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What is Xenium Onboard Analysis?

Xenium Onboard Analysis (XOA) is an on-instrument software pipeline that simultaneously collects and processes Xenium In Situ Gene Expression data on the Xenium Analyzer (XA).

The Xenium raw output data consists of decoded transcript counts and morphology images. These data reduce low-level internal sensor data, preserving details needed to assess decoded transcript quality. Raw output and other standard output files derived from them are included in the Xenium output directory for each region selected on the instrument. Because they represent raw data from the Xenium platform, decoded transcript counts and morphology images should be archived for possible off-instrument reprocessing and reproducibility. Learn more on the Archiving Xenium Data page.

The Xenium Analyzer (XA) instrument can generate Xenium Onboard Analysis outputs for the following 10x Genomics Xenium In Situ assay workflows:

Xenium In Situ assayXA v2.0XA v1.0-1.9
Gene Expression v1 + Cell Segmentation Staining (CG000749)-
Gene Expression v1 (CG000582)

XOA outputs can be visualized in Xenium Explorer and reanalyzed with Xenium Ranger. Refer to the following pages for software version compatibility (opens new tab):

  • Xenium Explorer compatibility
  • Xenium Ranger compatibility

Changes to nucleus and cell segmentation algorithms are noted in the Xenium Analyzer release notes. Refer to the Segmentation algorithm changes by software version table to view a summary of the changes by Xenium Analyzer and Xenium Ranger software versions.

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    Outputs

    Outputs at a glanceUnderstanding Xenium outputsAnalysis summary overviewExplore Zarr filesArchiving Xenium dataXenium Analyzer and XOA release notes
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    Algorithms

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    Other resources