VR-Omics: Exploration of Spatial Transcriptomics data in 3D (v2.0)

Spatial transcriptomics (ST) technologies produce complex, multi-dimensional data sets of gene expression information at subcellular levels that enable biologist to systematically investigate spatiotemporal gene expression patterns. However, analysis of SRT data remains broadly underpowered by complexity and lack of adequate software suited to non-computational users. We introduce VR-Omics, a freely available programme for comprehensive analysis, visualisation, and exploration of single or multi-section ST data generated from a variety of platforms as desktop application or immersive virtual environment. VR-Omics accommodates various ST technologies, including 10x Genomics' Visium and Xenium, Vizgen's MERFISH, open-source Tomo-seq, and custom ST data. The system can be implemented as a local 3D desktop application or as an immersive environment in virtual reality using head-mounted display. This allows biologists to interact with the data in novel ways that were previously inaccessible, which includes visually exploring the gene expression patterns of an organ and comparing genes based on their 3D expression profiles.