Provides hardware specifications, general image acquisition and analysis guidelines and image examples that are suitable for downstream analysis with Space Ranger.

Visium HD Spatial Applications Imaging Guidelines

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

Experimental Design

Experimental Planning and Design

Visium HD Spatial Gene Expression is a single cell scale, high resolution, CytAssist-enabled, whole transcriptome probe-based assay compatible with mouse or human FFPE tissue sections placed on glass slides.

Best practices for handling FFPE tissue samples and generating tissue slides. Protocol outlines deparaffinization, staining, and decrosslinking of tissue sections.

Tissue Prep & Staining

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 HD Spatial Gene Expression assay.

Probe Sets

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

Library Construction

Refer to instrument-specific documents for seamless instrument operation.

Instruments

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

HD Spatial Gene Expression

Overview

Documentation

Datasets

Videos

<div><Text as={'span'} size={'medium'} weight={'medium'}>{`This assay requires CytAssist instrument Firmware v2.0.0 or higher. Refer to the `}</Text><Anchor href={'/support/instruments/visium-cytassist/visium-cyt-assist-with-readiness-test'}><Text as={'span'} color={'inherit'} size={'medium'} weight={'medium'}>{'Visium CytAssist with Readiness Test User Guide (CG000542)'}</Text></Anchor><Text as={'span'} size={'medium'} weight={'medium'}>{' for details.'}</Text></div>

What is Visium HD Spatial Gene Expression?

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

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

Videos - Visium CytAssist Instrument

Visium CytAssist Instrument

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

Visium HD Spatial Applications Imaging Guidelines

Technical Note, CG000688

CG000688_VisiumHDSpatialApplicationsImagingGuidelines-TN_RevA.pdf