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Publication: Gray et al. Scientific reports 2016
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VirusMapper is an open-source software tool that enables high-resolution mapping of virus architecture using super-resolution microscopy and single particle analysis. It allows researchers to generate detailed molecular models of viruses by imaging thousands of individual virus particles labeled with fluorescent tags and averaging them together.

The key capabilities and workflow of VirusMapper are:

Segmentation - It automatically detects and segments thousands of individual fluorescently labeled virus particles from microscopy images. The particles are detected based on their shape and alignment, then cropped out and separated into individual images.

Seed selection - A subset of clearly aligned virus particle images are manually selected by the user as "seeds" to serve as templates for alignment of all the other particles. Multiple seeds representing different orientations can be selected.

Alignment and averaging - Each segmented virus particle is computationally aligned and registered to the seed templates based on rotational and translational shifts to maximize cross-correlation. Aligned particles are then averaged together, weighted by their similarity to the seeds.

Model generation - Alignment, registration and averaging are iteratively repeated using the newly generated averages as better seeds to progressively improve the final model. This allows models to be generated from very noisy individual particles.

Mapping - By labeling different virus components like outer proteins, genomes, etc. with separate fluorescent tags, models can be built independently and overlaid for multi-component mapping.

The key benefits are:

1) Molecular specificity - Unlike EM, fluorescent labeling allows specific virus proteins to be visualized

2) High resolution - Super-resolution microscopy enables sub-100nm resolution, surpassing optical diffraction limit

3) Statistical power - Thousands of single particles are analyzed compared to 10s by EM, improving accuracy

4) Context preservation - Viruses can be imaged in intact, natural states or in host cell contexts

5) Automation - VirusMapper performs automated, unbiased single particle analysis with little user input

The authors demonstrate VirusMapper by generating multi-component models of vaccinia virus architecture through SIM and STED super-resolution microscopy. They map the locations of different virus core proteins, genomes, and membranes within intact vaccinia virions. Measurements match previous EM data but also reveal new organizational details.

Additionally, by imaging cell-bound viruses, VirusMapper detects nanoscale structural changes in the virus core indicative of initial uncoating stages. This demonstrates how it can provide biological insights not accessible by EM.

VirusMapper is a powerful, open-source tool for mapping virus architecture at molecular resolution through computational processing of super-resolution microscopy images. It has the potential to uncover new structural-functional details of many viruses relevant to biomedicine and health.

Publications featuring NanoJ-VirusMapper

NanoPyx - super-fast bioimage analysis powered by adaptive machine learning
Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Preprint published in bioRxiv, August 2023
Technologies: CARE, NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and NanoPyx
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.08.13.553080
Mapping molecular complexes with super-resolution microscopy and single-particle analysis
Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques
Paper published in Open Biology, July 2022
Technologies: NanoJ-VirusMapper, Nuclear-Pores as references and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1098/rsob.220079
Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication
Emma Touizer, Christian Sieben, Ricardo Henriques, Mark Marsh, Romain F. Laine
Review published in Viruses, February 2021
Technologies: NanoJ-VirusMapper, Super-Beacons and ZeroCostDL4Mic
Funded by: Wellcome Trust
DOI: 10.3390/v13020233
Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion
Robert D. M. Gray, David Albrecht, Corina Beerli, Moona Huttunen, Gary H. Cohen, Ian J. White, Jemima J. Burden, Ricardo Henriques, Jason Mercer
Paper published in Nature Microbiology, July 2019
Technologies: NanoJ and NanoJ-VirusMapper
Funded by: BBSRC and Wellcome Trust
Blogs: Nature Microbiology Community
DOI: 10.1038/s41564-019-0488-4
Automating multimodal microscopy with NanoJ-Fluidics
Pedro Almada, Pedro M. Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Guillaume Charras, Buzz Baum, Romain F. Laine, Christophe Leterrier, Ricardo Henriques
Paper published in Nature Communications, March 2019
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and NanoJ-VirusMapper
Funded by: BBSRC and Wellcome Trust
News: Technology Times, MSN, DNYUZ and Express Informer
DOI: 10.1038/s41467-019-09231-9
NanoJ - a high-performance open-source super-resolution microscopy toolbox
Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, David Albrecht, Gabriel T Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M Pereira, Siân Culley, Ricardo Henriques
Paper published in Journal of Physics D - Applied Physics, January 2019
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
Septins recognize and entrap dividing bacterial cells for delivery to lysosomes
Sina Krokowski, Damian Lobato-Marquez, Arnaud Chastanet, Pedro Matos Pereira, Dimitrios Angelis, Dieter Galea, Gerald Larrouy-Maumus, Ricardo Henriques, Elias T Spiliotis, Rut Carballido-Lopez, Serge Mostowy
Published in Cell host & microbe, January 2018
Technologies: NanoJ-VirusMapper
Funded by: BBSRC
DOI: 10.1016/j.chom.2018.11.005
Open-source single-particle analysis for super-resolution microscopy with VirusMapper
Robert DM Gray, Jason Mercer, Ricardo Henriques
Paper published in JoVE, January 2017
Technologies: NanoJ-VirusMapper
Funded by: BBSRC
DOI: 10.3791/55471
VirusMapper - open-source nanoscale mapping of viral architecture through super-resolution microscopy
Robert DM Gray, Corina Beerli, Pedro Matos Pereira, Kathrin Maria Scherer, Jerzy Samolej, Christopher Karl Ernst Bleck, Jason Mercer, Ricardo Henriques
Paper published in Scientific reports, January 2016
Technologies: NanoJ-VirusMapper
Funded by: BBSRC
DOI: 10.1038/srep29132

Funding contributing to NanoJ-VirusMapper

Sub-cellular Metabolic Compartmentalization During Oocyte Development
Zita Carvalho dos Santos, Ricardo Henriques, Jorge Carvalho
Funded by: CZI - Measuring Metabolism Across Scales
Duration: January 2024 - December 2026
Enabling Live-Cell 4D Super-Resolution Microscopy Guided by Artificial Intelligence
Ricardo Henriques
Alias: SelfDriving4DSR
Funded by: ERC - Consolidator
Duration: September 2021 - September 2026
Publications: 23
Mapping the early stages of HIV-1 infection by live-cell 4D Super-Resolution Microscopy
Hannah Heil
Funded by: EMBO - Postdoctoral Fellowships
Duration: September 2021 - August 2023
Publications: 5
Optial Biology PhD programme
Michael Hausser, Ricardo Henriques, Antonella Riccio
Funded by: Wellcome Trust - 4-year PhD Programme in Science
Duration: August 2021 - August 2025
Unveiling live-cell viral replication at the nanoscale
Ricardo Henriques
Funded by: EMBO - Installation Grant
Duration: January 2021 - January 2026
Publications: 16
Minimal Model of Poxvirus Infection
David Albrecht
Funded by: Marie Curie - Postdoctoral Fellowships
Duration: September 2017 - August 2019