Visium Spatial Gene Expression

Map Gene Expression Within the Tissue Context

Visium Spatial Gene Expression is a next-generation molecular technology that allows you to classify tissue based on total mRNA. Map the whole transcriptome with morphological context to discover novel insights into normal development, disease pathology, and clinical translational research.

Spatial Gene Expression

Map the whole transcriptome

Spatially resolve total mRNA with morphological context.

Profile entire tissue sections

No need to select regions of interest—analyze the whole transcriptome from an entire section.

High resolution

1–10 cell resolution on average per spot depending on tissue type.

Streamlined data analysis

Combine histological and gene expression data with easy-to-use software.

One-day lab workflow

From tissue section to sequencing-ready library in one day.

Diverse sample compatibility

Demonstrated on a diverse set of organs across species (human, mouse, rat, and more).

Explore what you can do

  • Gain a complete view of disease complexity

  • Discover new biomarkers and identify novel cell types and states

  • Map the spatial organization of cell atlases

  • Identify spatiotemporal gene expression patterns

Proven Results

Proven Results


Search hundreds peer-reviewed publications using Spatial Gene Expression.


Watch how customers are using Spatial Gene Expression.


Find the latest app notes and other documentation Spatial Gene Expression.

Our End-to-End Solution

Visium Spatial Tissue Optimization Slides

Visium Spatial Tissue Optimization Slides

Easily adoptable within existing lab infrastructure, no need for a new instrument.

Visium Spatial Gene Expression Reagents

Visium Spatial Gene Expression Reagents

With our reagent kits, capture whole transcriptome gene expression with spatial resolution across an entire tissue section.

Analysis and Visualization Software

Analysis and Visualization Software

Our analysis pipelines

Our visualization software

World-Class Technical and Customer Support

World-Class Technical and Customer Support

Our expert support team can be contacted by phone or email.


  1. 1

    Prepare your sample

    Embed, section, and place fresh-frozen tissue onto a capture area of the gene expression slide. Each capture area has thousands of barcoded spots, each containing millions of capture oligonucleotides with spatial barcodes unique to that spot.

  2. 2

    Stain and image the tissue

    Utilize standard fixation and staining techniques, including Hematoxylin and Eosin (H&E) staining, to visualize tissue sections on slides using a brightfield microscope.

  3. 3

    Permeabilize tissue and construct library

    Permeabilize the tissue to release mRNA from the cells, which binds to the spatially-barcoded oligonucleotides present on the spots. A reverse transcription reaction produces cDNA from the captured mRNA. The barcoded cDNA is then pooled for downstream processing to complete a sequencing-ready library.

  4. 4


    The resulting 10x Barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers for massive transcriptional profiling of entire tissue sections.

  5. 5

    Analyze and visualize your data

    Use our Space Ranger analysis software to process your Spatial Gene Expression data and interactively explore the results with our Loupe Browser visualization software.

    Do I need to be a bioinformatician to use Loupe?

    Loupe is a point-and-click software that’s easy for anyone to download and use.


Frequently Asked Questions

It enables you to perform spatial transcriptomics, where histological spatial information is coupled with whole transcriptome analysis.

Visium is compatible with fresh-frozen tissues containing mRNA. A list of the tissues successfully tested in-house can be found below.

Visium is based on the Spatial Transcriptomics technology which has been demonstrated by a number of published peer review articles. You can find them on our publications page. For external validation of Visium, beta testers, such as Sanger, SciLife, Broad, USC, and Garvan, have been able to generate spatial gene expression profiles for a number of different sample types. In internal validation, 30+ different tissues were tested successfully.

10x Genomics provides 2 types of software that will help you analyze your data: Space Ranger and Loupe Browser. Space Ranger is an analysis software which will automatically overlay spatial gene expression information on your tissue image and identify clusters of spots with similar transcription profiles. You can then use Loupe Browser, a visualization software, to interactively explore the results. You can download Space Ranger and Loupe Browser from the 10x Support site at no cost.

While Visium Spatial Gene Expression is compatible with the targeted gene panels offered by 10x Genomics, it is not supported at this time. A supported protocol, along with software analysis for targeted panels used with Visium Spatial Gene Expression, will be coming in mid-2020.

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