CasaXPS: Quantification of a Survey Spectrum

This tutorial offers one of the many possible ways to quantify a survey spectrum in CasaXPS. The intention is to explain how the interacting components of the system aid the analyst to rapidly produce a quantification table suitable for inclusion in a customers report.

Step 1: Load the Spectrum

CasaXPS is designed for ISO-14976 formatted XPS spectra. A data file containing spectra stored in the ISO format may be selected via the Open VAMAS file dialog window shown in Figure 1. To select a VAMAS file press the toolbar button indicated in Figure 2 by the red box to invoke the Open VAMAS file dialog window.

Figure 1: Open VAMAS file Dialog Window

Figure 2: Toolbars. The red box points to the Open toolbar button.

Step 2: Select the Spectrum for Processing

Once the data file has been selected via the Open VAMAS file dialog window, the spectra held within the file will be displayed in a logical array where each data region is labeled by the VAMAS block identifier string and these block labels are arrange according to the element/transition strings recorded in the VAMAS file. Figure 3 shows the state of the CasaXPS windows after a spectral data file has been loaded.

Figure 3: CasaXPS program window after a file has been loaded.

When opened, the VAMAS file appears as an experiment-frame window, which is managed by the CasaXPS program frame and it in turn displays the file as a logical set of spectral blocks. These logical blocks labeled by name allow spectral regions to be selected and displayed in the left-hand-side of the experiment-frame. The current selection is that set of labels highlighted blue (default color scheme), and when the file is first opened the top row of spectra regions will be highlighted and displayed in the left-hand experiment-frame. If more than one spectrum appears on the first row of the right-hand-side, then the spectra will be displayed in the left-hand-side using a scrolled list of display tiles.

The left-hand mouse button and the cursor are used to make a new selection. Point the mouse at a block label within the array of labels on the right-hand-side and left-click. Any blocks currently selected will be deselected and the block under the mouse will become the current selection. Press the toolbar button indicated in Figure 4 to display the selection in the scrolled list on the left-hand-side of the experiment-frame.

Figure 4 Toolbar button to display spectra in the left-hand-side of the experiment-frame.

In this example, the spectrum of interest is the last in the sequence of survey spectra recorded in the data file. Figure 5 shows the state of the CasaXPS windows after a specific survey spectrum has been selected and displayed. Also note in Figure 5 that the experiment-frame window has been maximized within the program frame of CasaXPS.

Figure 5: CasaXPS ready to identify spectral features using the element library dialog window .

Step 3: Peak identification.

CasaXPS will load an element library called CasaXPS.lib located in the same directory as CasaXPS.exe. The element library is used to identify the peaks seen in the data and is central to rapidly creating quantification regions for a survey spectrum.

The Element Library dialog window is invoked or brought to the front of any CasaXPS dialog windows by pressing the toolbar button . The first property page of the element library dialog window is a scrolled list of line positions where the list is ordered by the energy of the entries. If the mouse is left-clicked on the spectrum displayed in the left-hand-side of the experiment-frame shown in Figure 5, then the scrolled list of element library entries will scroll to the energy indicated by the mouse click. Therefore, by pointing at the peaks in the spectrum via the mouse, the names for the various features can be brought into view and if the name field displayed in the scrolled list is selected, again using the mouse, a set of markers will appear on the spectrum positioned at the energies at which spectral lines should appear for the chosen element. Figure 6 shows the spectrum after the O 1s and C 1s lines have been activated via the element library scrolled list.

Figure 6: Peak identification via the element library.

If the name field of an element library entry is selected a second time, the element markers are removed from the display. The current set of active element markers can be view on the Periodic Table property page also located on the element library dialog window. The element markers may be activated and deactivated via the Periodic Table as well as the scrolled element list.

Step 4: Annotating Peaks Identified by the Element Markers

Once all the spectral lines are identified and markers have been placed on the displayed spectrum, the peaks can be annotated by the names stored in the element library. This step not only creates a labeled spectrum, but these annotation peak labels are used to create a set of quantification regions at the press of a button.

The annotation dialog window includes a property page entitled Peak Labels (Figure 7). All the peak markers active on a spectrum are listed on the Peak Labels property page and may be selected using the mouse and the control key (to add to the selection). When the Apply button is pressed those labels selected in the list of names on the Peak Labels property page become annotation labels on the spectrum. The peak labels are positioned on the spectrum according to the location of the nearest peak, so it is important that the spectrum is calibrated before this procedure is performed.

Figure 7: Peak Labels Property Page on the Annotation Dialog Window .

Step 5: Create Quantification Regions

The Quantification Parameters dialog window is available from the top toolbar button indicated in Figure 8. Integration regions are created and adjusted via the Quantification Parameters dialog window, where a scrolled list of region entries is offered. Each column in the scrolled list represents the set of parameters that define a quantification region.

The annotation for the peaks is used by the Create from Labels button at the bottom of the Quantification Parameters dialog window in Figure 8. Regions created in this way have the name and RSF set from the entries in the element library. The background type for each of the newly created regions is determined from the last background type entered on the Regions property page.

Figure 8: Creating Quantification Regions .

Step 6: Adjusting the Start and End points for the Quantification Regions

The Regions Property Page is used to manually adjust the values for the integration regions. The table of parameter fields offered in the scrolled list may be adjusted by selecting a field within the table using the left-hand mouse button and the cursor position. If a field can be altered, then selecting that field with the mouse will both highlight the column of parameters for that region and cause the selected field to become a text-edit field. Any changes are accepted only after the return-key is pressed.

Although manual input is achieved through the Regions property page, an easy way to check the start and end points for each integration region is to use the Zoom List toolbar buttons and adjust the integration limits under mouse control. Provided the Regions Property Page is the visible page on the Quantification Parameters dialog window, vertical bars will mark the integration regions on the active spectrum. The presence of these bars indicates that the limits for the regions can be adjusted under mouse control. If the cursor is dragged starting at the position of one of these vertical bars, the corresponding region end point will be adjusted when the mouse button is released.

The integration regions on a survey spectrum are typically too narrow to be adjusted in this way without the use of a zoomed display. To facilitate the use of the mouse, CasaXPS allows all the current integration regions to be entered onto the Zoom-List and then using the Zoom Out toolbar button (or Ctrl right-click of the mouse) the current set of integration regions can be zoomed into and adjusted.

Press the Zoom Reset toolbar button . The spectrum will be displayed showing the full set of data and any integration regions currently defined for the spectrum will be entered onto the Zoom-List. Now pressing the Zoom-Out toolbar button will cycle the set of zoom states and therefore sequentially display the regions.

Figure 9: Cycle through the integration regions using the Zoom Reset button followed by the Zoom Out button .

Step 7: Printing the results

Once the elemental composition has been defined using the integration regions, the results may be added to the spectrum display. This is achieved via the Annotation dialog window (Figure 10), where the Regions property page allows a table of atomic concentrations to be positioned on the spectrum. The entries in the quantification table are updated when changes are made to the set of integration regions so there is no problem about out-of-date quantification results being reported over a spectrum. If the Annotation History property page is the active page on the Annotation dialog window (Figure 10), then each annotation item will be displayed with a small position box attached. The annotation may be repositioned using these boxes. This is achieved by pointing the cursor at a box and then, with the left mouse button held down, the cursor is dragged to a new position. The annotation will move once the mouse button is released.

Figure 10: Annotating the spectra using the Quantification results. Note the drag box associated with the annotation.

The spectrum shown in Figure 10 is now ready to be printed. Any spectra visible in the left-hand-side of the sub-frame will be printed on a single page. If the left-hand-side is a scrolled list of spectra then each tile within the scrolled list will be printed as a separate page. If more than one spectrum is required on the same printed page then the Page Layout dialog window offers the means of sub-tiling a printed page (Figure 11 and Figure 12).

Figure 11: Page Layout dialog window .

Figure 12: Sub-tiling a printed page is achieved using the Page Layout dialog window .