scverse/squidpy

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Spatial Single Cell Analysis in Python

Stars: 598
Forks: 121
Open beginner issues: 0
Indexed issues: 79
Avg merge: 3d 11h
Merged PRs (30d): 3

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 10, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

79 open issues indexed

Bugs and problems in calculate_niche and in unreleased main. Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/squidpy#1293 · Opened Sep 15, 2026
In place shuffle dedup Open

scverse/squidpy#1289 · 1 assignee · Opened Sep 10, 2026
Make most of args kwargs only with PLR0917 Open

scverse/squidpy#1288 · 1 assignee · Opened Sep 10, 2026
Extensibility API for niche calling Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

scverse/squidpy#1285 · 10 comments · Opened Sep 2, 2026
Feedback on new niche implementation Open

scverse/squidpy#1277 · 3 comments · 3 reactions · 1 assignee · Opened Aug 24, 2026
using `TypedDict` instead of frozen dataclasses for the kwargs Open

scverse/squidpy#1275 · 1 assignee · Opened Aug 21, 2026
`spatial_scatter` uses inconsistent `spatial_key` for image validation and loading Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/squidpy#1269 · Opened Aug 19, 2026
spatial_autocorr crashes when the graph contains singletons Open

scverse/squidpy#1256 · 1 assignee · Opened Aug 10, 2026
Add automatic K selection (CellCharter's ClusterAutoK) for the cellcharter niche flavor Open

scverse/squidpy#1244 · 1 comment · 1 reaction · 1 assignee · Opened Jul 19, 2026
Radial kernel + cutoff for neighborhood graph Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#1241 · Opened Jul 7, 2026
Tutorial request: Stereo-seq (BGI STOmics) analysis — bin vs cellbin Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/squidpy#1228 · Opened Jun 24, 2026
Add persistence diagrams for persistent homology analysis Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#1225 · Opened Jun 22, 2026
pl.ligrec does not match pvaule table output Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/squidpy#1201 · 1 comment · Opened Jun 4, 2026
speed up _resolve_data in spatial neighbors when working with spatialdata Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

scverse/squidpy#1199 · 7 comments · Opened Jun 3, 2026
Public api change: rename adata to data and make it positional only Open

Difficulty 5/5 Over a week Newbie friendliness 42/100

scverse/squidpy#1180 · Opened May 15, 2026
spatial_neighbour_x should have serializable internals to avoid uns formats Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#1174 · Opened May 12, 2026
Why does co_occurence not use a pre-calculated spatial graph Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#1165 · Opened Apr 23, 2026
Feature request: contour-based inward/outward ring density for cells and transcripts around polygon annotations Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#1160 · 1 comment · Opened Apr 16, 2026
n-hop neighbors in spatial graph Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

scverse/squidpy#1159 · 5 comments · Opened Apr 14, 2026
rectangle as shape Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

scverse/squidpy#1155 · 1 comment · Opened Apr 10, 2026
spatial_neighbors unintended in-place change Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/squidpy#1154 · Opened Apr 9, 2026
Bring minimal `stalign` function Open

squidpy2.0

scverse/squidpy#1146 · 1 comment · 1 assignee · Opened Apr 2, 2026
We shouldn't use assert_adata_equal Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/squidpy#1143 · 1 comment · Opened Mar 16, 2026
Control verbosity, like Scanpy Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/squidpy#1141 · 2 comments · Opened Mar 12, 2026
replace manual variable checks with wrapper functions across codebase Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/squidpy#1137 · Opened Mar 3, 2026
rename functions in private modules to not have underscore for better IDE detection Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/squidpy#1136 · Opened Mar 3, 2026
ligrec does seed + worker_id antipattern Open

scverse/squidpy#1131 · 1 assignee · Opened Mar 2, 2026
Integration Testing CI Test Failure on python 3.13 with prerelease dependencies Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/squidpy#1127 · Opened Feb 25, 2026
`parallelize` progress bar causes zombie processes and deadlocks Open

scverse/squidpy#1123 · 1 assignee · Opened Feb 23, 2026
`test_parallelize` fails on local tests and is flaky Open

scverse/squidpy#1111 · 1 assignee · Opened Feb 2, 2026
Investigate why docutils<0.22 is needed. Open

scverse/squidpy#1098 · 1 assignee · Opened Jan 21, 2026
Consider having a `_typing.py` or a way to restructure common type aliases Open

scverse/squidpy#1085 · 3 comments · 1 assignee · Opened Dec 16, 2025
We should stop using non-public `scanpy.logging.info` Open

scverse/squidpy#1081 · 5 comments · 1 assignee · Opened Dec 14, 2025
Adding more tests for usage of given keys Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/squidpy#1055 · Opened Nov 7, 2025
Incorrect dataset link for `Analyze Xenium data` tutorial Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

scverse/squidpy#1049 · 4 comments · Opened Oct 23, 2025
Nothing is displayed in the image, but I can display it normally using official data in the same environment. Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/squidpy#1022 · 2 comments · Opened Aug 11, 2025
Function to remove points that don't fall into cell masks Open

enhancement :sparkles: squidpy2.0

scverse/squidpy#1017 · 1 assignee · Opened Jul 10, 2025
Function to subset the entire spatialdata object Open

enhancement :sparkles: squidpy2.0

scverse/squidpy#1007 · 6 comments · 1 assignee · Opened May 26, 2025
Consider switching to TrustedPublishing for PyPI uploads Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/squidpy#927 · Opened Dec 10, 2024
Handling Multiple Cells Sharing the Same Coordinates in Squidpy Neighborhood Analysis Open

scverse/squidpy#925 · 1 assignee · Opened Dec 7, 2024
[BUG] label harmonization across blocks Open

bug :bug:

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/squidpy#918 · 1 comment · Opened Nov 27, 2024
squidpy (non-graph) spatial statistics for multiple images Open

scverse/squidpy#917 · 3 reactions · 1 assignee · Opened Nov 26, 2024
Delegate plots to spatialdata-plot Open

enhancement :sparkles: plot :hibiscus:

scverse/squidpy#912 · 5 comments · 1 assignee · Opened Nov 8, 2024
Add parameter to `sliding_window` to end up with windows of (approximately) same number of cells Open

enhancement :sparkles: feature graph :spider_web: squidpy2.0

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/squidpy#908 · 2 comments · Opened Nov 4, 2024
Add SpaGFT-like method for identification of SVGs Open

enhancement :sparkles: graph :spider_web: squidpy2.0

scverse/squidpy#901 · 1 comment · 1 assignee · Opened Oct 15, 2024
How to draw co_occurrence plot with specific distance in x-axis? Open

scverse/squidpy#899 · 1 assignee · Opened Oct 11, 2024
CosMx FOVs being skipped Open

scverse/squidpy#894 · 2 comments · 1 assignee · Opened Oct 2, 2024
Mapping of Xenium 5k data Open

I/O :cd:

scverse/squidpy#889 · 5 comments · 1 assignee · Opened Sep 18, 2024
Edge correction in `squidpy.gr.ripley`? Open

enhancement :sparkles: graph :spider_web:

scverse/squidpy#886 · 1 comment · 1 assignee · Opened Sep 13, 2024
[doc improvment] inconsistent usage of img_key and img_res_key in code base Open

doc

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/squidpy#884 · 1 comment · Opened Sep 3, 2024

scverse/squidpy

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