DIVA: Natural Navigation Inside 3D Images Using Virtual Reality

Abstract

As three-dimensional microscopy becomes commonplace in biological research, there is an increasing need for researchers to be able to view experimental image stacks in a natural three-dimensional viewing context. Through stereoscopy and motion tracking, commercial virtual reality headsets provide a solution to this important visualization challenge by allowing researchers to view volumetric objects in an entirely intuitive fashion. With this motivation, we present DIVA, a user-friendly software tool that automatically creates detailed three-dimensional reconstructions of raw experimental image stacks that are integrated in virtual reality. In DIVA's immersive virtual environment, users can view, manipulate and perform volumetric measurements on their microscopy images as they would to real physical objects. In contrast to similar solutions, our software provides high-quality volume rendering with native TIFF file com-

Fast‐track virtual reality for cardiac imaging in congenital heart disease

“…The VR models of the patient's anatomy were generated using the DIVA software. 8,9 It was developed by using the popular Unity game engine and it includes two native interfaces: a desktop mode for volumetric viewing on a standard computer monitor and a VR mode to interact with medical images in an artificial environment through the use of a VR headset. The patient's imaging data were loaded directly from DICOM files and the volumetric renderings of the MRI are generated instantaneously by the software, without any human intervention.…”

Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality

“…While all these parameters could be defined within the VR interface, data visualization and analysis practices in the lab are often incompatible with long times passed within the VR environment. Hence, we developed a dynamic process where the user can switch from one interface to the other based on the specificity and complexity of the action, they wish to execute following the same design principles of DIVA ( El Beheiry et al, 2020 ). The VR interface allows visualization and navigation within the point cloud ( Figure 1 ; Supplementary Figure S3 ).…”

Challenges of intracellular visualization using virtual and augmented reality

“…The reason for using an immersive setup lies in the inherent benefits that an observer gains from a stereoscopic projection of 3D data ( Dwyer et al, 2018 ). Recently, members of this consortium have introduced platforms generating volumetric reconstructions from stacks of 3D + t microscopic images and facilitating efficient visualization, selection of structures of interest and quantitative analysis [DIVA (el Beheiry et al, 2020 )] ( Figures 1B,C ; Supplementary Video S1 ), as well as to visualize and analyze point clouds in VR, particularly adapted to SMLM data [Genuage ( Blanc et al, 2020 )] ( Figures 1D,E ). In both tools, data are imported in their raw format and visualized in VR using custom shaders.…”

“…In Section 2 , we review some of the visualization methods on flat screens and summarize their respective advantages but also limitations, with a focus on the temporal dimension. While not exhaustively, in Section 3 , we then review a list of significant tools in VR, already published by co-authors of this perspective paper, Genuage ( Blanc et al, 2020 ) and Diva (el Beheiry et al, 2020 ). In Section 4 , we present augmented reality (AR) approaches, using MorphoNet and based on AR Foundation using the Unity3D Game engine or HoloTracks developed using Microsoft Hololens.…”

“…(C) Dynamic exchange of mitochondria between cells using Tunneling Nanotubes (TNT) (Courtesy of Chiara Zurzolo’s lab, Institut Pasteur) visualized with DIVA in VR (see Supplementary Video S1 ). Rendering is performed by full volumetric ray casting (el Beheiry et al, 2020 ) and an adapted transfer function ( Guérinot et al, 2022 ). Note the possibility to have both the video running and the user interacting with the data.…”