After running Xenium Ranger, the output files will be saved in a directory called /outs:

Copy
├── analysis
│   ├── clustering
│   ├── diffexp
│   ├── pca
│   └── umap
├── analysis.zarr.zip
├── analysis_summary.html
├── aux_outputs
│   ├── per_cycle_channel_images/
│   └── fov_locations.json
├── cell_boundaries.csv.gz
├── cell_boundaries.parquet
├── cell_feature_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── cell_feature_matrix.h5
├── cell_feature_matrix.zarr.zip
├── cells.csv.gz
├── cells.parquet
├── cells.zarr.zip
├── experiment.xenium
├── gene_panel.json
├── metrics_summary.csv
├── morphology.ome.tif
├── morphology_focus.ome.tif
├── morphology_mip.ome.tif
├── nucleus_boundaries.csv.gz
├── nucleus_boundaries.parquet
├── transcripts.csv.gz
├── transcripts.parquet
└── transcripts.zarr.zip

For every Xenium Ranger analysis, the following file modifications will be made:

• In the experiment.xenium file, a new analysis_uuid will be generated (other UUIDs generated by the original XOA pipeline will remain the same).
• A xenium_ranger field will be appended to the experiment.xenium file. It provides the analysis run ID, Xenium Ranger version, and xeniumranger command(s).
• The analysis_summary.html will display similar Xenium Ranger metadata as above in a new panel on the Summary tab. It provides the analysis run ID, run timestamp, Xenium Ranger version, and xeniumranger command(s). If the same input dataset was rerun sequentially with Xenium Ranger multiple times, the commands will all be displayed in this panel.
• The import-segmentation pipeline generates new metrics in the metrics_summary.csv and Cell Segmentation tab of the analysis_summary.html.

Files that are not modified by a given Xenium Ranger subcommand will be copied from the original Xenium bundle directory (specified by --xenium-bundle).