vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy

Abstract

Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established 1,2 and its wide-spread adoption has led to the development of more than 36 software packages, dedicated to quantitative evaluation of the spatial and temporal detection of fluorophore photoswitching 3 . While the initial emphasis in the 3D SMLM field has clearly been on improving resolution and data quality, there is now a marked absence of 3D visualization approaches that enable the straightforward, highfidelity exploration of this type of data. Inspired by the horological phosphorescence points that illuminate watch-faces in the dark, we present vLUME (Visualization of the Universe in a Micro Environment, pronounced 'volume') a free-for-academic-use immersive virtual reality-based (VR) visualization software package purposefully designed to render large 3D-SMLM data sets. vLUME enables robust visualization, segmentation and quantification of millions of fluorescence puncta from any 3D SMLM technique. vLUME has an intuitive user-interface and is compatible with all commercial VR hardware (Oculus Rift/Quest and HTC Vive, Supplementary Video 1). vLUME accelerates the analysis of highly complex 3D point-cloud data and the rapid identification of defects that are otherwise neglected in global quality metrics.

CellexalVR: A virtual reality platform to visualise and analyse single-cell data

“…Here we present CellexalVR, a virtual reality (VR) platform that overcomes these barriers. VR is emerging as a potent tool to visualise scientific data, and its application thus far has been focused on image/volumetric 1 data [10][11][12]. By placing all DR plots and associated metadata in VR we have created an immersive and collaborative environment to explore and analyse scRNAseq experiments.…”