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What is Xenium Ranger?

Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Updated results can be visualized in Xenium Explorer. It includes the following pipelines:

  • xeniumranger relabel
  • xeniumranger resegment
  • xeniumranger import-segmentation

Each pipeline can be run individually or in combination.

Xenium Ranger (XR) is compatible with specific versions of the Xenium Onboard Analysis (XOA) pipeline outputs generated on the Xenium Analyzer (XA) instrument.

XR v1.7XR v1.6
XA v1.7 - v1.9-
XA v1.5 - v1.6
XA v1.0 - v1.4Partially supported*Partially supported*

*Output files or features that were added in more recent versions of the Xenium Onboard Analysis pipeline will not be generated for older versions. For example, Xenium Ranger will only produce the aux_outputs/ directory or a transcript density plot in the analysis_summary.html if they exist in the original XOA output bundle.

  1. 1

    Download and set up Xenium Ranger

    DownloadInstallSystem requirements
  2. 2

    Input

  3. 3

    Running pipelines

  4. 4

    Output