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Getting Started

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.

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

Xenium Onboard Analysis tiny example datasets

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

XR v2.0XR v1.7XR v1.6
XOA v2.0--
XOA v1.7 - v1.9-
XOA v1.5 - v1.6
XOA v1.0 - v1.4Partially supported*Partially 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.

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

Xenium Onboard Analysis versionXenium Ranger versionDAPI-ony cell segmentation algorithmMultimodal cell segmentation algorithm
XOA v3.0XR v3.0Fixed a bug to guarantee nucleus and cell segmentation masks are connected.-
XOA v2.0.1XR v2.0.1-Fixed a bug to ensure interior stain-based expansion extends all the way to the neighboring cell’s boundary.
XOA v2.0XR v2.0Introduces 5 µm distance default. Updates nucleus segmentation model to reduce false positive detection in tissues with bright non-nuclear DAPI signal.Introduces multimodal cell segmentation for cell segmentation staining workflow datasets and 5 µm nuclear expansion distance default.
XOA v1.7 - v1.9XR v1.7Fixed cell segmentation bug where elongated cells with straight edges were sometimes produced at an FOV boundary.-
XOA v1.3 - v1.6XR v1.6: Initial version of Xenium Ranger. Enables updating v1.0 - v1.5 dataset to the v1.6 segmentation algorithm models.Updated cell segmentation model to work on more diverse tissue types by training on human brain and human lung data.-
XOA v1.0 - v1.2-Introduces nuclear expansion segmentation with 15 µm nuclear expansion distance default.-
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    Download and set up Xenium Ranger

    DownloadInstallSystem requirementsRelease notes
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  3. 3

    Running pipelines

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