Software

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

Guillaume Jacquemet

Cell Migration Lab, Åbo Akademi University, Finland

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

Musa Mhlanga

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

Steven Lee

TheLeeLab, University of Cambridge, UK

Publications:

High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation
*Romain F Laine*, *Hannah S Heil*, *Simao Coelho*, Jonathon Nixon-Abell, Angélique Jimenez, Tommaso Galgani, Aki Stubb, Gautier Follain, *Siân Culley*, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, *Ricardo Henriques*
Published in bioRxiv, April 2022 (see preprint)
Research themes: New Methods, Software
Type: Preprint, Corresponding author

Mapping molecular complexes with Super-Resolution Microscopy and Single-Particle Analysis
*Afonso Mendes*, *Hannah S. Heil*, *Simao Coelho*, Christophe Leterrier, *Ricardo Henriques*
Published in arXiv, February 2022 (see preprint)
Research themes: Structural Biology, New Methods, Software
Type: Preprint, Corresponding author

DeepBacs: Bacterial image analysis using open-source deep learning approaches
*Christoph Spahn*, *Estibaliz Gómez-de-Mariscal*, *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*, 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*, Mike Heilemann, Guillaume Jacquemet, *Ricardo Henriques*
Published in Nature communications, April 2021 (see publication)
Research themes: New Methods, Software
Type: Paper, Corresponding author

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

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

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

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

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

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