Repository navigation
Issues with Exporting to Xenium Explorer #134
Description
Hello,
I've segmented a Xenium sample with segger, and I am attempting to export it to Xenium explorer. I ran the following script, and downloaded the segger.xenium and segger.zarr.zip file.
df = pd.read_parquet(args.path_to_segger_parquet)
df = df[df['segger_cell_id'] != "None"]
df = df.sort_values("segger_cell_id")
seg2explorer(
seg_df=df,
source_path=args.xenium_bundle,
output_dir=args.write_path,
cells_filename="segger",
analysis_filename="segger",
xenium_filename="segger.xenium",
analysis_df=None,
cell_id_columns="segger_cell_id",
area_low=10,
area_high=100,
)
The segger.zarr.zip file fails to be read by Xenium explorer, and when opening it in Python, has the structure
- cell_groups
- '0'
- indices
- indptr
How can I export a segger.zarr.zip that matches the format of the Xenium cells.zarr.zip?
Activity
jpark27 commentedon Mar 6, 2026
I encountered same issue that Xenium explorer can't read either seg_analysis.zarr.zip or seg_cells.zarr.zip from Seg2Explorer.
@VikramGanesanjs Did you happen to resolve the issue?
VikramGanesanjs commentedon Mar 7, 2026
No, I wasn't able to resolve the issue. @EliHei2 do you know the solution for this, or are there any more details I can provide to clarify the issue?
EliHei2 commentedon Mar 7, 2026
hey! we are moving to the new version which is present on https://github.com/dpeerlab/segger, for xenium explorer please take a look at the
release/v2-stablebranch. we're integrating everything into the new repo. thanks for your patience!