Lem-P

I get this in rapids_singlecell --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) Cell In[42], line 1 ----> 1 rsc.tl.leiden(adata, key_added="leiden_res0_25", resolution=0.25) 2 rsc.tl.leiden(adata, key_added="leiden_res0_5", resolution=0.5) 3 rsc.tl.leiden(adata, key_added="leiden_res0_1", resolution=0.1) File...

Maybe a noob question, but how? I have tried with ``` df = pd.DataFrame(adata.obsm["spatial"]) nan_count = df.isna().sum() print(nan_count) ``` and got 0 1 1 1 dtype: int64 But not sure...

```np.isnan(adata.obsm["spatial"]).sum()``` gives me 2 as output. How can I found out where it's coming from? (the data comes from spaceranger-2.0.1) How can I correct the dataset?

After some testing, it is the `sq.read.visium()` function that create the issue. If I create my AnnData with `sc.read_visium()` function, there are no NaN value in `adata.obsm["spatial"]` and I can...

No, I have the same number of observations/cells and variables/genes in both objects. But I found the problematic row. In the object made with Scanpy : `array([ 7335, 12140])` In...

Is there a temporary workaround to manually create the SpatialData data framework from Xenium ranger output? (I mean a tutorial/notebook/...)

Nobody have an idea about how to resolve this issue? Does anybody knows how to download the previous working version of Xenium Ranger (v3.0.0.0)? Or any tutorial to manually create...

After updating to Xenium Ranger v3.1, still not working. Nobody has any idea how to resolve this issue? `Traceback (most recent call last): File "./Read_Write_zarr.py", line 11, in sdata =...

Hi, I am back on this project! I have indeed polygons with less than 4 vertices in the cell_boundaries.parquet file and could filter them out of the cell boundaries file....

In line with @ConstensouxAlexis last comment, as it seems it is Xenium Ranger that introduces these problematic polygons, is there a (easy) way to generate the input files for SpatialData-io...