Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine

Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display. The application is structured to separate the biomolecular modeling and visualization systems. The biomolecular model loading and analysis system was developed as a stand-alone C# library and provides the foundation for the custom visualization system built in Unity. All visual models displayed within the tool are generated using Unity-based procedural mesh building routines. A 3D user interface was built to allow seamless dynamic interaction with the model while being viewed in 3D space. Biomolecular structure analysis and display capabilities are exemplified with a range of complex systems involving cell membranes, protein folding and lipid droplets

Virtual Reality bridge between Chemistry and Cultural Heritage: the "Sala degli Stemmi" Case Study

In this contribution, we present a multiscale and multidisciplinary VR architecture that aims at creating a common environment where cultural heritage and chemistry meet in order to strengthen the role already played by chemistry in the process of restoration of cultural goods. Our aim is to create a user friendly platform where experts of both fields can share data and ideas in a direct way, in order to achieve deeper insights into cultural goods combining the scientific and historical points of view. As a case study we present the 3D reconstruction of the "Sala degli Stemmi", which is one of the two historical rooms at Palazzo della Carovana in Pisa, presenting a number of artworks that underwent a process of chemical analysis and restoration in 2012. The whole architecture has been developed using the Unity game engine, and it is usable with HTC Vive headsets. The implementation of the VR environment and the potential applications, from both the scientific and educational points of view, are discussed in some detail

Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration

Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. Here, we use VR for visualization of 3D histology data, creating a novel interface for digital pathology. Our contribution includes 3D modeling of a whole organ and embedded objects of interest, fusing the models with associated quantitative features and full resolution serial section patches, and implementing the virtual reality application. Our VR application is multi-scale in nature, covering two object levels representing different ranges of detail, namely organ level and sub-organ level. In addition, the application includes several data layers, including the measured histology image layer and multiple representations of quantitative features computed from the histology. In this interactive VR application, the user can set visualization properties, select different samples and features, and interact with various objects. In this work, we used whole mouse prostates (organ level) with prostate cancer tumors (sub-organ objects of interest) as example cases, and included quantitative histological features relevant for tumor biology in the VR model. Due to automated processing of the histology data, our application can be easily adopted to visualize other organs and pathologies from various origins. Our application enables a novel way for exploration of high-resolution, multidimensional data for biomedical research purposes, and can also be used in teaching and researcher training