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

Imaging

### What is CytAssist Spatial Gene Expression for Fresh Frozen (FF)?

W﻿hole transcriptome analysis of mouse or human fresh frozen OCT embedded tissue sections utilizing probe-based chemistry.

T﻿his assay utilizes the following 10x products:

* V﻿isium CytAssist Spatial Gene Expression for FFPE Reagent Kits
* Visium CytAssist Instrument and Accessory Kit, to learn more [click here](/instruments/visium-cytassist)

T﻿his assay has been validated with the following:

* Fresh frozen OCT embedded tissue blocks
* 10-20 um section thickness
* H&E Staining
* Tissue types ([Tested Tissue List](/support/spatial-gene-expression-ffpe/documentation/workflows/cytassist-ffpe/steps/experimental-design-and-planning/visium-cytassist-spatial-gene-expression-for-fresh-frozen-tested-tissue-list))

### 10x Visium Kit Compatibility Table

| 10x Solution                                                                                     | FFPE Tissue | Fresh Frozen Tissue |
| ------------------------------------------------------------------------------------------------ | ----------- | ------------------- |
| [Visium CytAssist Spatial Gene Expression](/support/spatial-gene-expression-ffpe)                | <Check />   | <Check />           |
| [Visium Spatial Gene Expression for FFPE](/support/spatial-gene-expression-ffpe)                 | <Check />   | \-                  |
| [Visium Spatial Gene Expression for Fresh Frozen](/support/spatial-gene-expression-fresh-frozen) | \-          | <Check />           |

CytAssist-enabled whole transcriptome analysis of fresh frozen tissue sections utilizing probe-based chemistry.

CytAssist Spatial Gene Expression for Fresh Frozen

Visium CytAssist Instrument facilitates the transfer of analytes from standard glass slides to Visium slides. Find the Instrument Documentation via the button below.

Visium CytAssist Instrument Tour and Readiness Test

Additional Applications

CytAssist for FFPE

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 & Design

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

Tissue Prep

Deparaffinize, stain, image, and decrosslink tissue.

Tissue Staining

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

Probe Sets

Refer to instrument-specific documents for seamless instrument operation.

Instruments

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

Visium CytAssist Spatial Gene Expression for FFPE

FFPE

Experimental Planning and Design

For proper FFPE tissue sectioning and placement.