Error attempting to transform xenium transcript coordinate using transform() #1105

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1. LucaMarconato commented on Apr 4, 2026

   

   LucaMarconato

   on Apr 4, 2026

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

   👍React with 👍1Reacted by rached-97
2. rached-97 commented on May 8, 2026

   

   rached-97

   on May 8, 2026

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   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/[email protected]/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!
3. LucaMarconato

   closed this as completedin #1129on May 15, 2026