Alignment

Alignment

An alignment is a named set of per-section transforms. The currently active alignment determines how each section's image and traces are positioned. Switching alignments never changes the underlying images or trace coordinates — only how they are displayed.

Every series includes a special no-alignment entry (the identity transform). It can't be edited, renamed, or deleted, and you can't edit transforms while it is active — switch to a real alignment first.

Switching and managing alignments

• Switch the current alignment from the field's right-click menu (Series alignment submenu), which lists every alignment as a checkable item.
• Alignments ▸ Modify alignments (Ctrl+Shift+A) opens the alignment dialog, where you can create a New alignment (created as a copy of the current one), Rename, or Remove alignments. Objects can also carry a per-object alignment override (Change object alignment… in the object list).

Adjusting a section's transform

• Alignments ▸ Edit transformation (Ctrl+T) — enter the six transform numbers a b c d e f directly. (Blocked on locked sections and while in no-alignment.)
• Keyboard nudges (when no traces are selected, these move the section's transform; otherwise they move the selected traces):
  • Arrow keys — translate (medium step); Ctrl+arrows = small, Shift+arrows = big. Step sizes are set in Series ▸ Options.
  • Ctrl+Shift+Left / Ctrl+Shift+Right — rotate about the cursor.
  • F1–F4 (with Shift to reverse) — scale and shear in X/Y.

Assisted alignment

• Estimate affine transform — align the current section to the comparison ("B") section from matched traces. Select 3 or more traces of the same name on both sections (the same number on each); PyReconstruct computes the affine transform that best maps one set of centroids onto the other.
• Align by correlation (Ctrl+\) — automatically register the current image to the section beneath it by image cross-correlation (a translation-only adjustment).
• Propagate transform — record a transform adjustment and apply it across many sections: Start propagation recording, make your adjustment, then Propagate to start / Propagate to end (or simply navigate — while recording, moving to a new unlocked section applies the recorded change). A red dot is shown on the field while recording. Locked sections are skipped.

Importing transforms

Alignments ▸ Import alignments:

• .txt file — one line per section: section a b c d e f (the integer section number followed by the six transform numbers). Every section number must exist in the series; the translation terms are interpreted in pixels and scaled by the section magnification. The imported transforms are written to a new alignment named after the file (with the date appended), and the series switches to it.
• SWiFT project — import transforms from an AlignEM-SWiFT project; you choose the scale to import. The number of transforms must match the number of sections.

Transforms can also be imported from another series via Series ▸ Import ▸ from series… (an Alignments tab lets you pick which alignments to bring over).

Locking sections

A locked section's transform can't be changed by any means (manual edit, nudges, estimate/correlate, or propagation), and locked sections are protected from brightness/contrast changes, thickness edits, image-source edits, and deletion. Lock/unlock from the Section list (the Locked column or its context menu); unlock the current section quickly with Alignments ▸ Unlock current section (Ctrl+Shift+U).

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