Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data. It includes the following pipelines:

• Relabel transcripts with xeniumranger relabel
• Resegment cells with latest 10x segmentation algorithms with xeniumranger resegment
• Import your own segmentation data to assign transcripts to cells with xeniumranger import-segmentation
• Rename region or cassette names with xeniumranger rename

Each pipeline can be run individually or in combination. The updated results can be visualized in Xenium Explorer.

Looking for datasets to practice using Xenium Ranger? Check out these example datasets on the Xenium Onboard Analysis website:

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

^*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.

Changes to nucleus and cell segmentation algorithms are noted in the Xenium Analyzer release notes. This table summarizes those changes by Xenium Onboard Analysis (XOA) and Xenium Ranger (XR) software versions. Every row includes all the changes in the rows below it.