XRayImageScan is a plug-in written by 4pi that is compatible with 4pi SEII drivers. It is used to acquire X-ray maps from the SEII into NIH Image, Adobe Photoshop, IPLab Spectrum, or any program that works with Photoshop-compatible plug-ins. FPXDriver 5.0 (supplied with Revolution) is 100% backward-compatible with these programs via the XRayImageScan plug-in v4.4.1. Therefore, Revolution and any of these programs can be run side by side without any software reinstalls or changes or incompatibilities. Note that acquiring x-ray mapping data with these programs (via the plug-in) and Revolution simultaneously may work but is not a supported mode of operation and is not recommended. For reference, the diagram below shows the relationship of these software components:

Introduction

The raw data stream from the hardware is 16 bits deep. However, during acquisition, only 8 bits are displayed. Simultaneous acquisition of one of any of the 4 analog video channels is allowed. The number of x-ray maps that can be acquired simultaneously is limited only by the available memory. The maps generated display a true gray scale. The pixel value is the number of x-ray counts detected within the specified energy region-of-interest for that pixel location.

The X-ray ImageScan plug-in dwells at each pixel for a fixed livetime before proceeding to the next pixel. This method (commonly referred to as "slow" x-ray mapping) will enable future software versions to implement full quantitative analysis at every pixel and the saving of the raw spectral data for the entire image map.

Before attempting to acquire an x-ray map, the user should use SEMImageScan and DTSA (or FLAME) to perform all scanning and probe adjustments and calibrations.

Configuration

The XRayImageScan plug-in supports acquisition of maps from energy dispersive spectrometers. To start an acquisition, the user launches the preferred application (NIH Image, Adobe Photoshop, IPLab Spectrum, or any other application that supports Photoshop-compatible plug-ins). Pulling down the File>Acquire menu allows the user to select the plug-in. This act of selection puts the 4pi system directly into the probe mode and a Periodic Table is immediately displayed with other controls and settings:

The Size menu and the editable Dwell field are controlled and used in the same fashion as for the SEMIMageScan plug-in.

In this particular example, 128 x 128 pixel-maps are selected, with the livetime dwell for each pixel set to 10 ms. To enable acquisition of an element's x-ray image, select (single-click) the corresponding element button on the displayed periodic-table-of-elements window. In this example, Iron, Nickel, Copper, and a S(T)EM image are selected. Clicking on the Live radio button selection defines the dwell in livetime milliseconds; clicking on the Real radio button selection defines the dwell in realtime milliseconds. In the above example, data will be recorded at each pixel location until 10 ms of live time is accrued. Note that the actual acquire time will be longer than 10 ms per pixel (perhaps greatly so), depending on the deadtime accrued.

The calculation of estimated time to acquire has been updated for generic PCI Power Macintosh and generic 68k NuBus Macintosh. There may be variations for different machines. Estimated times for NuBus Macs may be somewhat less accurate than for PCI PowerMacs. You may click on either the live or real radio buttons for the appropriate estimated time information for either case. Note that when this window is on-screen, the 4pi system has not yet taken control of the microscope. Therefore, the input count, output count, and deadtime readings are a reflection of the positioning of your beam. Commonly, the microscope is in an internal scanning mode at this point; if you have a sample which emits x-rays in varying amounts as the beam scans, you will see the input count, output count, and probably the deadtime readings vary in like fashion. If you have the live radio button selected, then the estimated time can vary to a large degree as the beam scans. This variation may be so great as to make the estimate unusable. One solution is to put your microscope in a mode in which the beam is not scanning. However, in this case the estimated time will be accurate only if that part of the sample being illuminated is representative of the entire sample. Alternatively, you can select the real radio button which will ignore all deadtime corrections to the estimated acquire time. In this case, the estimate will be a minimum estimate of acquire time. There is no magic bullet here and there is no substitute for understanding the underlying physics of your situation!

To edit the ROI for an element, double-click on the element button. The following window will appear (Nickel, in this example):

ROI image titles can be different from the element symbol. For example the above image title can be "Nickel" instead of "Ni." Names are saved with all other information to an x-ray setup file. For each element, either ROI, K, L or M regions can be established (note that there are no M lines for Nickel, so they are not shown in this ROI). These regions can overlap. Also note that these regions do not have to correspond to K, L or M ROIs--they can be any energy region. The user has the option to include counts from any or all regions in the total count. Background ("bkg") images are similar to element images; however, only one ROI can be selected for each background image. Energies are used to allow for changes in the x-ray spectra channel-width and scaling. Other x-ray ROI setups (use the Open command in the X-Ray ImageScan element set-up screen) can be opened. This allows access to several typical setups for various samples. All information (with the exception of the image sizes) is saved in the ROI setups. Note: currently, color x-ray maps cannot actually be defined, although a color can be selected via the standard system color picker.

To access and change the available imaging parameters, double-click on the S(T)EM button. The following window will appear, allowing one to select any of the four available video channels, and set its mirror and name. Image sizes are flexible and follow the convention of the SEMImageScan plug-in.

Estimated Acquire Time. Calculated acquire time. When realtime is selected, the estimated acquire time is essentially the number of pixels multiplied by the pixel dwell. With no deadtime correction, this estimated time is a minimum time to map. When livetime is selected, the estimated acquire time is corrected for the reported deadtime. Note that the deadtime can vary from point to point in a sample. Thus, since there is no well-defined deadtime for the entire sample, the estimated acquire time may be inaccurate. The estimated acquire time remaining is updated as the maps are being generated.

8-16 Bit Selector.

There is no preferences record entry for this menu. Every time you launch the X-ray plug-in, it will default to 8-bit. If you are using 16-bit, you will have to remember to select it each time!

ROI Save As and Open

These buttons allow you to save and open custom ROI settings:

Using this feature, one might create a setup called "X-ray Setup 1" which consists of the element Nickel, and "X-ray Setup 2" which consists of the elements Iron and Aluminum. These setups could then be easily switched into or out of with the Open button. Or, one might, with enough work, define entire sets of ROIs that have no relationship to the common elements and their known K, L, and M lines. (To follow this example to its logical conclusion, one could also easily hack a duplicate plug-in with ResEdit or Resourcerer to change the element abbreviations on the buttons; this is beyond the scope of the normal user, but if you really want to know how to do this, send e-mail to 4pi support).

ROI Save To

The Save To button is used to define the destination folder for maps saved to disk:

Clicking the Save To button will present a standard Mac file-save dialog. You can navigate to any location in your mounted volume space (in this case to the NIH Image folder):

To create the destination folder, click on the New Folder button. In this example, a folder called "maps" is created:

Alternatively, one can just double-click on any existing folder to select as the folder to save to. At this point, clicking on the Save button will specify the maps folder at the repository for all acquired maps. Any text that is entered in the edit field is automatically prefixed to every file name. Therefore, in most cases this will be left blank.

Acquiring X-ray Maps

Save Spectra Menu

SCA Feature (optional purchase)

If the SCA outputs option was purchased, your SEII provides up to 16 single-channel-analyzer outputs. These outputs are physically located at one end of the board on a 34-pin connector. While in an ROI window, one can choose that ROI information to be echoed on any one of the SCA outputs simply by selecting a menu item:

For example, if SCA #9 is selected, whenever an x-ray pulse is deemed to fall within this ROI, a single TTL pulse will be sent through the SCA port. The SCAs are OR-ed together, so multiple ROIs can be assigned to the same SCA. Up to 48 different ROIs can be mapped to the 16 SCAs (in other words, overlap is allowed). Depending on the hardware options ordered, you may or may not have a pre-made cable for these connections. If one is shipped for the SEII from 4pi, the cable is likely to be a ribbon cable which connects the 34-pin SCA connector on the SEII to a special computer rear-panel connector not unlike a duplicate of the SEII's 37-pin rear-panel D-connector. The SCA header is a standard 34-pin header. The SCA outputs are the odd pins:

The polarity of the TTL SCA signal is set via a jumper (JMP1) on the SEII 2.2 board. When the jumper is present, the TTL pulses are positive-going. The polarity of all the SCA outputs is set collectively by the jumper. The SCA pulse is currently fixed at 10 microseconds.