Publications


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For a fully updated list of publications, check our Google Scholar profile.

Publications by our lab



2024

Structural Repetition Detector - multi-scale quantitative mapping of molecular complexes through microscopy
Afonso Mendes, Bruno M Saraiva, Guillaume Jacquemet, Joao I Mamede, Christophe Leterrier, Ricardo Henriques
Preprint published in bioRxiv, September 2024
Technologies: CARE, Nuclear-Pores as references and SReD
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1101/2024.09.16.613204
PhotoFiTT - A Quantitative Framework for Assessing Phototoxicity in Live-Cell Microscopy Experiments
Mario Del Rosario, Estibaliz Gómez-de-Mariscal, Leonor Morgado, Raquel Portela, Guillaume Jacquemet, Pedro M. Pereira, Ricardo Henriques
Preprint published in bioRxiv, July 2024
Technologies: CARE, DL4MicEverywhere, NanoJ-SRRF, PhotoFiTT and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022
DOI: 10.1101/2024.07.16.603046
DL4MicEverywhere - deep learning for microscopy made flexible, shareable and reproducible
Iván Hidalgo-Cenalmor, Joanna W. Pylvänäinen, Mariana G. Ferreira, Craig T. Russell, Alon Saguy, Ignacio Arganda-Carreras, Yoav Shechtman, Guillaume Jacquemet, Ricardo Henriques, Estibaliz Gómez-de-Mariscal
Paper published in Nature Methods, May 2024
Technologies: BioImage Model Zoo, DL4MicEverywhere and ZeroCostDL4Mic
Funded by: EMBO, ERC, H2021 and H2022
News: Labonline, MSN, AZoRobotics and Aamuset Kaupunkimedia
Blogs: news-medical.net
DOI: 10.1038/s41592-024-02295-6
Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus
Simon Schäper, António D. Brito, Bruno M. Saraiva, Georgia R. Squyres, Matthew J. Holmes, Ethan C. Garner, Zach Hensel, Ricardo Henriques, Mariana G. Pinho
Paper published in Nature Microbiology, March 2024
Technologies: CARE and NanoJ
Funded by: EMBO and ERC
DOI: 10.1038/s41564-024-01629-6
The rise of data‐driven microscopy powered by machine learning
Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Review published in Journal of Microscopy, March 2024
Technologies: NanoJ and NanoJ-Fluidics
Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022
DOI: 10.1111/jmi.13282
Harnessing artificial intelligence to reduce phototoxicity in live imaging
Estibaliz Gómez-de-Mariscal, Mario Del Rosario, Joanna W. Pylvänäinen, Guillaume Jacquemet, Ricardo Henriques
Perspective published in Journal of Cell Science, February 2024
Technologies: BioImage Model Zoo, CARE, DeepBacs, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1242/jcs.261545
CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data
Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet
Published in PLOS Biology, January 2024
Technologies: CARE, CellTracksColab and ZeroCostDL4Mic
DOI: 10.1371/journal.pbio.3002740
Nano-org, a functional resource for single-molecule localisation microscopy data
Sandeep Shirgill, Daniel J Nieves, Jeremy A Pike, Mohammad A Ahmed, Mohammed HH Baragilly, Kylie Savoye, Jonathan Worboys, Khodor Hazime, Adrian Garcia, David J Williamson
Preprint published in bioRxiv, January 2024
Technologies: nano-org
Funded by: EMBO, ERC, H2021 and H2022
DOI: 10.1101/2024.08.06.606779

2023

Decoding life's inner workings - advances in quantitative bioimaging
Ricardo Henriques, Christophe Leterrier, Aubrey Weigel
Editorial published in Open Biology, November 2023
DOI: 10.1098/rsob.230329
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, Theresa Wiesner, Damián Martínez, Tommaso Galgani, Louise Régnier, Aki Stubb, Gautier Follain, Samantha Webster, Jesse Goyette, Aurelien Dauphin, Audrey Salles, Siân Culley, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, Ricardo Henriques
Paper published in Nature Methods, November 2023
Technologies: CARE, NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoPyx and Nuclear-Pores as references
Funded by: CZI, EMBO, ERC, FCT, H2021, H2022, InnOValley and Wellcome Trust
News: Photonics.com, The Science Times, Optics.org and Phys.org
Blogs: Springer Nature Protocols and Methods Community
DOI: 10.1038/s41592-023-02057-w
Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth
Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann
Preprint published in bioRxiv, October 2023
Technologies: CARE, DeepBacs and ZeroCostDL4Mic
Funded by: EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.10.16.562172
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, FCT, H2021 and H2022
DOI: 10.1101/2023.08.13.553080
CLEM-Reg - An automated point cloud based registration algorithm for correlative light and volume electron microscopy
Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones
Preprint published in bioRxiv, May 2023
Technologies: CARE and ZeroCostDL4Mic
Funded by: CZI and ERC
DOI: 10.1101/2023.05.11.540445
Live-cell imaging in the deep learning era
Joanna W Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Review published in Current Opinion in Cell Biology, January 2023
Technologies: BioImage Model Zoo, CARE, DeepBacs, Fast4DReg, NanoJ, NanoJ-eSRRF, NanoJ-Fluidics, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC and H2021
DOI: 10.1016/j.ceb.2023.102271
Fast4DReg–fast registration of 4D microscopy datasets
Joanna W Pylvänäinen, Romain F Laine, Bruno MS Saraiva, Sujan Ghimire, Gautier Follain, Ricardo Henriques, Guillaume Jacquemet
Paper published in Journal of Cell Science, January 2023
Technologies: CARE, Fast4DReg, NanoJ and ZeroCostDL4Mic
Funded by: CZI and ERC
DOI: 10.1242/jcs.260728
This microtubule does not exist - Super-resolution microscopy image generation by a diffusion model
Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez-de-Mariscal, Iván Hidalgo-Cenalmor, Onit Alalouf, Ricardo Henriques, Yoav Shechtman
Preprint published in bioRxiv, January 2023
Technologies: CARE and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.07.06.548004
Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction
Simon Schaeper, Antonio D Brito, Bruno M Saraiva, Georgia R Squyres, Matthew J Holmes, Ethan C Garner, Zach Hensel, Ricardo Henriques, Mariana G Pinho
Preprint published in bioRxiv, January 2023
Technologies: NanoJ
Funded by: EMBO and ERC
DOI: 10.1101/2023.06.29.547026
Roadmap on deep learning for microscopy
Giovanni Volpe, Carolina Wählby, Lei Tian, Michael Hecht, Artur Yakimovich, Kristina Monakhova, Laura Waller, Ivo F Sbalzarini, Christopher A Metzler, Mingyang Xie, Kevin Zhang, Isaac CD Lenton, Halina Rubinsztein-Dunlop, Daniel Brunner, Bijie Bai, Aydogan Ozcan, Daniel Midtvedt, Hao Wang, Nataša Sladoje, Joakim Lindblad, Jason T Smith, Marien Ochoa, Margarida Barroso, Xavier Intes, Tong Qiu, Li-Yu Yu, Sixian You, Yongtao Liu, Maxim A Ziatdinov, Sergei V Kalinin, Arlo Sheridan, Uri Manor, Elias Nehme, Ofri Goldenberg, Yoav Shechtman, Henrik K Moberg, Christoph Langhammer, Barbora Špačková, Saga Helgadottir, Benjamin Midtvedt, Aykut Argun, Tobias Thalheim, Frank Cichos, Stefano Bo, Lars Hubatsch, Jesus Pineda, Carlo Manzo, Harshith Bachimanchi, Erik Selander, Antoni Homs-Corbera, Martin Fränzl, Kevin de Haan, Yair Rivenson, Zofia Korczak, Caroline Beck Adiels, Mite Mijalkov, Dániel Veréb, Yu-Wei Chang, Joana B Pereira, Damian Matuszewski, Gustaf Kylberg, Ida-Maria Sintorn, Juan C Caicedo, Beth A Cimini, Muyinatu A Lediju Bell, Bruno M Saraiva, Guillaume Jacquemet, Ricardo Henriques, Wei Ouyang, Trang Le, Estibaliz Gómez-de-Mariscal, Daniel Sage, Arrate Muñoz-Barrutia, Ebba Josefson Lindqvist, Johanna Bergman
Preprint published in arXiv, January 2023
Technologies: BioImage Model Zoo, CARE and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC and H2021
DOI: 10.48550/arXiv.2303.03793

2022

Mapping molecular complexes with super-resolution microscopy and single-particle analysis
Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques
Review 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
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
Paper published in Communications Biology, July 2022
Technologies: BioImage Model Zoo, CARE, DeepBacs, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: CZI, ERC, FCT and Wellcome Trust
DOI: 10.1038/s42003-022-03634-z
The LEGO® brick road to open science and biotechnology
Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C. Féral
Review published in Trends in Biotechnology, March 2022
Technologies: NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1016/j.tibtech.2022.02.003
Physical mechanisms of ESCRT-III–driven cell division
Lena Harker-Kirschneck, Anne E. Hafner, Tina Yao, Christian Vanhille-Campos, Xiuyun Jiang, Andre Pulschen, Fredrik Hurtig, Dawid Hryniuk, Siân Culley, Ricardo Henriques, Buzz Baum, Anđela Šarić
Paper published in Proceedings of the National Academy of Sciences, January 2022
Funded by: Wellcome Trust
DOI: 10.1073/pnas.2107763119
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
Paper published in ACS omega, January 2022
Funded by: EMBO, ERC and H2021
DOI: 10.1021/acsomega.2c05231
Expansion Microscopy on Saccharomyces cerevisiae
AG Korovesi, L Morgado, M Fumasoni, R Henriques, HS Heil, M Del Rosario
Paper published in microPublication Biology, January 2022
Technologies: CARE
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.17912/micropub.biology.000566
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
Preprint published in BioRxiv, January 2022
Technologies: BioImage Model Zoo and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC and H2021
DOI: 10.1101/2022.06.07.495102
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
Paper published in Frontiers in Immunology, January 2022
Technologies: NanoJ and NanoJ-SQUIRREL
Funded by: BBSRC, EMBO and ERC
DOI: 10.3389/fimmu.2022.868496

2021

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
Paper published in Biological Imaging, September 2021
Technologies: CARE
Funded by: ERC and Wellcome Trust
DOI: 10.1017/s2633903x21000027
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
Paper published in Nature Communications, April 2021
Technologies: CARE and DeepAutoFocus
Funded by: BBSRC and Wellcome Trust
News: Nanowerk
DOI: 10.1038/s41467-021-22526-0
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
Paper published in Nature Communications, April 2021
Technologies: CARE, FBSR-TFM, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
News: AZO Life Sciences, Drug Target Review, Nanotechnology Now and The Medical News
Blogs: Microbiome Digest - Bik's Picks
DOI: 10.1038/s41467-021-22518-0
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
Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding
Yue Yuan, Caron A. Jacobs, Isabel Llorente Garcia, Pedro M. Pereira, Scott P. Lawrence, Romain F. Laine, Mark Marsh, Ricardo Henriques
Paper published in Viruses, January 2021
Technologies: CARE
Funded by: ERC
DOI: 10.3390/v13010142
Avoiding a replication crisis in deep-learning-based bioimage analysis
Romain F Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet
Perspective published in Nature methods, January 2021
Technologies: CARE and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1038/s41592-021-01284-3
The field guide to 3D printing in microscopy
Mario Del Rosario, Hannah S Heil, Afonso Mendes, Vittorio Saggiomo, Ricardo Henriques
Review published in Adv. Biol., January 2021
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1002/adbi.202100994

2020

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, Ana Mafalda Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee
Paper published in Nature Methods, October 2020
Technologies: Nuclear-Pores as references, QuickPALM and vLume
Funded by: BBSRC and Wellcome Trust
News: La Razon (ESP), ZAP, Medium US and IEEE Spectrum
Blogs: Qubit, , Tech Explorist and Whats New
DOI: 10.1038/s41592-020-0962-1
Closed mitosis requires local disassembly of the nuclear envelope
Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum
Paper published in Nature, August 2020
Technologies: CARE, NanoJ, NanoJ-SRRF and Nuclear-Pores as references
Funded by: BBSRC and Wellcome Trust
News: Nature Asia
DOI: 10.1038/s41586-020-2648-3
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 A. M. de Bruin, Ricardo Henriques, Ambrosius P. Snijders, Anđela Šarić, Ann-Christin Lindås, Nicholas P. Robinson, Buzz Baum
Paper published in Science, August 2020
Technologies: NanoJ and NanoJ-SRRF
News: NRK, Scitech Daily, NCYT - Noticias de la Ciencia y la Technologia and UPI.com
DOI: 10.1126/science.aaz2532
The cell biologist's guide to super-resolution microscopy
Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, Ricardo Henriques, Christophe Leterrier
Review published in Journal of Cell Science, June 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SRRF, Nuclear-Pores as references and ZeroCostDL4Mic
Funded by: BBSRC and Wellcome Trust
News: ScienMag and EurekAlert!
DOI: 10.1242/jcs.240713
Between life and death - strategies to reduce phototoxicity in super-resolution microscopy
Kalina L Tosheva, Yue Yuan, Pedro Matos Pereira, Siân Culley, Ricardo Henriques
Review published in Journal of Physics D - Applied Physics, January 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab6b95
An Introduction to Live-Cell Super-Resolution Imaging
Siân Culley, Pedro Matos Pereira, Romain F Laine, Ricardo Henriques
Book chapter published in Imaging from Cells to Animals In Vivo, January 2020
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and QuickPALM
DOI: 10.1201/9781315174662-4
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
Paper published in Traffic, January 2020
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and Super-Beacons
Funded by: BBSRC and Wellcome Trust
DOI: 10.1111/tra.12728
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
Paper published in Current Biology, January 2020
Technologies: Sulfoscope
Funded by: Wellcome Trust
DOI: 10.1016/j.cub.2020.05.021
Fluctuation-based super-resolution traction force microscopy
Aki Stubb, Romain F Laine, Mitro Miihkinen, Hellyeh Hamidi, Camilo Guzmán, Ricardo Henriques, Guillaume Jacquemet, Johanna Ivaska
Paper published in Nano letters, January 2020
Technologies: CARE, FBSR-TFM, NanoJ, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC
DOI: 10.1021/acs.nanolett.9b04083

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
Paper published in Nature Methods, September 2019
Technologies: CARE, NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and Nuclear-Pores as references
Funded by: BBSRC and Wellcome Trust
News: Mirage News
DOI: 10.1038/s41592-019-0574-9
Artificial intelligence for microscopy - what you should know
Lucas von Chamier, Romain F. Laine, Ricardo Henriques
Review published in Biochemical Society Transactions, July 2019
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1042/bst20180391
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
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
Paper published in Nature Methods, April 2019
Technologies: NanoJ-SRRF and QuickPALM
Funded by: BBSRC
DOI: 10.1038/s41592-019-0364-4
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
TMEM16F activation by Ca2+ 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
Paper published in Scientific Reports, January 2019
Funded by: BBSRC
DOI: 10.1038/s41598-018-37056-x
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
Paper published in Single molecule spectroscopy and superresolution imaging XII, January 2019
Technologies: NanoJ and NanoJ-SRRF
DOI: 10.1117/12.2510761
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, January 2019
Technologies: CARE
Funded by: BBSRC
DOI: 10.1214/19-AOAS1240
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, January 2019
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SQUIRREL
Funded by: BBSRC and Wellcome Trust
DOI: 10.3389/fimmu.2019.00675

2018

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
Paper published in Nature Methods, November 2018
Technologies: CARE, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
News: Technology Networks, VBIO, Innovations Report and Informationsdienst Wissenschaft
DOI: 10.1038/s41592-018-0216-7
Heterogeneous localisation of membrane proteins in Staphylococcus aureus
Felix Weihs, Katarzyna Wacnik, Robert D. Turner, Siân Culley, Ricardo Henriques, Simon J. Foster
Paper published in Scientific Reports, February 2018
Technologies: NanoJ and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1038/s41598-018-21750-x
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
Paper published in Nature Methods, February 2018
Technologies: NanoJ, NanoJ-SQUIRREL, NanoJ-SRRF and QuickPALM
Funded by: BBSRC and Wellcome Trust
News: physicsworld.com
DOI: 10.1038/nmeth.4605
SRRF - Universal live-cell super-resolution microscopy
Siân Culley, Kalina L Tosheva, Pedro Matos Pereira, Ricardo Henriques
Paper published in The international journal of biochemistry & cell biology, January 2018
Technologies: NanoJ, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1016/j.biocel.2018.05.014
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
Published in Developmental cell, January 2018
Funded by: BBSRC
DOI: 10.1016/j.devcel.2018.03.009
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

2017

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

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
Paper published in PLOS Pathogens, November 2016
Funded by: BBSRC
News: Phys.org and Bionity
Blogs: The Toxoplasma Blog
DOI: 10.1371/journal.ppat.1006027
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
Paper published in The Journal of Immunology, October 2016
Funded by: BBSRC
DOI: 10.4049/jimmunol.1601132
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
Paper published in Nature Communications, August 2016
Technologies: QuickPALM
Funded by: BBSRC
News: Azom.com
DOI: 10.1038/ncomms12471
Infection Counter - Automated Quantification of in Vitro Virus Replication by Fluorescence Microscopy
Siân Culley, Greg Towers, David Selwood, Ricardo Henriques, Joe Grove
Paper published in Viruses, July 2016
Technologies: Infection-Counter
Funded by: BBSRC
DOI: 10.3390/v8070201
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
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
Paper published in Nature Communications, January 2016
Technologies: QuickPALM
Funded by: BBSRC and FCT
DOI: 10.1038/ncomms12629
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
Paper published in EMBO reports, January 2016
Funded by: BBSRC
DOI: 10.15252/embr.201541832

2015

PALM and STORM - Into large fields and high-throughput microscopy with sCMOS detectors
Pedro Almada, Siân Culley, Ricardo Henriques
Review published in Methods, January 2015
Technologies: QuickPALM
DOI: 10.1016/j.ymeth.2015.06.004
High-content 3D multicolor super-resolution localization microscopy
Pedro M Pereira, Pedro Almada, Ricardo Henriques
Book chapter published in Methods in cell biology, January 2015
Technologies: QuickPALM

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
Paper published in Journal of Cell Biology, January 2014
DOI: 10.1083/jcb.201307172

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
Paper published in Journal of Experimental Medicine, January 2013
Technologies: QuickPALM
DOI: 10.1084/jem.20130150

2012

Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion
Soudeh Ehsani, José Carlos Santos, Cristina D Rodrigues, Ricardo Henriques, Laurent Audry, Christophe Zimmer, Philippe Sansonetti, Guy Tran Van Nhieu, Jost Enninga
Paper published in Infection and immunity, January 2012
Technologies: QuickPALM
DOI: 10.1128/IAI.06391-11
Highly dynamic host actin reorganization around developing Plasmodium inside hepatocytes
Carina SS Gomes-Santos, Maurice A Itoe, Cristina Afonso, Ricardo Henriques, Rui Gardner, Nuno Sepulveda, Pedro D Simoes, Helena Raquel, Antonio Paulo Almeida, Luis F Moita, Friedrich Frischknecht, Maria M Mota
Paper published in PLoS One, January 2012
DOI: 10.1371/journal.pone.0029408
Enhanced epifluorescence microscopy by uniform and intensity optimized illumination
Sébastien Herbert, Ricardo Henriques
Perspective published in Cytometry Part A, January 2012
DOI: 10.1002/cyto.a.21177
Single-molecule localization super-resolution microscopy - deeper and faster
Sébastien Herbert, Helena Soares, Christophe Zimmer, Ricardo Henriques
Review published in Microscopy and microanalysis, January 2012
Technologies: QuickPALM
DOI: 10.1017/S1431927612013347
Superresolution imaging of HIV in infected cells with FlAsH-PALM
Mickaël Lelek, Francesca Di Nunzio, Ricardo Henriques, Pierre Charneau, Nathalie Arhel, Christophe Zimmer
Paper published in Proceedings of the National Academy of Sciences, January 2012
DOI: 10.1073/pnas.1013267109

2011

PALM and STORM - a super-resolution molecular view into living cells
C Griffiths, R Henriques, MM Mhlanga
Review published in Biotechnology International, January 2011
PALM and STORM - unlocking live‐cell super‐resolution
Ricardo Henriques, Caron Griffiths, E Hesper Rego, Musa M Mhlanga
Review published in Biopolymers, January 2011
Technologies: QuickPALM
DOI: 10.1002/bip.21586

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
Paper published in Nature Methods, January 2010
Technologies: QuickPALM
DOI: 10.1038/nmeth0510-339

2009

High-throughput SNP genotyping - combining tag SNPs and molecular beacons
Luis B Barreiro, Ricardo Henriques, Musa M Mhlanga
Book chapter published in Single Nucleotide Polymorphisms - Methods and Protocols, January 2009
DOI: 10.1007/978-1-60327-411-1_17
Chronic arthritis directly induces quantitative and qualitative bone disturbances leading to compromised biomechanical properties
J Caetano-Lopes, AM Nery, R Henriques, H Canhão, J Duarte, PM Amaral, M Vale, R Moura, PA Pereira, P Weinmann, S Abdulghani, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, M Viana Queiroz, YT Konttinen, L Graça, MF Vaz, JE Fonseca
Paper published in Clinical & Experimental Rheumatology, January 2009
Imaging host-pathogen interactions
Friedrich Frischknecht, Spencer Shorte, Ulrike Engel, Keira Melican, Agneta Richter-Dahlfors, Petra Rohrbach, Miguel Prudêncio, Maik J Lehmann, Nicolas Chenouard, Alexandre Dufour, Jean-Christophe Olivo-Marin, Ricardo Henriques, Musa M Mhlanga, Matthias F Langhorst, Joerg Schaffer, Bernhard Goetze, Freddy Frischknecht, Matthias Gunzer, Simone Lepper
Editorial published in Biotechnol. J, January 2009
DOI: 10.1002/biot.200900129
PALM and STORM - what hides beyond the Rayleigh limit?
Ricardo Henriques, Musa M Mhlanga
Review published in Biotechnology Journal - Healthcare Nutrition Technology, January 2009
DOI: 10.1002/biot.200900024
Frontiers in fluorescence microscopy
José Rino, José Braga, Ricardo Henriques, Maria Carmo-Fonseca
Review published in International Journal of Developmental Biology, January 2009
DOI: 10.1387/ijdb.072351jr

2008

Degradation of bone biomechanical properties secondary to quantitative and qualitative bone disturbances induced by arthritis in SKG mice
J Caetano-Lopes, AM Nery, R Henriques, H Canhao, J Duarte, P Amaral, M Vale, R Moura, PA Pereira, P Weinmann, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, L Graca, M Viana Queiroz, MF Vaz, JE Fonseca
Paper published in Calcified Tissue International, January 2008