Sophielsn

[BUG] pyscenic ctx error

2

**Describe the bug** I am trying to run the ctx step to get the regulon.csv result but I always got the Error. I am stuck here for over one week....

Tangram cell type annotation

1

Thanks for the great package! I noticed your `get_hard_labels `uses percentile clipping and min–max scaling before taking `idxmax`: ``` def get_hard_labels(self, df: pd.DataFrame) -> pd.Series: df = df.clip(df.quantile(1 - self.clip_percentile),...

I’m following the Tangram+Squidpy tutorial ([tutorial_tangram_with_squidpy.ipynb](https://github.com/broadinstitute/Tangram/blob/master/tutorial_tangram_with_squidpy.ipynb)) but working with 10x Xenium data instead of Visium. I’m unsure how to correctly define the image input (img) and/or adata.uns["spatial"] so that plotting...

 Here is the K-selection plot of my data. How to decide which k is better? 15 or 35?