20x Registration Adjustments

This page explains how to correct the placement of the 20x image on the 4x slice when it is clearly wrong.

This is usually not needed.

When this is actually necessary

Most 20x placements are already good enough out of the box.

Very small offsets do not matter for analysis.

Only adjust the 20x placement when it is visibly misplaced in a meaningful way.

Open the slice in the Registration view.

Click Adjust 20x.

Use the 4x image as the reference and compare the 20x overlay against it.

Move the corner points until the 20x image sits in the correct location.

Use overlay visibility and blending to compare both images while adjusting.

This changes the 20x placement only, not the atlas registration.

Focus on whether the 20x image sits naturally in the correct place on the 4x slice.

Do not chase tiny pixel-level differences.

Stop once the placement is clearly correct.

If the 20x placement looks fine but the atlas still does not match the anatomy, return to atlas registration adjustments instead.