Deparaffinize, stain, image, and decrosslink tissue.

Tissue Staining

Visium Spatial Gene Expression measures the whole transcriptome of FFPE tissue sections in a spatially resolved manner by mapping gene expression over a high-resolution microscope image of the H&E- or IF-stained tissue.

Find resources from protocols to free-to-use analysis tools.

Visium CytAssist

Compact instrument designed to simplify the Visium workflow by facilitating the transfer of analytes from standard glass slides to Visium slides.

Spatial Gene Expression for FFPE

Visium

Gene Expression

Probe-based assay allowing simultaneous analysis of molecular and imaging data from FFPE tissue sections.

Plan ahead by referring to the list of equipment, kits, and reagents needed for the Visium Spatial Gene Expression for FFPE protocols.

Experimental Design

Experimental Planning and Design

For proper FFPE tissue sectioning and placement.

Tissue Prep

For imaging hardware, general image acquisition and analysis guidelines, and example images.

Imaging

Find a list of probes targeting protein-coding genes in human or mouse transcriptome for the Visium for FFPE assay.

Probe Sets

Construct a sequencing-ready Visium spatial library from your FFPE tissue sections.

Library Construction

Sequence your Visium spatial library as per our provided recommendations.

Sequencing

Analyze your Visium spatial data using our pipelines and visualization tools.

Software Analysis

Workflow Documentation

Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Map the whole transcriptome with morphological context in FFPE or fresh frozen tissues to discover novel insights into normal development, disease pathology, and clinical translational research.

Immunofluorescence protein co-detection

Visium CytAssist Gene and Protein Expression

Map the whole transcriptome within the <em>tissue context</em>

Spatial Gene Expression

Protein co-detection

Spatial gene expression profiling and imaging data of fresh frozen or FFPE tissues.

Overview

User Guides

Datasets

Videos: FFPE

Publications

Visium Spatial Gene Expression analyzes the whole transcriptome of FFPE tissue sections in a spatially resolved manner by mapping gene expression over a high-resolution microscope image of the tissue.

What is Spatial Gene Expression for FFPE?

Videos - Visium Spatial Gene Expression for FFPE

Visium Spatial Gene Expression for FFPE Protocol

Visium Spatial Gene Expression for FFPE Tissue Preparation Guide

Find answers to common technical questions, from sample prep through data analysis, about Visium spatial workflows.

Read key peer-reviewed research publications offering greater insights into biology, enabled by 10x Genomics products and technologies.