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I've been using your package to deconvolute some visium data following the tutorial. I have successfully made it to the ad_map creation. However, when I try to plot I receive the below error and it lo…
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Hello
I am working with spatial transcriptomic data and would like to align data from several slices.
It's working very well on spatial data but now I would like to align the H&E images using the sa…
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empty figures
Hi
I am runing NCEM code from the scratch for coupling and cell enrichment analysis. Meanwhile, I wanted to save all the imaging output in png (or pdf) format. But except for the s…
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In the new theme we use for our docs, there are no links for either examples of tutorials. See screenshot below.
` or `sq.gr.co_occurrence()` with IMC test data, a runtime error is thrown. I believe this is to…
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Hi,
Each time I run sq.pl function and save the plot, such as sq.pl.ripley(adata, cluster_key="leiden", mode="L", save="c.pdf"), a wired file like "/" is generated in the directory. If I don't save t…
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It seems like a dask issue.
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dear all,
I have an image container with 3 layers:
**image**: y (15970), x (16512), z (1), channels (3)
image_smooth: y (15970), x (16512), z (1), channels (3)
**_segmented_stardist_*…
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Hello,
I'm using `squidpy.pl.spatial_scatter` and it doesn't seem to handle very well updating a color palette when a variable in .obs is updated.
```python
adata_vis = sq.datasets.visium_hne_a…
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## Description
``.shaped_metadata`` attribute doesn't seem to exist, although looking at the [diffs of previous version](https://github.com/cgohlke/tifffile/compare/v2022.4.8...v2022.4.22#diff-d8d5…