Sections through the Kim mouse atlas at centre AP −1.0 mm. Left/right tilt varies across columns and dorsal/ventral tilt across rows, from −10° to +10° in 5° steps. The teal frame marks the coronal section. All images use the same scale and intensity window.
All 25 images above come from the same Kim mouse atlas volume, cut through the same central AP position. We generated them by changing the angle of the cutting plane. Even within this range of angles, you can see the section outline change, along with the shape and symmetry of the anatomy inside it.
Compare the two ends of a row: reversing the left/right tilt changes which hemisphere is sampled further anteriorly. Moving down the centre column changes the relationship between dorsal and ventral anatomy instead. These differences can matter when you're registering a tissue section that looks broadly coronal but never quite matches a coronal atlas image.
A section can cross several AP levels
When you browse coronal atlas sections, changing AP moves the entire plane forwards or backwards through the brain. Every point in that plane remains at the same AP level. A tilted section cuts across those levels, so its centre can be at AP −1.0 mm while the anatomy towards its edges comes from positions further anterior or posterior.
You may recognise the consequence during registration. Moving to a neighbouring atlas section improves the match on one side of the tissue, but makes the other side less convincing. Or the dorsal anatomy looks plausible at an AP position that doesn't fit the ventral part of the section. If the tissue was cut obliquely, there may be no single coronal atlas image that captures those relationships.
The coronal reference and teal cutting plane share a centre at AP −1.0 mm. The teal plane has +10° left/right tilt and no dorsal/ventral tilt. The atlas-derived brain surface is smoothed for illustration.
In the 3D view, the two planes meet at the centre but pass through different tissue on either side. To reproduce the tilted section, we have to take a new cut through the atlas volume. Rotating an existing 2D atlas image on screen wouldn't change the anatomy it contains.
Once the tissue is cut, you have to work with that plane
Getting a mouse brain perfectly aligned for coronal sectioning is difficult. A small difference in how the tissue sits relative to the blade can affect a whole series of sections, even when the slices themselves are intact and well stained. By the time you examine the images, that orientation is part of the sample. You can't go back and change the cut.
This leaves you with tissue that may be entirely usable, but needs an atlas section taken at a corresponding angle. Adjusting the atlas plane gives you a more appropriate anatomical starting point before you refine the alignment. You'll still need to account for local deformation, folds or damage where they occur; those require attention to the individual section rather than a change in its overall angle.
Adjust the angle with the atlas and tissue side by side
In NeuroQP, you can adjust tilt for roughly coronal mouse and rat brain sections from the AP coordinate control in Registration. Enable Animal tilt to reveal the left/right and dorsal/ventral controls. The sliders let you explore the angle, while the chevrons and degree fields give you finer control. Top and side views show how the selected plane sits relative to a coronal reference.
The Animal tilt controls, shown here at −8° left/right and +20° dorsal/ventral. The panel also identifies the animal and the slices that share the setting.
The controls sit beside the viewers, so you can keep the tissue in sight as you make adjustments. NeuroQP reslices the atlas at the chosen AP position and angle, then updates both the atlas image and the region overlays on the microscopy image. A new section can take a moment to load. Once it appears, you can judge whether the change makes sense across the tissue, rather than repeatedly opening and closing the controls to compare it.
Compare landmarks in several parts of the section as you adjust the angle. If one boundary fits better but other recognisable structures move out of alignment, reconsider the angle. When the atlas plane looks appropriate, review the registration points and refine the fit to the tissue.
The tilt setting belongs to the animal and applies across its slices, each of which keeps its own AP coordinate and registration points. This represents a shared cutting orientation for the series. After saving a change, review the other affected registrations and run Process results to refresh their measurements. You can return the angles to zero with Reset tilt.
For now, you choose the angles manually. This release is intended for roughly coronal sections; automatic tilt estimation and sagittal or horizontal registration aren't included.
Region measurements need the same plane as the registration
A region boundary that moves across the image can change which cells fall within it. The area of that region intersected by the section can change too, which matters when calculating densities. These are changes to the anatomical mapping of the detections; cell detection and staining classification remain separate. Accounting for tilt in the viewer would be incomplete if the measurements still used an untilted atlas section.
NeuroQP uses the saved orientation for regional cell assignments and sampled region areas, as well as the atlas overlays in Training and Results. Anatomical cell and density plots also use the tilt-aware coordinates. Once you've reviewed the registrations and refreshed the results, you can use the region tables and plots without calculating separate angle corrections for them.
See the registration adjustment guide for the controls and review workflow.
Figures use NeuroQP's 20 µm Kim atlas volume. The unified anatomical labels are described by Chon et al., 2019, Nature Communications. The grid contains resliced atlas reference images; the 3D brain surface is illustrative.