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

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308 open issues indexed

aggregate(values, by=<labels with no non-background instance>) raises a misleading 'regions do not match' error Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: low

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

scverse/spatialdata#1250 · Opened Sep 13, 2026
aggregate(values, by=<multiscale labels>) crashes with AttributeError despite DataTree being a declared input type Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#1249 · Opened Sep 13, 2026
bounding_box_query(filter_table=True) crashes if the SpatialData object contains an orphan table Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

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

scverse/spatialdata#1248 · Opened Sep 13, 2026
Collection of minor issues found by an automated bug hunt (validation edge cases, misleading errors, small inefficiencies) Open

bug 🚨 needs: triage

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

scverse/spatialdata#1244 · Opened Sep 11, 2026
repr(sdata) reports the parquet row count for any points element that shares backing files, even after lazy filtering Open

API bug 🚨 element: points ⊙ needs: triage

Difficulty 3/5 1-2 days Newbie friendliness 76/100

scverse/spatialdata#1243 · Opened Sep 11, 2026
Joins on an element with duplicated index values duplicate rows (inner/right) instead of erroring Open

bug 🚨 element: shapes ▲ method: query needs: triage

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

scverse/spatialdata#1242 · Opened Sep 11, 2026
concatenate(): orphan tables crash the dict form; a generator input gives a misleading error Open

bug 🚨 method: concatenate needs: triage

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

scverse/spatialdata#1241 · Opened Sep 11, 2026
validate_table_in_spatialdata: the instance-key dtype-mismatch TypeError can never fire (`dtype is str`) Open

bug 🚨 element: table 📑 needs: triage

Difficulty 3/5 1-2 days Newbie friendliness 74/100

scverse/spatialdata#1240 · Opened Sep 11, 2026
unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster Open

bug 🚨 element: images 🌌 element: labels 🏷️ needs: triage

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1239 · Opened Sep 11, 2026
Multi-box bounding_box_query works on elements but crashes on a SpatialData object (TypeError: Unsupported type list) Open

bug 🚨 method: query needs: triage

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

scverse/spatialdata#1238 · Opened Sep 11, 2026
write_element(name, overwrite=True) can never overwrite an existing element, even purely in-memory tables/shapes Open

API enhancement ✨ I/O 💿 needs: triage

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

scverse/spatialdata#1237 · Opened Sep 11, 2026
rasterize(labels, value_key=...) crashes for categorical table columns and for labels absent from the table Open

bug 🚨 element: labels 🏷️ method: rasterization needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 75/100

scverse/spatialdata#1236 · Opened Sep 11, 2026
to_polygons(labels) turns a label containing a hole into an invalid MultiPolygon with the hole counted as area Open

bug 🚨 element: labels 🏷️ method: vectorize ◃ needs: triage priority: medium

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

scverse/spatialdata#1235 · Opened Sep 11, 2026
spatialdata.models.force_2d() silently drops interior rings (holes) of polygons Open

bug 🚨 element: shapes ▲ models needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1234 · Opened Sep 11, 2026
get_extent(circles, exact=True) (the default) is wrong for anisotropic/shearing transformations, while exact=False is right Open

bug 🚨 element: shapes ▲ method: transforms 🔃 needs: triage priority: medium

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

scverse/spatialdata#1233 · Opened Sep 11, 2026
bounding_box_query on circles ignores the radius (only the centre is tested), polygon_query does not Open

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

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

scverse/spatialdata#1232 · Opened Sep 11, 2026
A failing aggregate() leaves the internal __ones_column / __areas_column on the user's shapes element Open

bug 🚨 element: shapes ▲ method: aggregation 🔢 needs: triage

Difficulty 3/5 1-2 days Newbie friendliness 75/100

scverse/spatialdata#1231 · Opened Sep 11, 2026
aggregate(image, by=labels) crashes when the labels have no background (no zero pixels) Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1230 · Opened Sep 11, 2026
TableModel rejects int8/uint8 instance-key columns although the error message promises 'uint equivalents' (breaks aggregate/to_circles on uint8 labels) Open

bug 🚨 element: labels 🏷️ element: table 📑 models needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1229 · Opened Sep 11, 2026
Substring matching of element names against a single-region table (`element_name in regions` with `regions: str`) Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1228 · Opened Sep 11, 2026
match_sdata_to_table / filter_by_table_query crash for how='left_exclusive' and how='right_exclusive' Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

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

scverse/spatialdata#1227 · Opened Sep 11, 2026
Joins crash (IndexError / KeyError: None) when the element and the table share no instance Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1226 · Opened Sep 11, 2026
inner join on a Labels element returns table=None even with filter_label_pixels=True Open

bug 🚨 element: labels 🏷️ element: table 📑 method: query needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 76/100

scverse/spatialdata#1225 · Opened Sep 11, 2026
Points: the transform dict is shared between a dask DataFrame and every frame derived from it, so set_transformation on a copy/subset also modifies the original Open

bug 🚨 element: points ⊙ method: transforms 🔃 needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 74/100

scverse/spatialdata#1224 · Opened Sep 11, 2026
deepcopy() of a multiscale raster loads the original element into memory and detaches it from its Zarr backing Open

bug 🚨 element: images 🌌 element: labels 🏷️ needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1223 · Opened Sep 11, 2026
concatenate({'a': sdata1, 'b': sdata2}) renames the coordinate systems of the input objects in place Open

bug 🚨 method: concatenate needs: triage priority: medium

Difficulty 4/5 3-5 days Newbie friendliness 55/100

scverse/spatialdata#1222 · Opened Sep 11, 2026
Case-insensitive element-name uniqueness check only works when the existing name is lowercase Open

API bug 🚨 I/O 💿 needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/spatialdata#1221 · Opened Sep 11, 2026
rasterize() mis-positions the output by 0.5·(1 − s) units (up to half an output pixel) whenever the output pixel size s ≠ 1 Open

bug 🚨 method: rasterization needs: triage priority: medium

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

scverse/spatialdata#1220 · Opened Sep 11, 2026
transform(GeoDataFrame) uses geopandas' per-geometry affine_transform (Python loop): 41 s for 5.5 M polygons vs 1.8 s with shapely.transform Open

element: shapes ▲ method: transforms 🔃 needs: triage performance 🚀 priority: medium

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

scverse/spatialdata#1219 · Opened Sep 11, 2026
get_extent(shapes, exact=True) (default) transforms every geometry even without rotation, and the exact=False path uses a Python-level .apply: 49 s vs ~0.2 s possible on 5.5 M Visium HD bins Open

element: shapes ▲ needs: triage performance 🚀 priority: medium

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

scverse/spatialdata#1218 · Opened Sep 11, 2026
Opening a Visium HD store costs 7 GB of RAM because shapes and tables are loaded eagerly (lazy shapes/tables missing) Open

element: shapes ▲ element: table 📑 enhancement ✨ I/O 💿 needs: triage performance 🚀 priority: high

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

scverse/spatialdata#1217 · Opened Sep 11, 2026
to_circles(labels) crashes when the labels have a non-identity linear transformation (Scale/Affine) — i.e. on real data Open

bug 🚨 element: labels 🏷️ method: vectorize ◃ needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 74/100

scverse/spatialdata#1216 · Opened Sep 11, 2026
relabel_sequential() fails for every unsigned dtype: OverflowError: Python integer -1 out of bounds for uint16 Open

bug 🚨 element: labels 🏷️ needs: triage priority: high

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1215 · Opened Sep 11, 2026
inner/right joins fail with KeyError when the points element has more than one dask partition Open

bug 🚨 element: points ⊙ element: table 📑 method: query needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1214 · Opened Sep 11, 2026
ImageTilesDataset: tile extent ignores the region's coordinate transformation, and the input circles' radii are modified in place Open

bug 🚨 method: dataloader needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1213 · Opened Sep 11, 2026
`sdata.images = {...}` (and the other element setters) break cross-type name uniqueness; the resulting store cannot be read back Open

API bug 🚨 needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 74/100

scverse/spatialdata#1212 · Opened Sep 11, 2026
polygon_query on points resets the index and rewrites the coordinate systems (adds a bogus `global: Identity`) Open

bug 🚨 element: points ⊙ method: query needs: triage priority: high

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

scverse/spatialdata#1211 · Opened Sep 11, 2026
Image2DModel/Image3DModel.parse(DataArray) silently discards the channel names already present in the input Open

bug 🚨 element: images 🌌 models needs: triage priority: high

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

scverse/spatialdata#1210 · Opened Sep 11, 2026
rasterize_bins(value_key=None) declares dtype=uint32 while blocks hold X.dtype; writing the result silently zeroes non-integer values Open

bug 🚨 element: images 🌌 method: rasterization needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1209 · Opened Sep 11, 2026
_filter_labels_element rebuilds set(ids_to_keep) inside a comprehension: O(n_labels × n_keep) in right/inner joins with filter_label_pixels=True Open

bug 🚨 element: labels 🏷️ method: query needs: triage performance 🚀 priority: high

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1208 · Opened Sep 11, 2026
Points operations load the whole element into memory: polygon_query needs 17 GB / 15 s to return 25k of 42M transcripts Open

element: points ⊙ method: query needs: triage performance 🚀 priority: high

Difficulty 5/5 Over a week Newbie friendliness 38/100

scverse/spatialdata#1207 · Opened Sep 11, 2026
Categorical aggregate() (transcripts → cells count matrix) stores every (cell, gene) zero explicitly: memory ∝ n_cells × n_genes Open

bug 🚨 element: points ⊙ method: aggregation 🔢 needs: triage performance 🚀 priority: high

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

scverse/spatialdata#1206 · Opened Sep 11, 2026
Scale/Translation/Affine.__eq__ raise ValueError for a different number of axes (breaks aggregate on Xenium transcripts vs 2D cells) Open

bug 🚨 method: aggregation 🔢 method: transforms 🔃 needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 75/100

scverse/spatialdata#1205 · Opened Sep 11, 2026
aggregate(image, by=labels) silently ignores translations/offsets between the two rasters Open

bug 🚨 element: images 🌌 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: high

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

scverse/spatialdata#1204 · Opened Sep 11, 2026
Raster bounding_box_query/polygon_query: 1-pixel positioning error when the box minimum has a fractional part in (0, 0.5] Open

bug 🚨 element: images 🌌 element: labels 🏷️ method: query needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 76/100

scverse/spatialdata#1203 · Opened Sep 11, 2026
transform() of multiscale labels uses linear interpolation and invents label ids Open

bug 🚨 element: labels 🏷️ method: transforms 🔃 needs: triage priority: high

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#1202 · Opened Sep 11, 2026
coordinate system of xenium explorer and stada are inconsistent Open

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

scverse/spatialdata#1194 · Opened Aug 28, 2026
Investigate if `ome-zarr-py` Labels class __init__ leads to performance implications Open

performance 🚀

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

scverse/spatialdata#1190 · Opened Aug 21, 2026
No sharding configuration exposed for tables Open

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

scverse/spatialdata#1178 · 4 comments · Opened Aug 18, 2026
Bounding box query APIs slowed down by join operations Open

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

scverse/spatialdata#1177 · Opened Aug 18, 2026

scverse/spatialdata

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