Atlas Registrations Adjustments
This page explains how to manually improve the atlas registration for a slice so the anatomy matches well in the area that matters for analysis.
The goal is local anatomical accuracy, especially around the analyzed 20x area and the brain regions you selected.
What you are adjusting
In this view, you are matching landmarks between the atlas and the 4x slice image.
Each point pair tells Neuro QP which location on the atlas corresponds to which location on the slice.
As you add and move points, the atlas fit updates to better follow the tissue.
Open the Registration view
Select a slice from the left panel.
The atlas is shown on the left and the slice image on the right.
Start with slices where the anatomy is relatively easy to recognize.
Understand the layout
- Left side: Atlas viewer
- Right side: Slice viewer
- Left panel: Slice list grouped by animal
- Status indicators: Help identify slices that still need attention
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.
Neuro QP 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 edit existing points
Select an existing point pair.
Drag either side to improve the match.
Remove points that are clearly unhelpful or inaccurate.
Changes save automatically.
How to evaluate the fit
Focus on whether the atlas boundaries match the visible anatomy in the area that matters for analysis.
Pay special attention to the region covered by the 20x image and the brain regions you selected.
Cycle through stainings, because different anatomical boundaries can be easier to recognize in different channels.
The goal is not perfect alignment across the entire slice, but a good local match where the analysis depends on it.
When to stop
Stop when the atlas fit is clearly good in the relevant analysis area.
You do not need to keep adding points once the local registration is already reliable.
Well-placed points matter more than simply adding more points.
Final note
If the atlas registration is good but the 20x image itself looks misplaced, that is a separate problem and should be corrected in 20x Registration Adjustments.