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Hi Jan,
I am using SPATA2 on a Xenium dataset and used createGroupAnnotations to create the spatial annotation. However, I noticed that the outlines do not capture all the groups I want. In the i…
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Encountered an error while running `SCTransform` on a Xenium object created with `LoadXenium`. The error indicates that the `log_umi` cell attribute contains NA, NaN, or infinite values, which is prev…
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I am interested in using ATHENA to analyze tumor heterogeneity. I have data generated from the Xenium platform, and I was wondering if ATHENA supports this type of data.
Could you please confirm if…
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I am traying to segment a Xenium picture to subsequently use the npy mask with Xenium ranger to allocate my transcriptional data.
The xenium picture is 51206 x 95243 px
I generated training ROIs, …
Lem-P updated
2 weeks ago
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```
visualizer.save("Xenium-text-visualizer.vis")
/hpcwork/p0020567/enviroments/overlpy2/lib/python3.12/site-packages/anndata/_core/aligned_df.py:68: ImplicitModificationWarning: Transforming to s…
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Hi, I tried to convert bin2cell's AnnData to a SpatialData object using [this tutorial](https://spatialdata-notebooks.readthedocs.io/en/latest/notebooks/examples/squidpy_integration.html#using-the-con…
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### Report
I am trying to run CellCharter on a single sample, and I get the following error during the model train process: `model.train(early_stopping=True, enable_progress_bar=True)`
`ValueErr…
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`run_name` in the .xenium controls how samples appear in the xenium explorer
Right now `image_key` is used here which leads to all Xenium samples appearing as morphology_focus in the Xenium explorer.…
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Hello,
For Xenium 5k , there are two tissue sections in one capture area . I need to analyze every tissue section separately with Seurat.
So could you please tell me how spli…
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## Description
After running SOPA on my dataset, both the Xenium explorer file and the report contain codewords for non-genes including:
- `DeprecatedCodeword`
- `Intergenic_Region`
- `NegControlC…