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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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## Description
...
## Minimal reproducible example
```python
import numpy as np
import os
import scanpy as sc
import squidpy as sq
sc.logging.print_header()
print(f"squidpy=={…
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The latest Galaxy version comes with some nice assertions for imaging data: https://docs.galaxyproject.org/en/latest/dev/schema.html#assertions-for-image-data
When we update our instances/CI to Gal…
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I am watching [this talk](https://www.youtube.com/watch?v=dNnHlb4RfJY) from EuroPython 2023. I believe that use cases shown there could be adapted to SquidPy. For example, make interactive scatter plo…
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## Description
VisiumHD will now become one of the standards for single-cell level resolution on spatial data, but this seems to be too much for squidpy to handle as of now.
...
## Minimal r…
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... and see if it matches example notebook outputs
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Hello, I'm running `sq.gr.nhood_enrichment(adata, cluster_key=label_name, numba_parallel=False, n_jobs=1, backend=None)` but multiprocessing still seems to get at least initialized somehow, which I kn…
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Dear all,
I tried to follow this workflow (https://squidpy.readthedocs.io/en/stable/external_tutorials/tutorial_vizgen_mouse_liver.html) for the Human Liver cancer dataset (https://info.vizgen.co…
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## Description
I can not change the color map of the spatial transcriptomic data in Napari
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## Minimal reproducible example
viewer = napari.Viewer()
viewer.add_image(
img1,
…
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Hello!
I work with CODEX data across different conditions and I was wondering whether there is a way to visualise/summarise the differences in neighbourhood composition across the different cond…