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NaN value when importing Visium dataset

12

Hi, I am trying to import a dataset from 10X Visium H&E I am importing the dataset with: ```python adata = sq.read.visium('path') adata.var_names_make_unique() ``` Then pre-processing: ```python sc.pp.filter_cells(adata, min_counts =...

[BUG] running the Leiden algorithm doesn't support oversubscription

3

**Describe the bug** While running the leiden algorithm `rsc.tl.leiden(adata, key_added="leiden_res0_25", resolution=0.25` , I got a "CUDA error encountered 101 cudaErrorInvalidDevice invalid device ordinal" Just setting `rmm.reinitialize` `managed_memory` to `False` resolved...

Xenium Ranger 3.0.1.1 after Cellpose resegmentation - "ValueError: A linearring requires at least 4 coordinates."

15

After segmentation with cellpose, I ran Xenium Ranger 3.0.1.1 `xeniumranger import-segmentation --id=my_ID \ --xenium-bundle=$DIR/outs \ --nuclei=$DIR/outs/mask_nuclei.ome_cp_masks.tif \ --cells=$DIR/outs/mask_cells.ome_cp_masks.tif ` When I try to read the output folder with spatialdata_io (0.1.7.dev5+g82ff327),...