Xenium Analyzer

The Xenium platform delivers high-plex in situ at subcellular resolution with nanometer precision and offers a complete solution, including comprehensive panel offerings, to achieve fast and robust single cell spatial insights.

Characterize 100s to 1,000s of RNAs in cells and tissues with subcellular in situ resolution.

The ultimate single cell spatial biology experience

Xenium Catalyst Program: Discover the power of Xenium technology with our in-house pilot run service

Our Catalyst program lets you test drive the Xenium platform, evaluate its capabilities, and explore your spatial transcriptomics data alongside a team of scientific experts.

Build on your Xenium Spatial insights with comprehensive, whole transcriptome single cell and spatial analysis.

Seamlessly integrates transcript detection workflow, high-resolution imaging, decoding, and onboard data analysis.

Built to deliver exceptional image and data quality

Features state-of-the-art image acquisition and high-resolution optics with a nanometer-level localization precision.

Building on our years of innovation in single cell and spatial technologies, Xenium was designed to transform the way researchers can characterize RNA, protein, and cells in their native tissue environment.

Key Features

• Xenium offers industry-leading speed and throughput: Using multimodal cell segmentation, analyze 472 mm² of tissue per run, targeting up to 480 genes in < 3 days or up to 5,000 genes in < 6 days.
• Converts terabytes of 3D imaging data into biologically meaningful insights: One-of-a-kind onboard analysis software performs high-powered computation on-instrument. Internal image sensor data is converted into ready-to-explore formats as soon your run finishes.
• Delivers an unparalleled user experience: Simple run setup and cleanup operations, an intuitive touchscreen, and ergonomic design make instrument operation a breeze.
• Expands with upcoming innovations: Flexible fluidic architecture allows the Xenium Analyzer to leverage new functionalities, assay enhancements, and more.
• Gene and protein panels: Customizable ready-to-use panels or fully custom gene panels with add-on protein subpanels
• Xenium Analyzer instrument: Industry-leading speed and throughput for single cell spatial imaging
• Data analysis: Powerful on-board analysis and Xenium Explorer visualization software
• A first-of-its-kind fully optimized & automated solution for integrated high-plex spatial RNA and protein expression
• Validated, ready-to-use immuno-oncology-focused protein and gene panels eliminate the need for optimization
• Single-instrument workflow enables integrated analysis in Xenium Explorer, no data registration required
• <500-gene panels — Focused tissue and pathway characterization (Full custom panel option; Multiomic analysis with Xenium Protein subpanels)
• 5,000-gene panels — Broad discovery in human and mouse (Customizable with up to 100 additional genes; Explore across tissues, disease areas, and drug targets)
• Seamlessly integrates transcript detection workflow, high-resolution imaging, decoding, and onboard data analysis for fresh frozen or FFPE tissues
• Simple run setup and cleanup operations, an intuitive touchscreen, and ergonomic design make instrument operation a breeze
• Go from tissue section to data for up to 5,000 genes in ≤6 days or get even faster analysis times with smaller gene panels
• Immediate data access: Access your data as soon as the Xenium run is complete.
• Easy-to-use interface: Intuitively visualize morphology, protein markers, segmentation, cell typing, and transcript density—no bioinformatics experience required.
• Explore at any scale: Seamlessly explore your data at any scale, from whole tissue sections to single transcripts.
• Xenium Catalyst Program – End-to-end service completed in as few as 4 weeks
• Xenium Catalyst Program – Complete access to fully custom or 10+ panels

Applications

• Targeted gene expression (up to 5,000 genes)
• Multiomic gene and protein expression (up to 480 genes and 27 proteins)

Specifications

Xenium Analyzer
Dimensions (W x D x H)	52.5” x 27” x 31” (59” with door open); 133.3 cm x 68.5 cm x 78.7 cm (149.8 cm with door open)
Resolution	Transcript XY-localization precision < 30 nm and Z-localization precision < 150 nm; Pixel size = ~0.2 µm/pixel
Number of slides per run	2 slides
Throughput (area per time)	472 mm² of tissue per run when targeting up to 480 genes in < 3 days or up to 5,000 genes in < 6 days*
Total tissue area analyzable per run	~ 472 mm²
Sample prep	2–3 days sample prep with 4–6 hrs of hands-on time
Data output file formats	Cell-feature matrices: MEX, HDF5, Zarr; Transcripts and segmentation boundaries: CSV, Parquet, Zarr; Tissue images: OME-TIFF
Connectivity	Compatible with 10x Genomics Cloud instrument management
Chromium Single Cell platform
When to use	Comprehensive single cell data — Ideal for deep characterization of cell populations and states.
Xenium Spatial platform
When to use	High-resolution discovery — Understand complex tissues, neighborhoods, and cell to cell interactions.; Integration with other spatial-omics, histology, and morphology.
Visium Spatial platform
When to use	High-resolution discovery — Understand complex tissues, neighborhoods, and cell to cell interactions.; Integration with other spatial-omics, histology, and morphology.
Chromium Single Cell platform
Why use	Unbiased single cell discovery; High per-gene sensitivity
Xenium Spatial platform
Why use	Single cell spatial discovery; High per-gene sensitivity
Visium Spatial platform
Why use	Expanded spatial discovery
Chromium Single Cell platform
Applications	Whole transcriptome gene expression; Protein; TCR, BCR; CRISPR; ATAC
Xenium Spatial platform
Applications	Targeted gene expression (up to 5,000 genes); Multiomic gene and protein expression (up to 480 genes and 27 proteins)
Visium Spatial platform
Applications	Whole transcriptome gene expression
Chromium Single Cell platform
Resolution	Single cell
Xenium Spatial platform
Resolution	Subcellular
Visium Spatial platform
Resolution	Single cell–scale
Chromium Single Cell platform
Data readout	NGS-based
Xenium Spatial platform
Data readout	Imaging-based
Visium Spatial platform
Data readout	NGS-based
Chromium Single Cell platform
Sample compatibility	Single cell or nuclei suspensions from fresh, frozen, or FFPE samples
Xenium Spatial platform
Sample compatibility	Fresh frozen; FFPE
Visium Spatial platform
Sample compatibility	FFPE; Fresh frozen; Fixed frozen

Documents

• Get to know the Xenium platform (Brochure)
• Technical documentation
• Grant writing assistance (Grant resource)

Related Products

• Xenium platform
• Xenium Protein
• <500-gene panels
• <500-gene panels: Protein subpanels
• 5,000-gene panels
• Xenium Panels
• Xenium Analyzer
• Xenium analysis
• Xenium Catalyst Program
• Chromium Single Cell platform