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After uploading data and receiving "no errors detected", Preprocessing fails with this error
File "/home/adminuser/venv/lib/python3.9/site-packages/streamlit/runtime/scriptrunner/script_runner.py",…
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I used to use scanpy python package for down-stream analysis.
I wonder how the predicted gene expressions can be analyzed in Anndata (Scanpy).
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Filtering does not work if an extra table is present not related to an element (which is a use case to save analysis results).
```python
# napari_spatialdata/utils/_utils.py:361
for element_type,…
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[`_check_valid_name`](https://github.com/scverse/spatialdata/blame/95d69ff7138305ee2a530bcc45f8460a06e8118b/src/spatialdata/_core/_elements.py#L34-L40) implemented stricter naming constraints in https…
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Hi,
after following the tutorial part of [https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/napari_rois.html#extracting-cells-under-the-regions](url), I tried to apply …
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Hello,
Thank you for this amazing tool! It has been so helpful in dealing with spatial data, especially in a way that is reasonable in terms of memory and resources.
I was wondering if there wer…
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When I run mv.aggregate_peaks_10x with both the demo and my own data, I get this error: 'SparseCSCView' object has no attribute 'A'
How can I get around this?
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Hi!
in our lab (Schlesner Lab, recently moved from Heidelberg right into your neighborhood - Augsburg University), we have different use cases where it would be quite helpful if AnnData objects cou…
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Re: https://github.com/openjournals/joss-reviews/issues/4371#issuecomment-1511258256
@ivirshup, another attempt. This the thread in which JOSS editors are checking in. It'd be incredible if you res…
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Hi there,
I was trying to write my adata with `write_h5ad` which has my loom objects merged with my Seurat object in Python so that I can then convert it to Seurat object to use `SCP`, but it thre…