EFTEM SI Artifact Correction

Correcting EFTEM spectrum images after acquisition

EFTEM spectrum images (SI) are susceptible to x‑ray hits and sample drift during acquisition. X‑ray hits appear as isolated extreme pixel values within individual image planes, while sample drift causes misalignment between planes. If left uncorrected, these effects can introduce artifacts into extracted spectra, such as sharp discontinuities.

DigitalMicrograph^® software provides tools to reduce or eliminate both types of artifacts prior to analysis.

Remove x-ray artifacts

Use the Remove X‑rays function to identify and correct spurious pixel values caused by X‑ray hits.

Remove x‑rays

1. Select the EFTEM SI dataset.
2. Choose Remove X‑rays from the Volume submenu.

The software examines each image plane and identifies pixels that exceed a specified number of standard deviations above the local median (10 standard deviations by default).
 

When the process completes, the software reports the number of x‑ray hits removed.

Adjust x‑ray detection parameters

1. Hold down the Alt key while selecting Remove X‑rays to:
   1. Set the standard deviation threshold used to identify anomalous pixels.
   2. Define the maximum number of x‑ray hits to remove.

Correct spatial drift after acquisition

Because SI acquisition can take a significant amount of time, sample drift may cause individual energy planes to be spatially offset. The extent of drift depends on factors such as:

• Sample and microscope stability
• Exposure time
• Magnification

You should measure and correct spatial drift before performing any further analysis.

Measure drift (automatic)

Automatic drift measurement uses cross‑correlation to determine relative shifts between energy planes.

Procedure

1. Select the EFTEM SI dataset.
2. Choose EFTEM \ Measure Drift (Automatic) from the menu.

The software:

• Measures spatial drift between all planes of the STEM SI relative to the currently displayed plane.
• Uses cross‑correlation and image filtering as defined in the EFTEM Mapping Preferences.
• Displays the measured drift in a line plot, suitable for use with the Image Alignment palette or manual correction tools.

If any measurements fail the minimum quality criteria, a dialog appears at the end of the process, offering the option to continue with manual drift measurement.

Measure drift (manual)

Manual drift measurement provides interactive control for refining drift corrections in 3D image stacks.

Procedure

1. Select the EFTEM SI dataset.
2. Choose EFTEM \ Measure Drift (Manual) from the menu.

The manual drift correction tool opens with the following features:

• The image stack displayed alongside the alignment overlay.
• A line plot showing all currently measured drift values.
• Two draggable ROI markers used to select the image planes for alignment.
• Drift values reported relative to the reference plane (shown in gray).

You can change the active (green) plane using:

• The Plane buttons in the Image Alignment tool, or
• The Slice tool in the EFTEM SI dataset display

Note: If a line plot of drift measurements already exists when the tool is launched, those values are used initially.

• Click Cancel to retain the original measurements.
• Click OK to permanently replace them with the adjusted values.

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