10X Visium Digital Spatial Gene Expression

Delve deeper and thoroughly assess your samples with protein, total mRNA, and morphology in the same tissue section. Visualize protein and whole transcriptome expression and much more.

Features & Benefits

Map the whole transcriptome within the tissue context with 10X Visium® Digital Spatial Gene Expression. Unravel biological architectures in normal and diseased tissue and discover new biomarkers. Visualize the spatial organization of awe-inspiring cell types, states, and biomarkers.

1. Flexible - suitable for both FFPE & Fresh-frozen tissues

2. Comprehensive - analyze the whole transcriptome on entire tissue sections

3. Adaptable - combine with immunofluorescence protein detection

Service Overview

10x Visium Characterized Tissues

No experimental setup, no delays, and no hassle! 10x Visium characterized tissues, including elusive matched pair tissues, are ready to ship off the self. Review the tissues and the data unreservedly before you buy! Or request a custom project to have a bespoke tailored experience molded to you for further experiential control. (Shown: Mouse Brain Sagittal Anterior- Fresh Frozen - Whole Transcriptome, Visium-Characterized)

Visium Cost Calculator

Disclosure: Estimate only. Reagent cost not included. NGS services are requested separately and are dependent on project specifics. Only a general estimation is provided here.

A Simple Workflow for your Assays

Streamline experimentation with a ready-to-use, robust workflow that smoothly integrates easily into current laboratory methods and tools for whole tissue section analysis. With 10X Visium Digital Spatial Gene Expression you can gain a holistic view of disease complexity, discover new biomarkers, map the spatial organization of cell atlases and identify spatiotemporal gene expression patterns.

Researchers can leverage spatial discoveries with spatial capture technology. This can be achieved by the use of spatially barcoded mRNA – binding oligonucleotides. There are two methods in which mRNA molecules get a spatial barcode.

FFPE Tissues

  1. The tissues are permeabilized to release ligated probe pairs that bind to adjacent capture probes on the slide, allowing for the capture of gene expression information.
  2. Pairs of probes specific to each gene in the protein-coding transcriptome are hybridized to their gene target and then ligated to one another.
  3. The probe pairs are extended to incorporate complements of the spatial barcodes and sequencing libraries prepared.

Fresh-Frozen Tissues

  1. In fresh-frozen tissues, RNA is released by fixing and permeabilizing – which binds to adjacent capture probes to allow capture of gene expression information.
  2. Then sequencing libraries are prepared by synthesizing and capturing RNA.

Spatially Resolved Clustering

Spatially resolved clustering based on simultaneous gene expression and protein detection in the mouse brain.

A mouse brain section was labeled using immunofluorescence to visualize NeuN and then processed through the Visium Spatial Gene Expression workflow.

(A) an IF-only image

(B) an IF image overlaid with Visium data containing total UMI counts

(C) an IF image overlaid with Visium data for spatially naïve clustering based on total differentially expressed genes

(D) The top 10 genes that are more highly expressed in Cluster 6 are shown to the right along with example images.

Gain High-Resolution Characterization of Gene and Protein Expression

(A) Visium Spatial Gene Expression provides unbiased or targeted gene expression readout in intact sections from fresh-frozen tissue. The workflow is compatible with H&E to provide morphological context and IF staining to co-detect protein from the same tissue section.


(B) Shown on the left is an H&E image for a coronal mouse brain section, followed by an overlay of Visium data for total unique molecular identifiers (UMIs) for whole transcriptome analysis or spatially naïve spot clustering based on total differentially expressed genes. Listed on the far right are the most highly expressed genes in Cluster 4.

(Source: 10x Genomics)

Spatially Resolved Clustering & Gene Expression Analysis

Shown is the spatially resolved clustering and gene expression in the mouse kidney. Top Row: Top row depicts global analysis of tissue morphology, gene expression, and clustering. Bottom Row: The bottom row depicts gene-specific analysis of a few select genes. (Source: 10x Genomics)

A.  A coronal mouse kidney section was H&E stained, imaged, then processed through the Visium Spatial Gene Expression for fresh frozen tissue workflow. Shown is spatially naïve clustering based on total differentially expressed genes and image overlays containing data for:

  • (B) UMI counts
  • (C) total gene count

D. The top 11 genes that are more highly expressed in Cluster 4 (green) than any other cluster is shown to the far right. Examples of the many mRNAs that can be analyzed in a single experiment are also depicted, all coinciding with known expression patterns: (E) Slc22a8, (F) Slc34a1, (G) Slc22a12, (H) Umod.

Co-Detect Protein and Whole Transcriptome

Human breast ductal carcinoma in situ

Histological tools like in situ hybridization or immunohistochemistry are limited in the breadth of analysis they can perform. With protein detection by immunofluorescence one can visualize spatial patterns of gene expression.

The Visium spatial gene expression solution increases the level of precision by blending immunofluorescence protein detection and unbiased, spatial gene expression in the same tissue section alongside histological analysis.

The Significant Difference - the ability to localize rare cell subtypes in patient samples, characterize immune cell activation state, or resolve post-translational modifications and cell signaling in intact tissue, without letting go of whole transcriptome data. The combined workflow of Visium Spatial Gene Expression with Immunofluorescence makes it simpler to implement spatial transcriptomics technology into standard methods of tissue sectioning and immunofluorescence staining.

Interested in 10x Visium® or just want to learn more?

Reach out about your project with one click! Address all of your concerns or questions with our live spatial consulting to see what is best for you.

Streamlined Data Analysis

Space Ranger Analysis Pipelines:

  • Process Visium data with both brightfield and fluorescence microscope images.
  • Easy access to sample demultiplexing, image alignment, barcode processing, gene counting at your fingertips

Loupe Browser Visualization Software:

  • Rapidly locate important genes, cell types, and substructure without the need to program

Loupe Browser Data Exploration

Spot Selection

Over 125+ Publications & Preprints

Case Studies with 10X Visium

Spatial profiling reveals heterogeneous populations in ductal carcinoma in situ of the breast

Identified predictive biomarkers for classifying and optimizing treatment

Nagasawa S et al., Commun Biol, 2021

Spatial profiling of the immune infiltrate during chronic inflammation

Carlberg K et al., Scientific Reports, 2019

Spatiotemporal dynamics of molecular pathology in ALS (left)

Regional differences in microglia and astrocytes in ALS spinal cord (right)

Maniatis S et al., Science, 2019

Spatiotemporal gene expression and cell atlas of the developing human heart

Global Spatiotemporal Analysis of Three Cardiac Developmental Stages

Asp M et al., Cell, 2019

Spatially divergent expression patterns of fetal genes in cardiac biopsies

Therapy approaches could be improved by differentiating disease states with advanced biomarkers.

Asp et al. used spatial biology to study regions of cardiac biopsies and the spatial variations that occur within.

Asp M et al., Scientific Reports, 2017

Additional Resources


Inside Visium Spatial Capture Technology


Explore Data Visualization


Application Note: Visium FFPE Prostate Cancer

Disclaimer: Content in part from 10x Genomics. All rights reserved by respective original owners.

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