Image registration

Registration lines up two images of the same thing — a second round of staining over the first, a histology section over an atlas, a live frame over a fixed one. The result is a transform applied to the moving image’s layer, so the original file is untouched and you can undo it.

Aligning

With both images open (two layers in one Viewer, or two panes), open the moving image’s layer panel and choose Align to…, then pick the fixed image.

Choose a Transform type:

	Allows
Rigid	Rotation and translation
Similarity	Rigid plus uniform scale
Affine	Shear and non-uniform scale as well
B-Spline	A dense, non-rigid warp

Then either:

• press Start for an automatic registration, which optimises mutual information between the two images (works across modalities), or
• switch to landmark mode, click matching points on both images — three or more pairs — and press Run landmark registration.

Progress and the final metric are shown in the panel. Run again re-runs with new settings; the transform stack on the layer keeps each result so you can step back.

Tip

Start rigid. Move to affine only if the residual misalignment is a stretch, and to B-spline only when the tissue itself has deformed.