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Drift Correction & Animation

Two related workflows for working with a sequence of scans - typically repeated images of the same area taken over time - available from the thumbnail right-click menu after selecting two or more images.

Drift correction

Select two or more thumbnails of the same region taken at different times, then right-click -> Drift-correct and export.... This aligns every image to the first one in the selection using sub-pixel image registration (scikit-image's phase cross-correlation, falling back to OpenCV's ECC method if scikit-image isn't installed), then crops all frames to their common overlapping region so the whole stack shares one consistent field of view.

Note

Requires scipy. For the alignment step itself you also need scikit-image or opencv-python - without either, frames are still cropped to a common region but not actually shifted into alignment.

The Drift correction preview dialog that opens shows:

  • the measured shift (in pixels) for every frame, relative to the first
  • the resulting common crop size
  • an animated preview of the aligned stack, with a colormap picker and a playback-speed slider

From there, three outputs are available:

Button Result
Save aligned PNGs... Writes each aligned, cropped frame to disk as a PNG
Save animation... Saves the aligned stack directly as a GIF
Save corrected copies to thumbnails Inserts each aligned frame back into the thumbnail grid as a virtual copy

Animation from a selection

Select two or more thumbnails, then right-click -> Create animation from selection... to build a GIF, MP4, or PNG sequence directly from them - no alignment step. If the frames need registering first, use Drift correction instead (its own Save animation... button covers that case).

Note

Requires the imageio package.

Frames are always ordered alphabetically by filename, not by the order you selected them in. The Export animation dialog offers:

  • Format: GIF, MP4, or a numbered PNG sequence
  • FPS and Duration - linked, so changing one adjusts the other for the fixed frame count
  • Include scale bar / markers-overlays / molecules toggles
  • Resolution: Auto (native size), 720p, 1080p, or a custom width/height

A live preview canvas shows the assembled animation before you save it.