Unable to write to data.zarr file due to `ome-zarr (0.14.0)`

[mthimma]

---

TypeError Traceback (most recent call last)
Cell In[7], line 41
37 with tf.TemporaryDirectory() as tmpdir:
38 zarr_path = f"{tmpdir}/data.zarr"
39 #sdata.write(zarr_path)
40 print(zarr_path)
---> 41 sdata.write(zarr_path, overwrite=True)
42
43 sdata = sd.read_zarr(zarr_path)
44 sdata.pl.render_images("image_0").pl.render_shapes("shape_0", color="Gene001", table_name = "table_0", table_layer = "float_matrix").pl.show(coordinate_systems = "global")

File /Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/spatialdata/_utils.py:263, in _deprecation_alias..deprecation_decorator..wrapper(*args, **kwargs)
261 raise ValueError("version for deprecation must be specified")
262 rename_kwargs(f.name, kwargs, alias_copy, class_name, library, version)
--> 263 return f(*args, **kwargs)

File /Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-packages/spatialdata/_core/spatialdata.py:1176, in SpatialData.write(self, file_path, overwrite, consolidate_metadata, update_sdata_path, sdata_formats, shapes_geometry_encoding)
1173 store.close()
1175 for element_type, element_name, element in self.gen_elements():
-> 1176 self._write_element(
1177 element=element,
1178 zarr_container_path=file_path,
1179 element_type=element_type,
1180 element_name=element_name,
...
--> 204 raise TypeError(msg)
205 if not all(v > -1 for v in data_tuple):
206 msg = f"Expected all values to be non-negative. Got {data} instead."

TypeError: Expected an iterable of integers. Got ((3,), (512, 512, 512, 464), (512, 512, 512, 464)) instead.

[xinaesthete]

Can you explain in a little more detail what you did that lead to this so that it can be easily reproduced?

[mthimma]

Sorry about that.

I have python 3.14 and zarr=3.1.6, spatialdata module installed in my Mac host. I installed your dummy-spatialdata using pip install.

I followed your https://github.com/BIMSBbioinfo/dummy-spatialdata/blob/main/docs/notebooks/main.ipynb notebook to generate, visualise and save the spatial data objects to .zarr file.

It worked fine while creating and rendering the image of spatialdata. But failed while writing the object to .zarr

I used this
with tf.TemporaryDirectory() as tmpdir:
zarr_path = f"{tmpdir}/data.zarr"
sdata.write(zarr_path, overwrite=True)

This last line throws the TypeError.

Initially I thought it is due to memory chunking error and hence chunked the images using following function before writing the spatialdata object.

def rechunk_image_tree(img, c, y, x):
# works for DataTree-backed multiscale images and single-scale images
if hasattr(img, "keys"): # multiscale DataTree
for scale in list(img.keys()):
node = img[scale]
for var in list(node.data_vars):
node[var] = node[var].chunk({"c": c, "y": y, "x": x})
return img
else: # single DataArray / Dataset-backed image
for var in list(img.data_vars):
img[var] = img[var].chunk({"c": c, "y": y, "x": x})
return img

sdata.images["image_0"] = rechunk_image_tree(sdata.images["image_0"], 3, 512, 512)
sdata.images["image_1"] = rechunk_image_tree(sdata.images["image_1"], 1, 512, 512)

But with or without chunking, the objects are not written to data.zarr file.

It would be nice if you can help sort this out. I would be interested to generate some dummy spatial data and use it in our tool.

Hopefully this is detail enough to reproduce/debug the issue.

Thanks in advance for your support.

[xinaesthete]

For what it's worth, I have tried myself, not following exactly the same steps but I couldn't reproduce.

Environment created with

uv init
uv add dummy-spatialdata

For some reason import spatialdata_plot is not working for me (even after doing uv add "spatialdata[extra]" for good measure), but sdata.write is working ok on dummy objects generated with the library.

Not sure what the salient difference is in our environments.

[Artur-man]

ah ... this is due to the versions of ome-zarr (>0.13.0). See here: scverse/spatialdata#1090 scverse/spatialdata#1092

I have pinned the version below 0.14.0 in my envs, thus solves the issue, but newer versions of spatialdata (>0.7.2) handles the error.

[mthimma]

Hi Artur, After pinning the ome-zarr version to 0.13.0, it worked. Many thanks for helping to sort this out.

[xinaesthete]

I also just setup another environment in a similar way to before, and this time I also encountered the same issue and referred back to this for the fix.