scverse squidpy issues - Githubissues

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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issues

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[pre-commit.ci] pre-commit autoupdate

#849 pre-commit-ci[bot] closed 1 day ago
0
squidpy.im.ImageContainer cannot process some pyramid tiff (with z > 1)

#848 gdurif opened 2 days ago
2
fix precommit and add pre-release test

#847 giovp closed 1 week ago
0
obsm (spatial, spatial_fov) size seems unreasonably large.

#846 JonatanSahar opened 2 weeks ago
1
UnidentifiedImageError when reading in Nanostring CosMx Data

#845 keiven-kun opened 2 weeks ago
2
Documentation of spatial_scatter

#844 schae211 opened 2 weeks ago
1
Is squidpy.read.visium compatible with Visium HD data?

#843 sunyumail93 closed 6 days ago
1
compute graph base on spatialdata regions and add mask graph based on polygon

#842 giovp opened 3 weeks ago
1
Analyze Visium H&E data with h5ad

#841 asmlgkj opened 3 weeks ago
4
After removing rows with only NaN interactions, none remain.

#840 asmlgkj opened 4 weeks ago
4
Failed to open the url with default certificates, trying with certifi. HTTPError: HTTP Error 403: Forbidden

#839 asmlgkj closed 4 weeks ago
9
build spatial neighbors graph with spatialdata elements

#838 giovp opened 4 weeks ago
0
`var_by_distance` using polygons annotations

#837 giovp opened 4 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#836 pre-commit-ci[bot] closed 1 week ago
0
Vizgen-MERFISH multiple dataset integration/comparison

#835 HSvitina opened 1 month ago
0
neigh_correct when computing spatial graph

#834 wangjiawen2013 opened 1 month ago
1
When attempting to install, dependency "pygeos" gives: module 'configparser' has no attribute 'SafeConfigParser'

#833 azguan closed 2 days ago
1
[pre-commit.ci] pre-commit autoupdate

#832 pre-commit-ci[bot] closed 1 month ago
0
Add function for calculating niches

#831 LLehner opened 1 month ago
0
update releases and precommit

#830 giovp closed 1 month ago
0
Sliding window across spatial neighbourhood

#829 FrancescaDr opened 1 month ago
3
Update template to v0.4.0

#828 scverse-bot closed 1 month ago
0
matplotlib update leads to import error

#827 LouisK92 closed 1 month ago
8
`calculate_image_features()` error with tutorial data

#826 kimsjune opened 1 month ago
1
Stacking XYZ dimension images of mouse brain into 3D Volume

#825 sleepingcat4 opened 2 months ago
0
sort_order for pl.spatial_scatter

#824 JBreunig opened 2 months ago
1
[pre-commit.ci] pre-commit autoupdate

#823 pre-commit-ci[bot] closed 1 month ago
0
Clustering according to image features

#822 gboscagli opened 2 months ago
0
[pre-commit.ci] pre-commit autoupdate

#821 pre-commit-ci[bot] closed 2 months ago
0
Extracted cropped spot images

#820 KSimi7 closed 2 days ago
2
sq.gr.ligrec crashing kernel/script with VisiumHD (>100k spots/spatial barcodes) - Squidpy incompatible with single-cell level spatial technologies?

#819 Rafael-Silva-Oliveira opened 2 months ago
3
Should the raw H&E image (.tif) and the image stored in anndata be in the same orientation?

#818 ddzhang3 closed 4 weeks ago
1
Converting spatial seurat dataset to anndata

#817 SNOL2 closed 2 months ago
2
More robust co-occurrence calculation

#816 DPLemonade closed 1 month ago
3
KeyError: '72' when reading in Nanostring CosMx data

#815 josiejenyne closed 4 weeks ago
5
add zarr.zip to adata

#814 rkulchar closed 2 months ago
1
Ripley L measure with n_observations

#813 georgezakinih opened 3 months ago
0
The Kernel crashed while executing code in the current cell

#812 spatts14 opened 3 months ago
3
Using squidpy.pl.spatial_segment on Xenium data

#811 justinesjw closed 4 weeks ago
1
Xenium tutorial code does not work

#810 chiwwong closed 3 months ago
1
[pre-commit.ci] pre-commit autoupdate

#809 pre-commit-ci[bot] closed 2 months ago
1
pl.ligrec Value Error when following seqFish tutorial notebook

#808 DuncanBrady closed 2 months ago
4
Add method to calculate embeddings for variable by distance aggregation

#807 LLehner opened 4 months ago
3
Update template to v0.3.1

#806 scverse-bot closed 4 months ago
1
dated napari tutorial/documentation

#805 LinearParadox closed 4 months ago
1
[pre-commit.ci] pre-commit autoupdate

#804 pre-commit-ci[bot] closed 4 months ago
1
fixed reading 10x formatted visium mtx files

#803 LinearParadox closed 4 months ago
6
Issue reading visium data when the GEX file is a matrix

#802 LinearParadox closed 4 months ago
0
Visium analysis with missing highres images

#801 LinearParadox closed 4 months ago
0
EuroPython talk that can give feature insights to SquidPy

#800 inaciomdrs opened 4 months ago
2