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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

Add deprecation note #82

Closed votti closed 2 years ago

votti commented 2 years ago

I think it would be good to directly point users to Steinbock. Any other opinions?

jwindhager commented 2 years ago

Thanks for this, @votti! Not entirely sure we want to deprecate the IMC Segmentation Pipeline at this point, as steinbock is not a pipeline by design, and this repository is sort of the "reference implementation" for your RF-based segmentation approach. But no strong opinions on this from my side. Thoughts, @nilseling?

nilseling commented 2 years ago

Hi @votti if you don't mind, I'd like to update the pipeline to use readimc instead of imctools over the next couple of month and will maintain it as good as I can. I think a lot of people still rely on this pipeline and it's definitely worth to further support it.

jwindhager commented 2 years ago

See #85

nilseling commented 2 years ago

Closing for now due to #87