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

Tissue Prep & Staining

Next-generation Visium HD technology–powered assay with whole transcriptome coverage to gather broad information from diverse species.

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.

HD 3’ Spatial Gene Expression

Visium

Gene Expression

Unbiased whole transcriptome poly-A based gene expression assay at single cell scale, compatible with Fresh Frozen tissue sections

Plan ahead by referring to the list of equipment, kits, and reagents needed for Visium HD 3’ Spatial Gene Expression protocols.

Experimental Design

Experimental Planning and Design

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

Imaging

Construct a sequencing-ready Visium HD 3’ spatial library from Fresh Frozen tissue sections.

Library Construction

Refer to instrument-specific documents for seamless instrument operation.

Instruments

Sequence your Visium HD 3’ spatial library as per our provided recommendations.

Sequencing

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

Software Analysis

Workflow Documentation

Protein co-detection

Overview

User Guides

Datasets

Videos

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Single cell-scale resolution, unbiased, whole transcriptome, poly-A based gene expression assay compatible with Fresh Frozen tissue sections.

What is HD 3’ Spatial Gene Expression?

Access free, publicly available data from a number of different sample types generated with Visium HD 3’ Spatial Gene Expression

Visium CytAssist Instrument

Using the Visium CytAssist Alignment Aid, 6.5 mm

Key Techniques for Visium HD Slide Preparation & Use

Key Techniques for Tissue Slide Handling & Use

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