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Hello, I posted a question previously in Seurat (https://github.com/satijalab/seurat/issues/9036) but they don't have bandwidth to implement this feature. Since squidpy has a similar function (https:/…
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Hi,
I am wondering if it is possible to extract image features from a visium HD dataset using spatialdata and squidpy? Is this supported?
Thanks,
Sokratia
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Hi, I want to use baysor segmentation on my CosMx data and then visualize it in R/Python. CosMx usually outputs 5 files which are used by Seurat/Squidpy to create the object - metadata, tx, polygons, …
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We’re looking to use squidpy to generate comparative spatial statistics across multiple samples.
I see we can supply the sample key by ```library_key``` in ```squidpy.gr.spatial_neighbors``` so that …
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## Description
I try to build an `ImageContainer` using a "pyramid tiff" file storing an H&E stain image, i.e. an image with a `Z` dimension > 1.
> "The term "Pyramid TIFF" is used to describe a…
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https://github.com/scverse/squidpy/blob/16a9885976e24778664c81c05a9b592b2bd4a237/src/squidpy/_docs.py#L222-L223
The documentation for `legend_loc` in `spatial_scatter` refers to `matplotlib.legend.…
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Hi, thanks for your great work. I have a general question about benchmarking the clustering performances of different methods.
In you figure 3 (also 4), you considered Moran's I score as a me…
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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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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…