Writing spatialdata object fails in v0.7 #1108

Closed
Closed
Writing spatialdata object fails in v0.7#1108

Description

@lucas-diedrich
lucas-diedrich
opened on Apr 22, 2026

Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6

Steps to reproduce

# python 3.12, 3.13
pip install spatialdata
importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")

Returns the following error:

python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.

Session Info

spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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      Skip to content
      Writing spatialdata object fails in v0.7 #1108
      Closed
      Closed
      Writing spatialdata object fails in v0.7#1108
      Description
      @lucas-diedrich
      lucas-diedrich
      opened on Apr 22, 2026
      Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
      Steps to reproduce
      # python 3.12, 3.13
pip install spatialdata
      importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
      Returns the following error:
      python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
      Session Info
      spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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          Skip to content
          Writing spatialdata object fails in v0.7 #1108
          Closed
          Closed
          Writing spatialdata object fails in v0.7#1108
          Description
          @lucas-diedrich
          lucas-diedrich
          opened on Apr 22, 2026
          Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
          Steps to reproduce
          # python 3.12, 3.13
pip install spatialdata
          importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
          Returns the following error:
          python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
          Session Info
          spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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              Skip to content
              Writing spatialdata object fails in v0.7 #1108
              Closed
              Closed
              Writing spatialdata object fails in v0.7#1108
              Description
              @lucas-diedrich
              lucas-diedrich
              opened on Apr 22, 2026
              Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
              Steps to reproduce
              # python 3.12, 3.13
pip install spatialdata
              importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
              Returns the following error:
              python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
              Session Info
              spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

                  Skip to content
                  Writing spatialdata object fails in v0.7 #1108
                  Closed
                  Closed
                  Writing spatialdata object fails in v0.7#1108
                  Description
                  @lucas-diedrich
                  lucas-diedrich
                  opened on Apr 22, 2026
                  Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
                  Steps to reproduce
                  # python 3.12, 3.13
pip install spatialdata
                  importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
                  Returns the following error:
                  python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
                  Session Info
                  spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
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                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                      Skip to content
                      Writing spatialdata object fails in v0.7 #1108
                      Closed
                      Closed
                      Writing spatialdata object fails in v0.7#1108
                      Description
                      @lucas-diedrich
                      lucas-diedrich
                      opened on Apr 22, 2026
                      Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
                      Steps to reproduce
                      # python 3.12, 3.13
pip install spatialdata
                      importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
                      Returns the following error:
                      python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
                      Session Info
                      spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

                      Metadata
                      Metadata
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                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
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                        No projects
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                          No milestone
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                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

                          Skip to content
                          Writing spatialdata object fails in v0.7 #1108
                          Closed
                          Closed
                          Writing spatialdata object fails in v0.7#1108
                          Description
                          @lucas-diedrich
                          lucas-diedrich
                          opened on Apr 22, 2026
                          Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
                          Steps to reproduce
                          # python 3.12, 3.13
pip install spatialdata
                          importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
                          Returns the following error:
                          python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
                          Session Info
                          spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
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                              Writing spatialdata object fails in v0.7 #1108
                              Closed
                              Closed
                              Writing spatialdata object fails in v0.7#1108
                              Description
                              @lucas-diedrich
                              lucas-diedrich
                              opened on Apr 22, 2026
                              Hi! I currently get an error when trying to write spatialdata objects (version 0.7.2) on MacOS and Ubuntu. The write command fails for spatialdata 0.7.0 as well but not for spatialdata 0.6
                              Steps to reproduce
                              # python 3.12, 3.13
pip install spatialdata
                              importspatialdataassdsdata=sd.datasets.blobs()
sdata.write("./blobs.zarr")
                              Returns the following error:
                              python -c 'import spatialdata as sd; sdata = sd.datasets.blobs(); sdata.write("./blobs.sdata.zarr")'
Traceback (most recent call last):
File "<string>", line 1, in<module>
File "mamba-env/lib/python3.12/site-packages/spatialdata/_utils.py", line 263, in wrapper
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1176, in write
self._write_element(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py", line 1229, in _write_element
write_image(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 371, in write_image
_write_raster(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 197, in _write_raster
_write_raster_dataarray(
File "mamba-env/lib/python3.12/site-packages/spatialdata/_io/io_raster.py", line 275, in _write_raster_dataarray
write_single_scale_ngff(
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 648, in write_image
dask_delayed_jobs = _write_pyramid_to_zarr(
^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/ome_zarr/writer.py", line 751, in _write_pyramid_to_zarr
da.to_zarr(
File "mamba-env/lib/python3.12/site-packages/dask/array/core.py", line 4101, in to_zarr
z = root.create_array(name=array_name, **zarr_array_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 2739, in create_array
self._sync(
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 204, in _sync
return sync(
^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 159, in sync
raise return_result
File "mamba-env/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/group.py", line 1142, in create_array
return await create_array(
^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4907, in create_array
return await init_array(
^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 4721, in init_array
meta = AsyncArray._create_metadata_v3(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/array.py", line 777, in _create_metadata_v3
chunk_grid_parsed = RegularChunkGrid(chunk_shape=chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/chunk_grids.py", line 185, in __init__
chunk_shape_parsed = parse_shapelike(chunk_shape)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "mamba-env/lib/python3.12/site-packages/zarr/core/common.py", line 204, in parse_shapelike
raise TypeError(msg)
TypeError: Expected an iterable of integers. Got ((3,), (512,), (512,)) instead.
                              Session Info
                              spatialdata 0.7.2
---- ----
pyct 0.6.0
multipledispatch 1.0.0 (0.6.0)
pandas 2.3.3
wrapt 2.1.2
universal_pathlib 0.3.10
six 1.17.0
zstandard 0.25.0
pyproj 3.7.2
xarray-spatial 0.9.6
pytz 2026.1.post1
pooch 1.9.0 (v1.9.0)
shapely 2.1.2
scipy 1.17.1
cloudpickle 3.1.2
rich 15.0.0
Jinja2 3.1.6
charset-normalizer 3.4.7
h5py 3.16.0
spatial_image 1.2.3
numba 0.65.0
fsspec 2026.3.0
natsort 8.4.0
requests 2.33.1
typing_extensions 4.15.0
scverse-misc 0.0.3
idna 3.12
llvmlite 0.47.0
MarkupSafe 3.0.3
datashader 0.19.0
legacy-api-wrap 1.5
setuptools 82.0.1
dask 2026.1.1
scikit-image 0.26.0
psutil 7.2.2
platformdirs 4.9.6
dask-image 2025.11.0
tblib 3.2.2
anndata 0.12.11
tqdm 4.67.3
packaging 26.1
ome-zarr 0.15.0
urllib3 2.6.3
multiscale_spatial_image 2.0.3
donfig 0.8.1.post1
lazy-loader 0.5
numpy 2.4.4
session-info2 0.4.1
google-crc32c 1.8.0
narwhals 2.20.0
Deprecated 1.3.1
toolz 1.1.0
geopandas 1.1.3
python-dateutil 2.9.0.post0
pathlib_abc 0.5.2
zarr 3.1.6
PyYAML 6.0.3
pyarrow 24.0.0
networkx 3.6.1
annsel 0.1.2
more-itertools 11.0.2
xarray 2026.4.0
certifi 2026.4.22 (2026.04.22)
xarray-dataclass 3.0.0
msgpack 1.1.2
numcodecs 0.16.5
---- ----
Python 3.12.13 | packaged by conda-forge | (main, Mar 5 2026, 17:06:14) [Clang 19.1.7 ]
OS macOS-26.3-arm64-arm-64bit
Updated 2026-04-22 12:24

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