Registration Workflow and Best Practices

This page explains the practical workflow for getting good atlas registrations quickly.

Start with the automatic outline points

Begin with the points created by automatic registration.

Correct them so they match the visible outline of the anatomical reference image as well as possible.

This gives you the initial whole-slice fit before local refinement.

After correcting the outline points, add new points only where they clearly improve registration.

Focus on visible anatomical landmarks that help the atlas match the slice better.

Spread points across the relevant area instead of stacking many points in one small place.

Use landmarks that are easy to recognize in both the atlas and the slice image.

Good choices are strong outer contours, characteristic bends, and visible internal boundaries.

Avoid weak or ambiguous features.

For 4x reference + detail projects, refine atlas registration around the detail field and selected regions.

For high-res whole-slice projects, refine against the full high-resolution anatomical reference. There is no separate detail placement to adjust.

Different stainings reveal different anatomical structure.

Switch channels when needed to judge a boundary or landmark more confidently.

If a point is clearly wrong or pulls the fit in the wrong direction, move it or delete it.

A smaller number of good points is better than a larger number of poor points.

Stop when the atlas matches visible anatomy well in the area that matters for downstream analysis.

The goal is not to force every line to look perfect everywhere. The goal is trustworthy region assignment.