Xenium Analysis

Built for rapid data exploration and insights

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

Try the Xenium Explorer demo

Xenium Analyzer Onboard Analysis

Start exploring the data right after a run completes

Xenium processes data in parallel with imaging and biochemistry cycles, allowing for immediate access to interpretation-ready data, without time-consuming steps post-run.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.

Generate true single cell spatial data with multimodal segmentation

Trained on Xenium data, our AI algorithm provides flexible segmentation. It uses the best available signal for each cell and labels each cell with its segmentation method.

Freedom to store and analyze your data however you choose

Analysis journey after Xenium Analyzer

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 for spatial discovery

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

Download Xenium Explorer

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.
Correlate gene and protein expression
Visualize per-cell gene and protein expression in a single canvas in Xenium Explorer.
Compare gene and protein expression in cellular neighborhoods
Locate unique spatial niches then leverage the lasso tool to easily compare gene and optional protein expression in different tissue microenvironments.
Integrate with pathology workflows
Seamlessly import, align, and explore Xenium data directly overlaid on post-Xenium H&E or IF images from the same section.

More features coming in future releases

Create pathology annotations

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

Explore UMAP projection

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

Perform single cell style analysis

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

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.

Download Xenium Ranger