Xenium Analysis

Built for rapid data exploration and insights

Our best-in-class Onboard Analysis automatically processes data during a run, without needing waiting for hours of post-run processing. And with Xenium Explorer, our intuitive visualization software, in situ data exploration has never been easier.

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Xenium breast cancer sample data
Xenium Analyzer Onboard Analysis

Start exploring the data right after a run completes

Xenium enables immediate access to interpretation-ready data by processing images in parallel with imaging and biochemistry cycles. Xenium Onboard Analysis automatically decodes transcripts and segments cells and there is no need for complex and time consuming steps after the instrument run to process data.

Discover how Xenium transforms images into rich biological data

Immediate confidence in your data

Perform on instrument QC quickly and easily before exploring the data further in Xenium Explorer.

    Simplify your workflow with automatic cell segmentation

    Xenium's segmentation uses advanced neural network algorithms with manually labeled training data from diverse tissue types.


    Keep full ownership of your data at no extra cost

    Transfer data from the instrument to a storage location of your choosing. Your data is yours, at no additional charge.


    Flexible open file formats without additional processing

    Xenium Analyzer generates data in open formats, allowing you to use them with Xenium Explorer or community software.

Xenium Explorer

Seamless exploration of whole tissues to single transcripts

Xenium Explorer is a desktop application for Windows and MacOS that allows you to interactively visualize data generated by the Xenium Analyzer instrument.

View transcript localization at any scale

Xenium Explorer provides multiple high-performance options to visualize transcript data. At the tissue level, view a transcript density map or color cells by transcript density. At the cell level, zoom in to individual transcripts.

Compare gene expression and cellular neighborhoods

Locate unique spatial niches then leverage the lasso tool to easily compare gene expression in different tissue microenvironments.

Integrate with pathology workflows

Seamlessly align and explore Xenium data directly overlaid on H&E and DAPI images from the same section.

Align IF images to explore the link between RNA and protein

Use a simple interface to register and view same section H&E and IF images directly in Xenium Explorer.

Additional features coming in future releases

    Create pathology annotations

    Annotate tissue structures on the H&E or IF images and directly compare to the molecular readout.

    Annotation layer

    Explore UMAP projection

    Explore Xenium single cell data in a familiar dimensionality reduced projection.

    Alignment layer

    Perform single cell style analysis

    Define cell types and clusters, run differential expression between regions, and export high-res figures.

    Analysis clusters
Xenium Ranger

Reanalyze data with Xenium Ranger then visualize in Xenium Explorer

With compatibility across multiple Linux distributions, the Xenium Ranger analysis pipelines make it easy to reanalyze your Onboard Analysis data and visualize it in Xenium Explorer.

    Import segmentation

    Import segmentation

    Reassign transcripts in Xenium Ranger using segmentation results produced by a 3rd party tool and visualize in Xenium Explorer.

    Annotation layer


    Resegment Xenium data by adjusting cell expansion distance or nucleus intensity filter or by using our latest nucleus segmentation model.

    Analysis clusters


    Need to relabel transcripts after a Xenium Analyzer run? Use the Relabel pipeline to produce fully corrected Xenium data.

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Explore Xenium Data

In addition to the Human Breast, Mouse Brain Gene Expression panels or standalone custom panels, human brain, human lung, and multi-tissue mouse and human panels will be available soon.

Start your Xenium journey