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Hello!
```
git clone https://github.com/theislab/nicheformer.git
cd nicheformer
pip install -e .
```
I get an error which says a setup.py file is required. I created my own using the info…
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With https://github.com/ome/ome-zarr-py/pull/256 (work in progress) we hope to have AnnData tables available to `napari-ome-zarr`.
I've been using this to read "points" tables and display as tracks…
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## Description
due to the server network, I can not run
img = sq.datasets.visium_hne_image()
adata = sq.datasets.visium_hne_adata()
so I downloaded the visium_fluo.h5ad on another computer …
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On WINDOWS 11:
trying to import squidpy results in errors (different in python 3.11 and 3.12)
- if I install with `pip install 'squidpy[interactive]'`
- which does not happen after `pip instal…
Zaf4 updated
2 months ago
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## Description
I created my own color palette as a ListedColormap and verified that it was correct via `isinstance()`. However when I use it as the `palette` argument in `pl.spatial_scatter()` it f…
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I would like to visualize two features (`total_counts` and `n_genes_by_counts`) in the anndata obs of my spatial data by using `sq.pl.spatial_scatter.` I was not able to generate those figures for my …
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We can get some inspiration from [squidpy ](https://github.com/scverse/squidpy) for testing the output of the different plots that napari-sparrow generates:
- "Ground truth" matplotlib output is st…
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Hi,
When I run sq.gr.nhood_enrichment(sdata["table"], n_jobs=10, cluster_key='id'), the following error occurred:
https://github.com/scverse/squidpy/issues/867
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Hi,when I`m running example data on the Preprocessing transcriptomic library step, I encounter the problem.
![98adec7c81a075a584e7f534f283f83](https://github.com/user-attachments/assets/cd0b8f0a…
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### Description of feature
We are currently using custom code as a work-around as a replacement for the `to_legacy_anndata` function from `spatialdata_io`, which did not exist when the work with Spat…