How Registration Works
Registration tells Neuro QP where your tissue sits anatomically and where the analyzed high-resolution image belongs within that slice.
This is what allows the app to connect your images, detected cells, and selected brain regions.
The two parts of registration
Neuro QP works with two related placement steps:
- Brain slice to atlas registration: Aligns the 4x overview image to the atlas so the slice has the correct anatomical position and shape.
- 20x placement: Places the 20x image onto the 4x slice so the high-resolution analysis area is in the correct location.
Why both matter for analysis
Neuro QP needs to know both where the full slice belongs in the atlas and where the 20x image sits on that slice.
Together, these two placements allow the app to determine which brain regions are covered by the analyzed 20x area and assign detected cells to the right anatomical regions.
What happens automatically
After upload, Neuro QP creates an initial atlas registration automatically.
This automatic atlas registration is a coarse starting point for the full brain slice.
Neuro QP also places the 20x image automatically, and this is usually already very accurate.
What you usually need to review manually
In practice, the most important part to refine is the atlas registration in the area covered by the 20x image and the brain regions you selected for analysis.
That local accuracy matters more than making the entire slice look perfect everywhere.
The 20x placement usually does not need adjustment. Small differences of one or two pixels generally do not make a meaningful difference in the analysis.
What a good registration looks like
A good registration means the atlas boundaries match the anatomy well in the area that matters for your analysis.
The number of points needed depends on the slice and on how complex the local anatomy is.
In practice, around 10 to 20 points is usually enough for a very good registration.
Focus on placing points where they improve the fit in and around the relevant 20x region, rather than trying to add points everywhere.
Why manual refinement is important
Automatic registration gets you close, but it cannot know which local area matters most for your analysis.
Manual refinement lets you improve the anatomical accuracy exactly where it affects region assignment and quantification.