Dependency issue with `spatialdata`

[liz-is]

I'm trying to visualise some Xenium data, inspatialdata format, with Vitessce, using the functions in vitessce.data_utils for optimisation. However, I can't get versions of the spatialdata and vitessce-python packages to install that have all the functionality I need.

I'm using uv for environment management.

• If I install vitessce first:

uv add "vitessce[all]"
uv add spatialdata
uv add "setuptools<=81" # otherwise I get an import error

I get the following package versions (snipped to those I thought might be relevant, let me know if you need the full list):

Package                   Version
------------------------- -----------
ome-zarr                  0.10.2
spatialdata               0.5.0
vitessce                  3.8.3
zarr                      2.18.7

With these versions, I can't load a Zarr store of data processed with spatialdata version 0.7.3 (following the squidpy tutorial):

>>> sdata = read_zarr("../../data/Xenium-Human-Ovarian-Cancer/Xenium_Prime_Ovarian_Cancer_FFPE_processed.zarr")
Traceback (most recent call last):
  File "<python-input-1>", line 1, in <module>
    read_zarr("../../data/Xenium-Human-Ovarian-Cancer/Xenium_Prime_Ovarian_Cancer_FFPE_processed.zarr")
    ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/vitessce-pilot/env-testing/vitessce-first/.venv/lib/python3.13/site-packages/spatialdata/_io/io_zarr.py", line 74, in read_zarr
    f, f_store_path = _open_zarr_store(store)
                      ~~~~~~~~~~~~~~~~^^^^^^^
  File "/Users/vitessce-pilot/env-testing/vitessce-first/.venv/lib/python3.13/site-packages/spatialdata/_io/io_zarr.py", line 35, in _open_zarr_store
    f = store if isinstance(store, zarr.Group) else zarr.open(store, mode="r")
                                                    ~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/Users/vitessce-pilot/env-testing/vitessce-first/.venv/lib/python3.13/site-packages/zarr/convenience.py", line 139, in open
    raise PathNotFoundError(path)
zarr.errors.PathNotFoundError: nothing found at path ''
>>> import os
>>> os.path.exists("../../data/Xenium-Human-Ovarian-Cancer/Xenium_Prime_Ovarian_Cancer_FFPE_processed.zarr")
True

• If I install spatialdata first:

uv add spatialdata
uv add "vitessce[all]"

I get the following package versions (snipped to those I thought might be relevant, let me know if you need the full list):

Package                   Version
------------------------- -----------
ome-zarr                  0.15.0
spatialdata               0.7.3
vitessce                  3.5.1
zarr                      3.2.1

Then I can read the same Zarr store successfully:

>>> from spatialdata import read_zarr 
>>> sdata = read_zarr("../../data/Xenium-Human-Ovarian-Cancer/Xenium_Prime_Ovarian_Cancer_FFPE_processed.zarr")
>>> 

But vitessce-python==3.5.1 doesn't have the vitessce.data_utils functions that are used for optimisation, e.g. sdata_morton_sort_points, sdata_points_process_columns, etc.

Questions

• Is it intentional that recent versions of vitessce-python are only compatible with older versions of spatialdata? If so, can you provide some guidance as to the most recent suitable version of spatialdata I can use to be compatible with vitessce-python?
• How important are the optimisations? Is it worthwhile trying to visualise my data with an older version of vitessce-python where these helpers aren't available? I can't currently get the widget to work but I'm not sure if that's because of the version issues or something else (following this notebook but the example data URL gives a 404).

[keller-mark]

Hi @liz-is , thank you for the questions. We were overdue to update code here to support the latest spatialdata Python package version.

Can you please try with the latest version of the Python package (3.9.0)? I have also updated the Xenium dataset URL in the example notebook. Alternatively, you can manually download the xenium_rep1_io dataset from https://spatialdata.scverse.org/en/stable/tutorials/notebooks/datasets/README.html