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.

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

1. Input a brightfield image of your H&E-stained tissue into the Space Ranger pipeline
2. The software performs nuclei detection and expansion
3. 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.

Learn more about the Visium HD 3’ assay in this introductory webinar, including a Q&A with product experts.

10x Genomics is a proven leader in single cell research, expanding access to single cell with optimised protocols, end-to-end support, and easy-to-use analysis tools. 10x Genomics’ technology – backed by 10 years, over 2,200 patents, and > $1.5B in R&D investment – has empowered researchers to publish over 8,000 studies, including many high-impact applications of their tools.

10x Genomics’ complementary Visium and Xenium platforms offer an essential balance between unbiased discovery and precision insights and are leading the way in performance, flexibility, and ease-of-use. Being at the nexus of spatial biology means seeing what others may have missed: global cell-type organisation, cell–cell interactions, heterogeneous spatial niches, novel gene programs, critical ligand–receptor signalling networks, and spatial biomarkers of therapeutic response.