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

Alexander Spark, Alexandre Kitching, View ORCID ProfileDaniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, View ORCID ProfileLisa-Maria Needham, View ORCID ProfileAleks Ponjavic, Mafalda Da Cunha Santos, View ORCID ProfileJames McColl, View ORCID ProfileChristophe Leterrier, Simon J. Davis, View ORCID ProfileRicardo Henriques, View ORCID ProfileSteven F. Lee
doi: https://doi.org/10.1101/2020.01.20.912733
Alexander Spark
1Lume VR LIMITED
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Alexandre Kitching
1Lume VR LIMITED
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Daniel Esteban-Ferrer
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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  • ORCID record for Daniel Esteban-Ferrer
Anoushka Handa
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Alexander R. Carr
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Lisa-Maria Needham
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Aleks Ponjavic
3School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, United Kingdom
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Mafalda Da Cunha Santos
4Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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James McColl
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Christophe Leterrier
5Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France
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Simon J. Davis
4Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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Ricardo Henriques
6MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
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Steven F. Lee
2Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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  • For correspondence: sl591@cam.ac.uk
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Abstract

Super-Resolution (SR) Microscopy based on 3D Single-Molecule Localization Microscopy (SMLM) is now well established1,2 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 photoswitching3. 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, high-fidelity 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.

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Posted January 21, 2020.
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vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Mafalda Da Cunha Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
bioRxiv 2020.01.20.912733; doi: https://doi.org/10.1101/2020.01.20.912733
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vLUME: 3D Virtual Reality for Single-molecule Localization Microscopy
Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Mafalda Da Cunha Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
bioRxiv 2020.01.20.912733; doi: https://doi.org/10.1101/2020.01.20.912733

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