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New Xenium 5K output bundle incompatible with Squidpy #221

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SciComp8 opened this issue Sep 15, 2024 · 1 comment
Open

New Xenium 5K output bundle incompatible with Squidpy #221

SciComp8 opened this issue Sep 15, 2024 · 1 comment
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@SciComp8
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Description

Hello, Squidpy seems not to read the newly released Xenium 5K data (https://www.10xgenomics.com/datasets/preview-data-xenium-prime-gene-expression) correctly. In particular, the function sdata.write(zarr_path) outputs AssertionError: only one path". As a result, the transcripts folder under points folder is empty. How to address this issue? Any advice would be highly appreciated. Look forward to learning your expertise at your earliest convenience. Thank you so much.
...

Minimal reproducible example

ls ./Data/Raw/Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_outs
# analysis.zarr.zip		gene_groups.csv
# analysis_summary.html		gene_panel.json
# cell_boundaries.csv.gz		he_image.ome.tif
# cell_boundaries.parquet		he_imagealignment.csv
# cell_feature_matrix.h5		metrics_summary.csv
# cell_feature_matrix.zarr.zip	morphology.ome.tif
# cell_groups.csv			morphology_focus
# cells.csv.gz			nucleus_boundaries.csv.gz
# cells.parquet			nucleus_boundaries.parquet
# cells.zarr.zip			transcripts.parquet
# experiment.xenium		transcripts.zarr.zip
import spatialdata as sd
from spatialdata_io import xenium
import matplotlib.pyplot as plt
import seaborn as sns
import scanpy as sc
import squidpy as sq
xenium_path = "./Data/Raw/Xenium_Prime_Human_Lymph_Node_Reactive_FFPE_outs"
sdata = xenium(xenium_path)
zarr_path = "./Data/Derived/Xenium_5K_Human_Lymph_Node"
sdata.write(zarr_path)

Traceback

"sdata.write(zarr_path)
/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/tifffile/tifffile.py:9437: UserWarning: <tifffile.TiffPage 0 @16> reading array from closed file
  warnings.warn(
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/spatialdata/_core/spatialdata.py", line 1159, in write
    self._write_element(
  File "/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/spatialdata/_core/spatialdata.py", line 1207, in _write_element
    write_points(points=element, group=element_type_group, name=element_name, format=parsed["points"])
  File "/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/spatialdata/_io/io_points.py", line 74, in write_points
    points.to_parquet(path)
  File "/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/dask/dataframe/core.py", line 5642, in to_parquet
    return to_parquet(self, path, *args, **kwargs)
  File "/Users/xyz/.pyenv/versions/3.9.19/lib/python3.9/site-packages/dask/dataframe/io/parquet/core.py", line 851, in to_parquet
    assert len(_paths) == 1, "only one path"
AssertionError: only one path"

Version

print(squidpy.__version__)

1.6.1
...

@SciComp8
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Hello team, any updates on this issue? With gratitude.

@timtreis timtreis transferred this issue from scverse/squidpy Oct 15, 2024
@timtreis timtreis assigned LLehner and unassigned michalk8 Oct 21, 2024
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