Researchers at the Murdoch Children’s Research Institute (MCRI) have developed a groundbreaking software tool, VR-Omics, that enables scientists to visualize and analyze the spatial genetic architecture of human tissue in both 2D and immersive 3D environments. The platform is already providing new insights into cardiac rhabdomyoma, the most common heart tumor in children, according to a study published in Genome Biology.
Cardiac rhabdomyomas are typically detected during pregnancy or infancy. While most cases resolve spontaneously, some tumors can grow large enough to obstruct blood flow, leading to serious complications like respiratory distress, arrhythmias, and heart failure. Treatment options for these severe cases are limited, often requiring partial heart removal—a risky intervention with high morbidity.
“Unfortunately, it’s not well understood why these tumors form,” said Professor Mirana Ramialison, PhD, senior author of the study and lead developer of VR-Omics. Seeking to address this knowledge gap, Ramialison and her team applied VR-Omics to heart tissue from three pediatric patients diagnosed with cardiac rhabdomyoma.
Using spatial transcriptomics data, the tool produced detailed 3D reconstructions of gene expression across tissue sections, enabling what the authors describe as “immersive single-cell spatial exploration.” According to the study, VR-Omics revealed “previously undetected transcriptional activity within tumor cell populations,” including clusters enriched in cell-cycle and neurogenesis-related pathways—hallmarks often associated with disease progression.
“VR-Omics generates 3D visualizations of the cells within human tissue based on large collections of patient data. This could allow for greater analysis of human tissue compared to other methods,” said Ramialison.
Crucially, VR-Omics was benchmarked against existing spatial analysis tools like Seurat and Scanpy. The authors found that VR-Omics outperformed all methods in accuracy, reproducibility, and interpretability across multiple tasks, including segmentation and marker detection. The platform also integrates an intuitive virtual reality interface using the Unity engine, enabling researchers to navigate through dense tissue maps and interact with substructures in ways that traditional screens can’t replicate.
“VR-Omics has a unique capacity to analyze large datasets, which allows it to explore new biological mechanisms in rare tissue sections, like those from cardiac rhabdomyoma,” Ramialison said.
While the study focused on a rare cardiac tumor, the tool’s broader utility is clear. VR-Omics supports multimodal data integration, real-time hypothesis generation, and collaborative exploration, making it applicable to a wide range of pediatric and adult diseases. Ramialison envisions it accelerating discoveries in congenital disorders, cancer biology, and regenerative medicine.
The study represents a collaboration between MCRI, the Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (CardioRegen), the University of Konstanz, Monash University, and reNEW at the University of Melbourne. With childhood conditions often underrepresented in biomedical tool development, VR-Omics marks a significant step toward precision diagnostics in pediatric care.
As Ramialison notes, “The technology will enable more biological discoveries that could help better understand many childhood conditions.”
