Detail Image Registration Adjustments

This page applies only to 4x reference + detail projects.

It explains how to correct the placement of a 10x or 20x detail image on the anatomical reference image when the placement is clearly wrong.

High-res whole-slice projects do not use this workflow because there is no separate 4x reference plus detail image alignment.

When this is necessary

Most detail-image placements are already good enough out of the box.

Very small offsets usually do not matter for analysis.

Only adjust placement when the detail image is visibly misplaced in a meaningful way.

Open the slice in the Registration view.

Click Adjust 10x or Adjust 20x, depending on the project detail magnification.

Use the anatomical reference image as the reference and compare the detail-image overlay against it.

Move the corner points until the detail image sits in the correct location.

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

This changes only detail-image placement. It does not change atlas registration.

Focus on whether the detail image sits naturally in the correct place on the anatomical reference image.

Do not chase tiny pixel-level differences.

Stop once the placement is clearly correct.

If detail-image placement looks fine but atlas boundaries still do not match anatomy, return to atlas registration adjustments.