Visium Spatial Proteomics

Tissue Profiling with Transcriptomics and Protein Co-detection

Combine whole transcriptome spatial analysis with immunofluorescence protein detection in the same tissue section. Gain a deeper, more holistic understanding of tissue organization with colocalized protein detection and gene expression analysis.

Spatial Proteomics
  • Maximize your insights

    Maximize your insights

    Gain a deeper, more complete assessment of your samples with protein, total mRNA, and morphology in one.

  • Profile entire tissue sections

    Profile entire tissue sections

    Visualize protein and whole transcriptome expression, without selecting regions of interest.

  • Accessible technology

    Accessible technology

    Use standard microscopy, immunofluorescence staining protocols, and antibodies.

  • Streamlined data analysis

    Streamlined data analysis

    Combine histology or protein expression profiles with gene expression data in easy-to-use software.

  • One-day lab workflow

    One-day lab workflow

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

  • Diverse sample compatibility

    Diverse sample compatibility

    Demonstrated on multiple mouse and human tissues

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

Flexible Multiomic Spatial Profiling

Gain multiomic insights by combining protein expression data with whole transcriptome analysis or focus on your genes of interest using targeted gene expression panels.

Targeted Gene Expression Panels (Coming soon)

Choose from pre-designed cancer, immunology, neuroscience and gene signature panels with the ability to add up to 200 custom genes, or design fully custom panels. Optimized protocol, support, and software for targeted panels with Visium Spatial Gene Expression coming Fall 2020.

Highly Multiplexed Protein Detection (Coming soon)

Perform multiomic analysis by leveraging Feature Barcode technology to vastly increase the number of proteins detected compared to fluorescently labeled approaches.

With our comprehensive solution you get:

Powerful discovery

Envision the spatial organization of newly discovered cell types, states, and biomarkers with protein detection and whole transcriptome analysis.

Seamless integration

Validate discoveries or explore new hypotheses with the ability to transition seamlessly between whole transcriptome and targeted analysis from the same library preparation.

Focused expansion

Guided by protein expression patterns, scale up from a few genes of interest to all relevant genes and pathways by combining high-throughput spatial gene expression with the efficiency of targeted panels.

Proven Results

Proven Results


Watch how customers are using Spatial Gene Expression.


Search hundreds peer-reviewed publications 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.

Products Required

Visium Spatial Proteomics is enabled with these 10x Genomics products:

Analysis and visualization software:

Additional materials required:

  • Equipment and reagents necessary to support histology or immunofluorescence staining protocols
  • Microscopy equipment for digital image capture and export
  • Sequencing equipment

Our Support page provides a detailed summary of products used in the Visium Spatial Workflow, and recommended compatible products.


  1. 1Step 1

    Prepare your sample

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

  2. 2Step 2

    Stain and image the tissue

    Utilize standard fixation and staining techniques, such as Hematoxylin and Eosin (H&E) staining for morphology, or immunofluorescence (IF) for protein detection. Visualize tissue sections on slides using either brightfield or fluorescent microscopy to capture tissue images used to complement spatial gene expression data in downstream analyses.

  3. 3Step 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. 4Step 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. 5Step 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

With the release of Visium Spatial Gene Expression with Immunofluorescence, Visium analysis and visualization software can now display up to six fluorescent signals at a time from immunostained samples. 10x Genomics has verified detection of four fluorescent signals using the Visium Spatial Gene Expression with Immunofluorescence workflow and supports up to three antibodies plus DAPI. The maximum number of proteins that can be detected will ultimately be governed by your experimental design and imaging system configuration.

Yes, there are several key differences between standard IF and the IF protocol used with Visium. Please refer to the IF Demonstrated Protocol for additional detail.

Impact on Visium performance may vary from tissue to tissue due to the high sensitivity of the Visium assay. However, the spatial organization of gene expression and cell cluster detection is comparable between H&E and IF.

Visium is compatible with fresh-frozen tissues containing mRNA. Right now, Visium Spatial Gene Expression is not compatible with fixed sample types. However, it is something that we are actively working to enable in the future.

10x Genomics provides two types of software to help you analyze your data: Space Ranger and Loupe Browser. Space Ranger is an analysis software which automatically overlays spatial gene expression information on your tissue image and identifies 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 Genomics Support site at no cost.

Single Cell Gene Expression

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