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Hello,
I've noticed a mismatch between histology pixel coordinates and spots (spatial coordinates) when using the `tg.plot_cell_annotation_sc` function, which went away when I manually supplied the…
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Hi,
I have an anndata object, and the spatial distances are stored in the obsp key:
https://squidpy.readthedocs.io/en/stable/auto_examples/graph/compute_spatial_neighbors.html
Then I run:
hs = h…
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## Description
Issue with using the sq.gr.ligrec function, same error on multiple datasets and haven't been able to get the function to run.
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## Minimal reproducible example on a sample datase…
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## Description
When loading Visium data from Cell Ranger outputs, `squidpy.read.visium()` appears to read the `hires` and `lowres` images into the `uns['spatial'][{library_id}]['images']` keys `hires…
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## Description
When you receive adata paired with images, the collaborates might put more info in the adata file than you expect. In my case I have multiple scalefactors in the adata, see here wher…
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Hi,
we can find neighbors with both sq.gr.spatial_neighbors() of squidpy and sc.pp.neighbors() of scanpy. here's my question:
1, what's the difference between them and which one should I use …
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Hello,
Thank you for your great work on this package, it is very clearly documented and well-implemented.
I am using Domino with transcriptomic data from mouse, using gene conversion via the `gene_c…
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## Description
Newer verions of squidpy (require z dim) do not load ImageContainer that were generated on another version of squidpy
## Minimal reproducible example
```python
# requires Ima…
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## Description
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/var/folders/hy/xgyntz3j1y57…
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### Type of the feature
- [ ] New function in `sqduipy.im`?
- [ ] New function in `squidpy.gr`?
- [ ] New function in `squidpy.pl`?
- [ ] Change an existing functionality, such as default behavi…