scverse/napari-spatialdata

View on GitHub

Interactive visualization of spatial omics data

Stars: 90
Forks: 25
Open beginner issues: 0
Indexed issues: 68
Avg merge: 22m
Merged PRs (30d): 1

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 8, 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

68 open issues indexed

Title: Labels categorical coloring fails for label ids missing from table rows when `*_colors` is present in `adata.uns` Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/napari-spatialdata#392 · 1 comment · 1 reaction · Opened Apr 10, 2026
Allow colormap scaling to reflect raw counts instead of hard-coded [0, 1] range Open

Difficulty 3/5 1-2 days Newbie friendliness 67/100

scverse/napari-spatialdata#387 · 4 comments · Opened Feb 16, 2026
Support both `r`, `g`, `b` and `R`, `G`, `B` for displaying images Open

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

scverse/napari-spatialdata#382 · Opened Dec 23, 2025
KeyError: 'SpatialData' Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#381 · 2 comments · Opened Dec 15, 2025
Installation problem Open

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

scverse/napari-spatialdata#379 · Opened Nov 18, 2025
Migrate to scverse cookiecutter template Open

scverse/napari-spatialdata#378 · 1 assignee · Opened Nov 10, 2025
Points subsampling Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/napari-spatialdata#372 · 2 comments · Opened Aug 26, 2025
How to visualize specific gene `transcripts` and specific cell-type `cell_boundaries` within `napari-spatialdata`? Open

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

scverse/napari-spatialdata#369 · 1 comment · 1 reaction · Opened Jul 7, 2025
Shift-E on point elements doesn't retain annotations (i.e. additional DataFrame columns) Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#367 · 3 comments · Opened Jun 25, 2025
`add_elements` not adding elements using Interactive Open

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

scverse/napari-spatialdata#362 · Opened May 13, 2025
RuntimeError when trying to run napari-spatialdata Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

scverse/napari-spatialdata#361 · Opened May 4, 2025
how to indicate the shape of spatialDATA to subset spatial_adata Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/napari-spatialdata#359 · Opened Apr 23, 2025
Multiscale image visualization Open

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

scverse/napari-spatialdata#352 · Opened Apr 1, 2025
Is it possible to show two different channels of the same image as different layers? Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

scverse/napari-spatialdata#351 · 2 comments · Opened Mar 28, 2025
Widget to explain Color code of shapes Open

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

scverse/napari-spatialdata#350 · 2 reactions · Opened Mar 28, 2025
why `len(unique) <= len(res) // 100` Open

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

scverse/napari-spatialdata#346 · 1 comment · Opened Feb 10, 2025
about Interactive(sdata) Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/napari-spatialdata#344 · 2 comments · Opened Jan 21, 2025
[test-bot] Benchmark tests failing Open

bug

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

scverse/napari-spatialdata#341 · 1 comment · Opened Jan 19, 2025
Legend (categorical obs column) for scatterplot widget not consistent Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/napari-spatialdata#339 · 1 comment · 1 reaction · Opened Jan 5, 2025
Teardown problems in scatterplot widget tests still present Open

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

scverse/napari-spatialdata#335 · Opened Dec 17, 2024
Next steps after the scatterplot PR Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/napari-spatialdata#333 · 1 comment · Opened Dec 17, 2024
2.5D visualization Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/napari-spatialdata#330 · 2 comments · Opened Nov 8, 2024
Colors categorical column in table annotated by a labels layer not correct in napari-spatialdata Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#328 · 4 comments · Opened Oct 30, 2024
Is "polygon_query" function working properly? Open

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

scverse/napari-spatialdata#327 · 4 comments · Opened Oct 23, 2024
make multicolor images Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/napari-spatialdata#326 · 6 comments · 1 reaction · Opened Oct 23, 2024
RGB Colormap missing Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

scverse/napari-spatialdata#325 · 1 comment · Opened Oct 14, 2024
Cannot set custom colors for categorical variables Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/napari-spatialdata#324 · 10 comments · Opened Oct 9, 2024
Test for shapes Open

good first issue

Difficulty 2/5 1-3 hours Newbie friendliness 62/100

scverse/napari-spatialdata#322 · 1 comment · Opened Oct 1, 2024
Test plotting annotations Open

good first issue

Difficulty 3/5 1-2 days Newbie friendliness 30/100

scverse/napari-spatialdata#321 · Opened Oct 1, 2024
Add design schema for napari-spatialdata and interacting plugins Open

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

scverse/napari-spatialdata#313 · Opened Sep 8, 2024
Public API to refresh element lists Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/napari-spatialdata#312 · Opened Sep 8, 2024
Saving and reloading images directly on sdata within napari Open

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

scverse/napari-spatialdata#310 · 3 comments · Opened Sep 6, 2024
Refine support for tables annotating dataframes Open

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

scverse/napari-spatialdata#305 · Opened Aug 23, 2024
Coordinate system widget shown twice Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#286 · Opened Aug 9, 2024
The channel slider works only for a single channel image. Open

macos

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

scverse/napari-spatialdata#273 · 2 comments · Opened Jul 14, 2024
napari can only save the first shape Open

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

scverse/napari-spatialdata#272 · 1 comment · Opened Jul 12, 2024
Saving with Shift+E seems to fail when the object is not backed. Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/napari-spatialdata#271 · Opened Jul 11, 2024
plot theme Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/napari-spatialdata#268 · 3 comments · Opened Jul 10, 2024
Named axes and pixel resolution Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

scverse/napari-spatialdata#263 · Opened Jun 26, 2024
annotation widget mac specific issues Open

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

scverse/napari-spatialdata#250 · 1 comment · Opened Jun 10, 2024
Shapes performance Open

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

scverse/napari-spatialdata#249 · 1 comment · Opened Jun 10, 2024
Remove `_models.py` Open

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

scverse/napari-spatialdata#248 · 4 comments · 1 reaction · Opened Jun 10, 2024
Error when filtering on multiple tables Open

bug

scverse/napari-spatialdata#244 · 1 comment · 1 assignee · Opened May 23, 2024
NaN values colored if non-NaN values are only one Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#238 · 2 comments · Opened Apr 29, 2024
Improvements around saving annotations to disk Open

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

scverse/napari-spatialdata#234 · Opened Apr 11, 2024
Colorbar and slider broken Open

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

scverse/napari-spatialdata#227 · 1 comment · Opened Mar 29, 2024
Warn about element/table mismatches. Coloring the background Open

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

scverse/napari-spatialdata#221 · Opened Mar 24, 2024
"Color by:" disappears after changing and going back to a layer. Proposed alternative approach Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/napari-spatialdata#220 · Opened Mar 24, 2024
Fix default size for points elements Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/napari-spatialdata#214 · Opened Mar 21, 2024
remove _pkg_constants Open

Task

Difficulty 1/5 Under an hour Newbie friendliness 35/100

scverse/napari-spatialdata#206 · Opened Mar 13, 2024

scverse/napari-spatialdata

Get new issues in your inbox