Hi hi,

I wanted to share my experience running SCS on 10x Xenium data - I'm trying to add it to the nf-core spatialxe pipeline ( nf-core/spatialxe#130 ). I found that the default background threshold (stain_bg_threshold=10) does not work well for Xenium data, since almost all pixels have values above 10. This results in no background being detected and the model failing to train properly. That's a pull request related to the issue I just opened #21 . Please find in the attachment my test code Test_SCS2Visium.ipynb using the breast cancer tumor Xenium data (https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast), and the screenshot of the results:

I hope it's fine that I prepared a pull request to adjust for that. Summary of changes:

- Added an argument to the preprocess funcion called stain_bg_percentile that allows users to specify a percentile-based adaptive background threshold for stain intensity.
- Added a note in the README and example scripts about using stain_bg_percentile for Visium/H&E data.
- Clarified that the default threshold is for low-range fluorescence images, and percentile-based thresholding is recommended for H&E.

Let me know if you'd like any further changes. Thanks for maintaining SCS!

Cheers,
Kasia