Acquiring Elemental Images
In AugerMap 2, elemental images are separate from topographic SEM (SED, ABS video) images.
Before acquiring, you’ll want to ensure that you are acquiring clean Auger data using AugerScan. You’ll also want to use AugerScan to ensure peak and background positions. See
your AugerScan documentation for more information.
To acquire an elemental image(s), click Elemental Region in the Acquisition menu. This will bring up the Setup Elemental Acquisition dialog. From this
dialog, you can acquire (or re-acquire) multiple images. If you have not
already acquired an elemental image, you may also setup your images without acquiring
by clicking the Apply button. You may also acquire more than one of each elemental region (for
example, if you want to acquire two Si images at different resolutions)
Elemental Acquisition Dialog
Element List
The Element List is a list of all the elemental region images for this map. To add an element
image, simply click the Add button. To remove an element, select the element from the list and click the Remove button. To remove all the elements, click the Remove All button.
When you click the Add button to add an element, you’ll be presented with the Select Element dialog. From here, you can click one
or more elements to add. Note that you can also edit the element table from
this dialog. Click here for more information on editing the element table.
The following all refer to the selected element:
Energy
These parameters determine what kinetic energies will be used to acquired data
for the selected element. Each element can be acquired using data from the
peak energy only (not normally recommended), from the peak minus one background
energy (recommended), and from the peak minus the intersection of two
backgrounds (used in special cases).
The Peak energy is always selected. To select either the Background E1 or Background E2 energies, check the boxes next to the edit fields. Note that you cannot use
the Background E2 energy unless the Background E1 energy is selected.
The default values for the peak and background energies are provided by the element table. However, these values are not always recommended, as they will often not
result in good images. The best way to obtain these values is to use AugerScan
to do a quick survey of the area.
You must always specify a peak energy by entering a value in the Peak energy field. This energy should normally be the actual maximum count value
of this element’s signature.
The Background E1 energy is normally a kinetic energy (higher than the peak value) at which the
signature of the peak reaches a minimum. When this energy is selected, the
resulting data is the Peak – Background E1, which should yield a stable, noise free image.
The Background E2 energy is normally a stable minimum that occurs at an energy lower than the
peak energy. When this background is selected, the actual background used (for
peak – background data) occurs at the intersection of the peak with a line drawn
between the E1 and E2 backgrounds. This is useful when the E1 (higher energy)
background is fluctuating, which may occur if there is another peak near this
higher energy.
Keep in mind that the acquisition time is adversely affected by selecting two
backgrounds, and, if the situation does not warrant it, will not necessarily
result in a better image.
Resolution
Use this drop-down box to select the resolution (XxY pixels) of the image.
The choices available are 64x64, 128x128, 256x256, 512x512, and 1024x1024. It’s a good idea to take a 64x64 image first, to determine whether the parameters
setup result in reasonable image quality. 256x256 is probably the best
compromise between time and quality if you do not require high resolution.
Time Per Step
This value determines the amount of time (in milliseconds) spent acquiring
data at each energy, for each pixel of the image. For example, if you were using
the peak and one background, data would be acquired at 10ms for the peak and
10ms for the background, for a total of 20ms per pixel.
A good default value here is 10ms. Longer times may result in better signal
to noise ratios (and resulting images), but at great cost to acquisition time.
Comment
Type a comment in this field (optional) for the selected image. The comment
will also appear in the Project Window, and on the printout, so it can be a useful reference.
Acquire All
Click this box if you wish to automatically acquire all the elemental region
images in the list. If unchecked, only the selected acquisition will be
acquired at this time. You can always acquire the other acquisitions later.
Acquire
Click this button to acquire the selected image, or all the images if you have
that option selected (see above).
Apply
Click this button to apply the current settings for all images, without
actually acquiring. You can then save the file, and use it later as a template.
Note that, if you have acquired any elemental images, this button is inactive.
Acquisition Control
Evaluating Data During Acquisition
AugerMap displays the image as it is being acquired, so you can often easily
tell if there are problems with the image quality. As new data is acquired, the
image gray-scale range is automatically adjusted to take into account the min
and max of the new data. Therefore, you may see the contrast of the image
fluctuate as it adjusts to accommodate. The status bar at the bottom of the main
AugerMap window will update with the current line being acquired, counts, and
estimated time remaining. The counts may vary anywhere from the hundreds to
thousands, depending on the type of image being acquired and the current settings.
The overall range is usually not important, but if you are only see a
fluctuation of less than a hundred, you will probably notice a lack of image depth and
quality, and need to make some adjustments to your image setup to compensate.
Note that for elemental regions, the full set of energies are acquired on a
line-per-line basis. This means that the image you see on the screen is updated
with peak-background information. Acquiring in this manner also ensures that
any drift may affect the image spatially, but will not result in incorrect
background pixels being subtracted from their associated peaks (and resulting in
noise).
To cancel the rest of an image acquisition (and any other images queued up
afterwards), click Stop Now from the Acquisition menu. The acquisition will stop immediately. Note that this removes any
previously collected data (for that image), since it is incomplete. To cancel any
queued-up acquisitions after this one is complete, click Stop from the Acquisition menu.
After Acquisition
After acquisition, there are a number of actions you can take. You can annotate the image, or add a microm marker. You can also process, enhance, colorize, and invert the image. All of these commands are available from the image menu. You can
also use the Project Window to delete the image.
Often, an image will need some adjustments to brightness and contrast before
the quality is acceptable. This may be the case if there is any noise in the
image. If there are a few pixels with very high counts in an image, this will
lower the overall contrast. Brightness and contrast are adjusted using the Threshold and Gamma controls available from the Processing command in the Image menu. Click here for more information on image processing.
Keep in mind that, for elemental images, the resulting image should be
representative of the underlying data. Adjusting the processing or enhancing an
elemental image will obviously changed the way the grey-scale image maps to the
underlying data, and may no longer reflect an accurate representation.
Elemental images can be most useful as part of a composite (especially if overlayed on an SED or ABS image). Before using an elemental image as top layer in a composite, you
must colorize the data.
Lastly, saving, exporting and printing commands are covered in the File Management topic.