BSE Field Correction

13 min

Requires AMICS 5.2.1 or newer.

BSE Field Correction corrects two common imaging artifacts in backscattered electron images:

Vignetting — radial brightness falloff where the center of each field appears brighter than the edges, caused by detector geometry and optics

Photometric drift — per-field brightness and contrast shifts caused by temperature fluctuations, beam instability, or detector gain changes over the course of a long measurement

{{FIG: Before/after comparison showing a multi-field mosaic with visible vignetting (brightness rings) on the left and the corrected uniform image on the right | BSE field correction before/after}}

When to Use BSE Field Correction

Use BSE Field Correction when:

You can see brightness rings or center-to-edge falloff within individual fields

Adjacent fields have noticeably different brightness despite measuring the same material

Long measurements show progressive brightness drift across the dataset

Quantitative BSE analysis requires consistent grey levels across all fields

Note: BSE Field Correction and BSE Adjustor (offset-based correction) are mutually exclusive. Activating one deactivates the other. Choose the method that best fits your artifact type.

Artifact	Best Tool
Uniform brightness offset between fields	BSE Adjustor
Radial brightness falloff (vignetting) + drift	BSE Field Correction
Both vignetting and uniform offset	BSE Field Correction

Accessing BSE Field Correction

From the Process ribbon Processing tab:

Click the BSE Adjust dropdown in the Tools panel

Select BSE Field Correction

{{FIG: Process ribbon Tools panel showing BSE Adjust dropdown with BSE Field Correction option | BSE Adjust dropdown menu}}

Workflow

First-Time Correction

Click BSE Adjust → BSE Field Correction

AMICS prompts: "Perform BSE correction?" → Click Yes

A progress bar appears while correction parameters are calculated

The corrected BSE images are displayed immediately

{{FIG: Progress dialog during BSE field correction parameter calculation | BSE correction progress}}

Re-Applying Existing Correction

If correction parameters have already been calculated for this measurement:

Click BSE Adjust → BSE Field Correction

AMICS prompts: "Correction already available. Recalculate?"

Yes — recalculate from scratch (use if you've modified the dataset)

No — apply the existing parameters immediately (faster)

Cancel — abort

Toggling Correction On/Off

Once calculated, the correction can be toggled:

Use the Apply BSE Shift checkbox to switch between corrected and original BSE images

This lets you compare the before and after images instantly

Saving

Correction is applied in-memory only until you explicitly save

Original BSE images in the FLD files are never modified — the correction is non-destructive

When you save, correction parameters are written as a JSON file in the MRE folder

Parameters include: vignetting polynomial coefficients, per-tile gain and offset values

How the Correction Works

Step 1: Vignetting Correction (Flat Field)

AMICS samples approximately 200 random fields and computes a radial brightness profile — measuring how intensity varies from the center to the edges. A 4th-degree polynomial is fit to this profile, and a flat-field correction image is generated.

The flat-field image is the same for all fields in the measurement, since vignetting is caused by the optical system geometry.

Step 2: Photometric Correction (Per-Field Gain/Offset)

For each pair of overlapping fields, AMICS compares the pixel intensities in the overlapping region using QQ-regression (quantile-quantile regression), which is robust to outliers. This produces a gain and offset value describing how one field's brightness relates to its neighbor's.

These pairwise relationships are propagated across the entire measurement grid using a least-squares optimization, producing a consistent global gain and offset for each field.

Step 3: Apply Correction

Each pixel is corrected as:

corrected = pixel × flat_field × gain + offset

With these rules:

Background pixels (grey level 0-25) are left unchanged

Zero pixels (empty/masked) remain zero

All other pixels receive the full vignetting + photometric correction

Results are clamped to a minimum of 1 (non-zero pixels never become zero)

Performance

BSE Field Correction is optimized for large datasets:

Flat-field calculation uses random tile sampling (not all tiles)

QQ-regression is parallelized across tile pairs

Per-pixel correction is trivially parallelizable

Memory cost: one additional BSE image copy per loaded field (same as BSE Adjustor)

Correction Parameters

Correction values are automatically clamped to prevent extreme adjustments:

Parameter	Range	Purpose
Gain	0.5 — 2.0	Per-tile brightness scaling
Offset	-50 — +50	Per-tile brightness shift
Background range	0 — 25	Grey levels treated as background (uncorrected)

Limitations

Requires overlapping fields — the photometric correction uses overlap regions to compute gain/offset between neighbors. Non-overlapping measurements cannot be corrected for photometric drift (vignetting correction still works).

Extremely sparse datasets (few fields) may produce less accurate photometric corrections due to limited overlap data.

The correction is calculated from the BSE images as they exist — if the BSE images have been modified by other tools, recalculate the correction.

Reverting Correction

To remove BSE Field Correction:

Click BSE Adjust → BSE Adjust Revert to undo the last correction

Click BSE Adjust → Clear ALL BSE Offsets to remove all BSE corrections

These buttons apply to whichever correction mode (BSE Adjustor or BSE Field Correction) is currently active.