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fix(visium): build the circles from the spot coordinates again #416

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Merged
LucaMarconato merged 2 commits into from
Sep 9, 2026
Merged

fix(visium): build the circles from the spot coordinates again #416

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1e07786
fix(visium): build the circles from the spot coordinates again
LucaMarconato Sep 8, 2026
e19b01e
remove ai-generated visium test as it is not using real data
LucaMarconato Sep 9, 2026
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,12 @@ Release notes for `v0.7.1` and earlier are available on the [Releases][] page.
documentation builds, `mypy` type checking of `src` and `tests`, `biome`/`pyproject-fmt`/`zizmor` pre-commit hooks,
and Dependabot updates.

### Fixed

- `visium()`: the circles are built again from the spot coordinates instead of from the raw `tissue_positions` table,
which made the reader raise `TypeError: ShapesModel.parse() does not support the type
<class 'pandas.core.frame.DataFrame'>`.

### Removed

- Support for Python 3.11.
7 changes: 5 additions & 2 deletions src/spatialdata_io/readers/visium.py
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Expand Up @@ -174,7 +174,10 @@ def visium(

assert isinstance(adata.obs, pd.DataFrame)
adata.obs = pd.merge(adata.obs, coords, how="left", left_index=True, right_index=True)
adata.obsm["spatial"] = adata.obs[[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y]].values
# `coords` above is the raw `tissue_positions` table; the circles are built from the
# spot coordinates in the order of `adata`, so keep them in a separate variable
spot_coords = adata.obs[[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y]].to_numpy()
adata.obsm["spatial"] = spot_coords
adata.obs = pd.DataFrame(adata.obs)
adata.obs.drop(columns=[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y], inplace=True)
adata.obs["spot_id"] = np.arange(len(adata))
Expand Down Expand Up @@ -204,7 +207,7 @@ def visium(
)
shapes = {}
circles = ShapesModel.parse(
coords,
spot_coords,
geometry=0,
radius=scalefactors["spot_diameter_fullres"] / 2.0,
index=adata.obs["spot_id"].copy(),
Expand Down
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