-
## Description
VisiumHD will now become one of the standards for single-cell level resolution on spatial data, but this seems to be too much for squidpy to handle as of now.
...
## Minimal r…
-
## Description
...
## Minimal reproducible example
```python
...
```
adata = sq.read.nanostring(path = sample_dir,
counts_file = counts_file,
meta_file = meta_file,
…
-
The current design of the data structure to represent WSI contains several drawbacks. This issue is to discuss if there are better solutions or if the current one is already acceptable.
Another thi…
-
Hi, whenever I run this
```
res = sq.gr.ligrec(
adata,
n_perms=100,
cluster_key="cell_type",
copy=False,
use_raw=False,
transmitter_params={"categories": "ligand"},
…
-
Hello, I wonder if Seurat supports some advanced analysis of the images in the Visium HD data? I have fluorescence staining images aligned with the data and I only wanted to select bins that have posi…
-
## Description
I got the following error when using squidpy.read.visium to read Visium HD Space Ranger output dir:
FileNotFoundError: [Errno 2] No such file or directory: /outs/binned_outputs/square…
-
## Description
was unable to load datasets which are included in squidpy (visium_hne_adata())
...
## Minimal reproducible example
import squidpy as sq
adata = sq.datasets.visium_hne_a…
-
Hi folks:
When i download files via API, the download completes, but file size is different than when I download via browser. Consequently, API-downloaded files wouldn't open with gzip or viewers..…
-
## Description
Got the error **ValueError: buffer source array is read-only** when trying to plot using sq.pl.spatial_segment() on CosMx demo data.
Any pointer for debugging? Thank you!
#…
-
Hi, when I run the tutorials of flowsig with default parameters and python 3.8 environment, I have the following bug:
```
Temporary checkpoint directory: /tmp/tmpv1t2fq2f
0002 numerical instabili…