The rename pipeline allows you to change the sample region_name and cassette_name throughout all the Xenium Onboard Analysis output files that contain this information. This pipeline does not upgrade or change the output file format beyond the metadata renaming. Please see the other Xenium Ranger subcommand options to upgrade file formats.

The input files for rename are the Xenium output bundle generated by the Xenium Onboard Analysis pipeline (see Input overview), in particular, these three files are required:

• experiment.xenium
• analysis_summary.html
• metrics_summary.csv

The xeniumranger rename command line arguments and character limits are described on the Xenium Ranger command line arguments page.

Make sure to edit the paths to input/output files in the examples below for your own datasets.

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# Example renaming region name and cassette name

xeniumranger rename --id=rename-demo \
                     --xenium-bundle=/path/to/xenium/files \
                     --region-name="replicate 1" \
                     --cassette-name="cassette 1"

After the pipeline completes, check the output outs/ directory (see Output overview). The following files will include the renamed region name and/or cassette name:

• experiment.xenium
• analysis_summary.html
• metrics_summary.csv