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.
| XR v3.1 | XR v3.0 | XR v2.0 | XR v1.7 | XR v1.6 | |
|---|---|---|---|---|---|
| XOA v3.2 | - | - | - | - | |
| XOA v3.0 - v3.1 | - | - | - | ||
| XOA v2.0 | - | - | |||
| XOA v1.7 - v1.9 | - | ||||
| XOA v1.5 - v1.6 |
Partial support: Output files or features that were added in more recent versions of the
Xenium Onboard Analysis pipeline will not be generated for XOA v1.0 - v1.4. 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.
| XOA version | XR version | DAPI-ony cell segmentation algorithm | Multimodal cell segmentation algorithm |
|---|---|---|---|
| XOA future releases | XR v3.1 | - | Improved algorithm by filtering incorrect segmentation and merging segmentations of boundary-stain images. |
| XOA v3.0 - v3.2 | XR v3.0 | Fixed a bug to guarantee nucleus and cell segmentation masks are connected. | Improved algorithm by filtering incorrect segmentations of the boundary-stain images. |
| XOA v2.0.1 | XR v2.0.1 | - | Fixed a bug to ensure interior stain-based expansion extends all the way to the neighboring cell’s boundary. |
| 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. | N/A |
| 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. | N/A |
| XOA v1.0 - v1.2 | N/A | Introduces nuclear expansion segmentation with 15 µm nuclear expansion distance default. | N/A |
- 1
Download and set up Xenium Ranger
- 2
Input
- 3
Running pipelines
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Output