Dataset Viewer
The dataset viewer is not available for this split.
Cannot load the dataset split (in streaming mode) to extract the first rows.
Error code: StreamingRowsError
Exception: ArrowInvalid
Message: Mismatching child array lengths
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/utils.py", line 147, in get_rows_or_raise
return get_rows(
dataset=dataset,
...<4 lines>...
column_names=column_names,
)
File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
return func(*args, **kwargs)
File "/src/services/worker/src/worker/utils.py", line 127, in get_rows
rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
File "/src/services/worker/src/worker/utils.py", line 478, in safe_iter
yield from ds.decode(False) if ds.features else ds
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2818, in __iter__
for key, example in ex_iterable:
^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2355, in __iter__
for key, pa_table in self._iter_arrow():
~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2380, in _iter_arrow
for key, pa_table in self.ex_iterable._iter_arrow():
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 87, in _generate_tables
pa_table = _recursive_load_arrays(h5, self.info.features, start, end)
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 273, in _recursive_load_arrays
arr = _recursive_load_arrays(dset, features[path], start, end)
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 273, in _recursive_load_arrays
arr = _recursive_load_arrays(dset, features[path], start, end)
File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/hdf5/hdf5.py", line 294, in _recursive_load_arrays
sarr = pa.StructArray.from_arrays(values, names=keys)
File "pyarrow/array.pxi", line 4306, in pyarrow.lib.StructArray.from_arrays
File "pyarrow/error.pxi", line 155, in pyarrow.lib.pyarrow_internal_check_status
return check_status(status)
File "pyarrow/error.pxi", line 92, in pyarrow.lib.check_status
raise convert_status(status)
pyarrow.lib.ArrowInvalid: Mismatching child array lengthsNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
# Mouse Brain Visium · 3 complementary sections
Curated, ready-to-load spatial transcriptomics dataset.
## Source
- Paper: [10x Genomics public datasets](https://www.10xgenomics.com/datasets)
- Canonical download: cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_*
## Scale
| Property | Value |
|---|---|
| Technology | 10x Genomics Visium |
| Species | Mus musculus |
| Tissue | Mouse brain (sagittal anterior, sagittal posterior, coronal) |
| Sections / slices | 3 |
| Total cells / spots | 8,816 |
## Files
- `Visium_sagittal-anterior2/V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5`
Visium_sagittal-posterior2/V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5Visium_coronal/V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5Each `.h5ad` follows the AnnData spec: - `.X` — gene expression matrix (cells × genes), sparse where natural - `.obs` — per-cell annotations (see "Metadata" below) - `.obsm['spatial']` — `(n_cells, 2)` float32 spatial coordinates - (where present) `.layers['count']` — raw integer counts - (where present) `.obsm['spatial3d']` — `(n_cells, 3)` float32 (x, y, z=section) ## Metadata (`obs` columns) `in_tissue`, `array_row`, `array_col` ## Notes Three 10x Visium mouse-brain serial sections offering complementary tissue views. Original 10x outputs (filtered h5 + spatial/) kept in conventional subfolders so `sc.read_visium(folder)` works directly. After filtering to in_tissue==1: 2825 / 3289 / 2702 spots respectively. ## Usage ```python
import scanpy as sc from huggingface_hub import snapshot_download d = snapshot_download(repo_id='Shaow/mousebrain_visium_3section', repo_type='dataset') adata_st_list = [] for sub, h5 in [ ('Visium_sagittal-anterior2', 'V1_Mouse_Brain_Sagittal_Anterior_Section_2_filtered_feature_bc_matrix.h5'), ('Visium_sagittal-posterior2', 'V1_Mouse_Brain_Sagittal_Posterior_Section_2_filtered_feature_bc_matrix.h5'), ('Visium_coronal', 'V1_Adult_Mouse_Brain_filtered_feature_bc_matrix.h5'), ]: a = sc.read_visium(f'{d}/{sub}', count_file=h5) a.var_names_make_unique() adata_st_list.append(a[a.obs['in_tissue'] == 1].copy())
## Citation
If you use this dataset, please cite the source paper above.
## License
MIT for the curation/preparation. Underlying data inherits the license of
the upstream publication (typically CC-BY-4.0); please see the source paper.
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