Generalized Stain Normalization

[drbeh]

Stain normalization in MONAI consists of two components stain extraction and stain normalization. Right now, they are specific to Hematoxylin and Eosin stains but both of these components can be generalized to supports any or at least many stains.

#3505 generalized normalization part to be independent of the stain matrix but the stain extraction needs further investigation to see whether it can be generalized to common stains in histopathology. Also it would be great to know if we can use our stain normalization with arbitrary predefined stain matrices.

Moreover, changes are needed to be fit into the overall structure of MONAI Pathology #4005.

[shaneahmed]

This might be a good resource

https://github.com/Peter554/StainTools https://tia-toolbox.readthedocs.io/en/latest/usage.html#stain-extraction https://tia-toolbox.readthedocs.io/en/latest/usage.html#stain-normalization

[drbeh]

Hi @shaneahmed,

Thank you very much for the references. We also were looking into make it compatible with scikit-image operations: https://scikit-image.org/docs/stable/auto_examples/color_exposure/plot_ihc_color_separation.html

Also a discussion here: https://github.com/scikit-image/scikit-image/issues/6333

What do you think?