The following output files from Xenium Onboard Analysis (XOA) are required as inputs for Xenium Ranger:

1. transcripts.zarr.zip or transcripts.zarr
2. cells.zarr.zip or cells.zarr
3. morphology.ome.tif
4. morphology_mip.ome.tif (required for XOA v1.0 - 1.9 datasets)
5. 2D autofocus image(s):
   • morphology_focus/ directory (required for XOA v2.0 and later datasets)
   • morphology_focus.ome.tif (required for XOA v1.0 - 1.9 datasets)
6. experiment.xenium
7. metrics_summary.csv
8. analysis_summary.html
9. gene_panel.json (required for XOA v1.0 - 1.4 datasets)

For descriptions of these files, see the Xenium Onboard Analysis documentation. Xenium Ranger expects these files in one directory, which is specified by the --xenium-bundle argument.

Here is an example for a XOA v2.0 dataset with Cell Segmentation Staining:

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└── outs
    ├── analysis_summary.html
    ├── cells.zarr.zip
    ├── experiment.xenium
    ├── gene_panel.json
    ├── metrics_summary.csv
    ├── morphology.ome.tif
    ├── morphology_focus
    │   ├── morphology_focus_0000.ome.tif
    │   ├── morphology_focus_0001.ome.tif
    │   ├── morphology_focus_0002.ome.tif
    │   └── morphology_focus_0003.ome.tif
    └── transcripts.zarr.zip

Depending on the Xenium Ranger pipeline, additional input files include:

• For the relabel pipeline: the gene panel JSON file to use for relabeling decoded transcripts
• For the import-segmentation pipeline: Xenium Ranger accepts segmentation files from XOA and community-developed tools. Compatible file formats and specifications are described here.