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Spatial Gene Expression for FFPE

What is Spatial Gene Expression for FFPE?

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.

Get startedFind User Guides


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

Experimental Planning & Design

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

Tissue Prep

Best practices for handling tissue samples and slides before and after sectioning. Guidance for removing hard coverslips from archived tissue slides.

Tissue Staining

Deparaffinize, stain, image, and decrosslink tissue.


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

Probe Sets

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


Refer to instrument-specific documents for seamless instrument operation.

Library Construction

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


Sequence your Visium spatial library as per our provided recommendations.

Analysis Software

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

Additional Applications


Access free, publicly available data from a number of different sample types generated with Visium Spatial solutions

View datasets

Videos - Visium CytAssist Spatial Gene Expression for FFPE

Visium CytAssist Instrument Tour and Readiness Test video
How-to series
Visium CytAssist Instrument Tour and Readiness Test
Tissue Preparation Guide video
Demonstrated Protocol series
Tissue Preparation Guide
Deparaffinization, H&E Staining, Imaging & Decrosslinking video
Demonstrated Protocol series
Deparaffinization, H&E Staining, Imaging & Decrosslinking
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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.