10x Genomics Support/Xenium Ranger/Analysis/

Choosing a Pipeline

  • Xenium Ranger provides a set of analysis pipelines that reprocess Xenium In Situ Gene Expression data.
  • Start by choosing a computing option to set up and run Xenium Ranger.

Click the links below to read documentation on each pipeline. The xeniumranger subcommand line arguments are described on the Xenium Ranger command line arguments page.

xeniumranger relabelRelabel decoded transcript gene labels.
xeniumranger resegmentRerun nucleus and cell segmentation using Xenium segmentation algorithms.
xeniumranger import-segmentationImport 2D nucleus and/or cell segmentation results from community-developed tools or a prior Xenium Onboard Analysis output bundle to regenerate Xenium Onboard Analysis output files.