`pl.show()` leading to `ValueError` due to mismatch between number of axes and number of panels

[LucaMarconato]

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Blocking a release. To reproduce please run notebook_spatial_query.ipynb from spaitaldata-notebooks.

Some notebooks started throwing some ValueError due to a mismatch between the number of axes and the number of panels in the plot. If possible, I would try to be backward compatible.

INFO - SpatialData object, with associated Zarr store: /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata-sandbox/visium/data.zarr
INFO - ├── Images
INFO - │ ├── 'ST8059048_hires_image': DataArray[cyx] (3, 2000, 1969)
INFO - │ ├── 'ST8059048_lowres_image': DataArray[cyx] (3, 600, 591)
INFO - │ ├── 'ST8059050_hires_image': DataArray[cyx] (3, 2000, 1968)
INFO - │ └── 'ST8059050_lowres_image': DataArray[cyx] (3, 600, 590)
INFO - ├── Shapes
INFO - │ ├── 'ST8059048': GeoDataFrame shape: (2987, 2) (2D shapes)
INFO - │ └── 'ST8059050': GeoDataFrame shape: (3497, 2) (2D shapes)
INFO - └── Tables
INFO - └── 'table': AnnData (6484, 31053)
INFO - with coordinate systems:
INFO - ▸ 'ST8059048', with elements:
INFO - ST8059048_hires_image (Images), ST8059048 (Shapes)
INFO - ▸ 'ST8059048_downscaled_lowres', with elements:
INFO - ST8059048_lowres_image (Images), ST8059048 (Shapes)
INFO - ▸ 'ST8059050', with elements:
INFO - ST8059050_hires_image (Images), ST8059050 (Shapes)
INFO - ▸ 'ST8059050_downscaled_lowres', with elements:
INFO - ST8059050_lowres_image (Images), ST8059050 (Shapes)
INFO - 
INFO - Ending Cell 3------------------------------------------
INFO - Executing Cell 4---------------------------------------
INFO - Ending Cell 4------------------------------------------
INFO - Executing Cell 5---------------------------------------
INFO - /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:170: UserWarning: The table is annotating 'ST8059050', which is not present in the SpatialData object.
INFO - self.validate_table_in_spatialdata(v)
INFO - /Users/macbook/embl/projects/basel/spatialdata-integration-testing/dependencies/spatialdata/src/spatialdata/_core/spatialdata.py:170: UserWarning: The table is annotating 'ST8059050', which is not present in the SpatialData object.
INFO - self.validate_table_in_spatialdata(v)

Again, session_info2 seems to be uninformative. Please let me know if you can't reproduce and I will dig deeper.

Versions

| Dependency | Version |
| ----------------------------- | ------- |
| sphinxcontrib-devhelp | 2.0.0 |
| sphinxcontrib-htmlhelp | 2.1.0 |
| sphinxcontrib-serializinghtml | 2.0.0 |
| session-info2 | 0.3 |
| sphinxcontrib-qthelp | 2.0.0 |
| sphinxcontrib-bibtex | 2.6.5 |
| sphinxcontrib-jsmath | 1.0.1 |
| sphinxcontrib-applehelp | 2.0.0 |
| setuptools | 80.9.0 |

| Component | Info |
| --------- | -------------------------------------------------------------------------------- |
| Python | 3.13.0 | packaged by conda-forge | (main, Nov 27 2024, 19:18:26) [Clang 18.1.8 ] |
| OS | macOS-26.5.1-arm64-arm-64bit-Mach-O |
| Updated | 2026-07-02 17:52 |

[LucaMarconato]

This was occurring in the notebooks visium and spatial_query. As a workaround I pass coordinate_systems explicitly in pl.show() (see scverse/spatialdata-tutorials#169). But this at times is very verbose, so I advocate for a fix please.