POE analysis fails on run_starfysh about starfysh HOT 5 OPEN

setting up hchannel=True on preprocess_image (#31 run_starfysh error with poe argument) works but the image looks horrible:

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Hi @Jorges1000,

Thanks for using Starfysh! We'll try to reproduce the RGB dimension error you reported and get back later (will release a new version if it's a confirmed package error).

For your follow-up question with 1-D PoE, Starfysh performs H&E color deconvolution to pick only hematoxylin channels via histomicstk link, where we empirically found the positive correlations between H-channel and cell density.

From the uploaded image, the color segmentation picks up a lot of background noise distribution (repeated white blobs) + fiducial points (boundary black dots). However, Starfysh only input pixel patches mapped with valid Visium coordinates (img_metadata['map_info'][['imagerow', 'imagecol']]) while most of the background values should be dropped. Does your raw tissue consist of four separate tissues?

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Hi, thanks for the reply, it seems to be enhancing small differences in the background of the slide. Here is the source image:

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And here is the estimated tissue density; it seems that the background is affecting it more than cell density

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Thanks for the follow-up. We fixed the RGB issues and you can install through the GitHub version to run histology integration. I also looked into the 1D PoE: the Haematoxylin channel might either captures nucleus or the background depending on the color comparison w/ background (examples attached). We might extend it as a user option whether to flip the 1D intensities.

• Provided histology:
  

• Our sample histology vs. smoothed library size:
  
  
  

Please let me know which intensity preprocessing setup makes more sense to you?

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