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.
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.
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.
Additional features coming in future releases
Align immunofluorescence (IF) images
Use a simple interface to register and view IF images directly in Xenium Explorer to enrich Xenium analysis with a custom protein readout.
Create pathology annotations
Annotate tissue structures on the H&E or IF images and directly compare to the molecular readout.
Perform single cell style analysis
Filter cells to define new clusters, run differential expression between regions, explore UMAP projections, and export high-res figures.
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
Reassign transcripts in Xenium Ranger using segmentation results produced by a 3rd party tool and visualize in Xenium Explorer.
Resegment
Resegment Xenium data by adjusting cell expansion distance or nucleus intensity filter or by using our latest nucleus segmentation model.
Relabel
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.
Human Breast
Use the Xenium Explorer Demo to explore a Xenium In Situ dataset from a 0.4 cm² human breast cancer FFPE section using a 280-gene Xenium Human Breast Gene Expression Panel with 33 additional custom genes.
Mouse Brain Neurobiology
Use the Xenium Explorer Demo to explore a Xenium In Situ dataset from a 0.66 cm² fresh frozen mouse brain coronal section using a pre-designed 248-gene Xenium Mouse Brain Gene Expression panel.