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 relabelxeniumranger resegmentxeniumranger 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 Ranger (XR) is compatible with specific versions of the Xenium Onboard Analysis (XOA) pipeline outputs generated on the Xenium Analyzer (XA) instrument.
| XR v2.0 | XR v1.7 | XR v1.6 | |
|---|---|---|---|
| XOA v2.0 | - | - | |
| XOA v1.7 - v1.9 | - | ||
| XOA v1.5 - v1.6 | |||
| XOA v1.0 - v1.4 | Partially 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.
| Xenium Onboard Analysis version | Xenium Ranger version | DAPI-ony cell segmentation algorithm | Multimodal cell segmentation algorithm |
|---|---|---|---|
| XOA v2.0 | XR v2.0 | Introduces 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 - v1.9 | XR v1.7 | Fixed cell segmentation bug where elongated cells with straight edges were sometimes produced at an FOV boundary. | - |
| XOA v1.3 - v1.6 | XR 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
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Input
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Running pipelines
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Output