How to obtain well-aligned Level 0 images?

[670768312]

What an outstanding job! I currently have ndpi data for ER, HR, KI, PR, and TP. Which configuration should I use to achieve Level 0 registration results? Ultimately, I want to obtain registered patch-level image pairs.

[MWod]

It depends - if your samples are consecutive slides then you can basically use the default affine + nonrigid configuration as in the provided examples. For consecutive slides increasing the image resolution does not improve the registration quality.

However, if your slides are restained and you would like to achieve as high registration quality as possible - it will require a patch-based pipeline that is not available yet but will be released soon.