NaVis: a virtual microscopy framework for interactive, high-resolution navigation of spatial transcriptomics data

Despite the wide adoption of spatial transcriptomics (ST) into the biomedical community, its practical use remains constrained by a fundamental resolution-coverage trade-off and by reliance on computationally intensive and static workflows. As a result, transcriptome-wide spatial data are typically interpreted as ad-hoc processed outputs rather than explored dynamically as one would do with stained or fluorescence tissue images, limiting ST accessibility and slowing biological insight. Here we introduce NaVis, a web-based virtual microscopy framework that redefines how spatial transcriptomics is experienced. NaVis enables near-real-time, on-demand super-resolution inference from low-resolution whole-transcriptome platforms (10x Genomics Visium V1/V2, Cytassist and VisiumHD), generating high-resolution reconstructions that approach microscopy-level detail while preserving transcriptome-wide coverage. Unlike conventional interpolation approaches that produce fixed images, NaVis computes and refines spatial reconstructions interactively as users navigate tissue sections, transforming resolution from a platform-imposed constraint into a dynamic, user-controlled parameter. Also, NaVis is delivered through a fully point- and-click browser interface requiring no coding expertise, thus removing computational mediation and allowing clinicians, pathologists and experimental researchers to directly interrogate spatial molecular architecture. By coupling high-resolution inference with immediate visual interaction, NaVis shifts spatial transcriptomics from a static computational analysis to an exploratory, microscopy-like modality, broadening both its accessibility, conceptual reach, and potential for biological discoveries.