search

spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
225 stars 67 forks source link

add color deconvolution preprocessing #1197

Open neuromusic opened 5 years ago

neuromusic commented 5 years ago

This is needed to support chromogenic assays.

See https://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html

ttung commented 5 years ago

Would this just be a filter operation that groups by ch?

neuromusic commented 5 years ago

actually, I think it's just linear unmixing ... https://spacetx-starfish.readthedocs.io/en/latest/api/image/index.html?highlight=unmixing#starfish.image.Filter.LinearUnmixing