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.

Align by correlation, then propagate across a range

The Ctrl+\ correlation shift can be recorded and propagated across a range of sections, exactly like a manual transform — but you must start recording before you correlate:

1. Navigate to the section you want to align.
2. Alignments ▸ Propagate transform ▸ Start propagation recording.
3. Press Ctrl+\ (Align by correlation). This aligns the current section and records the shift.
4. Either navigate through the sections (each unlocked section you visit receives the recorded shift) or use Propagate to start / Propagate to end to apply it across a bulk range at once.
5. Alignments ▸ Propagate transform ▸ End propagation recording.

Order matters: starting recording resets the accumulator, so pressing Ctrl+\ before you start recording will not capture that alignment — always start recording first. As with manual transforms, locked sections are skipped during propagation.

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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