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

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70 issues indexed so far

Visium HD: empty `dataset_id` default produces an unnamed coordinate system that napari-spatialdata can't select Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 58/100

scverse/spatialdata-io#422 · Opened Sep 16, 2026
AI-generated: macsima() uses the OME plane positions as pixel padding widths, truncated Open

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

scverse/spatialdata-io#419 · 1 comment · Opened Sep 9, 2026
MCMICRO reader does not support new nf-core/mcmicro output formats Open

Difficulty 5/5 Over a week Newbie friendliness 48/100

scverse/spatialdata-io#409 · 1 reaction · Opened Jul 22, 2026
Visium in matrix market format Open

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

scverse/spatialdata-io#408 · Opened Jul 15, 2026
Feature request: lazy parsing of the pyramidal OME-TIFF morphology focus in Xenium Open

xenium

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

scverse/spatialdata-io#407 · Opened Jul 12, 2026
CosMx Reader Incorrectly Assumes Image Dimension Order Open

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

scverse/spatialdata-io#403 · 2 comments · Opened Jun 4, 2026
Xenium Fails to read third party segmentation Open

bug xenium

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

scverse/spatialdata-io#402 · 1 comment · 2 reactions · Opened May 29, 2026
Xenium transcript dask DataFrame has non-unique index; `transcript_id` is the natural unique key Open

xenium

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

scverse/spatialdata-io#397 · Opened May 15, 2026
Handling of case-variant column names in CosMx data Open

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

scverse/spatialdata-io#393 · 1 comment · Opened Apr 28, 2026
filtered_counts_file parameter for cell-segmented matrices Open

visium-hd

Difficulty 3/5 1-2 days Newbie friendliness 65/100

scverse/spatialdata-io#390 · Opened Apr 8, 2026
Add Xenium Explorer GeoJSON import Open

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

scverse/spatialdata-io#385 · 1 comment · Opened Mar 12, 2026
BMKS300 Open

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

scverse/spatialdata-io#384 · 2 comments · Opened Mar 10, 2026
spatialdata.write fails on Xenium sdata in env with pandas 3.0.0 Open

xenium

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

scverse/spatialdata-io#364 · 4 comments · 2 reactions · Opened Feb 3, 2026
Error reading Xenium data: morphology file missing Open

xenium

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

scverse/spatialdata-io#362 · 2 comments · Opened Feb 1, 2026
Error with spatialdata_io.xenium() reader Open

xenium

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

scverse/spatialdata-io#361 · 2 comments · 1 reaction · Opened Jan 30, 2026
visium_hd reader: load_segmentations_only = False still loads segmentation results Open

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

scverse/spatialdata-io#359 · 4 comments · Opened Jan 22, 2026
Anndata compatible version with spatialdata-io 5.1/5.0 Open

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

scverse/spatialdata-io#346 · 1 comment · Opened Nov 18, 2025
Improve the contribution guide by adding some examples Open

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

scverse/spatialdata-io#340 · 1 reaction · Opened Nov 1, 2025
PyArrow OSError: Unexpected end of stream Open

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

scverse/spatialdata-io#334 · 4 comments · Opened Oct 27, 2025
proposal for friendly spatialdata_io.stereoseq function Open

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

scverse/spatialdata-io#355 · 1 comment · Opened Sep 17, 2025
Xenium read error Open

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

scverse/spatialdata-io#325 · 9 comments · Opened Sep 17, 2025
How to read BGI's STOmics spatial transcriptomics data? Open

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

scverse/spatialdata-io#322 · Opened Sep 7, 2025
Recommended approach for reading multiple Xenium slides with mutual panel at once Open

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

scverse/spatialdata-io#319 · 1 comment · Opened Sep 2, 2025
ENHANCEMENT: to_legacy_anndata support with region > 1 Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/spatialdata-io#318 · 12 comments · Opened Sep 1, 2025
Cosmx reader: CellOverlay is skipped Open

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

scverse/spatialdata-io#313 · 1 comment · 1 reaction · Opened Aug 11, 2025
`xenium_aligned_image` assumes the image has 3 or 4 channels Open

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

scverse/spatialdata-io#311 · Opened Jul 31, 2025
Unable to read xenium data Open

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

scverse/spatialdata-io#309 · Opened Jun 30, 2025
`xenium` fails on imported segmentation Open

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

scverse/spatialdata-io#308 · 1 reaction · Opened Jun 17, 2025
`spatialdata_io.xenium` results in `NA` feature names in the `transcripts` Spatial Element Open

Difficulty 3/5 1-2 days Newbie friendliness 50/100

scverse/spatialdata-io#306 · Opened May 21, 2025
VisiumHD: Reading in raw_probe_bc_matrix.h5 Open

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

scverse/spatialdata-io#300 · Opened Apr 8, 2025
Unique cell_ID issue with cosmx reader Open

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

scverse/spatialdata-io#291 · 3 comments · Opened Mar 18, 2025
Use `scanpy` for reading matrixes Open

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

scverse/spatialdata-io#288 · Opened Mar 15, 2025
Read `cell_feature_matrix` in market format Open

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

scverse/spatialdata-io#287 · 4 comments · Opened Mar 13, 2025
VisiumHD: load scalefactor microns_per_pixel in anndata Open

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

scverse/spatialdata-io#286 · 5 comments · Opened Mar 11, 2025
Python Environment Open

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

scverse/spatialdata-io#277 · 1 comment · Opened Feb 14, 2025
Add `dataset_id` prefix to tables in Visium HD Open

visium-hd

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

scverse/spatialdata-io#273 · 1 reaction · Opened Feb 6, 2025
Load Visium HD generated without microscopy image Open

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

scverse/spatialdata-io#270 · 8 comments · Opened Jan 31, 2025
Problem of reading dbit-seq image Open

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

scverse/spatialdata-io#267 · 1 comment · Opened Jan 26, 2025
failure to import spatialdata_io Open

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

scverse/spatialdata-io#263 · 1 comment · Opened Jan 14, 2025
z_index = 0 for polygons in MERSCOPE Open

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

scverse/spatialdata-io#256 · 3 comments · Opened Jan 5, 2025
Change points to shapes for stereo-seq Open

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

scverse/spatialdata-io#253 · 12 comments · Opened Jan 3, 2025
Selecting specific stains when reading merscope files into a sdata object. Open

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

scverse/spatialdata-io#250 · 3 comments · Opened Dec 12, 2024
In `.geojson` parsed, the index should be parsed from `.geojson` Open

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

scverse/spatialdata-io#249 · 2 comments · 1 reaction · Opened Dec 12, 2024
Update MACSima reader when stitching is supported Open

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

scverse/spatialdata-io#243 · 1 comment · 1 reaction · Opened Nov 27, 2024
Xenium cell segmentation mask export requires coordinate flipping among y-axis Open

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

scverse/spatialdata-io#240 · 1 comment · Opened Nov 18, 2024
Missing tiles in Xenium H&E image Open

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

scverse/spatialdata-io#235 · 4 comments · Opened Nov 6, 2024
Reduce readers' memory consumption Open

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

scverse/spatialdata-io#229 · 1 comment · Opened Oct 28, 2024
Remove dummy channel from `xenium` Open

xenium

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

scverse/spatialdata-io#226 · Opened Oct 23, 2024
We're storing spot locations as int64 (and maybe more) - should be sth smaller Open

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

scverse/spatialdata-io#220 · 3 comments · Opened Oct 10, 2024
cosmx - ValueError: Affine matrix must be homogeneous. Open

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

scverse/spatialdata-io#213 · 7 comments · Opened Oct 2, 2024

scverse/spatialdata-io

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