Publications

You can find the complete publication list on our Google Scholar profile. A complete list of bioRxiv preprints on our Rxivist profile.

2023

Fast4DReg – fast registration of 4D microscopy datasets Joanna W Pylvänäinen, *Romain F Laine*, Sujan Ghimire, Gautier Follain, *Ricardo Henriques*, Guillaume Jacquemet Published in Journal of Cell Science, February 2023 (see publication) Research themes: New Methods, Software Type: Paper

2022

Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy Daria Aristova, Roman Selin, *Hannah Sophie Heil*, Viktoriia Kosach, Yuriy Slominsky, Sergiy Yarmoluk, Vasyl Pekhnyo, Vladyslava Kovalska, *Ricardo Henriques*, Andriy Mokhir, Svitlana Chernii Published in American Chemical Society, December 2022 (see publication) Research themes: New Methods, Probes Type: Paper

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

DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches *Christoph Spahn*, *Estibaliz Gómez-de-Mariscal*, *Romain F Laine*, *Pedro M Pereira*, *Lucas von Chamier*, Mia Conduit, Mariana G Pinho, Guillaume Jacquemet, Séamus Holden, Mike Heilemann, *Ricardo Henriques* Published in Nature Communications Biology, July 2022 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis Wei Ouyang, Fynn Beuttenmueller, *Estibaliz Gómez-de-Mariscal*, Constantin Pape, Tom Burke, Carlos Garcia-López-de-Haro, Craig Russell, Lucía Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, Dominik Kutra, Maksim Novikov, Martin Weigert, Uwe Schmidt, Peter Bankhead, Guillaume Jacquemet, Daniel Sage, *Ricardo Henriques*, Arrate Muñoz-Barrutia, Emma Lundberg, Florian Jug, Anna Kreshuk Published in bioRxiv, June 2022 (see preprint) Research themes: New Methods, Software Type: Preprint

Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration David Tomaz, *Pedro Matos Pereira*, Nadia Guerra, Julian Dyson, Keith Gould, *Ricardo Henriques* Published in Frontiers in immunology, June 2022 (see publication) Research themes: Cell Signalling Type: Paper, Corresponding author

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

Expansion Microscopy on Saccharomyces cerevisiae Artemis G. Korovesi, *Leonor Morgado*, Marco Fumasoni, *Ricardo Henriques*, *Hannah S. Heil*, *Mario Del Rosario* Published in microPublication Biology, April 2022 (see publication) Research themes: Microbiology, Structural Biology Type: Paper

The LEGO® brick road to open science and biotechnology Etienne Boulter, Julien Colombelli, *Ricardo Henriques*, Chloé C Féral Published in Trends in Biotechnology, March 2022 (see publication) Research themes: New Methods, Hardware Type: Review, Corresponding author

Physical mechanisms of ESCRT-III–driven cell division Lena Harker-Kirschneck, Anne E Hafner, Tina Yao, Andre Arashiro Pulschen, Fredrik Hurtig, Christian Vanhille Campos, Dawid Hryniuk, *Sian Culley*, *Ricardo Henriques*, Buzz Baum, Andela Šarić Published in PNAS, January 2022 (see publication) Research themes: Microbiology, Structural Biology Type: Paper

2021

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

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* Published in Viruses, January 2021 (see publication) Research themes: Cell Signalling, Host-Pathogen Interactions, Microbiology, Structural Biology Type: Review

Single-molecule super-resolution imaging of T-cell plasma membrane CD4 redistribution upon HIV-1 binding *Yue Yuan*, *Caron Jacobs*, Isabel Llorente Garcia, *Pedro M Pereira*, Scott P.Lawrence, *Romain F Laine*, Mark Marsh, *Ricardo Henriques* Published in Viruses, January 2021 (see publication) Research themes: Cell Signalling, Host-Pathogen Interactions, Microbiology, Structural Biology Type: Paper, Corresponding author

2020

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

Closed mitosis requires local disassembly of the nuclear envelope Gautam Dey, *Siân Culley*, Scott Curran, *Ricardo Henriques*, Wanda Kukulski, Buzz Baum Published in Nature, August 2020 (see publication or preprint) Research themes: Cell Division, Microbiology Type: Paper

The proteasome controls ESCRT-III–mediated cell division in an archaeon Gabriel Tarrason Risa, Fredrik Hurtig, Sian Bray, Anne E Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, Dimitra Papatziamou, Delyan R Mutavchiev, Catherine Fan, Leticia Meneguello, Andre Arashiro Pulschen, Gautam Dey, *Siân Culley*, Mairi Kilkenny, Diorge P Souza, Luca Pellegrini, Robertus AM de Bruin, *Ricardo Henriques*, Ambrosius P Snijders, Anđela Šarić, Ann-Christin Lindås, Nicholas P Robinson, Buzz Baum Published in Science, August 2020 (see publication or preprint) Research themes: Cell Division 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

2019

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

Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion *Robert DM Gray*, *David Albrecht*, Corina Beerli, Moona Huttunen, Gary H Cohen, Ian J White, Jemima J Burden, *Ricardo Henriques*, Jason Mercer Published in Nature microbiology, July 2019 (see publication) Research themes: Host-Pathogen Interactions, Microbiology, Structural Biology Type: Paper, 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

TMEM16F activation by Ca 2+ triggers plasma membrane expansion and directs PD-1 trafficking Christopher Bricogne, Michael Fine, *Pedro M Pereira*, Julia Sung, Maha Tijani, Youxue Wang, *Ricardo Henriques*, Mary K Collins, Donald W Hilgemann Published in Scientific reports, January 2019 (see publication) Research themes: Cell Signalling Type: Paper

2018

Septins recognize and entrap dividing bacterial cells for delivery to lysosomes Sina Krokowski, Damián Lobato-Márquez, Arnaud Chastanet, *Pedro Matos Pereira*, Dimitrios Angelis, Dieter Galea, Gerald Larrouy-Maumus, *Ricardo Henriques*, Elias T Spiliotis, Rut Carballido-López, Serge Mostowy Published in Cell host & microbe, December 2018 (see publication) Research themes: Host-Pathogen Interactions, Microbiology Type: Paper

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

Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration David Tomaz, *Pedro Matos Pereira*, Nadia Guerra, Julian Dyson, *Ricardo Henriques*, Keith Gould Published in bioRxiv, August 2018 (see preprint) Research themes: Cell Signalling Type: Preprint

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

The role of mitotic cell-substrate adhesion re-modeling in animal cell division Christina L Dix, Helen K Matthews, Marina Uroz, Susannah McLaren, Lucie Wolf, Nicholas Heatley, Zaw Win, *Pedro Almada*, *Ricardo Henriques*, Michael Boutros, Xavier Trepat, Buzz Baum Published in Developmental cell, April 2018 (see publication) Research themes: Cell Division Type: Paper

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

Heterogeneous localisation of membrane proteins in Staphylococcus aureus Felix Weihs, Katarzyna Wacnik, Robert D Turner, *Siân Culley*, *Ricardo Henriques*, Simon J Foster Published in Scientific reports, April 2018 (see publication) Research themes: Microbiology Type: Paper

2017

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

2016

K63-linked ubiquitination targets Toxoplasma gondii for endo-lysosomal destruction in IFNγ-stimulated human cells Barbara Clough, Joseph D Wright, *Pedro M Pereira*, Elizabeth M Hirst, Ashleigh C Johnston, *Ricardo Henriques*, Eva-Maria Frickel Published in PLoS pathogens, November 2016 (see publication) Research themes: Host-Pathogen Interactions, Microbiology Type: Paper

HIV-1 Nef impairs the formation of calcium membrane territories controlling the signaling nanoarchitecture at the immunological synapse Joana G Silva, Nuno P Martins, *Ricardo Henriques*, Helena Soares Published in The Journal of Immunology, November 2016 (see publication) Research themes: Host-Pathogen Interactions, Microbiology Type: Paper

Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti Janine Scholefield, *Ricardo Henriques*, Anca F Savulescu, Elisabeth Fontan, Alix Boucharlat, Emmanuel Laplantine, Asma Smahi, Alain Israël, Fabrice Agou, Musa M Mhlanga Published in Nature communications, September 2016 (see publication) Research themes: Cell Signalling, Structural Biology Type: Paper, Co-first 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

Mitochondria mediate septin cage assembly to promote autophagy of Shigella Andrea Sirianni, Sina Krokowski, Damián Lobato‐Márquez, Stephen Buranyi, Julia Pfanzelter, Dieter Galea, Alexandra Willis, *Siân Culley*, *Ricardo Henriques*, Gerald Larrouy‐Maumus, Michael Hollinshead, Vanessa Sancho‐Shimizu, Michael Way, Serge Mostowy Published in EMBO reports, July 2016 (see publication) Research themes: Host-Pathogen Interactions Type: Paper

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

2015

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

2014

TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO–IKK supramolecular structures Nadine Tarantino, Jean-Yves Tinevez, Elizabeth Faris Crowell, Bertrand Boisson, *Ricardo Henriques*, Musa Mhlanga, Fabrice Agou, Alain Israël, Emmanuel Laplantine Published in Journal of Cell Biology, January 2014 (see publication) Research themes: Cell Signalling Type: Paper

2013

Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse Helena Soares, *Ricardo Henriques*, Martin Sachse, Leandro Ventimiglia, Miguel A Alonso, Christophe Zimmer, Maria-Isabel Thoulouze, Andrés Alcover Published in Journal of Experimental Medicine, October 2013 (see publication) Research themes: Cell Signalling Type: Paper

2010

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