. Then use Acquire -- Elements/Cations to open the Element Properties for that element and hand edit the peak position. This position will then be used for subsequent samples if they are based on this sample setup.

    Acquiring Standard Samples

    1. Ensure that all necessary standards have been added to the run via the Standard Menu, they have correct XYZ positions, all elements are in current sample, analytical conditions are correct, count times are correct, PHA settings are correct, etc. etc.
    2. Click Select Standards to highlight all standards that are both in the run and which have positions in the Automate window.
    3. Select Automatation Actions and check Acquire Standard Samples. Recommend not having any other AAs selected for initial sweep of standard positions.
    4. Recommend using Use Last Unknown Sample for consistent measurement during standardization. Can use Digitized Conditions or Digitized Sample Setups for complete control, but this is typically done for unknowns only.
    5. Two choices for acquisition of standard samples: Normal PFE measurement measures all elements in sample on all standards (benefit is built-in check of blank values, background validity, and interference calibration) vs. Quick Standards which will acquire only the elements for which the given sample is the primary calibration standard. Example: Normal: all elements measured on Amelia Albite vs. only Na and Si measured on same.
    6. Number of standard points. Important issues regarding number of standard points used for calibration:
      Standard Points to Acquire (SPA): number of x-ray intensity measurements acquired for each standard sample in the automation sequence (i.e., a global number).
      If SPA is set to 5 and all standards have 5 explicitly digitized positions, these positions will be used for calibration on each standard. This is the recommended method.
      If SPA exceeds number of explicitly digitized positions, virtual positions will be generated for those standards with a number of positions less than SPA. The virtual positions use the last digitized position and increment the stage x-axis by the amount entered in Standard X increment (um). If the increment is 5 um then each virtual point will be place 5 um higher in x position from the previous. While this works on large well polished standard grains it is not preferred as pits or the edge of the standard grain could be reached. Suggest using explicitly digitized points instead (they can be random, line traverse, etc.).
    7. If Acquire Standard Samples (again) is used during the run, and virtual standard points are necessary, the stage is further incremented by the y-axis value entered in Restandard Y increment (um).
    8. Click Run Selected Samples yellow bar and cycle through all standards to measure all elements.


    Analyze Window


    Analyze Window Components and Uses

    1. Analyze In PFE the ZAF/PRZ correction is performed on demand by clicking on the Analyze button.
      Unless the Output menu is used, all analysis output is printed to the log window.
    2. Use Output Menu -- Save to Disk Log if you really want all output saved to a text file. This is not normally done since all analyses are performed on demand.
    3. Multi-select standards or unknowns to analyze those materials or to modify the calculation settings which are assigned on both a per-element and per-sample basis.
    4. Data prints raw count data to the log file.
    5. Kraws prints raw k-ratio data to the log file.
    6. Calculation Options (button and window)
      Calculate oxygen by stoichiometry (note for standards if oxygen not calculated by stoichiometry you will get specified oxygen from the standard.mdb entry).
      Calculate detection limits, sensitivity, homogeneity (n>3 points required).
      Specified element treatment: Difference, Stoichiometry, etc.
      Formula basis output.
      EDS element measurement
      Carbon coat treatment (simplified)
    7. Standard Assignments standards assigned on per-element and per-sample basis. Primary standard is used for both peaking and primary calibration.
    8. Elements/Cations used for generation of element and sample setups, adding specified elements to selected samples in analysis list.
    9. Name/Description used to rename or correct an incorrectly named phase inherited from automated analysis using Automate, or to add additional comments to a sample.
    10. Specified Concentrations used to enter fixed wt% data for elements not formally analyzed. Can enter directly on a per-sample basis, or use the standard database or existing samples in the run as a source for routinely used matrix compositions.
    11. Note regarding Sample Setups Sample setups are generated from a new sample, edit necessary measurement parameters, and finally saving the sample setup using the Elements/Cations button and Save Sample Setup button. If sample setup does not contain measurement data, can edit analysis parameters from Analyze window at a later time (e.g., Conditions, Count Times).


    12. Deletion/Disabling of Samples and Data Lines
    13. Delete Selected Samples disables an entire sample. If a standard sample is disabled, then it is not used for correction and is removed from the drift correction calculation.
    14. Delete/Undelete Selected Lines and Analyze Selected Lines allows disabling/re-enabling of individual point data in a sample, or analysis of only that point.


    15. Report Features
    16. Report generates a text report on a per sample basis.


    17. Combined Sample Processing
    18. Combined Sample Features Combining samples means that individual sub-sets of a composite analysis can be performed then combined for the final composite analysis. Two samples, each with the same number of points, represent subsets of a complex analysis (i.e., element list requiring crystal flip or different analytical conditions) which are combined and analyzed on demand.
      Conbine Selected Samples
      Combine Analysis Lines from Selected Samples
      Combine Data Lines from Selected Samples
      Combine the Selected Samples into a New Sample

    Evaluating Calibration on Standard Samples

    1. Important points: The Calculation Options for Standards and Samples are essentially unique while they are derived from the initial sample. If you forgot to add Oxygen as a specified element, this will need to be remedied by adding oxygen to all standards in the acquired list.
    2. Remember that all settings in Analyze window can be on either a per sample basis (analytical conditions, calculation options, etc.) or a per-element basis (standard assignments, interference assignments, etc.). When setting parameters for per-sample basis, you need to select all or individual samples in position list in order to assign the parameters to the desired samples, otherwise you would have to open each sample and set the parameters individually.
    3. Example: Select all standards in position list, select Calculation Options, and set Calculate Oxygen by Stoichiometry. This will use stoichiometric oxygen value computed from measured elements rather than pulling in oxygen as a specified element from the standard database.
    4. Next, select standards with common chemistry and oxygen basis (i.e., all olivines with 4 oxygens), click on Calculation Options, and select formula basis and pull down menu for oxygen.
    5. Click Analyze to perform ZAF/PRZ correction and evaluate the analysis. Pay attention to measured vs. published values and use several standards to compare primary calibration. Analysis of secondary standards gives best indication of accuracy and calibration problems.
    6. Standard Assignments can be modified on a per sample basis by seleting the standard in the list, and clicking on Standard Assignments to assign a different standard to one or more elements.


    Guide to Picture Snap



    Guide to Picture Snap
    Use Picture Snap to load a digital image of any type, calibrate it, and use it for microprobe analysis

    1. Open the Picture Snap window using Run -- Display Picturesnap.
    2. Use the Picture Snap File menu to open the digital image for calibration. It can be a .bmp, .jpg, or .gif image. It can be a backscattered-electron image or mosaic, a composite x-ray map, a reflected light mosaic, etc. so any source can be used.
    3. Use the Window menu to select Calibrate Image to Stage Coordinates. This opens the calibration window.
    4. Calibration method:
      Three point calibration: Use the three point calibration if rotation needs to be corrected and if there is a tilt to the image requiring a z-axis planar fit to the calibration data.
      Two point calibration: The two point calibration is obviously quicker but does not correct for rotation or include z-axis correction for a tilted sample.
    5. Inspect the image and decide on two or three points that have a significant range for both x and y. For the three point calibration an equilateral triangle is best.
    6. Drive the stage to each calibration point.
      Click Read Current Stage Coordinate. Check that a valid and correct set of xy coordinates has been read.
      Click Pick Pixel Coordinate on Picture and click the exact position that the stage is currently located.
      Repeat this for the other points.
      When finished, click on Calibrate Picture.
    7. The calibrate function generates an .acq file which has the calibration data for twips (VB image pixel values) and xyz stage calibration points used for the calibration procedure.
      Note that if the entire stage block is being loaded each time and a generic calibration is desired, one can copy the .acq file to a new name and then recalibrate the image or use the rough calibration as-is.<<
      Remember that you can also use the static images in the Stage window or the JEOL/Cameca software to generically drive around on the stage mount.
    8. Display Calibration Points can be used to confirm the location of points on the picture. It does not guarantee that the xy coordinates are correct, however. Turn this off before exiting the Calibration window.
    9. The image should now be click-able and should have a scale bar present. Confirm the image calibration by double clicking on the image, wait for the stage to drive to that location, and determine if the calibration is valid.
    10. If the calibration is not satisfactory, repeat the calibration procedure. If the image is not internally consistent due to image distortion you will not get a consistent calibration.
    11. To display the locations of position samples (of type standard, unknown, or wavescan), select the approrpriate submenu from the Picture Snap Display menu. Note: these are the locations of digitized position samples.
    12. To show labels for digitized position samples, select the appropriate sub menu from the same Display menu. Note: these are the labels and numbers of position samples, not analysis numbers. To understand this point, if a given position sample is repeatedly used for automated analysis then the analysis number increments but the digitized position sample does not.
    13. To display the positions and labels for analyzed samples, use the Run menu to select the display of acquired sample types and their labels on the Picture Snap image. The display of analyzed samples is intended for use after completion of part of a run, or using PFE on a remote computer to view the positions of analyses after completion of a run.
    14. The Picture Snap image with markers for position or analyzed samples can be captured using a screen capture utility. Note that the red circles and labels are not part of the Picture Snap image so this utility is necessary to capture an annotated PS image.


    Guide to Automated Analysis



    Guide to Automated Analysis

    Perform Automated Analysis of Standards, Unknown Samples, and Wavescan Samples

    Automate Window Components

    Positions List

    1. This list which shows the position samples of type standard, unknown, and wavescan.
      Position samples are selected by clicking, multi-clicking, and dragging, or by using Select All Standards or Select All.
      Samples that have been digitized or imported from a .pos file will appear in this list.
      The radio button for Standard, Unknown, and Wavescan samples is used to list these position sample types.
      Generally you will operate on one sample type at a time:
      Use Standard positions for Confirm, Peaking, Acquire Standard Samples.
      Use Unknown positions for Confirm, Acquire Unknown Samples, etc.
      Use Wavescan positions for Confirm, Acquire Wavescan Samples, etc.
    2. Selecting all standards. Click Select Standards to automatically select all standards that are currently in the run. This should be done before Confirm, Acquire, etc. to conveniently select the necessary standards.
    3. Select All. Select all positions samples of this type, generally used to select which position samples will be exported to a .pos file.
    4. Delete All. Deletes all position samples of this type from the position.mdb database.
      Important to export position samples to a .pos text file before deleting positions from the position.mdb database.
    5. Positioning to a specific positions sample. Selecting the sample in the list, then click the Go button, and the stage will drive to the xyz coordinates for that position.
    6. Updating a specific position sample. Select the sample in the list, click Go button to drive to the xyz position, correct the position by driving the stage and adjusting z as necessary. Click on the Update button to update the position sample.
    7. Changing analysis order. Use up/down buttons to move position samples in list window to change the analysis order of samples.
    8. Reload button. Use reload button to force a reload of the position list if necessary. This is necessary after position names have been edited, etc.
    9. Correcting the name of a position sample (use for Unknown and Wavescan samples).
      Click on Move button, Positions button, Select sample in list, Edit Sample button, change name or edit any other sample parameter.
    10. Duplicating Standard Positions as Unknown or Wavescan positions. To generate position samples on standards for use as unknowns or wavescans.
      Click Move button, Positions, Select Sample(s) in list, Click Duplicate as (appropriate type).

    Automation Actions

    1. The actions of Confirm, Peak, and Acquire operate on the position samples in the list window.
      The selected position samples must be of the correct type for Automation Actions to use (i.e., you can only Acquire Standard Samples on position samples of type Standard so the Position List and Automation Actions must be compatible).
    2. Recommended procedure for processing of standards:
      Use separate processes for quality control (i.e., review peaking before acquiring standard samples)
      Confirm Standard Samples
      Peak Spectrometers (on Standard Samples)
      Acquire Standard Samples
      Evaluate the calibration, then proceed to running unknown samples.
    3. Recommended procedure for processing of unknowns:
      Digitize unknowns in groups of same phase if possible (simplifies assignment of sample setups, other options).
      Run a few samples to confirm proper setup.
      Run standards again to monitor calibration and drift during longer runs.

    Automation Options: Upper Section

    1. Peak on Assigned Standards. Recommend: always checked. Use assigned standards (only) for peaking. If not selected an attempt is made to peak all elements on all standards, and this is not recommended. Seleted by default.
    2. Use Quick Standards. Recommend: not checked. If selected, only the elements which have been assigned a given standard are measured on that standard. Example, if Albite (NaAlSi3O8) is used for Na and Si then only those elemetns will be measured on that standard. No measurement of other elements is performed
      Pros: Faster standardization run times as only subset of elements is measured on assigned standards.
      Cons: No ability to perform standard checking with redundant measurement of elements (e.g., Si in silicate runs), no built-in interference correction capabilities, reduced capability to identify problem calibrations.
    3. Use Filament Standby Afterwards. Ramps filament current down to parked value and presents dialog box at end of automation sequence to ramp filament back up to operating conditions.
    4. Use Confirm During Acquisition. Recommended. Presents dialog box with countdown timer to permit correction of xyz coordinates during automated analysis. Note that if a position is adjusted for a multipoint sample, all other points are adjusted as internal consistency is assumed.
    5. Use Beam Deflection for Position. TBD.
    6. Confirm All Positions in Sample (CAPS). If checked, will allow/require confirmation of all points in a position sample. If not checked, only first point is confirmed and all other points are assumed to be internally consistent.
      Suggest using CAPS for detailed explicit points which require individual positioning.
      For grids, etc. do not use as first point can be used to reposition the entire grid.
    7. Use ROM Auto Focus. If checked performs ROM auto focus on: New sample only, Every point, as digitized, or at a specific interval.
    8. Standard Points to Acquire (SPA). Number of points to use for standard calibration. Important points:
      If explicit digitized points exist, they are used for measurement.
      If SPA exceeds number of digitized points for given standard, virtual points are created using last digitized point and Standard X Increment (um) value.
      If Acquire -- Acquisition Options -- Use Only Digitized Standard Positions is checked, then only explicit digitized positions will be used and SPA value will not be reached.
      Note that value set in Replicates also determines number of measurements acquired per digitized point.
    9. Standard X Increment (um). Value used to increment x-axis for generation of virtual points.
    10. Re-Standard Y Increment (um), Value used to increment y-axis for generation of virtual points. During re-standardization if virtual points are required, both x and y values are incremented to generate the virtual point positions.
    11. Automate Confirm Delay (sec). Value of count-down clock used for confirm dialog during automated sequences.
    12. Re-standard Interval (hrs). Time in hours during automated run where a restandardization is triggered.

    Automation Options: Lower Section Analysis Modes

    1. Use Last Unknown Sample Default mode which uses all sample parameters without modification for subsequent samples. That is, analytical conditions, element list, count times, standard assignments, calculation options, etc. are all nominally used by default. Note that processing options can always be modified after acquisition (e.g., standard assignments, calculation options). The parameters established for the most recent unknown sample are used as the analysis template.
      Use Acquire New Sample to generate a new unknown sample, modify parameters as necessary. This template is then used for all subsequent samples until changed. For example, the initial sample is used as the template for acquisition of all standard samples until a new sample is generated and modified.
      No parameters are assigned in the Automate list window, each unknown is acquired using current sample parameters.
      Select Use Last Unknown Sample to use this mode (default).
      Mult-select all position samples to be run.
      Use Run Selected Samples to start the automated run.

    2. Use Digitized Conditions Only Analytical Conditions (Acc. voltage, probe current, beam diameter, scan mode (spot vs. raster), analytical magnification, and beam shift) are assignable on a per sample basis in the Automate list window.
      All other parameters (element list, calculation options, etc.) are nominally based on current sample.
      To assign Digitized Conditions:
      Select Use Digitized Conditions.
      Multi-select all position samples to be used for assignment.
      Click Conditions button and set Analytical Conditions as desired.
      Repeat for all position samples.
      Use Run Selected Samples to start the automated run.

    3. Use Digitized Sample Setups Allows complete customization of sample parameters for assignment to position samples for an automated run. See section on Sample Setups for complete information and recommended procedure.
      To assign Digitized Sample Setups (assumes you have generated the sample setups already):
      Select Use Digitized Sample Setups.
      Multi-select all position samples to be used for assignment.
      Click Sample Setups button and select a single setup from setups list.
      Repeat for all position samples.
      Use Run Selected Samples to start the automated run.

    4. Use File Setups This is the same as the import procedure in Acquire -- New Sample where you browse to a PFE run database and load a sample setup in from a pre-existing run. Recommend using this mode only if all peak positions and standard intensities are up to date. This mode is equivalent to browsing for sample setups from a number of existing files for assignment on a per-sample position sample basis.
      To assign Digitized File Setups (assumes the files have valid sample setups):
      Select Use Digitized File Setups.
      Multi-select all position samples to be used for assignment.
      Click File Setups button and browse to file, select sample from file.
      Repeat for all position samples.
      Use Run Selected Samples to start the automated run.

    5. Use Digitized Multiple Setups This allows the assignment of multiple sample setups to a position sample. The typical use is for multiple kV thin film work where the same element list is analyzed at several accelerating voltages. All sample setups must be previously generated and available within the current run.
      To assign Digitized Multiple Setups (assumes the sample setups have already been generated):
      Select Use Digitized Multiple Setups.
      Multi-select all position samples to be used for assignment.
      Click Multiple Setups button and multi-select the sample setups to be assigned.
      Repeat for all position samples.
      Use Run Selected Samples to start the automated run.


    About the Position Database vs. User Database Files


    About the Position Database and Differences with User Database Files

    1. There are important differences between the position.mdb database and all user *.mdb files that you will deal with.
    2. All position samples are stored in position.mdb which is a binary file. There is only one copy of this file. You will not typically back up the position.mdb file, instead you will export samples to .pos text files.
    3. Each user sets up a database file for their microprobe run which has a specific name (i.e., Carpenter 8-15-2011.mdb) which inherently is protected from overwriting and deletion by virtue of the specific name. That is, the only way data is lost is to delete the entire mdb file.
    4. During routine sample analysis, as each sample is analyzed the measurement data including the xyz coordinates are added to the user mdb file. These xyz points can be recalled using the Locate window and the points can be displayed using Picturesnap.
    5. The xyz positions in the user mdb file are not in the format for reading and display in the Automate position window. For this reason you need to back up the position samples using the export procedure.

    Exporting Position Samples from position.mdb to a .pos text file

    1. Position samples in the position.mdb database must be manually exported using the following procedure:
      Select all position samples of the sample type (standard, unknown, wavescan)
      Click on Automate -- Export Selected Samples to *.pos
      Save these position samples to a text file with a .pos extension using this method.
      Suggest: Standard positions backed up multiply (original file, working file, additional backups)
      Suggest: User .pos files saved to user folders and must be done as needed during the run and after final automated run sequence.
    2. If sample positions are not exported to .pos files and positions are seleced in Automate window then deleted, position data has been lost.
    3. For community labs the friendly policy is to select all unknown points, then export to user folder as a .pos file.

    Importing Position Samples from a .pos text file into position.mdb

    1. Any .pos file can be reloaded into the position.mdb database for reuse by using the import function. This can be done at any time as the position samples are simply xyz data points.
    2. To import position samples from a .pos file back into the position.mdb database (for use in the Automate window), first delete unknown or wavescan samples as necessary. Then use Automate -- Import from ASCII to load a .pos file.
    3. You will be presented with a dialog box to transform xy coordinates. To do this you need the following.
      First, the .pos file must have transformation coordinates in the first three lines (confirm this by opening the file and inspecting). These are the xyz positions of the fiducial marks.
      To transform the points, drive to the three xyz fiducial coordinates used for transformation purposes, confirm those positions, the software will transform them and you can then use the positions.
      If you do not transform the positions, you can still apply multiplicative shift values to the position samples since typically the mount is positioned in a way that requires shifting of either x or y preferrentially. This window appears after you click No on the transformation dialog.
    4. After reloading, the position samples are ready for use.


    Sample Setups



    Guide to Sample Setups

    1. A Sample Setup is the template for a given sample, with a unique list of elements, analytical conditions, count times, standard assignments, calculation options, etc.
    2. Sample setups must be set up within the current run but can be used from the New Sample window, or assigned for use in the Automate window. When you use File Import you are loading a Sample Setup from another run, then using that template as your master sample.
    3. Suggest using a master sample with all elements to be used in current run and disabling the acquisition of selected elements for analysis of a subset of phases. Disabling rather than deleting the elements allows you to turn the element back on without having to re-enter the element data.

    Procedure for Generating Sample Setups

    1. Use Acquire -- New Sample to generate a new sample of type unknown (this assumes generating sample setups for quantitative analysis of unknowns). You will use this empty sample only for generating a setup (it will not contain measurement data and therefore you can make changes to the setup at a later time if necessary).
    2. If you have a master list of elements, the first sample setup you generate should be the master list for eventual recall at a later time. That master list then does not have to be edited to re-enable elements or set conditions and count times back to the original values, for example.
    3. Give the new sample the name of the setup and include specific information (if necessary) for parameters pertinent to that setup. Example: Olivine setup 25 nA 5 um beam.
    4. If elements need to be disabled, use Elements/Cations and open the specific element properties window, then check both DA (disable acquisition) and DQ (disable quant) for that element. It will still appear in the printout list but will not be measured or used for the correction. (NOTE: If you disable the first element on a spectrometer and TDI is being used this can cause problems, so make sure you have the correct settings for measurement if you have disabled a critical element in the setup).
    5. Edit all measurement parameters that are specific to this sample setup (beam current, diameter, count times, element measurement order, etc.) by making changes in the Acquire window. If using different Analytical Conditions, set these parameters and enforce the conditions.
    6. Use the Analyze window to edit the parameters that are used for calculation in the analysis, such as number of oxygens, specified elements (if any), standard assignments, etc.
    7. Make sure you have set all parameter for this sample setup.
    8. Use either the Analyze -- Elements/Cations button or the yellow Add to Setup button to open the dialog and add the sample setup to the list of available setups. You can rename the setup before adding to the list if necessary.
    9. Repeat this procedure (new sample, name, measurement parameters, calculation parameters, etc.), then add to sample setup list as discussed. This can be done at any point in the run, but understand that if spectrometers are repeaked then all setups will need to have their peak positions edited. This can be done from the Analyze window and only if the sample setup does not contain data.
    10. Remember that the Sample Setup is a pointer that refers back to the specific sample in the mdb that is used as a template for subsequent analyses.

    Procedure for Using Sample Setups

    1. Sample Setups can be recalled for one-by-one analysis using the Acquire -- New Sample window, then use Sample Setups to recall the setup for analysis. That setup will then be the default setup for subsequent analysis and can be used either for measurements from Acquire or from Automate (with the measurement mode set to Use Last Unknown Sample. That is, you have loaded a Sample Setup and can use it indefinitely.
    2. The more powerful use of Sample Setups is to digitize points on your samples, then assign Sample Setups to those points for automated analysis. This allows customized control of the analysis for your samples. This procedure is outlined next.
    3. In the Automate window, use the Digitize button to perform the normal digitizing of sample positions. Try to group digitize sample positions together because you will be assigning Sample Setups by multi-clicking these position samples in the Automate position list. You can digitize a few, or as many position samples as necessary, then run them, and repeat the process.
    4. Set the analysis mode to Use Digitized Sample Setups on the lower right of the Automate window. This allows assignment and processing using Sample Setups.
    5. Multi-select all position samples in the Automate position list by dragging or control-clicking with the mouse.
    6. Click on the Automate -- Sample Setups button and select the appropriate Sample Setup for use on these position samples. Confirm that choice.
    7. Repeat this procedure until all the position samples have been assigned the appropriate Sample Setup.
    8. You can confirm the assignment of the specific Sample Setups by double clicking on a position sample in the list and noting the setup assignment number at the bottom of the Automate window (the setup number is the mdb data row number, not 1st or 2nd setup).
    9. Now select all position samples that are to be run. Make sure the Acquire Unknown Samples checkbox is selected (and no previous standard checkboxes). This indicates the total list of position samples to be run.
    10. Run these samples by clicking on the Run Selected Samples yellow bar in the Automate window.

    Standard Assignment



    About Standards, Positions, and Standard Assignments

    1. Standard Database The standard.mdb database contains the compositions of all standards. It is accessed using the Standard Menu -- Standard Database, or by running Standard.exe externally. Standard numbers are assigned and the composition of the standard is entered into the standard.mdb file.
      The standard.mdb database does not contain xyz coordinates, these are set using Stage.exe or PFE using the Automate window and Digitize button.
    2. Standard Positions The standard xyz coordinates are stored in the standard position samples. The Automate window (or Move window -- Positions button) is used to display these standard position samples, which are the xyz locations of standards. No compositional information is stored in the position.mdb database.
    3. Calibration on a standard requires that the standard be added to the run (the standard number and compositional information exist in the run .mdb file) and an xyz position sample exists for recalling the location of the standard (Automate Position List)
      The composition and position are not linked so that standards may exist on multiple mounts.
    4. If you add a standard to the run but no position exists for that standard, then it will not be highlighted when you click Automate -- Select Standards and no automation action or recall procedure can be used.
    5. If a standard has a position entry in positionl.mdb, but has not been added to the run, the PFE program will not expect it to be used. Again, the standard position entry will not be highlighted when you click Automate -- Select Standards.
    6. Use the Run menu to list the Standards currently in the run, their compositions, and the standard intensities that have been measured in the run.

    Adding and Assigning Standards

    1. Add or confirm that standards are added to the run. Use Standard Menu -- Add/Remove Standards To/From run (also can be done from Acquire -- New Sample, and from Automate -- Digitize).
    2. Default standard assignments will be made during the run if you do not explicitly change the standard assignments. The default assignment uses the standard with the highest concentration as the primary standard for that element.
      You should always check the standard assignments prior to making extensive measurements.


    3. Standard Assignment
    4. Open the Analyze window and display appropriate sample type (standard or unknown) in the position list.
    5. Standards are assigned on a per-sample basis.
      Standards and samples can have different and unique standard assignments.
    6. Multi-select the samples in the list to choose all samples of a given type for standard assignment.
    7. Click Standard Assignments button. This opens the Standard and Interference Assignments window.
    8. Click on the row of the element to change assignments. This opens the Assignment Properties window.
      The Assignment Properties window is used for Standard, Interference, TDI, and Blank assignments.
    9. Select the Assigned (Primary) Standard from the pull down menu. Click Ok to close the window.
    10. Repeat this for all elements needing changes in standard assignment.
    11. When you click on Ok to close the Standard and Interference Assignments window, these assignments are made to all selected samples in the list window.

    12. Notes
    13. It is important that this standard be of the appropriate composition as this is not checked until measurements or correction is attempted. Meaning: the standard needs to have sufficient concentration for peaking and calibration.
    14. If you delete an element from a sample, the standard assignment linking needs to be reviewed. For this reason it is preferrable to disable acquisition (DA) and disable quant (DQ) rather than delete an element from the sample.


    Peak Interference Setup



    Declaring Peak Interferences

    There are two types of interferences, on the peak, and on a background.
    On-peak interferences are treated with the interference correction (Example: Ti K-beta peak on V K-alpha peak).
    Background interferences are corrected with appropriate background offsets or MAN background correction.


      Interference Assignment
    1. Open the Analyze window and display appropriate sample type (standard or unknown) in the position list.
    2. Interference declarations are assigned on a per-sample basis.
      Standards and samples can have different and unique interference assignments.
    3. Multi-select the samples in the list to choose all samples of a given type for inteference assignment.
    4. Click Standard Assignments button. This opens the Standard and Interference Assignments window.
    5. Click on the row of the element to change assignments. This opens the Assignment Properties window.
      The Assignment Properties window is used for Standard, Interference, TDI, and Blank assignments.
    6. Inspect the Interference Standard Assignments for Interfered Element: XX-xx. Up to 5 intefering elements can be declared along with the appropriate interference standards to use.
    7. Select the first interfering element, the order of the intefering line, and the interference standard to be used.
      For the example of Ti Kb intefering on V ka you would:
      Select V from the Standard and Interference Assignments window (i.e., the element list for the sample). This opens the Assignment Properties window.
      Enter Ti, 1, and the appropriate V-free Ti standard (e.g., Ti metal or TiO2). This declares Ti to be the interfering element, the 1st order Ti Ka peak is the interfering line, and the apparent V intensity is to be measured on a V-free standard, either Ti metal or TiO2.
      That is all that needs to be done.
    8. When you click on Ok to close the Standard and Interference Assignments window, these assignments are made to all selected samples in the list window.

    9. Notes:
      For multiple spectrometer / aggregate intensity setups it is important to use the correct instance of the interfering element (e.g. Ti Ka measured on spectrometer 3 vs. 5 to correct for V measured on, say, spectrometer 3.


    TDI Evaluation



    Evaluating Time-Dependent Intensity Behavior

    The TDI correction treats time-dependent x-ray intensity emission from beam-sensitive materials regardless of the physical process involved.
    The correction performs incremental counting using the first element on each spectrometer only and projects to time zero to evaluate the initial x-ray intensity.


    TDI Data Collection

    1. TDI data collection is enabled from Acquire window -- Special Options button. (See Special Options window discussion). After data collection is set to TDI, all further data will perform incremental measurement for the first element on each spectrometer only.
    2. If standards are to be treated with TDI, enable this as well. However, a defocused beam should be a priority on beam-sensitive standards.
    3. Use Acquire window -- Acquisition Options to select each element and set the measurement order using User Specified Order to force the measurement of required elements to be first for TDI correction.
    4. Note that this necessitates placing elements that exhibit TDI behavior (e.g., Na, Si) on different spectrometers.


    TDI Data Evaluation
    1. Open the Analyze window and display appropriate sample type (standard or unknown) in the position list.
    2. TDI correction options are nominally assigned on a per-sample basis.
      Standards and samples can each have been acquired with TDI turned on.
    3. Multi-select the samples in the list to choose all samples of a given type for TDI inspection.
    4. Click Standard Assignments button. This opens the Standard and Interference Assignments window.
    5. Click on the row of the element to select for viewing. This opens the Assignment Properties window.
      The Assignment Properties window is used for Standard, Interference, TDI, and Blank assignments.
    6. The Time Dependent Intensity (TDI) section is used to turn TDI on and off on a per-sample basis, and to select the type of TDI fit used for correction.
    7. Remember that Analyze Menu -- Analysis Options has the global on/off flag for TDI correction.
    8. Select TDI Self or TDI Assigned Calibration Correction.
    9. Click on yellow Display TDI Fit to observe the TDI behavior. Note that the data range is expanded to fill the available graph range. Samples with multiple points will show them in different colors on the plot.


    10. Exporting TDI Plot Data
    11. Use the Output Menu -- Save Custom Analysis etc. TDI output selection. This will save the TDI intensity vs. time data to .dat files based on sample name, and to an Excel sheet using a new worksheet for each sample (note that for Excel there is a 99 worksheet maximum and after that number no additional TDI sheets will be generated in the Excel workbook.


    Blank Correction Assignment



    Blank Value

    Processing of samples using a standard with a known low level or trace concentration of an element.

    Blank Value Assignment

    1. Open the Analyze window and display appropriate sample type (standard or unknown) in the position list.
    2. Blank value assignment is on a per-sample basis.
    3. Multi-select the samples in the list to choose all samples of a given type for blank value assignment.
    4. Click Standard Assignments button. This opens the Standard and Interference Assignments window.
    5. Click on the row of the element to select for viewing. This opens the Assignment Properties window.
      The Assignment Properties window is used for Standard, Interference, TDI, and Blank assignments.
    6. The Blank Correction Sample Assignment section is used to add or remove the blank correction using a selected standard.
    7. Select a blank standard for use and enter the known concentration of the given element in the text field.
    8. Remember that Analyze Menu -- Analysis Options has the global on/off flag for blank correction.


    Mean Atomic Number Background Setup




    Output of Analyzed Data Using Output Menu



    Output of Data from PFE Analysis Runs

    The Output Menu is used to correct all analyses in a run and generate Excel sheets with all data. There are many options for output format.

    Output of Data

    1. Output Menu has a number of options for output of analytical data (see help file and user guide)
      Custom output formats (1-9): specific output formats requested by users, Carpenter=9
      Custom output formats (10-11): wavescan output for spreadsheet use
      Custom output format (12): TDI intensity data
      Custom output format (14): Trace element statistics output
      Save User Specified Format Output output specified analysis parameters (uses probewin.ini default settings)
      Save analysis in Calczaf file input format for Calczaf processing (compare ZAF algorithms, mac data sets)
      Excel link for raw writing of data to Excel during analysis
      Open the Analyze window and display appropriate sample type (standard or unknown) in the position list.


    2. To correct and dump all samples or standards in the run, select a given output format. All analyses will be processed and data is generally written to two files:
      A .dat file that is tab delimited
      An Excel workbook that can be used for further calculations and data processing.

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    Page last updated on: by Paul Carpenter