New Methods

Team members:

Ricardo Henriques

Group Leader at IGC and Honorary Professor at UCL

Daniel Krentzel

Internship Student
Crick Sandwich Student
Alumni

Collaborators:

Alan Lowe

Artificial Intelligence for Quantitative Biology Lab, University College London, UK

Andela Šarić

Šarić Lab, University College London, UK

Buzz Baum

Cell Morphogenesis Lab, University College London, UK

Bassam Hajj

Cell Organization Imaging and Control Lab, Institut Curie, France

Christophe Leterrier

NeuroCyto Lab, INP, CNRS, Aix-Marseille University, France

Ed Cohen

Cohen Group, Imperial College London, UK

Ewa Paluch

Paluch Lab, Trinity College, University of Cambridge, UK

Gautam Dey

Cell Morphogenesis Lab, University College London, UK

Guillaume Jacquemet

Cell Migration Lab, Åbo Akademi University, Finland

Isabel Llorente-García

Llorente-García Lab, University College London, UK

Joe Grove

Grove Lab, University College London, UK

Johanna Ivaska

Cell Adhesion and Cancer Adhesion Lab, University of Turku, Finland

Jason Mercer

Viral Cell Biology Lab, University of Birmingham, UK

Lucy Collinson

Electron Microscopy Science Technology Platform, Francis Crick Institute, UK

Mike Heilemann

Single Molecule Biophysics, Goethe University Frankfurt, Germany

Mariana Pinho

Bacterial Cell Biology laboratory, ITQB NOVA, Portugal

Mark Marsh

Cellular Mechanisms of Virus Entry and Assembly Lab, University College London, UK

Musa Mhlanga

Gene Expression & Biophysics Lab, University of Cape Town, South Africa

Steven Lee

TheLeeLab, University of Cambridge, UK

Publications:

DeepBacs: Bacterial image analysis using open-source deep learning approaches
*Christoph Spahn*, *Romain F. Laine*, *Pedro Matos Pereira*, *Estibaliz Gómez-de-Mariscal*, *Lucas von Chamier*, Mia Conduit, Mariana Gomes de Pinho, Guillaume Jacquemet, Séamus Holden, Mike Heilemann, *Ricardo Henriques*
Published in bioRxiv, November 2021 (see preprint)
Research themes: New Methods, Software
Type: Preprint, Corresponding author

Avoiding a replication crisis in deep-learning-based bioimage analysis
*Romain F Laine*, Ignacio Arganda-Carreras, *Ricardo Henriques*, Guillaume Jacquemet
Published in Nature methods, October 2021 (see publication)
Research themes: New Methods, Software
Type: Paper

eHooke: a tool for automated image analysis of spherical bacteria based on cell cycle progression
*Bruno M Saraiva*, Ludwig Krippahl, Sérgio R Filipe, *Ricardo Henriques*, Mariana G Pinho
Published in Biological Imaging, September 2021 (see publication)
Research themes: New Methods, Software
Type: Paper

The Field Guide to 3D Printing in Optical Microscopy for Life Sciences
*Mario Del Rosario*, *Hannah S. Heil*, *Afonso Mendes*, Vittorio Saggiomo, *Ricardo Henriques*
Published in Advanced Biology, May 2021 (see publication)
Research themes: New Methods, Software, Hardware
Type: Review, Corresponding author

FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division
Kevin D Whitley, Calum Jukes, Nicholas Tregidgo, Eleni Karinou, *Pedro Almada*, Yann Cesbron, *Ricardo Henriques*, Cees Dekker, Séamus Holden
Published in Nature communications, April 2021 (see publication or preprint)
Research themes: Microbiology, New Methods, Software, Hardware
Type: Paper

Democratising deep learning for microscopy with ZeroCostDL4Mic
*Lucas von Chamier*, *Romain F Laine*, Johanna Jukkala, *Christoph Spahn*, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loïc A Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, *Ricardo Henriques*
Published in Nature communications, April 2021 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

An Introduction to Live-Cell Super-Resolution Imaging
*Siân Culley*, *Pedro M Pereira*, *Romain F Laine*, *Ricardo Henriques*
Published in Imaging from Cells to Animals In Vivo, November 2020 (see publication)
Research themes: New Methods
Type: Book Chapter

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
Published in Nature methods, October 2020 (see publication or preprint)
Research themes: New Methods, Software
Type: Paper

The cell biologist’s guide to super-resolution microscopy
Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, *Ricardo Henriques*, Christophe Leterrier
Published in Journal of Cell Science, June 2020 (see publication)
Research themes: New Methods, Software, Hardware
Type: Review, Corresponding author

Live Imaging of a Hyperthermophilic Archaeon Reveals Distinct Roles for Two ESCRT-III Homologs in Ensuring a Robust and Symmetric Division
Andre Arashiro Pulschen, Delyan R Mutavchiev, *Siân Culley*, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, *Ricardo Henriques*, Buzz Baum
Published in Current Biology, June 2020 (see publication or preprint)
Research themes: Cell Division, Microbiology, New Methods, Hardware
Type: Paper

Super-Beacons: open-source probes with spontaneous tuneable blinking compatible with live-cell super-resolution microscopy
*Pedro M Pereira*, *Nils Gustafsson*, Mark Marsh, Musa M Mhlanga, *Ricardo Henriques*
Published in Traffic, March 2020 (see publication or preprint)
Research themes: New Methods, Probes
Type: Paper, Corresponding author

Fluctuation-Based Super-Resolution Traction Force Microscopy
Aki Stubb, *Romain F Laine*, Camilo Guzmán, *Ricardo Henriques*, Guillaume Jacquemet, Johanna Ivaska
Published in Nano Letters, March 2020 (see publication)
Research themes: New Methods, Software
Type: Paper

Between life and death: strategies to reduce phototoxicity in super-resolution microscopy
*Kalina L Tosheva*, *Yue Yuan*, *Pedro Matos Pereira*, *Siân Culley*, *Ricardo Henriques*
Published in Journal of Physics D: Applied Physics, January 2020 (see publication)
Research themes: Cell Division, New Methods
Type: Review, Corresponding author

Nuclear pores as versatile reference standards for quantitative superresolution microscopy
Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, *Pedro Matos Pereira*, *Ricardo Henriques*, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries
Published in Nature methods, October 2019 (see publication)
Research themes: Structural Biology, New Methods
Type: Paper

A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores
Lekha Patel, *Nils Gustafsson*, Yu Lin, Raimund Ober, *Ricardo Henriques*, Edward Cohen
Published in The annals of applied statistics, September 2019 (see publication)
Research themes: New Methods, Software
Type: Paper

Artificial intelligence for microscopy: what you should know
*Lucas von Chamier*, *Romain F Laine*, *Ricardo Henriques*
Published in Biochemical Society Transactions, August 2019 (see publication)
Research themes: New Methods, Software
Type: Review, Corresponding author

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software
Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M Hagen, Jean-Baptiste Sibarita, Jonas Ries, *Ricardo Henriques*, Michael Unser, Seamus Holden
Published in Nature methods, May 2019 (see publication)
Research themes: New Methods, Software
Type: Paper

Fix your membrane receptor imaging: Actin cytoskeleton and CD4 membrane organization disruption by chemical fixation
*Pedro M Pereira*, *David Albrecht*, *Siân Culley*, *Caron Jacobs*, Mark Marsh, Jason Mercer, *Ricardo Henriques*
Published in Frontiers in immunology, April 2019 (see publication)
Research themes: Cell Signalling, New Methods
Type: Paper, Corresponding author

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*
Published in Nature communications, March 2019 (see publication)
Research themes: New Methods, Hardware
Type: Paper, Corresponding author

Real time multi-modal super-resolution microscopy through Super-Resolution Radial Fluctuations (SRRF-Stream)
Justin Cooper, Mark Browne, Hugh Gribben, Martin Catney, Colin Coates, Alan Mullan, Geraint Wilde, *Ricardo Henriques*
Published in SPIE, February 2019 (see publication)
Research themes: New Methods
Type: Conference Paper, Corresponding author

NanoJ: a high-performance open-source super-resolution microscopy toolbox
*Romain F Laine*, *Kalina L Tosheva*, *Nils Gustafsson*, *Robert DM 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*
Published in Journal of Physics D: Applied Physics, February 2019 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

Content-aware image restoration: pushing the limits of fluorescence microscopy
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, *Siân Culley*, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, *Ricardo Henriques*, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W Myers
Published in Nature methods, December 2018 (see publication)
Research themes: New Methods, Software
Type: Paper

SRRF: Universal live-cell super-resolution microscopy
*Siân Culley*, *Kalina L Tosheva*, *Pedro Matos Pereira*, *Ricardo Henriques*
Published in The international journal of biochemistry & cell biology, August 2018 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

Quantitative mapping and minimization of super-resolution optical imaging artifacts
*Siân Culley*, *David Albrecht*, *Caron Jacobs*, *Pedro Matos Pereira*, Christophe Leterrier, Jason Mercer, *Ricardo Henriques*
Published in Nature methods, April 2018 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

Standard and super-resolution bioimaging data analysis: a primer
Ann Wheeler, *Ricardo Henriques*
Published in John Wiley & Sons, October 2017 (see publication)
Research themes: New Methods
Type: Book, Editor

Open-source single-particle analysis for super-resolution microscopy with VirusMapper
*Robert DM Gray*, Jason Mercer, *Ricardo Henriques*
Published in JoVE (Journal of Visualized Experiments), April 2017 (see publication)
Research themes: Microbiology, Structural Biology, New Methods, Software
Type: Paper, Corresponding author

Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations
*Nils Gustafsson*, *Siân Culley*, George Ashdown, Dylan M Owen, *Pedro Matos Pereira*, *Ricardo Henriques*
Published in Nature communications, August 2016 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

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*
Published in Scientific reports, July 2016 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

Infection counter: automated quantification of in vitro virus replication by fluorescence microscopy
*Siân Culley*, Greg J Towers, David L Selwood, *Ricardo Henriques*, Joe Grove
Published in Viruses, July 2016 (see publication)
Research themes: New Methods, Software
Type: Paper

PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors
*Pedro Almada*, *Siân Culley*, *Ricardo Henriques*
Published in Methods, October 2015 (see publication)
Research themes: New Methods, Hardware
Type: Review, Corresponding author

High-content 3D multicolor super-resolution localization microscopy
*Pedro M Pereira*, *Pedro Almada*, *Ricardo Henriques*
Published in Methods in cell biology, January 2015 (see publication)
Research themes: New Methods
Type: Bookchapter, Corresponding author

QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ
*Ricardo Henriques*, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga
Published in Nature methods, May 2010 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author