Atlas Registrations Adjustments
This page explains how to manually improve atlas registration for a slice.
The goal is local anatomical accuracy in the areas that matter for analysis.
What you are adjusting
You are matching landmarks between the atlas and the project's anatomical reference image.
Depending on acquisition mode, the anatomical reference may be a 4x, 10x, or 20x image.
Each point pair tells NeuroQP which location on the atlas corresponds to which location on the slice image.
As you add and move points, the atlas fit updates.
Open the Registration view
Select a slice from the left panel.
The atlas is shown on one side and the slice image on the other.
Start with slices where anatomy is relatively easy to recognize.
Main controls and shortcuts
- Move: Pan and zoom the viewers
- Add Points: Create corresponding landmarks
- Link: Move both viewers together
- S: Switch to Move mode
- A: Switch to Add Points mode
- L: Link or unlink the viewers
- D: Cycle through stainings
- F: Cycle brain region display
How to add adjustment points
Switch to Add Points.
Click a recognizable landmark in one viewer.
NeuroQP places the corresponding point in the other viewer as a starting estimate.
Drag the points so both mark the same anatomical feature.
Repeat across the relevant area until the fit improves.
How to evaluate the fit
Focus on whether atlas boundaries match visible anatomy in the analysis area.
Cycle through stainings when different channels reveal different anatomical boundaries.
The goal is not perfect alignment everywhere. The goal is a trustworthy local match where region assignment affects quantification.
When to stop
Stop when the fit is clearly good in the relevant analysis area.
Well-placed points matter more than simply adding more points.
If atlas registration is good but a detail image looks misplaced in a 4x reference + detail project, use Detail Image Registration Adjustments instead.