scverse/spatialdata-io

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Stars: 103
Forks: 65
Open beginner issues: 0
Indexed issues: 70
Avg merge: 1h 8m
Merged PRs (30d): 3

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 9, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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70 open issues indexed

Merscope - not loading vpt output Open

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

scverse/spatialdata-io#208 · 1 comment · Opened Sep 18, 2024
Export the real global coordinates of cells (Xenium) Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

scverse/spatialdata-io#205 · 1 comment · Opened Sep 9, 2024
Confusion on constructing SpatialData object from the ground up Open

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

scverse/spatialdata-io#203 · 3 comments · Opened Sep 6, 2024
Xenium: use physical units instead of pixel units as references Open

xenium

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

scverse/spatialdata-io#198 · 6 comments · Opened Aug 14, 2024
Segmented CODEX data in QuPath csv to squidpy Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

scverse/spatialdata-io#197 · 1 comment · Opened Aug 13, 2024
Xenium cells with 2 nuclei Open

xenium

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

scverse/spatialdata-io#188 · Opened Aug 2, 2024
Verify compatibility with Xenium Onboard Analysis 3.0 Open

xenium

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

scverse/spatialdata-io#180 · 11 comments · Opened Jul 31, 2024
Inquiry about Visium HD Open

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

scverse/spatialdata-io#177 · 2 comments · Opened Jul 25, 2024
Alignment image with xenium Open

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

scverse/spatialdata-io#168 · 24 comments · Opened Jul 2, 2024
bounding_box_query does not work on cellpose result stored in spatialdata Open

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

scverse/spatialdata-io#166 · 10 comments · Opened Jun 27, 2024
Stereoseq expected directory structure Open

documentation

Difficulty 2/5 Half a day Newbie friendliness 65/100

scverse/spatialdata-io#161 · 13 comments · Opened Jun 18, 2024
How to represent rounds and channels in ISS data Open

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

scverse/spatialdata-io#159 · 11 comments · Opened Jun 17, 2024
Wrong file loaded when building new SpatialData Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

scverse/spatialdata-io#147 · 2 comments · Opened May 17, 2024
Cannot load VisiumHD data without image Open

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

scverse/spatialdata-io#140 · Opened Apr 27, 2024
store probe set for image-based transcriptomics in spatialdata Open

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

scverse/spatialdata-io#138 · 3 comments · 1 reaction · Opened Apr 23, 2024
Wrong Visium radii? Open

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

scverse/spatialdata-io#124 · 1 comment · Opened Mar 18, 2024
How to load Merscope data missing cell_boundaries.parquet file? Open

scverse/spatialdata-io#71 · 6 comments · 1 assignee · Opened Jul 19, 2023
Nanostring TileDB export, new format Open

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

scverse/spatialdata-io#85 · 3 comments · 3 reactions · Opened Jul 1, 2023
API for reading in raw MCD files from IMC experiments Open

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

scverse/spatialdata-io#66 · 3 comments · Opened Jun 27, 2023
Using MultiValueEnum for MCMICRO Open

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

scverse/spatialdata-io#29 · 1 comment · Opened Apr 2, 2023

scverse/spatialdata-io

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