sd.concatenate throws ValidationError on queried sdatas

[fbnrst]

Bug Description

Concatenating two SpatialData objects extracted from bounding boxes fails with a ValidationError.

To Reproduce

import spatialdata as sd

sdata = sd.datasets.blobs()
sdata1 = sdata.query.bounding_box(('x', 'y'), min_coordinate=2*[0], max_coordinate=2*[100], target_coordinate_system='global')
sdata2 = sdata.query.bounding_box(('x', 'y'), min_coordinate=2*[100], max_coordinate=2*[200], target_coordinate_system='global')
sdata_concat = sd.concatenate({'s1': sdata1, 's2': sdata2})

Error Message

---------------------------------------------------------------------------
ValidationError                           Traceback (most recent call last)
Cell In[1], line 6
      4 sdata1 = sdata.query.bounding_box(('x', 'y'), min_coordinate=2*[0], max_coordinate=2*[100], target_coordinate_system='global')
      5 sdata2 = sdata.query.bounding_box(('x', 'y'), min_coordinate=2*[100], max_coordinate=2*[200], target_coordinate_system='global')
----> 6 sdata_concat = sd.concatenate({'s1': sdata1, 's2': sdata2})

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_core/concatenate.py:139, in concatenate(sdatas, region_key, instance_key, concatenate_tables, obs_names_make_unique, modify_tables_inplace, attrs_merge, **kwargs)
    136     raise TypeError("`sdatas` must be a `Iterable`")
    138 if isinstance(sdatas, dict):
--> 139     sdatas = _fix_ensure_unique_element_names(
    140         sdatas,
    141         rename_tables=not concatenate_tables,
    142         rename_obs_names=obs_names_make_unique and concatenate_tables,
    143         modify_tables_inplace=modify_tables_inplace,
    144     )
    146 ERROR_STR = (
    147     " must have unique names across the SpatialData objects to concatenate. Please pass a `dict[str, SpatialData]`"
    148     " to `concatenate()` to address this (see docstring)."
    149 )
    151 merged_images = {**{k: v for sdata in sdatas for k, v in sdata.images.items()}}

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_core/concatenate.py:251, in _fix_ensure_unique_element_names(sdatas, rename_tables, rename_obs_names, modify_tables_inplace)
    249 sdatas_fixed = []
    250 for elements, tables in zip(elements_by_sdata, tables_by_sdata, strict=True):
--> 251     sdata = SpatialData.init_from_elements(elements, tables=tables)
    252     sdatas_fixed.append(sdata)
    253 return sdatas_fixed

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:2299, in SpatialData.init_from_elements(cls, elements, tables, attrs)
   2297         for name, table in tables.items():
   2298             elements_dict["tables"][name] = table
-> 2299 return cls(**elements_dict, attrs=attrs)

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_utils.py:270, in _deprecation_alias.<locals>.deprecation_decorator.<locals>.wrapper(*args, **kwargs)
    268     raise ValueError("version for deprecation must be specified")
    269 rename_kwargs(f.__name__, kwargs, alias_copy, class_name, library, version)
--> 270 return f(*args, **kwargs)

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:156, in SpatialData.__init__(self, images, labels, points, shapes, tables, attrs)
    151     duplicates = {x for x in element_names if element_names.count(x) > 1}
    152     raise KeyError(
    153         f"Element names must be unique. The following element names are used multiple times: {duplicates}"
    154     )
--> 156 with raise_validation_errors(
    157     title="Cannot construct SpatialData object, input contains invalid elements.\n"
    158     "For renaming, please see the discussion here https://github.com/scverse/spatialdata/discussions/707 .",
    159     exc_type=(ValueError, KeyError),
    160 ) as collect_error:
    162     if images is not None:
    163         for k, v in images.items():

File ~/miniforge3/envs/workshop_2025_spatial/lib/python3.12/site-packages/spatialdata/_core/validation.py:382, in raise_validation_errors.__exit__(self, exc_type, exc_val, exc_tb)
    380 # Exceptions were collected that we want to raise as a combined validation error.
    381 if self._collector.errors:
--> 382     raise ValidationError(title=self._message, errors=self._collector.errors)
    383 return True

ValidationError: Cannot construct SpatialData object, input contains invalid elements.
For renaming, please see the discussion here https://github.com/scverse/spatialdata/discussions/707 .
  tables/table-s1: Regions in the AnnData object and `region` do not match.

Expected Behavior

The concatenate function should successfully merge the two bounding box subsets of sdata.

System Info

• OS: macOS 14.7.5
• Python version: 3.12.9
• SpatialData version: 0.3.0

Package Versions

Package	Version
spatialdata	0.3.0
numpy	2.1.3
pandas	2.2.3
xarray	2025.3.1
dask	2024.11.2
zarr	2.18.5
pyproj	3.7.1
shapely	2.1.0
scikit-image	0.25.2
anndata	0.11.4
ome-zarr	0.10.3
multiscale_spatial_image	2.0.2