scverse/spatialdata

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An open and interoperable data framework for spatial omics data

Stars: 394
Forks: 95
Open beginner issues: 10
Indexed issues: 308
Avg merge: 4d 3h
Merged PRs (30d): 7

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 11, 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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308 open issues indexed

Problem with indices with `left_exclusive` join Open

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

scverse/spatialdata#824 · 1 comment · Opened Jan 13, 2025
questions about alignment in Figure 2b Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

scverse/spatialdata#816 · 4 comments · Opened Jan 3, 2025
How to open the current Zarr based image data as OME-Zarr Open

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

scverse/spatialdata#805 · 3 comments · 1 reaction · Opened Dec 9, 2024
Elements should be validated before starting to write Open

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

scverse/spatialdata#804 · 1 comment · 1 reaction · Opened Dec 9, 2024
Why is it necessary to produce invalid OME-Zarr images? Open

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

scverse/spatialdata#803 · 4 comments · 1 reaction · Opened Dec 6, 2024
Harmonize artifical dataset creation Open

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

scverse/spatialdata#796 · 1 comment · Opened Nov 27, 2024
Rename SpatialElements Open

enhancement ✨

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

scverse/spatialdata#793 · 1 comment · 2 reactions · Opened Nov 22, 2024
idea: point on-disk representation using OME-NGFF Open

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

scverse/spatialdata#789 · 4 comments · 1 reaction · Opened Nov 14, 2024
Annotating coordinate systems Open

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

scverse/spatialdata#780 · 1 comment · Opened Nov 13, 2024
Recommending a workflow for tiling (deep learning use case) Open

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

scverse/spatialdata#774 · 2 reactions · Opened Nov 12, 2024
User documentation on how to setup jobs or run large analysis Open

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

scverse/spatialdata#768 · 1 comment · Opened Nov 7, 2024
User documentation on different methods of benchmarking with SpatialData Open

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

scverse/spatialdata#763 · Opened Nov 6, 2024
User notebook showcasing SpatialData speed Open

docs 📜

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

scverse/spatialdata#762 · 1 comment · 1 reaction · Opened Nov 6, 2024
Having auto-completion when using spatialdata-plot Open

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

scverse/spatialdata#755 · 1 comment · Opened Nov 5, 2024
New docs section: how to integrate `spatialdata` in your tool Open

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

scverse/spatialdata#751 · 1 comment · Opened Nov 1, 2024
New easier table notebook Open

docs 📜

Difficulty 5/5 Over a week Newbie friendliness 28/100

scverse/spatialdata#749 · 2 comments · Opened Nov 1, 2024
New easier intro notebooks Open

docs 📜

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

scverse/spatialdata#748 · 1 comment · Opened Nov 1, 2024
Make a biological transformation notebook Open

docs 📜

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

scverse/spatialdata#747 · 1 comment · Opened Nov 1, 2024
CLI for `get_data_extent()` and `bounding_box_query()` Open

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

scverse/spatialdata#746 · Opened Nov 1, 2024
CLI for modular creation/edit/concatenation of `SpatialData` objects Open

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

scverse/spatialdata#745 · Opened Nov 1, 2024
Faster version `aggregate()` method available Open

method: aggregation 🔢 needs: triage performance 🚀 priority: high

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

scverse/spatialdata#744 · 6 comments · 1 reaction · Opened Oct 31, 2024
Parallelize `aggregate()` Open

performance 🚀

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

scverse/spatialdata#743 · 1 comment · Opened Oct 31, 2024
Benchmark geopandas query methods Open

performance 🚀

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

scverse/spatialdata#742 · 1 comment · Opened Oct 31, 2024
Benchmarks performance on HPC Open

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

scverse/spatialdata#741 · 1 comment · Opened Oct 31, 2024
Benchmark spatial partitioning in dask geopandas Open

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

scverse/spatialdata#739 · 1 comment · Opened Oct 31, 2024
Any way to map the probes sequences with the bins? Open

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

scverse/spatialdata#738 · 1 comment · Opened Oct 31, 2024
Importing Mass Spec Imaging Data into SpatialData Open

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

scverse/spatialdata#737 · 8 comments · 2 reactions · Opened Oct 30, 2024
Transformation inconsistency between on-disk and in-memory usage Open

method: transforms 🔃 needs: triage priority: medium

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

scverse/spatialdata#736 · 3 comments · Opened Oct 29, 2024
Detach SpatialData object from its Zarr store Open

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

scverse/spatialdata#733 · 3 comments · Opened Oct 17, 2024
Expose interpolation `kwargs` for `dask_image.ndinterp.affine_transform()` Open

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

scverse/spatialdata#725 · Opened Oct 3, 2024
Performance improvement of query and aggregate with cuspatial Open

method: aggregation 🔢 method: query performance 🚀

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

scverse/spatialdata#724 · 1 comment · Opened Oct 3, 2024
Respect xarray coordinates for ImageContainers Open

method: transforms 🔃

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

scverse/spatialdata#723 · 4 comments · Opened Oct 3, 2024
UserWarning: ignoring keyword argument 'read_only' when reading zarr created by older version Open

maint 🏗️

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

scverse/spatialdata#717 · 3 comments · Opened Sep 30, 2024
`TableModel().validate()` intentionally skips check for unique `instance_key` values (grouped by `region_key` values) Open

element: table 📑 models needs: triage priority: low

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

scverse/spatialdata#715 · 1 comment · Opened Sep 28, 2024
registration got unmatched images Open

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

scverse/spatialdata#712 · 1 comment · Opened Sep 24, 2024
The SpatialData object is not self-contained Open

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

scverse/spatialdata#710 · 2 comments · 1 reaction · Opened Sep 18, 2024
Is there currently a way to plot 3D data? Open

scverse/spatialdata#708 · 2 comments · 1 assignee · Opened Sep 10, 2024
Image Functions Open

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

scverse/spatialdata#704 · 3 comments · Opened Sep 9, 2024
Streamline datasets for documenation Open

docs 📜

Difficulty 5/5 Over a week Newbie friendliness 32/100

scverse/spatialdata#700 · 3 comments · Opened Sep 3, 2024
Adding `.pipe` to `SpatialData` Open

enhancement ✨

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

scverse/spatialdata#695 · 6 comments · Opened Aug 30, 2024
Parallel computation Open

question ❓

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

scverse/spatialdata#694 · 1 comment · Opened Aug 29, 2024
Extent calculation doesn't account for radius of Points Open

bug 🚨 method: transforms 🔃

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

scverse/spatialdata#693 · 1 comment · Opened Aug 28, 2024
Sparse Array in Labels? Open

element: labels 🏷️ enhancement ✨

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

scverse/spatialdata#691 · 3 comments · Opened Aug 27, 2024
Tool to migrate data between SpatialData versions Open

format

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

scverse/spatialdata#680 · 5 comments · 1 reaction · Opened Aug 15, 2024
Get elements in a coordinate sytem Open

API method: transforms 🔃 question ❓

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

scverse/spatialdata#679 · 1 comment · Opened Aug 15, 2024
spatialdata aggregate 3D support + relatively slow on large images Open

enhancement ✨ method: aggregation 🔢

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

scverse/spatialdata#677 · 2 comments · Opened Aug 14, 2024
Bounding box query vs polygon query for circles Open

element: shapes ▲ method: query needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 64/100

scverse/spatialdata#669 · 3 comments · Opened Aug 9, 2024
Disallow zero-len dataframes when parsing Open

element: labels 🏷️ element: points ⊙ needs: triage priority: low

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

scverse/spatialdata#662 · 1 comment · Opened Aug 6, 2024
simplify tests where `Identity()` was needed as last transformation in a sequence Open

method: transforms 🔃

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

scverse/spatialdata#645 · 1 comment · Opened Jul 25, 2024
Faster implementation available for `vectorize()` Open

enhancement ✨

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

scverse/spatialdata#634 · 5 comments · Opened Jul 11, 2024

scverse/spatialdata

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