Deeper Spatial Discovery with Visium HD 3′
Visium HD 3' is here! Explore more species - Now Shipping
Introducing 10x Genomics‘ Visium HD 3’, a novel assay for unbiased cross-species spatial gene expression profiling of fresh frozen tissue sections mounted on a standard glass slide. The Visium HD’s array has a gapless design that enables integration of unsupervised gene expression clustering data with microscope H&E images from the same tissue section, allowing precise profiling of finer anatomical features with high tissue coverage at single cell-scale resolution.
Furthermore, this novel reverse transcription-based assay generates cDNA products compatible with both short reads and long reads sequencing, extending its applications beyond gene expression analysis to enable immune profiling and the discovery of isoforms and novel transcripts on a spatial level.
Key Features
Visium HD 3’ assay, which delivers whole transcriptome spatial analysis with a 3’ poly(A) capture-based chemistry. This assay provides:
- Flexibility to explore the spatial biology of fresh frozen samples from any species
- De novo spatial discovery power, including isoforms, TCRs/BCRs, and SNVs
- True single cell resolution with new cell segmentation software
- Streamlined slide handling and high spatial fidelity powered by the Visium CytAssist instrument
Space Ranger v4.0.1 is now live! Expand the power of Visium HD with cell segmentation
Improve cell-type resolution with nuclei expansion–based cell segmentation available in Space Ranger version 4.0 software. Importantly, Space Ranger v4.0 now supports cell and nucleus segmentation with H&E images. So you can reprocess existing Visium HD data through the new Space Ranger pipeline to derive these nuclei and cell segmentation outputs alongside the square bins
- Input a brightfield image of your H&E-stained tissue into the Space Ranger pipeline
- The software performs nuclei detection and expansion
- The Space Ranger pipeline outputs custom binning files viewable in Loupe Browser software
The new version can be found at: https://www.10xgenomics.com/support/software/space-ranger/latest
Some other notable features are:
- A new UMI-based registration algorithm for Visium HD and Visium HD 3′ data.
- You can now visualize and analyse Visium HD / Visium HD 3′ cell segmentation in Loupe Browser v9.
Watch introductory webinar on-demand
Learn more about the Visium HD 3’ assay in this introductory webinar, including a Q&A with product experts.
Build your own Visium HD 3’ experiment
Use 10x Genomics’ interactive tool to design your Visium HD 3’ experiment. Answer questions about your sample types and experimental goals, and get kit recommendations.
Other Resources
Press Release: 10x Genomics Expands Visium Platform with Launch of Visium HD 3’ Gene Expression, Unlocking Deeper Spatial Recovery
Grant application resources for Visium products
AACR Annual Meeting (Chicago) Visium HD 3′ poster: Visium HD 3’ enables unbiased whole transcriptome spatial profiling of Tumor microenvironment in fresh frozen cancer tissues at single cell scale resolution.
