NOTE: Before any spectra can be acquired with Revolution, several steps must be completed, namely, the physical connection of the 4pi system to the pulse processor. The system comes complete with an interface box and cable. The interface box must be connected to the SEII computer card with the included ribbon cable. The interface box must be connected to the pulse processor with the included cable, and turned on. The microscope must be on and in working order, and the X-ray detector must eb connected to the pulse processor, cooled, and in proper working order. In addition, the FPXDriver and hasp software must be installed. Review and perform the Hardware and Software Installation procedures before proceeding!
EDS spectrum display and acquisition functions are controlled from the EDS Spectrum Toolbar. If the toolbar is not visible at the top of your screen, selecting Mode → EDS Spectra from the top menu will make it appear:
The tool bar is divided into five sections:
Spectra Options. Used to set the beam energy and current, and to perform the following functions:
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Display markers for K, L, and M lines of selected elements | |
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Superimpose selected regions of interest on the spectrum | |
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Perform automatic peak identification | |
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Perform Quant analysis and generate report |
Acquire Spectra. Used to set the amount of time during which the spectrum will be acquired, and to perform the following functions:
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Clear current spectrum | |
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Start spectrum acquisition |
Tools. Used to select tools for visual spectrum manipulation. In order from left to right, these are:
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Switch to magnify-cursor. Used to zoom in spectra. Use the option key (Macintosh) or alt key (Windows) to temporarily zoom out. | |
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Switch to demagnify-cursor. Used to zoom out spectra. Use the option key (Macintosh) or alt key (Windows) to temporarily zoom in. | |
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Switch to hand-cursor. Used to drag spectrum around in zoomed mode. | |
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Switch to pointer-cursor. Used for selecting any item with a valid handle in a spectrum. | |
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Switch to text-cursor. Used to create or edit text annotations in a spectrum. |
Status. Lists useful information about the current operational state, including deadtime in percent, input count-rate (Fast Channel), and output count-rate.
When a spectrum is first acquired and displayed on the computer screen, the spectrum is unlikely to look correct (if it appears at all), and the quant routines cannot run correctly. Before accurate spectra can be acquired, several procedures must be followed. These procedures can be repeated at any time, but should not be required more than once:
Select the correct hardware
Calibrate the spectrum
Before acquisition, select the correct pulse processor in Hardware Setup (select the Edit → Preferences... menu to get the Preferences window on screen):
| Select Hardware Setup from the prefs list and choose the correct pulse processor from the Processor menu in the Pulse Processor Settings: |  |
| Select X-ray Probe prefs to inspect and adjust the display dimensions of the spectrum windows: |  |
Revolution and the Spectral Engine II card allow both manual and automatic calibration to be performed. Manual calibration is a mandatory first step! It is strongly recommended that the manual calibration be as accurate as possible. The automatic calibration will then be simpler, quicker, and much more likely to produce satisfactory results.
Operating note 1: accurate calibration is crucial to accurate Quant results. 4pi tech support has found that 95% of the problems with Quant results can be traced to bad calibration.
Operating note 2: Proper autocalibration requires a preliminary detector setup procedure to be performed!
To begin the calibration procedure, select Options → Calibrate Spectra. The following window appears:
The spectrum calibration window is a self-contained acquisition window, with tools available for zooming in and out, sliding channels left and right, and scaling the spectrum. The realtime and livetime counters are also available.
| To begin the calibration procedure, select from the Sample menu according to the type of sample in the microscope... |  |
... and select the Acquire Spectra button: |  |
KLM reference markers are automatically placed in the spectrum according to the sample selected. A spectrum will acquire for the amount of time entered in the EDX Spectra Toolbar dwell field (see top of this page). As the calibration is being performed, the spectrum will update in real time. The goal of course is to align the spectrum lines with the KLM reference markers. If extensive adjustments are required, the clr button should be used to restart the spectrum as needed.
For this procedure to work well, the calibration sample loaded into the microscope should have a minimal number of well-known x-ray lines in both a lower and a higher energy range. A common and effective choice is any sample that contains both Aluminum and Copper. Al-Cu will be assumed for rest of this discussion.
The manual calibration process is to iterate the adjustment of the gain and offset controls of the Scanning Interface Unit (SIU) until the spectrum comes into alignment (for systems without an SIU, the gain and offset controls of the pulse processor itself must be used).
The general rule of thumb when performing a calibration is that the offset control is used to adjust low-energy peaks while the gain control is used to adjust high-energy peaks. Note: condensed spectrum snapshots are shown to conserve space.
| Initially, it is quite likely that the element peaks will appear at the wrong energies: |  |
| The first step is to change the offset control of the SIU or pulse processor until the low-energy (copper) peak is adjusted (upward in this example) to the correct energy: |  |
| Use the mag control to zoom in on the spectrum to perform a precise adjustment of the lowest energy. It is not unusual for lines at a higher energy (here, Al) to still be out of adjustment: |  |
| Next, adjust the gain control of the SIU or pulse processor to make the high-energy (copper) peak line up to the markers: |  |
| By iterating back and forth between the low-energy and high-energy peaks, the SIU or pulse processor offset and gain controls can be used to dial in the correct calibration. Once the high and low energy peaks are calibrated, the intermediate peak(s) will be also: |  |
The most precise calibration is performed with the lowest low-energy and highest high-energy peaks available. The choice of calibration sample is dependent on the user's needs and available samples. To improve the calibration and lock it in to the software, the autocalibration step must be performed (below).
Operating Note: As a general rule, the manual calibration shown above is acceptable for the autocal step but is not sufficient for accurate Quant results.
Remember: Autocalibration must always be performed after the manual calibration is completed (see above). Do not skip the manual step - a relatively good manual calibration is required for the autocalibration to work properly.
As the above manual adjustment is being made, the measured peak values are continually updated in comparison with the known values of peak energy for the sample(s) selected (see blue highlights in diagram below). The most precise calibration will show a close match between the actual and measured peaks. Due to the statistics of the x-ray process, there will always be a fluctuation in the measured value, so a perfect match is not realistic. The equivalent Manganese FWHM is continuously calculated to indicate detector performance (see red highlight in diagram below). The end result for a Copper/Aluminum sample should be very comparable to the following example:
The autocalibration is performed for the entire time the window is open. When a satisfactory result has been achieved (as determined by the closeness of the actual and measured line energies), hit the OK button to record the calibration preferences. All spectra acquired after this point will have the calculated software correction applied.
Operating note: any spectrum that has already been acquired into any catalog can be cut and pasted into this Calibrate window and used to perform the autocalibration.
| Select File → New Catalog to create a new blank catalog window: |  |
| The catalog is simply a collection of spectra. To create new spectra within a catalog, select File → New. Each new spectrum will be added to the catalog and can be selected with the spectrum menu: |  |
| When the catalog is created, the appropriate tools on the toolbar become available. The klm and roi buttons are always available. The PeakID and Quant buttons are available depending on the purchased feature set: |  |
| To acquire a spectrum into a catalog, click on the acquire button | → |  |
| The spectrum will be captured into the catalog and added to the spectrum menu. As many new spectra as desired can be created by selecting File → New and starting another acquisition: |  |
| Each spectrum display can be manipulated independently from the others with the zoom-in, zoom-out, and slider tools in the toolbar, and the scaling tools in the catalog window: |  zoom in (toolbar) |
 zoom out (toolbar) |
 slider (toolbar) |
 scaling (catalog window) |
To zoom in, click on the magnifying glass (+) tool button and click inside the spectrum window. Each click in the spectrum window will zoom in on the area of the spectrum centered on the eV position of the magnifying glass. To zoom out, click on the magnifying glass (-) tool button and click inside the spectrum window. Each click in the spectrum window will zoom out from the area of the spectrum centered on the eV position of the magnifying glass. Hold down the alt key (Windows) or option key (Macintosh) to swap (+) & (-).
To drag the spectrum to the left or right, click on the slider (hand) tool and drag inside the spectrum window. While holding the mouse button down, drag the spectrum left or right. To adjust the vertical scale (number of counts), use the Scale Menu above the spectrum. A pop-down menu will appear (default setting is Autoscale). A specific full-scale fixed value can be selected from the list, as can logarithmic scaling (default scaling is linear). Auto 80% autoscales the peaks to 80% of the maximum displayable height. To adjust the counts axis in steps without using the scale menu, use the green up and down arrow buttons in the Spectrum window.
The acquisition will accrue x-ray counts until the amount of time specified in the Dwell field of the toolbar. The Erase Spectra button (clr) will clear all counts out of a spectrum without stopping acquisition; this is a convenient way to observe a rapidly shifting spectrum during calibration or when deciding which area of the sample to probe.
When the toolbar first appears on screen, it displays in the upper right corner the Input Count Rate (Input) in counts/sec, the Output Count Rate (Output) in counts/sec, and the deadtime (Dead) percentage, all as reported by the pulse processor. Please review Tech Support Note 2000-1 regarding the measurement and interpretation of these values, in particular the deadtime value.
The Realtime and Livetime counters are updated in the upper left corner of the catalog window and measure seconds. Realtime is the total running clock time. Livetime is the total amount of time during which the pulse processor has not rejected pulses due to pileup. Please review Tech Support Note 2000-1 for more detailed information, including how the deadtime is calculated.
If the pulse processor and detector are properly installed and connected to the 4pi system, and the calibration steps above have been performed, a correct spectrum should appear immediately.
Selecting a catalog window's close box initiates a save via the close warning:
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Selecting Save from the Close Warning dialog, or selecting Save or Save As from the File menu, creates the save dialog box shown below:
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Operating Note: Catalogs can be saved only in Revolution's proprietary format.
Operating Note: Catalogs are automatically saved with a .mbd extension. It is not necessary to add this extension to the file name.
Operating Note: Performing Save As saves the position of the spectrum window and which spectrum is frontmost.
Opening a catalog can be done in any of the usual ways: File → Open, double click on a catalog data file, or drag a data file onto the Revolution application icon.
Operating Note: double-clicking a file when Revolution is already open is not an issue; however, if a file is double-clicked and that action launches Revolution from scratch, it is not necessarily true that the correct version of Revolution will open if multiple copies exist. For this reason, 4pi recommends that all previous versions of Revolution be archived in a non-functional state, or removed from the hard drive entirely.
The data from any acquired spectrum within a catalog can be saved to disk by selecting File → Export, resulting in a save dialog with multiple export formats:
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Operating Note: Spectra are automatically saved with the correct file extension. It is not necessary to add an extension to the file name.
Operating Note: Revolution will remember the last format selected. Known Issue: unlike for the imaging/mapping modules, the File Format selector for X-ray Spectra Probe settings does not set the default value in this dialog. 4pi will change this behavior in an upcoming release.
The export formats available are:
EMSA 1.0. Industry-standard plain-text format that can be imported into any X-ray microanalysis software that understands the EMSA 1.0 format. The file consists of a header followed by a listing of the counts in each channel. If the header is removed with a text-editor, the channel data are easily imported into a database or spreadsheet. File extension is .ems.
Xraytor. Saves the data in a special file format designed for encoding spectrum-at-every-pixel information. File extension is .xrt.
Excel-Results. Saves the qual-quant results only in a Microsoft Excel spreadsheet format. Note: The Excel menu item will not appear if no quant results have been displayed for the spectrum. File extension is .xls.
BMP (Windows) or PICT (Macintosh) or JPEG (Win/Mac). This format does not save the spectrum data, but instead saves the spectrum as a picture in an OS-native graphics format, convenient for pasting into a report or publishing on the web. File extension is .bmp or .jpg (PICT is not an option for Windows, and so never is appended to a file).
Any Revolution spectrum file (EMSA 1.0 format, .ems extension) can be opened by double-clicking on the file. EMSA files by default open individually in a single-spectrum mode that does not support all the features of spectrum catalogs; to access full capability, single-spectrum EMSA files must be copied and pasted into catalogs or directly imported into a catalog using File → Import. A single-spectrum Xraytor file (Xraytor format, .xrt file extension) opens into single spectrum just as an EMSA file does.
Operating Note: double-clicking a file when Revolution is already open is not an issue; however, if a file is double-clicked and that action launches Revolution from scratch, it is not necessarily true that the correct version of Revolution will open if multiple copies exist. For this reason, 4pi recommends that all previous versions of Revolution be archived in a non-functional state, or removed from the hard drive entirely.
Opening any spectrum saved as a graphic in JPEG, BMP, or PICT format will merely open that image file. There is no EDX data to work with, and Revolution cannot distinguish such a file from any other image.
KLM markers and/or manually-defined Regions of Interest (ROIs) can be overlaid independently on any spectrum in any catalog via special periodic tables that appear in floating windows on the screen.
| To access the KLM floating window, use the klm button in the toolbar, or the contextual menu by right-clicking inside the spectrum: |  |
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Click on any elements in the floating window to immediately place the KLM marker overlay(s) on the spectrum. Click again to immediately turn the marker(s) off (result shown below): Unique to the KLM window, the keyboard arrow keys can be used to highlight the markers, with the KLM markers on the spectrum moving accordingly. The spacebar toggles "sticky" activation of an element's markers. |
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| The KLM marker colors can be changed by right-clicking in the spectrum and selecting "Edit Display". |  |
| The KLM markers that will be displayed can be selected by option-clicking (Macintosh) or alt-clicking (Windows) any element in the KLM perioduc table (Copper shown as example): |  |
| To access the ROI floating window, use the roi button in the toolbar, or the contextual menu by right-clicking inside the spectrum: | |
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Click on any elements in the floating window to immediately place the ROI overlay(s) on the spectrum. Click again to immediately turn the ROI(s) off (result shown below): |
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| To edit any individual manual ROI, alt-click (Windows) or option-click (Macintosh) any element button in the X-ray Probe ROIs window (Copper shown here): |  |
The Image Title is the name associated with the manual ROI. |
| The Include checkboxes determine whether the manual ROI definition consists of K, L, or M lines (if applicable). The energy limits of each manual ROI (min/max) can be edited to suit the user (hence the term "manual"). Default values are supplied for most elements. See the discussion of the Auto ROI function for an important caveat. | ||
| The Set Color button accesses the operating system's color-picking services, and allows you to select the manual ROI color. This color is applied to ROI overlays in any x-ray spectrum, and also to the ROI image in any x-ray map. |
Important Operating Note: The KLM and ROI periodic tables are floating windows whose settings apply to whatever spectrum has focus. If a new spectrum takes focus, the periodic table settings assume default values. The settings for each individual spectrum are remembered as the focus changes.
| A data flag can be overlaid independently on any spectrum in a catalog using the arrow button in the toolbar: |  |
| With the arrow button selected, double-click anywhere in the spectrum to make the flag appear: |  |
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The flag can be moved anywhere in the spectrum by dragging anywhere on the vertical black marker, to display the channel number, the number of counts in that channel, and the energy: To remove the flag, drag it off the spectrum to the right or left. |
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| The flag can be precisely positioned to inspect the data for any channel (magnified, Cu marker shown, flag is one channel away from the actual line at 8.04 KeV): |  |
| If the relevant ROI is also turned on (above, this page), the flag appends the total count summed over the whole ROI: |  |
| If background subtraction is also turned on, the flag appends the background-subtracted count summed over the whole ROI: |  |
Revolution allows the user to superimpose any number of spectra one atop another. From any source spectrum in any open catalog, select Options → Spectra Overlays to activate the overlay editor:
| The source spectrum (in this example, PbS) is placed "In View." |  |
| Select any other spectrum from any other (open) catalog to place it In View. |  |
| Press the Add button to add the spectrum to the overlay list. |  |
Important Operating Notes: The originating spectrum will continue to be shown "filled in," but will not be labelled. The "In View" spectrum (always red) will obscure the actual color of the overlay if that spectrum has been added, but only in this dialog, and only while that same spectrum is In View.
As many spectra as desired can be added to the overlay list. Use the Overlay menu to select any overlay list item for editing. Use the Edit Name button to change the name of the spectrum. Use the Color button to change the overlay color. Overlay items can of course be removed with the Delete button. When finished, hit the OK button to exit the editor and return to the Catalog:
| The original spectrum from the catalog is replaced with the overlaid version of same. |  |
| As a separate example, overlays can be used to follow the long term drift of spectra: |  |
Some 4pi Spectral Engine II boards have the capability to generate a TTL pulse stream that can be used to drive the dot-mapping input on a microscope. This will only work if you have the correct 4pi hardware (SEII 2.2 or 2.3 card with the Single Channel Analyzer hardware installed) AND the correct dot-mapping input jack on the microscope. To enable and use the dot-mapping capability, follow these simple instructions:
Click the roi button in the upper left of the toolbar to open the Region Of Interest periodic table:
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To see or change individual ROI settings, option-click (Mac) or alt-click (PC) on the element of choice. The following window will appear (Nickel shown here):
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The Image Title pertains only to acquisitions that use the Spectral Engine x-ray mapping capability. Ignore that here. |
| The Include checkboxes determine whether the ROI consists of K, L, or M lines (if applicable). The energy limits of each ROI (min/max) can be edited to suit the user. Default values are supplied for most elements. | |
| The Set Color button pertains only to acquisitions that use the Spectral Engine x-ray mapping capability. Again, ignore that here. |
Use the Enable SCA menu allow a user to select a Single Channel Analyzer output. In standard installations, there is only one dot-mapping channel, and it is almost always SCA #1. If you do not have more information about the hardware configuration, select #1.
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In the X-ray Probe Preferences, select the Turn on SCAs checkbox.
When an acquisition is started (described in the content above on this page), TTL pulses will be streamed from the Spectral Engine's SCA outputs to the dot-mapping inputs on the microscope.