Aligning a Junction

Line up the two slices of the current junction: move the green (moving) slice onto the magenta (fixed) one until shared structure turns gray.

Moving the Slice

• Drag with the left mouse button to move the moving slice; arrow keys nudge by 1 pixel, Shift plus arrow by 10

• The dx, dy, and rotation fields show the current transform and accept typed values

• Any manual move clears the confidence score, since it no longer reflects the current position

Auto Align and Confidence

• Auto-align estimates dx and dy by phase correlation on the declared slice pair (a boundary map is used for label stacks); it runs coarse-to-fine but does not estimate rotation, so set that by hand

• Each run reports a confidence score (overlap correlation) in the viewer footer: above 0.5 is good, at or below is poor, and below 0.3 raises a warning

• If confidence stays low, confirm the pair shows the same physical section, check for a large rotation, and fall back to manual alignment, using the flicker toggle to verify the fit

Per-Junction Buttons

• Auto-align: estimate the transform automatically

• Reset: clear dx, dy, and rotation back to zero and drop the confidence score