The following output files from Xenium Onboard Analysis (XOA) v3.0 and later are required as inputs for Xenium Ranger relabel, resegment, and import-segmentation because they regenerate the entire XOA output bundle set of files:

1. transcripts.zarr.zip or transcripts.zarr
2. cells.zarr.zip or cells.zarr
3. morphology.ome.tif
4. 2D autofocus images: morphology_focus/ directory
5. experiment.xenium
6. metrics_summary.csv
7. analysis_summary.html
8. gene_panel.json

These files are only required for datasets generated on previous XOA versions (noted in parentheses):

1. morphology_mip.ome.tif (required for XOA v1.0 - 1.9 datasets)
2. 2D autofocus image: morphology_focus.ome.tif (required for XOA v1.0 - 1.9 datasets)
3. 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 v4.0 and later dataset with Cell Segmentation Staining:

Copy
└── outs
    ├── analysis_summary.html
    ├── cells.zarr.zip
    ├── experiment.xenium
    ├── metrics_summary.csv
    ├── gene_panel.json
    ├── morphology.ome.tif
    ├── morphology_focus
    │   ├── ch0000_dapi.ome.tif
    │   ├── ch0001_atp1a1_cd45_e-cadherin.ome.tif
    │   ├── ch0002_18s.ome.tif
    │   └── ch0003_alphasma_vimentin.ome.tif
    └── transcripts.zarr.zip

The following output files from Xenium Onboard Analysis (XOA) are required as inputs for Xenium Ranger rename because it only modifies the names in these files (if provided, the remaining XOA files will be copied from the originals):

1. experiment.xenium
2. analysis_summary.html
3. metrics_summary.csv

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.