-
The [Squidpy notebook](https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/technology_visium_hd.ipynb) shows an error liked to rasterizatation. @Sonja-Stockhaus could you ple…
-
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
-
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, …
-
Greetings all,
I'm trying to create a `SpatialData` object from an `Anndata` object using the `from_legacy_anndata` function. The Anndata file was created with Squidpy's `read_nanostring` (Squidpy ve…
-
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 …
-
When I used squidpy to draw Co-occurrence figure:
sq.gr.spatial_neighbors(adata)
sq.gr.nhood_enrichment(adata, cluster_key="Level1_Filt")
sq.pl.nhood_enrichment(adata, cluster_key="Level1_Filt"…
-
## 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…
-
Routinely listing improvement we can make to the docs:
- [ ] add `rasterize_bins()` example in Visium HD notebook;
- [ ] show how to use `get_element_instances()` in the annotation notebook.
-
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.…
-
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…