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fix bug #154

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Merged
dariarom94 merged 1 commit into from
Jun 24, 2026
Merged

fix bug #154

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9 changes: 7 additions & 2 deletions src/methods_segmentation/custom_segmentation/script.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import anndata as ad
import os
import shutil
import pandas as pd

## VIASH START
par = {
Expand All @@ -20,14 +21,18 @@
assert par["labels_key"] in sdata.labels, f"Key '{par['labels_key']}' not found in input data."

print(f"Copy segmentation from '{par['labels_key']}'", flush=True)
metadata = sdata.tables["metadata"]
# Select only the columns that exist — Xenium provides cell_id and region,
# Vizgen uses different column names (or an empty obs) so we take what's available.
obs_cols = [c for c in ["cell_id", "region"] if c in metadata.obs.columns]
sdata_segmentation_only = sd.SpatialData(
labels={
"segmentation": sdata[par["labels_key"]]
},
tables={
"table": ad.AnnData(
obs=sdata.tables["metadata"].obs[["cell_id", "region"]],
var=sdata.tables["metadata"].var[[]]
obs=metadata.obs[obs_cols],
var=metadata.var[[]]
)
}
)
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