Error attempting to transform xenium transcript coordinate using `transform()`

[rached-97]

Describe the bug

I am getting "ValueError: The number of items in 'lengths' does not match the number of partitions. 4 != 13" when attempting to transform xenium transcript coordinates using spatialdata (sd) sd.transform()

I noticed a similar error reported previously (issue #1064) but I am under the impression that it was resolved and closed.

Thank you for your help.

>>> sdata = xenium(xenDataDir, cells_as_circles=False)

>>> get_transformation(sdata["transcripts"])
Scale (x, y)
 [4.70588235 4.70588235]

>>> sd.transform(sdata["transcripts"], to_coordinate_system = "global")
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[23], line 1
----> 1 sd.transform(sdata["transcripts"], to_coordinate_system = "global")

File /opt/homebrew/Cellar/python@3.14/3.14.3_1/Frameworks/Python.framework/Versions/3.14/lib/python3.14/functools.py:982, in singledispatch.<locals>.wrapper(*args, **kw)
 979 if not args:
 980 raise TypeError(f'{funcname} requires at least '
 981 '1 positional argument')
--> 982 return dispatch(args[0].__class__)(*args, **kw)

File .venv/lib/python3.14/site-packages/spatialdata/_core/operations/transform.py:443, in _(data, transformation, maintain_positioning, to_coordinate_system)
 441 arrays = []
 442 for ax in axes:
--> 443 arrays.append(data[ax].to_dask_array(lengths=True).reshape(-1, 1))
 444 xdata = DataArray(da.concatenate(arrays, axis=1), coords={"points": range(len(data)), "dim": list(axes)})
 445 xtransformed = transformation._transform_coordinates(xdata)

File .venv/lib/python3.14/site-packages/dask/dataframe/dask_expr/_collection.py:1422, in FrameBase.to_dask_array(self, lengths, meta, optimize, **optimize_kwargs)
 1418 lengths = tuple(self.map_partitions(len).compute())
 1420 arr = self.values
-> 1422 chunks = self._validate_chunks(arr, lengths)
 1423 arr._chunks = chunks
 1425 if meta is not None:

File .venv/lib/python3.14/site-packages/dask/dataframe/dask_expr/_collection.py:2471, in FrameBase._validate_chunks(self, arr, lengths)
 2468 lengths = tuple(lengths)
 2470 if len(lengths) != self.npartitions:
-> 2471 raise ValueError(
 2472 "The number of items in 'lengths' does not match the number of "
 2473 f"partitions. {len(lengths)} != {self.npartitions}"
 2474 )
 2476 if self.ndim == 1:
 2477 chunks = normalize_chunks((lengths,))

ValueError: The number of items in 'lengths' does not match the number of partitions. 4 != 13

To Reproduce

pip freeze | grep spatialdata
napari-spatialdata==0.7.0
spatialdata==0.7.2
spatialdata-io==0.6.0
spatialdata-plot==0.3.2

pip freeze | grep dask 
dask==2026.1.1
dask-image==2025.11.0

Expected behavior
I expected the transcript data to be scaled to the global coordinate system (more specifically the coordinates of the Images in the spatialdata object) by the scaling factor returned by get_transformation()

Desktop (optional):

• OS: MacOS running on Apple M1 Max
• Version: Tahoe 26.2

[LucaMarconato]

Hi, thanks for reporting. Seems to be related to #1095. @melonora do you have updates regarding the issue? Thanks!

[rached-97]

Dear dev team,

I attempted the operation again in spatialdata v0.7.3 and received a different error "ValueError: cannot reindex on an axis with duplicate labels"

---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[7], line 1
----> 1 sd.transform(sdata["transcripts"], to_coordinate_system = "global")

File /opt/homebrew/Cellar/python@3.14/3.14.4_1/Frameworks/Python.framework/Versions/3.14/lib/python3.14/functools.py:982, in singledispatch.<locals>.wrapper(*args, **kw)
 979 if not args:
 980 raise TypeError(f'{funcname} requires at least '
 981 '1 positional argument')
--> 982 return dispatch(args[0].__class__)(*args, **kw)

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/spatialdata/_core/operations/transform.py:466, in _(data, transformation, maintain_positioning, to_coordinate_system)
 462 new_ax = xtransformed[:, indices]
 463 # TODO: discuss with dask team
 464 # This is not nice, but otherwise there is a problem with the joint graph of new_ax and transformed, causing
 465 # a getattr missing dependency of dependent from_dask_array.
--> 466 new_col = pd.Series(new_ax.data.flatten().compute(), index=transformed.index)
 467 transformed[ax] = new_col
 469 old_transformations = cast(dict[str, Any], get_transformation(data, get_all=True))

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/pandas/core/series.py:493, in Series.__init__(self, data, index, dtype, name, copy, fastpath)
 490 name = ibase.maybe_extract_name(name, data, type(self))
 492 if index is not None:
--> 493 index = ensure_index(index)
 495 if dtype is not None:
 496 dtype = self._validate_dtype(dtype)

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/pandas/core/indexes/base.py:7715, in ensure_index(index_like, copy)
 7713 return Index(index_like, copy=copy, tupleize_cols=False)
 7714 else:
-> 7715 return Index(index_like, copy=copy)

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/pandas/core/indexes/base.py:529, in Index.__new__(cls, data, dtype, copy, name, tupleize_cols)
 527 raise cls._raise_scalar_data_error(data)
 528 elif hasattr(data, "__array__"):
--> 529 return cls(np.asarray(data), dtype=dtype, copy=copy, name=name)
 530 elif not is_list_like(data) and not isinstance(data, memoryview):
 531 # 2022-11-16 the memoryview check is only necessary on some CI
 532 # builds, not clear why
 533 raise cls._raise_scalar_data_error(data)

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/dask/dataframe/dask_expr/_collection.py:460, in FrameBase.__array__(self, dtype, **kwargs)
 459 def __array__(self, dtype=None, **kwargs):
--> 460 return np.array(self.compute())

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/spatialdata/models/_accessor.py:72, in wrap_method_with_attrs.<locals>.wrapper(self, *args, **kwargs)
 64 raise RuntimeError(
 65 "Invalid .attrs: expected an accessor (`AttrsAccessor`), "
 66 f"got {type(self.attrs).__name__}. A common cause is assigning a dict, e.g. "
 67 "my_dd_object.attrs = {...}. Do not assign to 'attrs'; use "
 68 "my_dd_object.attrs.update(...) instead."
 69 )
 71 old_attrs = self.attrs.copy()
---> 72 result = original_method(self, *args, **kwargs)
 73 # the pandas Index do not have attrs, but dd.Index, since they are a subclass of dd.Series, do have attrs
 74 # thanks to our accessor. Here we ensure that we do not assign attrs to pd.Index objects.
 75 if hasattr(result, "attrs"):

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/dask/base.py:377, in DaskMethodsMixin.compute(self, **kwargs)
 353 def compute(self, **kwargs):
 354 """Compute this dask collection
 355 
 356 This turns a lazy Dask collection into its in-memory equivalent.
 (...) 375 dask.compute
 376 """
--> 377 (result,) = compute(self, traverse=False, **kwargs)
 378 return result

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/dask/base.py:685, in compute(traverse, optimize_graph, scheduler, get, *args, **kwargs)
 682 expr = expr.optimize()
 683 keys = list(flatten(expr.__dask_keys__()))
--> 685 results = schedule(expr, keys, **kwargs)
 687 return repack(results)

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/dask/dataframe/dask_expr/_expr.py:1957, in assign(df, *pairs)
 1955 if isinstance(val, Callable):
 1956 val = val(df)
-> 1957 df[name] = val
 1958 return df

File ~/Documents/python_virtual_environments/py3env_spatialAnalysis_20260508/lib/python3.14/site-packages/pandas/core/indexes/base.py:4436, in Index.reindex(self, target, method, level, limit, tolerance)
 4433 raise ValueError("cannot handle a non-unique multi-index!")
 4434 elif not self.is_unique:
 4435 # GH#42568
-> 4436 raise ValueError("cannot reindex on an axis with duplicate labels")
 4437 else:
 4438 indexer, _ = self.get_indexer_non_unique(target)

ValueError: cannot reindex on an axis with duplicate labels

dask==2026.1.1
dask-image==2025.11.0
multiscale_spatial_image==2.0.3
napari-spatialdata==0.7.1
spatial_image==1.2.3
spatialdata==0.7.3
spatialdata-io==0.7.0
spatialdata-plot==0.3.3
xarray-spatial==0.9.9

Thank you for your help and effort!