RT Journal Article
SR Electronic
T1 Exploration and analysis of molecularly annotated, 3D models of breast cancer at single-cell resolution using virtual reality
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.06.28.448342
DO 10.1101/2021.06.28.448342
A1 Dario Bressan
A1 Claire M. Mulvey
A1 Fatime Qosaj
A1 Robert Becker
A1 Flaminia Grimaldi
A1 Suvi Coffey
A1 Sara Lisa Vogl
A1 Laura Kuett
A1 Raul Catena
A1 Ali Dariush
A1 Carlos Gonzalez-Fernandez
A1 Eduardo A. Gonzalez-Solares
A1 Mohammad Al Sa’d
A1 Aybüke Küpcü Yoldaş
A1 Tristan Whitmarsh
A1 Ilaria Falciatori
A1 Spencer S. Watson
A1 CRUK IMAXT Grand Challenge Team
A1 Johanna A. Joyce
A1 Nicholas Walton
A1 Bernd Bodenmiller
A1 Owen Harris
A1 Gregory J. Hannon
YR 2021
UL http://biorxiv.org/content/early/2021/06/29/2021.06.28.448342.abstract
AB A set of increasingly powerful approaches are enabling spatially resolved measurements of growing numbers of molecular features in biological samples. While important insights can be derived from the two-dimensional data that many of these technologies generate, it is clear that extending these approaches into the third and fourth dimensions will magnify their impact. Realizing biological insights from datasets where thousands to millions of cells are annotated with tens to hundreds of parameters in space will require the development of new computational and visualization strategies. Here, we describe Theia, a virtual reality-based platform, which enables exploration and analysis of either volumetric or segmented, molecularly-annotated, three-dimensional datasets, with the option to extend the analysis to time-series data. We also describe our pipeline for generating annotated 3D models of breast cancer and supply several datasets to enable users to explore the utility of Theia for understanding cancer biology in three dimensions.Competing Interest StatementDario Bressan, Robert Becker, Flaminia Grimaldi, and Gregory J. Hannon are shareholders of Suil Interactive Ltd, the commercial entity which produced the VR software described in this manuscript. No other author has competing interests to declare.