CI
b59203a4af
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-h86dl
Source commit: 6ae6ad1936
Source message: deploy: 00cafd63af52decfa15830ba20bc88f7a9384965
47 lines
1.2 KiB
Python
47 lines
1.2 KiB
Python
import sys
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from spatialdata_io import xenium
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## VIASH START
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par = {
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"input": "./resources_test/xenium_tiny",
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"output": "./test/xenium_tiny.zarr",
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"cells_boundaries": True,
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"nucleus_boundaries": True,
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"cells_as_circles": None,
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"cells_labels": True,
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"nucleus_labels": True,
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"transcripts": True,
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"morphology_mip": True,
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"morphology_focus": True,
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"aligned_images": True,
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"cells_table": True,
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"n_jobs": 1,
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}
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meta = {"resources_dir": "src/utils"}
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## VIASH END
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sys.path.append(meta["resources_dir"])
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from setup_logger import setup_logger
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logger = setup_logger()
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logger.info("Reading in Xenium data...")
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sdata = xenium(
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par["input"],
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cells_boundaries=par["cells_boundaries"],
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nucleus_boundaries=par["nucleus_boundaries"],
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cells_as_circles=par["cells_as_circles"],
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cells_labels=par["cells_labels"],
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nucleus_labels=par["nucleus_labels"],
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transcripts=par["transcripts"],
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morphology_mip=par["morphology_mip"], # only available in version < 2.0.0
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morphology_focus=par["morphology_focus"],
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aligned_images=par["aligned_images"],
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cells_table=par["cells_table"],
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n_jobs=par["n_jobs"],
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)
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logger.info("Writing out SpatialData object to Zarr...")
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sdata.write(par["output"], overwrite=True)
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