# Read failure with aligned example data; fails on "shapes"

**URL:** <https://discourse.scverse.org/t/read-failure-with-aligned-example-data-fails-on-shapes/2437>\
**Category:** spatialdata\
**Created:** [August 7, 2024, 12:13pm UTC](https://discourse.scverse.org/t/read-failure-with-aligned-example-data-fails-on-shapes/2437 "2024-08-07T12:13:49Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![stvjc](https://avatars.discourse-cdn.com/v4/letter/s/2acd7d/32.png) [@stvjc](https://discourse.scverse.org/u/stvjc)\
**Post date:** [August 7, 2024, 12:13pm UTC](https://discourse.scverse.org/t/read-failure-with-aligned-example-data-fails-on-shapes/2437/1 "2024-08-07T12:13:49Z")

</div>

`wget https://s3.embl.de/spatialdata/spatialdata-sandbox/xenium_rep1_io_aligned.zip`

unzip to find folder `data_aligned.zarr`

```auto
>>> sdata = sd.read_zarr("data_aligned.zarr")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/exouser/.local/lib/python3.10/site-packages/spatialdata/_io/io_zarr.py", line 121, in read_zarr
    shapes[subgroup_name] = _read_shapes(f_elem_store)
  File "/home/exouser/.local/lib/python3.10/site-packages/spatialdata/_io/io_shapes.py", line 33, in _read_shapes
    coords = np.array(f["coords"])
  File "/home/exouser/.local/lib/python3.10/site-packages/zarr/hierarchy.py", line 511, in __getitem__
    raise KeyError(item)
KeyError: 'coords'

```

The read will succeed with `sd.read_zarr("data_aligned.zarr", selection=["points", "images"])` but if “shapes” is added, it fails as above.

```auto
>>> session_info.show(dependencies=True)
-----
session_info 1.0.0
spatialdata 0.2.1
-----
PIL 10.4.0
anndata 0.10.7
asciitree NA
attr 21.2.0
certifi 2020.06.20
chardet 4.0.0
cloudpickle 3.0.0
colorama 0.4.4
cycler 0.12.1
cython_runtime NA
dask 2024.8.0
dask_expr 1.1.10
dask_image NA
datashader 0.16.3
datatree 0.0.14
dateutil 2.9.0.post0
exceptiongroup 1.2.1
fsspec 2023.6.0
geopandas 1.0.1
h5py 3.11.0
idna 3.3
importlib_metadata NA
jinja2 3.0.3
kiwisolver 1.4.5
lazy_loader 0.4
llvmlite 0.42.0
markupsafe 2.0.1
matplotlib 3.9.0
more_itertools 8.10.0
msgpack 1.0.8
multipledispatch 0.6.0
multiscale_spatial_image 1.0.1
natsort 8.4.0
networkx 3.3
numba 0.59.1
numcodecs 0.13.0
numpy 1.26.4
ome_zarr NA
packaging 24.0
pandas 2.2.2
param 2.1.1
pkg_resources NA
platformdirs 2.5.1
pooch v1.8.2
psutil 5.9.0
pyarrow 17.0.0
pyct 0.5.0
pygments 2.18.0
pyparsing 2.4.7
pyproj 3.6.1
pytz 2022.1
requests 2.25.1
rich NA
scipy 1.13.1
shapely 2.0.5
sitecustomize NA
six 1.16.0
skimage 0.24.0
spatial_image 1.1.0
tblib 3.0.0
tlz 0.12.1
toolz 0.12.1
tqdm 4.66.4
typing_extensions NA
tzdata 2024.1
urllib3 1.26.5
xalt_python_pkg_filter NA
xarray 2024.7.0
xarray_dataclasses 1.8.0
xarray_schema 0.0.3
xrspatial 0.4.0
yaml 5.4.1
zarr 2.18.2
zipp NA
zoneinfo NA
zope NA
-----
Python 3.10.12 (main, Jul 29 2024, 16:56:48) [GCC 11.4.0]
Linux-6.5.0-44-generic-x86_64-with-glibc2.35
-----
Session information updated at 2024-08-07 12:13

```

---

<div class="post-metadata">

**Author:** ![LucaMarconato](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/lucamarconato/32/661_2.png) [@LucaMarconato](https://discourse.scverse.org/u/LucaMarconato)\
**Post date:** [August 7, 2024, 12:41pm UTC](https://discourse.scverse.org/t/read-failure-with-aligned-example-data-fails-on-shapes/2437/2 "2024-08-07T12:41:27Z")

</div>

Hi, thanks for reporting the issue. Please check this link to see an explanation on why the issue occurs: [Error on the tutorial Deep learning example on image tiles · Issue #652 · scverse/spatialdata · GitHub](https://github.com/scverse/spatialdata/issues/652).

The solution is already prepared, we just need to cut a new release. I will be doing it later today.

---

<div class="post-metadata">

**Author:** ![LucaMarconato](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/lucamarconato/32/661_2.png) [@LucaMarconato](https://discourse.scverse.org/u/LucaMarconato)\
**Post date:** [August 7, 2024, 1:12pm UTC](https://discourse.scverse.org/t/read-failure-with-aligned-example-data-fails-on-shapes/2437/3 "2024-08-07T13:12:19Z")

</div>

I just made a release for spatialdata, spatialdata-io, napari-spatialdata and spatialdata-plot. The packages should be available via pip within minutes, and should be available in conda earliest in a few hours and latest in 1-2 days.