Drift Correction

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Drift Correction#

Drift correction aligns an image stack by estimating pairwise shifts, reducing them to absolute correction shifts, and applying those shifts to the original images.

The drift-correction workflow adapts the pairwise image-registration approach described by de Jong et al., Ultramicroscopy 213, 112913 (2020), DOI: 10.1016/j.ultramic.2019.112913.

If you use the drift-correction workflow in published work, please cite:

de Jong et al., Ultramicroscopy 213, 112913 (2020), DOI: 10.1016/j.ultramic.2019.112913.

On top of the algorithm, pyLEEM provides additional features to improve the performance and the workflow.

Tuning#

The implemented drift correction prioritizes LEEM experiments, where only transformational corrections (x, y shifts) are applied. The drift correction varies from experiment to experiment, here we outline the parameters and how each would change the drift correction behavior.

Parameters for drift correction (calculate_drift):

  • sigma: Gaussian smoothing.

    • For noisy data, increase sigma. Value too high would blur features.

  • crop_size: Center crop used for drift correction.

    • Can increase the drift correction speed.

  • upsample_factor: Pixel precision for correlation and shift.

    • 10 means 0.1 pixel precision.

    • Larger values are slower and usually only help after the pair registration is already stable.

  • max_workers: Number of worker threads for multi-threading.

    • Recommended: 4–8 depending on the CPU.

  • chunk_size: Number of image-pairs per threaded task.

    • Recommended: 16–64 depending on the CPU.

  • max_distance: Pairing window size.

    • 1 means correct image based on the adjacent frames.

    • If there are a lot of frames with contrast or feature change, use higher values to calculate the overall correlation.

    • Higher values are much slower (1 is log(n), 2 is log(n^2), 3 is log(n^3), etc.)

    • Higher values may result in jitter depending on the data.

  • reference_index: Center frame to reference the shift.

    • The reference index is important especially for ROI selection.

Parameters for the shift application (apply_shifts):

  • expand: Whether to expand the canvas to fit all shifted content.

    • By default, the shifted content is cropped at the original boundary.

  • cval: Fill value for empty pixels introduced by shifting.

    • Defaults to 0 (black).

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