10x Genomics Xenium In Situ Spatial Platform

What the platform does

These specifications are from 10x Genomics’ current Xenium Analyzer information.

How Xenium works

The basic workflow is:

1. Tissue preparation
A tissue section—typically FFPE or fresh-frozen—is placed on a Xenium slide.

2. Probe hybridization and target recognition
Gene-specific probes bind target RNA molecules.

3. Padlock/rolling-circle amplification
Xenium uses a padlock-probe chemistry with rolling-circle amplification to amplify detected transcripts. This contributes to sensitivity and enables detection of relatively short or degraded transcripts, including those found in FFPE tissue.

4. Fluorescence imaging
The amplified targets undergo successive rounds of fluorescent probe hybridization and imaging.

5. Transcript decoding
The instrument identifies the optical signature corresponding to each targeted gene.

6. Cell segmentation and spatial analysis
The system generates spatial maps of transcripts together with cell/nucleus boundaries and tissue morphology.

7. Data exploration
Xenium Onboard Analysis and Xenium Explorer allow visualization from whole-tissue scale down to individual transcripts.

Main applications

Xenium is particularly suited to:

• Cancer research — tumor microenvironment, tumor/normal boundaries and rare cell populations
• Neuroscience — neuronal populations, brain architecture and cellular neighborhoods
• Immunology — immune-cell localization and cell–cell interactions
• Developmental biology — spatial organization of developing tissues
• Pathology — molecular characterization alongside tissue morphology
• Biomarker discovery
• Cellular neighborhood analysis
• Cell–cell communication studies
• Spatial validation of single-cell RNA-seq findings

The major advantage is that gene-expression information remains connected to the native tissue architecture.

Xenium Analyzer

The Xenium Analyzer is the dedicated instrument that performs transcript detection, high-resolution imaging, decoding and onboard computational analysis. Current specifications list two slides per run and approximately 472 mm² of analyzable tissue per run. Depending on panel size, 10x Genomics reports approximately <3 days for up to 480 genes or <6 days for up to 5,000 genes.

The instrument is substantial laboratory equipment: approximately 133 × 69 × 79 cm, with an additional vibration-isolation table and analysis computer. The published environmental requirements include approximately 19–25 °C and 30–80% non-condensing relative humidity.

Xenium vs conventional RNA sequencing

A conventional bulk RNA-seq experiment can tell you:

“These genes are expressed in this tissue.”

Xenium can provide a much more spatially resolved question:

“These genes are expressed in these individual cells, at these locations, and these cells are immediately adjacent to these other cell types.”

That spatial context is the central value of Xenium.

Xenium vs 10x Visium

A useful distinction is:

Xenium → targeted, imaging-based, subcellular spatial resolution

Visium → sequencing-based, broader/whole-transcriptome spatial profiling at approximately single-cell-scale resolution

10x Genomics currently describes Xenium as supporting targeted gene expression of up to 5,000 genes, while its Visium platform provides broader spatial discovery through NGS-based approaches.

Key components of a Xenium system

A laboratory installation generally involves:

1. Xenium Analyzer
2. Xenium Analysis Computer
3. Vibration-isolation table
4. Xenium slides/consumables
5. Gene-expression probe panels
6. Tissue-preparation reagents
7. Xenium analysis software
8. Xenium Explorer for visualization

The analysis computer is integrated into the instrument workflow and converts the large imaging dataset into formats suitable for downstream analysis.

In short: Xenium is essentially a high-plex molecular microscope for tissue—combining spatial transcriptomics, high-resolution fluorescence imaging, cell segmentation and computational analysis to determine what genes are expressed, in which cells, and where those cells are located.

Official Xenium In Situ Platform
Xenium Analyzer specifications