Support homeXenium Ranger 2.0Analysis
Output Overview

Output Overview

Xenium Ranger subcommands generate the same output files as the Xenium Onboard Analysis (XOA) pipeline with some modifications. The general output file specifications are described in the Xenium Onboard Analysis documentation.

A typical xeniumranger analysis will display the following after completion (here the --id=tiny-test):

...

Outputs:
- metrics_summary:                            /tiny-test/outs/metrics_summary.csv
- transcripts:                                /tiny-test/outs/transcripts.zarr.zip
- Transcript info CSV:                        /tiny-test/outs/transcripts.csv.gz
- Transcript info parquet:                    /tiny-test/outs/transcripts.parquet
- Cell info CSV:                              /tiny-test/outs/cells.csv.gz
- Cell info parquet:                          /tiny-test/outs/cells.parquet
- Cell segmentation result:                   /tiny-test/outs/cells.zarr.zip
- Cell segmentation nucleus polygons CSV:     /tiny-test/outs/nucleus_boundaries.csv.gz
- Cell segmentation cell polygons CSV:        /tiny-test/outs/cell_boundaries.csv.gz
- Cell segmentation nucleus polygons parquet: /tiny-test/outs/nucleus_boundaries.parquet
- Cell segmentation cell polygons parquet:    /tiny-test/outs/cell_boundaries.parquet
- Clustering result in zarr.zip format:       /tiny-test/outs/analysis.zarr.zip
- Cell-feature matrix in zarr.zip format:     /tiny-test/outs/cell_feature_matrix.zarr.zip
- Cell-feature matrix in h5 format:           /tiny-test/outs/cell_feature_matrix.h5
- morphology:                                 /tiny-test/outs/morphology.ome.tif
- CS multi-file OME-TIFF (AUTOFOCUS):         /tiny-test/outs/morphology_focus
- Metadata for Xenium Explorer:               /tiny-test/outs/experiment.xenium
- Customer-facing web summary:                /tiny-test/outs/analysis_summary.html
- Cell-feature matrix in MEX format:          /tiny-test/outs/cell_feature_matrix
- Clustering result in csv format:            /tiny-test/outs/analysis
- Auxiliary output files:
    morphology_fov_locations:    null
    overview_scan:               null
    overview_scan_fov_locations: null
    per_cycle_channel_images:    null
- Gene panel JSON:                            /tiny-test/outs/gene_panel.json

Pipestance completed successfully!

The /outs directory contains all the output files. Xenium Ranger v2.0 output structure matches the outputs from XOA v2.0:

β”œβ”€β”€ analysis
β”‚   β”œβ”€β”€ clustering
β”‚   β”œβ”€β”€ diffexp
β”‚   β”œβ”€β”€ pca
β”‚   └── umap
β”œβ”€β”€ analysis.zarr.zip
β”œβ”€β”€ analysis_summary.html
β”œβ”€β”€ aux_outputs
β”‚   β”œβ”€β”€ per_cycle_channel_images/
β”‚   └── fov_locations.json
β”œβ”€β”€ cell_boundaries.csv.gz
β”œβ”€β”€ cell_boundaries.parquet
β”œβ”€β”€ cell_feature_matrix
β”‚   β”œβ”€β”€ barcodes.tsv.gz
β”‚   β”œβ”€β”€ features.tsv.gz
β”‚   └── matrix.mtx.gz
β”œβ”€β”€ cell_feature_matrix.h5
β”œβ”€β”€ cell_feature_matrix.zarr.zip
β”œβ”€β”€ cells.csv.gz
β”œβ”€β”€ cells.parquet
β”œβ”€β”€ cells.zarr.zip
β”œβ”€β”€ experiment.xenium
β”œβ”€β”€ gene_panel.json
β”œβ”€β”€ metrics_summary.csv
β”œβ”€β”€ morphology.ome.tif
β”œβ”€β”€ morphology_focus/
β”‚   β”œβ”€β”€ morphology_focus_0000.ome.tif
β”‚   β”œβ”€β”€ morphology_focus_0001.ome.tif # (0001-0003 for cell segmentation staining workflow data)
β”‚   β”œβ”€β”€ morphology_focus_0002.ome.tif
β”‚   └── morphology_focus_0003.ome.tif
β”œβ”€β”€ nucleus_boundaries.csv.gz
β”œβ”€β”€ nucleus_boundaries.parquet
β”œβ”€β”€ transcripts.csv.gz
β”œβ”€β”€ transcripts.parquet
└── transcripts.zarr.zip

For every Xenium Ranger analysis, the following file modifications will be made to the input XOA files:

  • 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).