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!