-
Hello
This matplotlib pluggin is great but it doesnt seam to work on my spatial transcriptomic data ....
I launched it with squidpy
Many thanks
Sophie
. Installed squidpy, scanpy etc. via Mamba using conda-forge.…
-
To begin with, how we should introduce the data to start the analysis?
In the tutorial, it's mentioned that loading data is like this:
```
img = sq.datasets.visium_hne_image()
adata = sq.data…
-
*This is for internal use only; if you'd like to open an issue or request a new feature, please open a bug or enhancement issue*
# Design Doc - `AnnData` Conversion
This design doc proposes a ne…
-
Hi,
The sc.read_visium() function needs to be updated. Because 10x genomics changed the position files (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/spatia…
-
## Read Flow Cytometry Standard (fcs) files
Reading files in fcs format is not yet supported by squidpy. However, e.g. [the output of CODEX experiments](https://help.codex.bio/codex/mav/technical-…
-
## Imege rotation
Hi,
when plotting cell position on top of images (sc.pl.spatial) would it be possible to apply a predefined rotation to it? This could either be an argument in the function ca…
-
When running the tutorial notebook for Nanostring data, I'm encountering an error when running "sq.pl.spatial_segment".
Just as in the tutorial I run:
`sq.pl.spatial_segment(
adata,
co…