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Probably fix with a [`testcleanup` directive](https://www.sphinx-doc.org/en/master/usage/extensions/doctest.html).
These files were added to the gitignore in #630.
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When we modify in-memory an object that is not backed, we need to write it to disk in order to update the changes. For backed objects we have to check if changes are written to disk immediately (as it…
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Dear all,
I have been playing around with spatialdata.models and was trying to build a custom ShapesModel object with Polygon geometry.
I have started with a set of Polygon points, and kept ge…
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The latest version of scvi-tools `1.0.4` works for scVI and totalVI but causes errors and warnings when running multiVI: https://discourse.scverse.org/t/error-when-training-model-on-m3-max-mps/1896
…
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There is an issue with Leiden Clustering in cugraph version 23.06.
The issue has been reported https://github.com/rapidsai/cugraph/issues/3749.
For the meantime please use rapids-23.04
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The behavior appears for instance with this dataset: https://github.com/giovp/spatialdata-sandbox/blob/main/visium/to_zarr.py.
A fix would be to use the same logic as here: https://github.com/scver…
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### Describe the bug
**context**
When including a plot in a jupyter notebook, mystnb renders it way larger than it appears in the jupyter notebook.
**expectation**
Plot sizes between the origin…
grst updated
7 months ago
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Hi,
Thank you for this package. I'm trying to extract a polygon from Xenium data.
```type(polygon)``` returns shapely.geometry.polygon.Polygon and ```polygon``` gives the below image.
…
EST09 updated
8 months ago
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Hi @LucaMarconato ! A few days ago, following the instructions in the **Use landmark annotations to align multiple -omics layers** section, I successfully aligned the layers using data from visium and…
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The following code:
```
adata = sc.read_10x_mtx(os.path.join(path_data,"filtered_gene_bc_matrices/hg19"))
adata.obs["organism_ontology_term_id"] = "NCBITaxon:9606"
preprocessor = Preprocessor(do…