Closed Jorges1000 closed 4 weeks ago
setting up hchannel=True on preprocess_image (#31 run_starfysh error with poe argument) works but the image looks horrible:
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?
Hi, thanks for the reply, it seems to be enhancing small differences in the background of the slide. Here is the source image:
And here is the estimated tissue density; it seems that the background is affecting it more than cell density
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?
Hi @YinuoJin, many thanks for the improvements, i will try soon. I think there may be a benefit of applying a threshold to the H-channel to eliminate low counts, as it appears that the nuclei intensities are well above the background.
Great package! When trying to run
I get the following error:
When running with poe = False it works. I attach the model and the img_metadata. model_img.zip
Thanks for any help!