Plotting UMAP converts cell_id to category --> hinders plotting with spatialdata.plot #3960
Description
Please make sure these conditions are met
- I have checked that this issue has not already been reported.
- I have confirmed this bug exists on the latest version of scanpy.
- (optional) I have confirmed this bug exists on the main branch of scanpy.
What happened?
Hi,
I'm using sc.pl.umap to plot a UMAP embedding in a SpatialData object sdata.tables. In this case, I'm using the anndata object cell_segmentations.
sc.pl.umap(sdata.tables["cell_segmentations"], color = "n_genes")
shows a notification: "...storing 'cell_id' as categorial"
Plotting the segmented cells on an HE image withspatialdata_plot throws an Error:
TypeError: Only int, np.int16, np.int32, np.int64, uint equivalents or string allowed as dtype for instance_key column in obs. Dtype found to be category
Same occurs with location_id for binned sdata.tables.
Minimal code sample
import scanpy as sc
import spatialdata as sd
import spatialdata_plot
sc.pl.umap(sdata.tables["cell_segmentations"], color = "n_genes")
sdata.pl.render_images("H914Apex2_hires_image").pl.render_shapes(elements = "H914Apex2_cell_segmentations",
color='n_genes',
).pl.show("H914Apex2", figsize = (8,4))Error output
sdata = sd.SpatialData(
145 images=self._sdata.images if images is None else images,
146 labels=self._sdata.labels if labels is None else labels,
147 points=self._sdata.points if points is None else points,
148 shapes=self._sdata.shapes if shapes is None else shapes,
149 tables=self._sdata.tables if tables is None else tables,
150 )
151 sdata.plotting_tree = self._sdata.plotting_tree if hasattr(self._sdata, "plotting_tree") else OrderedDict()
153 return sdata
File /wuppertal/gpfjz/miniforge3/envs/spatialdata_2601/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:178, in SpatialData.__init__(self, images, labels, points, shapes, tables, attrs)
176 for k, v in tables.items():
177 with collect_error(location=("tables", k)):
--> 178 self.validate_table_in_spatialdata(v)
179 self.tables[k] = v
181 self._query = QueryManager(self)
File /wuppertal/gpfjz/miniforge3/envs/spatialdata_2601/lib/python3.12/site-packages/spatialdata/_core/spatialdata.py:203, in SpatialData.validate_table_in_spatialdata(self, table)
183 def validate_table_in_spatialdata(self, table: AnnData) -> None:
184 """
185 Validate the presence of the annotation target of a SpatialData table in the SpatialData object.
186
(...) 201 The dtypes of the instance key column in the table and the annotation target do not match.
202 """
--> 203 TableModel().validate(table)
204 if TableModel.ATTRS_KEY in table.uns:
205 region, _, instance_key = get_table_keys(table)
File /wuppertal/gpfjz/miniforge3/envs/spatialdata_2601/lib/python3.12/site-packages/spatialdata/models/models.py:1096, in TableModel.validate(self, data)
1093 if data.obs[instance_key].isnull().values.any():
1094 raise ValueError("`table.obs[instance_key]` must not contain null values, but it does.")
-> 1096 self._validate_table_annotation_metadata(data)
1098 return data
File /wuppertal/gpfjz/miniforge3/envs/spatialdata_2601/lib/python3.12/site-packages/spatialdata/models/models.py:1044, in TableModel._validate_table_annotation_metadata(self, data)
1033 if (dtype := data.obs[attr[self.INSTANCE_KEY]].dtype) not in [
1034 int,
1035 np.int16,
(...) 1041 "O",
1042 ] or (dtype == "O" and (val_dtype := type(data.obs[attr[self.INSTANCE_KEY]].iloc[0])) is not str):
1043 dtype = dtype if dtype != "O" else val_dtype
-> 1044 raise TypeError(
1045 f"Only int, np.int16, np.int32, np.int64, uint equivalents or string allowed as dtype for "
1046 f"instance_key column in obs. Dtype found to be {dtype}"
1047 )
1048 expected_regions = attr[self.REGION_KEY] if isinstance(attr[self.REGION_KEY], list) else [attr[self.REGION_KEY]]
1049 found_regions = data.obs[attr[self.REGION_KEY_KEY]].unique().tolist()
TypeError: Only int, np.int16, np.int32, np.int64, uint equivalents or string allowed as dtype for instance_key column in obs. Dtype found to be categoryVersions
Details
| Package | Version |
| ---------------- | ------- |
| anndata | 0.12.0 |
| spatialdata | 0.6.1 |
| scanpy | 1.12 |
| spatialdata-plot | 0.2.13 |
| celltypist | 1.7.1 |
| Dependency | Version |
| ------------------------ | --------------------- |
| ome-zarr | 0.12.2 |
| cytoolz | 1.1.0 |
| zarr | 3.1.5 |
| charset-normalizer | 3.4.4 |
| matplotlib-inline | 0.2.1 |
| setuptools | 80.10.2 |
| jaraco.text | 4.0.0 |
| pathlib_abc | 0.5.2 |
| tqdm | 4.67.1 |
| lz4 | 4.4.5 |
| tblib | 3.2.2 |
| cycler | 0.12.1 |
| babel | 2.17.0 |
| traitlets | 5.14.3 |
| scipy | 1.17.0 |
| matplotlib-scalebar | 0.9.0 |
| idna | 3.11 |
| google-crc32c | 1.8.0 |
| xarray-schema | 0.0.3 |
| jaraco.context | 6.1.0 |
| debugpy | 1.8.19 |
| pure_eval | 0.2.3 |
| toolz | 1.1.0 |
| pyct | 0.6.0 |
| llvmlite | 0.46.0 |
| requests | 2.32.5 |
| kiwisolver | 1.4.9 |
| multiscale_spatial_image | 2.0.3 |
| colorama | 0.4.6 |
| multipledispatch | 0.6.0 |
| donfig | 0.8.1.post1 |
| legacy-api-wrap | 1.5 |
| pillow | 12.1.0 |
| Pint | 0.25.2 |
| scikit-learn | 1.8.0 |
| attrs | 25.4.0 |
| asttokens | 3.0.1 |
| comm | 0.2.3 |
| xarray-dataclass | 3.0.0 |
| numcodecs | 0.16.5 |
| parso | 0.8.5 |
| geopandas | 1.1.2 |
| pandas | 3.0.0 |
| flexcache | 0.3 |
| xarray-spatial | 0.5.2 |
| torch | 2.7.1 |
| PySocks | 1.7.1 |
| platformdirs | 4.5.1 |
| typing_extensions | 4.15.0 |
| dask-image | 2025.11.0 |
| ipython | 9.9.0 |
| python-dateutil | 2.9.0.post0 |
| msgpack | 1.1.2 |
| decorator | 5.2.1 |
| MarkupSafe | 3.0.3 |
| session-info2 | 0.3 |
| networkx | 3.6.1 |
| PyYAML | 6.0.3 |
| jupyter_core | 5.9.1 |
| defusedxml | 0.7.1 |
| pyproj | 3.7.2 |
| executing | 2.2.1 |
| rich | 14.3.1 |
| packaging | 26.0 |
| urllib3 | 2.6.3 |
| scikit-image | 0.26.0 |
| spatial_image | 1.2.3 |
| h5py | 3.15.1 |
| fast-array-utils | 1.3.1 |
| tornado | 6.5.4 |
| shapely | 2.1.2 |
| natsort | 8.4.0 |
| dask | 2024.11.2 |
| prompt_toolkit | 3.0.52 |
| wcwidth | 0.5.0 |
| jedi | 0.19.2 |
| numba | 0.63.1 |
| stack_data | 0.6.3 |
| Pygments | 2.19.2 |
| pytz | 2025.2 |
| six | 1.17.0 |
| backports.zstd | 1.3.0 |
| xarray | 2026.1.0 |
| datashader | 0.18.2 |
| pyparsing | 3.3.2 |
| threadpoolctl | 3.6.0 |
| Jinja2 | 3.1.6 |
| ipykernel | 7.1.0 |
| universal_pathlib | 0.3.8 |
| lazy_loader | 0.4 |
| cloudpickle | 3.1.2 |
| flexparser | 0.4 |
| psutil | 7.2.2 |
| pyarrow | 23.0.0 |
| jaraco.functools | 4.4.0 |
| numpy | 2.3.5 |
| Brotli | 1.2.0 |
| certifi | 2026.1.4 (2026.01.04) |
| matplotlib | 3.10.8 |
| backports.tarfile | 1.2.0 |
| jupyter_client | 8.8.0 |
| pyzmq | 27.1.0 |
| more-itertools | 10.8.0 |
| joblib | 1.5.3 |
| fsspec | 2026.1.0 |
| Component | Info |
| --------- | ------------------------------------------------------------------------------ |
| Python | 3.12.12 | packaged by conda-forge | (main, Jan 26 2026, 23:51:32) [GCC 14.3.0] |
| OS | Linux-5.15.0-1093-nvidia-x86_64-with-glibc2.35 |
| Updated | 2026-01-29 10:50