Adjustments

Spatial drift correction

Thermal effects and mechanical instabilities in the microscope can cause the sample to drift relative to the electron beam. Because Spectrum Image (SI) acquisition may take a significant amount of time, uncorrected drift can smear features or shift the acquired data away from the intended sample region. Drift effects increase at higher magnifications and may vary between microscopes and even between sessions on the same instrument.

Spatial drift correction compensates for this movement by periodically measuring and correcting beam position offsets during SI acquisition.

How spatial drift correction works

Spatial drift correction uses cross‑correlation between:

A reference scan of a user‑defined region, and
Subsequent scans of the same region acquired during SI acquisition.

For best results, the drift measurement region should contain distinct spatial features with sufficient contrast.

Workflow:

A reference scan is acquired from a selected region of the survey image.
At the start of SI acquisition, the first drift measurement scan is taken from the same region.
Cross‑correlation measures any positional shift.
The system corrects drift by offsetting the beam scan coordinates.
Drift measurements are repeated periodically based on the selected correction frequency.

Measurement results are reported in the DigitalMicrograph^® results window. If the survey image is calibrated, reported shifts are shown in calibrated units.

After acquisition completes, you can review the applied corrections using Show Correction from the SI menu.

Note: Because drift images are acquired during SI acquisition, the detector used for drift measurement must not interfere with spectrum acquisition when inserted.

Set up spatial drift correction

Acquire and assign a survey image for SI acquisition.
Enable the Drift button in the STEM SI palette.
A rectangular ROI labeled Spatial Drift appears on the survey image.
Adjust and accept the correction frequency settings.
Resize and reposition the Spatial Drift ROI as needed.
(Optional) Configure advanced drift correction settings.

Choose a correction frequency

The optimal correction frequency depends on the magnitude and stability of sample drift. Selecting a frequency involves balancing:

Shorter total acquisition time, and
Improved spatial fidelity in the SI.

Frequency options based on spatial features (pixels, rows, or frames) generally produce smoother results than time‑based options.

Adjust the Spatial Drift ROI

Use the mouse to resize and move the Spatial Drift ROI:

The measurement area should be at least twice the maximum expected drift between corrections.
Choose a region with distinct, high‑contrast features.
Avoid overlapping the drift ROI with the main SI acquisition area whenever possible.

Access advanced drift options

To open the drift correction options directly:

Click the Drift button while holding the Alt key.

This opens the Spectrum Imaging Setup dialog at the drift correction options page.

Viewing point spectra

When configuring spectrometers for SI acquisition (for example, to determine optimal pixel dwell time), it is often useful to view a continuous spectrum from a specific location in the survey image.

The Spot function allows you to position the beam anywhere within the survey image and observe the corresponding spectra.

View the spectrum at a specific point

Acquire and assign a survey image.
Enable Spot mode in the Scan palette.
A cursor labeled Beam appears on the survey image.
1. If the survey image is currently being acquired, the cursor is labeled Park.
2. Stop the scan to obtain a stationary beam.
Start continuous acquisition using the View button in the appropriate Spectral Acquisition palette.
Drag the beam cursor to view spectra from different locations.

The spectrum display updates continuously as the cursor is moved. Use this mode to optimize acquisition parameters before starting SI acquisition.

Beam Safe Point

To minimize beam damage when acquisition is paused or completed, the system attempts to move the beam away from the sample.

If a safe point is defined, the beam moves to that location.
Otherwise, beam control returns to the microscope.

Note: During an active scan, the cursor is labeled Park. When no scan is active and the beam is stationary, the label changes to Beam.

Set up a Beam Safe Point

Ensure a survey image is assigned.
Enable Spot mode in the Scan palette.
Position the Beam cursor at the desired safe point (a vacuum region is recommended).

When SI acquisition is paused or terminated, the beam automatically returns to this location.