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Dear Community,
I am working on CODEX Datasets and want to use squidpy to analyze the spatial charateristics. Unfortunately I cant seem to generate the anndata object from the .csv export from …
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While updating the Visium HD notebook I have tried converting the bins to points and plotting them, and I found that this leads to an error in `spatialdata-plot`.
Here is how to reproduce (I also c…
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I'm working on tutorial notebooks right now and ran into a minor hiccup when running `sq.gr.spatial_neighbors()`. @giovp already ported the function to work with `spatialdata` (thanks!) but the functi…
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Hi,
I followed the update instructions detailed in #61 but Ive gotten a new issue importing now...
```
---------------------------------------------------------------------------
ImportErro…
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Idea for enhancement:
Add a filter option to the spatialdata object, where it is possible to filter out certain cells, based on a column in the table.
This can be relevant to for example large cel…
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Bounding box query selects circles whose center is contained inside the box, polygon query selects circles that intersect the box in any point.
You can reproduce with this code:
```python
##
fro…
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### What kind of feature would you like to request?
Additional function parameters / changed functionality / changed defaults?
### Please describe your wishes
10X updated to Space Ranger v3.0, and …
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There should be tutorials giving a general introudction to
* spatial anlaysis with squidpy
* how to use spatialdata
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Dear scverse Team,
First of all, thank you for your effort on developping integrative frameworks for spatial transcriptomics data.
Now, I'm analyzing MERFISH data using spatialdata. When I use c…
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Asked by @berombau.
One public function similar to this is here https://github.com/scverse/spatialdata/blob/4c6c1e9613310acc8844ff186a66084e8d5b85e4/src/spatialdata/_utils.py#L170.
- [ ] We could…