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Fix morphology marker names that have forward slashes in them
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sopa/io/reader/cosmx.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -510,7 +510,7 @@ def _get_morphology_coords(images_dir: Path) -> list[str]:
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channels = re.findall(r'"ChannelId": "(.*?)",', description)
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channel_order = list(re.findall(r'"ChannelOrder": "(.*?)",', description)[0])
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return [substrings[channels.index(x)] if x in channels else x for x in channel_order]
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return [substrings[channels.index(x)].replace("/", ".") if x in channels else x for x in channel_order]
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def _get_protein_name(image_path: Path) -> str:

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