AttributeError: type object 'MultiscaleSpatialImage' has no attribute 'from_dict'
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Description
When running the vignette Use landmark annotations to align multiple -omics layers, I run into an attribute error on cell #2
xenium_sdata = sd.read_zarr("xenium.zarr")
xenium_sdata
The error is
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[5], line 1
----> 1 xenium_sdata = sd.read_zarr("xenium.zarr")
2 xenium_sdata
File ~/miniconda/envs/serial_integration/lib/python3.10/site-packages/spatialdata/_io/io_zarr.py:80, in read_zarr(store, selection)
78 f_elem = group[subgroup_name]
79 f_elem_store = os.path.join(f_store_path, f_elem.path)
---> 80 element = _read_multiscale(f_elem_store, raster_type="image")
81 images[subgroup_name] = element
82 count += 1
File ~/miniconda/envs/serial_integration/lib/python3.10/site-packages/spatialdata/_io/io_raster.py:86, in _read_multiscale(store, raster_type, fmt)
79 data = node.load(Multiscales).array(resolution=d, version=fmt.version)
80 multiscale_image[f"scale{i}"] = DataArray(
81 data,
82 name=name,
83 dims=axes,
84 coords={"c": channels} if channels is not None else {},
85 )
---> 86 msi = MultiscaleSpatialImage.from_dict(multiscale_image)
87 _set_transformations(msi, transformations)
88 return compute_coordinates(msi)
AttributeError: type object 'MultiscaleSpatialImage' has no attribute 'from_dict'
Any help would be appreciated
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Research direction
Reproduce cell #2 of the “Use landmark annotations to align multiple -omics layers” vignette, starting with sd.read_zarr("xenium.zarr"). Inspect spatialdata/_io/io_raster.py around _read_multiscale and the MultiscaleSpatialImage API shown in the traceback. Done means the vignette can read the Zarr store without the reported AttributeError.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100