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.

For atlases with named anatomical labels, you can change the atlas slice with the label picker instead of typing a coordinate. For example, spinal cord projects can use spinal segment labels such as C1, T9, or L3.

You can also enter a coordinate in millimetres or step through neighbouring atlas slices. Coordinates entered in the positioning controls are rounded to the nearest available atlas slice.

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

Adjust the section position and tilt

For brain atlases, click the AP coordinate above the viewers to open the positioning panel.

The AP coordinate sets the position of the current slice. Animal tilt adjusts the section’s orientation and applies to every slice assigned to the same animal. Each slice keeps its own AP coordinate and registration points.

1. Select a slice with clearly recognisable anatomy.
2. Adjust its AP coordinate.
3. Enable Animal tilt.
4. Adjust Left / right tilt and Dorsal / ventral tilt using the sliders, arrow buttons or degree fields.
5. Compare the updated atlas and region boundaries with the tissue image.
6. Click Save to apply the changes.

The top and side previews compare the section with a coronal reference plane. Both viewers update as you adjust the controls; allow the atlas to finish loading before judging the fit.

You can pan and zoom while the panel is open. Adding, moving and deleting registration points becomes available again after closing the panel and loading the selected atlas section.

Revert discards unsaved positioning changes. Closing the panel with × or Esc also discards them. Reset tilt sets both angles to zero; click Save to keep that change.

Tilt adjustment supports roughly coronal mouse and rat brain sections, with up to ±25° on each control. Sagittal, horizontal and spinal-cord tilt adjustment are not supported.

Review other slices after changing animal tilt

Changing animal tilt affects all slices assigned to that animal. Existing registration points remain in place, so check whether they still match the updated anatomy.

A reminder identifies slices that have not yet displayed the new tilt in Registration. It clears automatically when the current atlas section has loaded in the editable viewer. This records that the section was displayed, not that its registration was approved.

Review representative slices across the animal before refining individual landmarks. After saving positioning changes, run Process results to update affected measurements.

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.