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:
NOTE: Before any spectra can be acquired with Revolution, several steps must be completed, namely, the physical connection of the 4pi system to the x-ray detector. In addition, the microscope must be on and in working order, and the X-ray detector must be cooled and in proper working order. These steps are outside the scope of this operating manual.
The tool bar is divided into four sections:
EDX Spectra. Used to set the amount of time for which the spectrum will be acquired (dwell), and to perform the following functions:
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Clear current spectrum | |
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Start spectrum acquisition |
Options. Used to set the beam energy and current, and to perform the following functions:
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Perform automatic peak identification | |
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Perform Quant analysis |
Tools. Used to select tools for visual spectrum manipulation, described in the Basic Operating Principles
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:
Setup parameters and hardware
Calibrate the spectrum
Before acquisition, hit the Setup button to set most of the spectrum parameters that will not change after the installation:
| Although these parameters are usually set once at the beginning, they can be reset at any time. See below for a list of the meanings of all settings. |
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Lower Level Discriminator - SEII. The LLD setting for the Spectral Engine II is similar to a low energy discriminator. Our algorithms are pulse processor baseline-sensitive, and constantly compare that baseline to the pulses received. The LLD is interpreted as a minimum difference between the baseline and the current pulse stream (in units of channels). The setting is somewhat sensitive and can be used to accept pulses with very low energy; however, if set too low, the SEII will pick up the noise baseline as part of the spectrum. From a display standpoint, all channels below the LLD will be set to zero before display. The default value of 10 should be optimum for most setups. The actual number you use will depend on your noise, your pulse processor and your application. Starting from the default, work down or up to get the desired result.
Lower Level Discriminator - USE. The LLD setting for the Universal Spectral Engine is purely a display setting. All channels below the LLD will be set to zero before display. The default value of 10 should be optimum for most setups. The actual number you use will depend on your noise, your pulse processor and your application. Starting from the default, work down or up to get the desired result.
Acquire/Display Channels. Selects the default number of channels either acquired by or displayed in a spectrum window. Selections are 10-based for plotting and display purposes, and power-of-two-based for traditional displays related to channel numbers. Note that these settings will not affect already-opened spectrum windows; they only operate on windows opened after the settings have been made.
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Preset. The preset (operating mode) can either be realtime or livetime:
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In realtime mode, no deadtime information is used to time the acquisition, and the spectrum will acquire for time set in the EDS Toolbar. In livetime mode, the SEII internal livetime counter only increments when the pulse processor allows it to, thus incorporating deadtime information; when selected, an acquire time of 1000 seconds (for example) will take longer than 1000 actual seconds, depending on the deadtime statistics. |
Enable SCA Outputs. This checkbox is accessible only on older Spectral Engine II systems. It enables streaming of TTL-compatible Single Channel Analyzer pulses from the SEII to a microscope with dot-mapping input capability. See dot-mapping for more information.
Acquire into New Spectrum. This setting can be either be New or Current:
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In New mode, every acquisition into a new catalog will create a new spectrum, and older spectra in that catalog will not be explicitly overwritten unless it is done manually by cutting and pasting. In Current mode, any new spectrum will overwrite the existing one; however, if the data has been saved in any way, a dialog will warn and give an opportunity to cancel the overwrite. |
Edit Default Display. Hitting the button opens the following dialog, with which the user can set all default colors used in the x-ray spectrum windows. Note that these settings will not affect already-opened spectrum windows; they only operate on windows opened after the settings have been made.
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Selecting any button will open the operating system's color services, allowing the user to select the color for that particular aspect of the spectrum display. Note: the axis color also sets the color of the axis label text. The default KLM marker text size can also be set. The unlabeled menu sets the default autoscaling: 100% means the spectrum's maximum value will be drawn at the top (100%) of the y-axis; 80% means the spectrum's maximum value will be drawn 1/5 below the top (80%) of the y-axis. |
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The default spectrum plotting style can be selected. |  |
The default scaling of KLM markers can be selected. |
Analog Pulse Processor (SEII systems only)
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A list of common pulse processors that the SEII interfaces to are shown to the left. To configure the setup, select the Pulse Processor model via the menu. This selection determines the logic definitions for several hardware signals that are part of the pulse processor interface. The Custom setting allows the user to implement his or her own polarity definitions. |
TTL Polarity (SEII systems only)
Deadtime. Also referred to as Livetime if the polarity definition is switched, this is a TTL signal from the pulse processor indicating that x-ray pulses are not being processed due to a pulse pileup condition. A real time clock in the SEII counts off total seconds since the acquisition was started. A parallel live time clock increments with the real time but is stopped by the pulse processor via this signal whenever deadtime is being accrued. At the bottom of the pulse processor menu appears a Custom selection which allows the user to define the Deadtime polarity as desired.
Pulse Reject. A TTL signal from the pulse processor indicating that pulse pileup has occurred and that the analog signal on the PHA Input line should be considered invalid and ignored. As a general rule, pulse processors with a step-function output (see below) do not send a pulse reject signal. At the bottom of the pulse processor menu appears a Custom selection which allows the user to define the Pulse Reject polarity as desired.
ADC Deadtime. Also known as ADC Busy, this is a TTL signal sent to the pulse processor by the SEII. It indicates that the MCA is busy and temporarily cannot accept any new pulses. This signal is sent to the pulse processor for deadtime correction. In some cases this line is not present or can be left disconnected with little error. However, for some pulse processors (notably Kevex), this signal acts as a start-of-conversion pulse and must be present for proper operation. At the bottom of the pulse processor menu appears a Custom selection which allows the user to define the ADC Deadtime polarity as desired.
Note: Choosing incorrect polarities will not harm anything, but may cause the system to appear to stop acquiring a spectrum, or lead to results which are not easily interpreted.
Pulse Type (SEII systems only). For analog pulse processors the output pulse type is either a step function or a quasi-gaussian (no-step) function. For the SEII Rev 2.2 card and above, the software automatically selects the pulse type according to the pulse processor selected. For Rev 2.1 cards (PCI or NuBus) this will be a selectable option if a custom pulse processor is chosen. If your pulse processor is configured in a non-standard fashion, or if your pulse processor does not appear in the dialog list, please consult with 4pi before making the final setting. Incorrect pulse type will lead to spectrum artifacts.
Digital Pulse Processor (USE systems only). The Universal Spectral Engine contains a digital pulse processor whose time constants can be changed in software. Select the desired time constant via the menu. Larger values yield the best spectral resolution, but the concomitant high count rates cannot be accommodated without incurring a lot of deadtime. Lower values are just the opposite; high count rates can be accommodated, but spectral resolution will suffer. This is the nature of pulse processors. The Link All TC Settings checkbox automatically locks the time constant to be the same value for spectrum acquisition and x-ray mapping.
Revolution allows both manual and automatic calibration to be performed on any Spectral Engine system. Manual calibration is a mandatory first step! It is strongly recommended that the manual calibration be as accurate as possible, within reason. 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 Analyze → Calibrate Spectra from the menus. 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. Note: the lower section of this window (bracketed in red above) is only seen on Universal Spectral Engines.
| 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 the discussion involving Spectral Engine II systems. Mn will be assumed for the discussions involving Universal Spectral Engine systems. Note: the principles for calibrating both SEIIs and USEs are essentially the same; If you have a USE, you should still read the sections below about the SEII.
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 analog 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. The calibrate window provides continuous feedback about whether the desired peaks are being found in software, and where the adjustment is at the present time. A certain amount of fluctuation is expected for both the line positions (± 2eV or more) and also the calculation of the resolution. Note: condensed spectrum snapshots are shown to conserve space.
| Initially, it is quite likely that the element peaks will appear at the wrong energies: |  |
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| 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: |  |
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| 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 other energies (here, Cu-L) to still be out of adjustment; in fact, even the Al line is still not perfectly in position: |  |
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| Next, adjust the gain control of the SIU or pulse processor to make the high-energy (copper) peak line up to the markers: |  |
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| 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: |  |
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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. It is generally impossible to get the peaks lined up even as well as shown above without tedious effort. Therefore, accuracy to a few tens of channels is acceptable for the manual calibration. Unfortunately, this manual calibration is not good enough for accurate Quant results! To improve the calibration and lock it in to the software, the autocalibration step (below) must be performed.
Unlike the SEII, which is a 2-point calibration, the Universal System is a 1-point calibration - only the gain is adjusted; the digital pulse processor takes care of the zero.
The same general rule of thumb as for the SEII applies: use the gain to adjust the high-energy peak in question.
| Initially, it is quite likely that the element peaks will appear at the wrong energies, and the software will be unable to locate the peaks: |  |
| Change the gain value until the high-energy (Manganese) peak is adjusted (upward in this example, although by mistake to an energy too high). Note: the gain value behaves counter-intuitively; lower gain values will move the spectrum up, and vice versa. |
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| By adjusting the gain value, a closer calibration can be dialed in. Once the high-energy peak is close enough, the software is able to locate it and also calculate a detector resolution. Note that the calibration could still be better; the final autocal step is described further below: |
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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). Note that the settings for fast, slow, restore, and baseline are set by the installer, and should not be changed in the field without consulting 4pi technical support; in addition, the gain adjustment step must be performed for each time constant (TC) present in the menu (normally 4). 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 manual 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. In fact, an error of +-10eV per peak is quite acceptable. 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 correction is calculated for the entire time the window is open. When a satisfactory result via manual adjustment has been achieved, hit the OK button to lock the autocalibration into the 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.
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 the SEII discussion above). The most precise manual 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. Although an error of ±10eV can be overcome in software, a better match is achievable and should be sought. The equivalent Manganese FWHM is continuously calculated to indicate detector performance. The end result for a Manganese sample should be very comparable to the following example:
| After the manual calibration is complete (above), click on the Calibrate button. The software will calculate a precise gain value that can achieve sub-channel accuracy for the peak location: |
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The autocalibration correction is calculated every time the Calibrate button is pressed. Allow the spectrum to acquire for a while, and press the Calibrate button. A couple of iterations, or just one if the manual calibration is close enough, should be sufficient to make the measured and actual peaks quite close. When a satisfactory result has been achieved, stop the acquisition. If this is the last calibration to be performed, hit the OK button to lock the autocalibration into the preferences. If the other time constants have not had this procedure done, switch to those time constants and repeat. All spectra acquired after this window exits 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.
| To acquire a spectrum into a catalog, click on the acquire button | → |  |
Alternately, select File → New Catalog to create a new blank catalog window, and then hit the Acquire button. |
| 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: |  |
| 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 and drag tools in the toolbar, and the scaling tools in the catalog window: |  zoom out (toolbar) |
 zoom in (toolbar) |
 drag (toolbar) |
 scaling (catalog window) |
To zoom in (out), click on the appropriate magnifying glass tool button and click inside the spectrum window. Each click in the spectrum window will zoom in (out) on the area of the spectrum centered on the eV position of the magnifying glass. To zoom out (in), switch to the opposite tool. As per standard usage guidelines, each of the magnifying tools can have its function reversed by holding down the alt key (Windows) or option key (Macintosh).
To drag the spectrum to the left or right, click on the drag (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.
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.
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 (Windows left, Macintosh right):
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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 (Windows top, Macintosh bottom). Use the usual rules for your operating system to navigate to the desired save location:
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 (Windows top, Macintosh bottom). Use the usual rules for your operating system to navigate to the desired save location:
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.
The export formats available are:
MSA 1.0 [XY]. 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. Note: in the "normal" format (no XY), the count information is organized into 4 comma-delimited columns. Thus the number of rows of data is [number of channels] divided by 4. In the XY format, there are 2 columns of information: energy (as calculated with the eV/chan information), and number of counts at that energy.
Xraytor. Saves the data in a special file format designed for encoding spectrum-at-every-pixel information. File extension is .xrt.
JPEG [& MSA XY]. JPEG saves the data as a jpeg image of the spectrum, at the size that it appears on your computer screen. Note that the JPEG format alone does not save the spectrum data, but instead saves the spectrum as a picture, convenient for pasting into a report or publishing on the web. If the MSA XY option is also selected, two separate files are created: 1) the same jpeg image of the spectrum, and 2) an MSA XY text file (see above) of the data.
Excel-Results. Saves the qual-quant results (only the results) 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). These formats do not save the spectrum data, but instead save the spectrum as a picture in an OS-native graphics format, convenient for pasting into a report. File extension is .bmp or or .pct.
Any Revolution spectrum saved as an EMSA or Xraytor file can be opened by double-clicking on the file, and by default open individually in a single-spectrum window that does not support all the features of spectrum catalogs; to access full capability, these single-spectrum files must be copied and pasted into catalogs or directly imported into a catalog using File → Import.
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. If multiple copies of Revolution are being kept, we recommend that files only be opened using File → Open or File → Import.
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 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 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 right-clicking any element in the KLM periodic table and selecting Edit Lines (Copper shown as example): |  |
Important Operating Note: The KLM periodic table is a floating window 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 Show ROIs is turned on, 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 labeled. 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: |  |