Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps

TL;DR

Vitessce Link is a web-based hybrid visualization tool combining 3D mixed reality and 2D displays to facilitate interactive analysis of complex 3D tissue maps in spatial omics research.

Contribution

It introduces a novel, browser-based framework that integrates mixed reality with 2D visualization for 3D tissue data analysis, supporting seamless interaction and data exploration.

Findings

Enhances segmentation evaluation and spatial relationship interpretation.

Supports integration with computational notebooks and cross-device synchronization.

Demonstrated effectiveness in nephrology and oncology case studies.

Abstract

Advances in spatial omics and high-resolution imaging enable the creation of three-dimensional (3D) tissue maps that capture cellular organization and interactions in situ. While these data provide critical insights into tissue function and disease, their exploration is often constrained by tools limited to 2D displays or stereoscopic rendering without analytical integration. We present Vitessce Link, a web-based hybrid framework that unites a 3D stereoscopic view in mixed reality with a synchronized 2D display environment. Users can navigate volumetric data with intuitive hand gestures while controlling channels, filters, and derived data views through the Vitessce platform. Built on open standards and running entirely in the browser, Vitessce Link minimizes friction, supports integration with computational notebooks, and synchronizes interactions across devices via a lightweight WebSocket architecture. Case studies in nephrology and oncology demonstrate how the hybrid approach enhances segmentation evaluation, distance measurement, and interpretation of spatial relationships. Vitessce Link establishes a paradigm for integrative, web-native analysis of 3D tissue maps.