Issues with Exporting to Xenium Explorer

[VikramGanesanjs]

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?

[jpark27]

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]

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]

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-stable branch. we're integrating everything into the new repo. thanks for your patience!