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

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

Imaging

Single cell scale resolution whole transcriptome probe-based gene expression assay compatible with FFPE, Fresh Frozen, & Fixed Frozen tissue sections.

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

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

Tissue Prep & Staining for FFPE

Best practices for preparing and handling Fixed Frozen tissue samples and generating tissue slides. Protocol outlines rehydration, staining, and decrosslinking of tissue sections.

Tissue Prep & Staining for Fixed Frozen

Best practices for preparing and handling Fresh Frozen tissue samples and generating tissue slides. Protocol outlines fixation, staining, and permeabilization of tissue sections.

Tissue Prep & Staining for Fresh Frozen

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 HD spatial library from your FFPE, Fresh Frozen, or Fixed Frozen 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

User Guides

Workflow Documentation

Datasets

Videos

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

What is Visium HD Spatial Gene Expression?

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

Documentation

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_RevB.pdf