Unable to read xenium data
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调研方向
从 xenium 入口点和 readers/xenium.py 开始，尤其检查 traceback 中显示的 _get_tables_and_circles 调用。使用列出的新 Xenium 输出 bundle 重现该故障，并验证 reader 能够处理其中的 .zarr 文件，而不会尝试打开缺失的 cell_feature_matrix.h5 文件。
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描述
Hi,
I have installed the latest development version of spatialdata-io using pip install git+https://github.com/scverse/spatialdata-io.git@main.
Then I tried the below code:
from spatialdata_io import xenium
sdata = xenium(path_to_xenium_folder)
I get the FileNotFoundError.
Error log:
INFO reading /Users/riyapodder/Downloads/Sample_13666_Region_1/cell_feature_matrix.h5
/var/folders/rd/07ft8cf97nzgfgsy6gfk0lzc0000gp/T/ipykernel_16029/698948949.py:1: DeprecationWarning: The default value of cells_as_circles will change to False in the next release. Please pass True explicitly to maintain the current behavior.
sdata = xenium("/Users/riyapodder/Downloads/Sample_13666_Region_1")
FileNotFoundError Traceback (most recent call last)
Cell In[19], line 1
----> 1 sdata = xenium("/Users/riyapodder/Downloads/Sample_13666_Region_1")
File /opt/miniconda3/envs/spatial_analysis_2/lib/python3.10/site-packages/spatialdata_io/_utils.py:47, in deprecation_alias..deprecation_decorator..wrapper(*args, **kwargs)
45 class_name = f.qualname
46 rename_kwargs(f.name, kwargs, aliases, class_name)
---> 47 return f(*args, **kwargs)
File /opt/miniconda3/envs/spatial_analysis_2/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:185, in xenium(path, cells_boundaries, nucleus_boundaries, cells_as_circles, cells_labels, nucleus_labels, transcripts, morphology_mip, morphology_focus, aligned_images, cells_table, n_jobs, imread_kwargs, image_models_kwargs, labels_models_kwargs)
182 cells_table = True
184 if cells_table:
--> 185 return_values = _get_tables_and_circles(path, cells_as_circles, specs)
186 if cells_as_circles:
187 table, circles = return_values
File /opt/miniconda3/envs/spatial_analysis_2/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:523, in _get_tables_and_circles(path, cells_as_circles, specs)
520 def _get_tables_and_circles(
521 path: Path, cells_as_circles: bool, specs: dict[str, Any]
522 ) -> AnnData | tuple[AnnData, AnnData]:
--> 523 adata = _read_10x_h5(path / XeniumKeys.CELL_FEATURE_MATRIX_FILE)
524 metadata = pd.read_parquet(path / XeniumKeys.CELL_METADATA_FILE)
525 np.testing.assert_array_equal(metadata.cell_id.astype(str), adata.obs_names.values)
...
File h5py/_objects.pyx:57, in h5py._objects.with_phil.wrapper()
File h5py/h5f.pyx:102, in h5py.h5f.open()
FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/Users/riyapodder/Downloads/Sample_13666_Region_1/cell_feature_matrix.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
my xenium folder contains these files:
analysis_summary.html cell_feature_matrix.zarr cells.zarr.zip transcripts.zarr
analysis.zarr cell_feature_matrix.zarr.zip experiment.xenium transcripts.zarr.zip
analysis.zarr.zip cells.zarr morphology.ome.tif
I understand that the data that I have is the new xenium output bundle. Is the xenium reader function not updated to handle this data? Or am I missing something? Requesting your kind assistance.
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