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squidpy
Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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fix precommit and add pre-release test
#847
giovp
closed
1 day ago
0
obsm (spatial, spatial_fov) size seems unreasonably large.
#846
JonatanSahar
opened
1 week ago
0
UnidentifiedImageError when reading in Nanostring CosMx Data
#845
keiven-kun
opened
1 week ago
0
Documentation of spatial_scatter
#844
schae211
opened
1 week ago
0
Is squidpy.read.visium compatible with Visium HD data?
#843
sunyumail93
opened
2 weeks ago
0
compute graph base on spatialdata regions and add mask graph based on polygon
#842
giovp
opened
2 weeks ago
1
Analyze Visium H&E data with h5ad
#841
asmlgkj
opened
2 weeks ago
3
After removing rows with only NaN interactions, none remain.
#840
asmlgkj
opened
3 weeks ago
3
Failed to open the url with default certificates, trying with certifi. HTTPError: HTTP Error 403: Forbidden
#839
asmlgkj
closed
3 weeks ago
9
build spatial neighbors graph with spatialdata elements
#838
giovp
opened
3 weeks ago
0
`var_by_distance` using polygons annotations
#837
giovp
opened
3 weeks ago
0
[pre-commit.ci] pre-commit autoupdate
#836
pre-commit-ci[bot]
closed
1 day ago
0
Vizgen-MERFISH multiple dataset integration/comparison
#835
HSvitina
opened
3 weeks ago
0
neigh_correct when computing spatial graph
#834
wangjiawen2013
opened
4 weeks ago
0
When attempting to install, dependency "pygeos" gives: module 'configparser' has no attribute 'SafeConfigParser'
#833
azguan
opened
4 weeks ago
1
[pre-commit.ci] pre-commit autoupdate
#832
pre-commit-ci[bot]
closed
4 weeks 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
2
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
1 month ago
0
sort_order for pl.spatial_scatter
#824
JBreunig
opened
2 months ago
0
[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
opened
2 months ago
1
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
3 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
3 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
3 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
[pre-commit.ci] pre-commit autoupdate
#799
pre-commit-ci[bot]
closed
4 months ago
1
Maint/fix warnings
#798
michalk8
closed
4 months ago
1
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