10x Genomics Visium Spatial Gene Expression

Visualize gene expression on tissue sections

Gain novel insights by adding tissue context to your transcriptome data

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Spatial transcriptomics with Visium 

The Visium Spatial Gene Expression solution by 10x Genomics allows you to analyze the whole transcriptome on a fresh frozen or FFPE tissue section. Discover the spatial organization of cell types, states, and biomarkers. 

At Single Cell Discoveries, we offer Visium Spatial Gene Expression as a complete service. All you need to do is prepare the tissue slides in your own lab. 

This is a Pilot ProgramClick here to find out what this means for your Visium project. 

Fresh Frozen Samples

Visium Spatial Gene Expression works with slides developed by 10x Genomics. Each slide contains 4 capture areas with 5,000 barcoded spots. Each spot contains millions of capture oligonucleotides.  

You place and fix the tissue sections on the capture area of the slide. In our lab, we stain and permeabilize the tissue.

The permeabilization step releases the mRNA that then binds to spatially barcoded capture spots. cDNA is then synthesized from captured mRNA and prepared into a sequencing library.  

After sequencing, the data can be analyzed and visualized with 10x Genomics Space Ranger and Loupe Browser.  

FFPE Samples

Visium for FFPE works with similar slides as the fresh frozen samples. However, there is a difference in how the mRNA is captured.

In the protocol, the probe pairs target specific sequences of the RNA. The probe pairs target around 18,000 genes in both human and mouse samples.  Once they hybridize with their target gene and are ligated to one another, the tissue is permeabilized.

Then, the ligated probe pairs are captured on the Visium slide by binding to the barcoded spots. Followed by library preparation and sequencing. This data can also be analyzed and visualized with 10x Genomics Space Ranger and Loupe Browser.

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Key benefits of Visium

  • Add tissue context to your transcriptomics data
    Visium allows you to place transcriptomics data within its tissue context. Analyze different cell types within their spatial organization.
  • Compatible with FFPE tissue
    With an adjusted protocol offered by us, Visium can be performed on FFPE tissue.
  • High spatial resolution
    Visium captures 1-10 cells on average per spot. This allows you to link spatial information to a tissue section in great detail.


Step 0: Tissue optimization

This step is necessary if you're working with fresh frozen samples, and not applicable to FFPE.

If it’s your first Visium experiment or you’re working with new tissue, it is required to optimize for this type of tissue. This is done by using the Visium Spatial Tissue Optimization Slide, which contains 8 capture areas.

We send you the optimization slide and you place the tissue sections on the slide in your own lab and send it back to us. By processing your optimization slide, we can select the optimal permeabilization time.

When this is determined and everything looks good, we can start with step 1: sample preparation.

10x Genomics Visium Spatial Gene Expression
Sample processing of bulk RNA seq

Step 1: Sample preparation

After we send you the Visium Spatial Gene Expression slides, you can start with the sample preparation. In your own lab, you will prepare the slide. You place the tissue on the capture area of the gene expression slide and send the slides back to us. 

Check out the resources by 10x Genomics linked below to find out how this works. 


Step 2: Sample processing

When we receive your slides, we start by processing the optimization slide for fresh frozen tissues. 

Then, we process the Visium Gene Expression Slides using the 10x Genomics fresh frozen or FFPE protocol to synthesize cDNA. The cDNA is then pooled so we can complete the library preparation and send it out for sequencing. 


RNA purification of Bulk RNA seq
Data analysis

Step 3: Sequencing and data analysis

We send the NGS libraries to one of our sequencing partners for Next-Generation Sequencing on the Illumina NovaSeq 6000. 

When we’ve received the sequencing data, we map it to the appropriate reference transcriptome 

Mapping of sequencing data and initial quality control reports are done with the standard 10x Genomics Space Ranger pipeline. You'll be provided with a cloupe data file for browsing the data with the 10x Genomics Loupe Browser. 

Pilot Program

Since we are still gaining experience in offering Visium Spatial Gene Expression as a service, we have decided to offer it as a pilot for now. 

For your project, this means that: 

  • We may process your tissue type of interest for the first time. 
  • You get an attractive discount on Visium as long as it is a pilot program. 
  • The results (images, cluster plots) can be used for marketing purposes, but we will always check this with you first. 

The Visium Pilot Program is a temporary version of our Visium Spatial Gene Expression service. After this, we will offer it as a full service, and you can no longer make use of the attractive discounts. 


As with all of our services, we provide ongoing support from our single-cell sequencing specialists. For each Visium Spatial Gene Expression project, we provide the following: 

  • Regular email updates during sample processing 
  • Raw sequencing data (FASTQ files)
  • A standard Space Ranger QC report 
  • A standard Loupe Browser visualization file (cloupe) 
  • Mapped count tables for downstream analysis 
  • A preliminary differential gene expression analysis 


No. The barcoded spots capture 1-10 cells per spot. However, 10x Genomics is working on Visium HD, a single-cell spatial transcriptomics solution and plans on releasing it Q1, 2022

 At the moment, we don’t offer this as part of service.

We do not yet perform a customized preliminary cluster analysis. We do deliver you the standard output by Space Ranger.

Internally, 10x Genomics has optimized Visium for different tissues derived from human, mouse, rat, and zebrafish. However, Visium should be compatible with most mRNA-containing tissues.  Working with FFPE tissue? Then Visium is only possible for human and mouse samples so far.

You don’t have to, but we recommend it because we process the entire slideIf you don’t use all the capture areas, the costs remain the same.

Visium Pilot Program

Ready to proceed? Use the form below to sign up for our Visium Pilot Program. We'll get in touch as soon as possible.


Julia Strengers

Account Manager

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