Top Publications


Most cited publications by our lab from the last 5 years


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
Citations: 470
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
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
Citations: 302
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
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
Citations: 176
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
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
Citations: 80
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
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
Citations: 55
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
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
Citations: 53
Technologies: CARE, NanoJ, NanoJ-Fluidics and NanoJ-SQUIRREL
Funded by: BBSRC and Wellcome Trust
DOI: 10.3389/fimmu.2019.00675
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
Citations: 28
Technologies: CARE
Funded by: ERC
DOI: 10.3390/v13010142
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
Citations: 24
Technologies: CARE
Funded by: BBSRC
DOI: 10.1214/19-AOAS1240
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
Citations: 12
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
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
Citations: 8
Technologies: NanoJ and NanoJ-SRRF
DOI: 10.1117/12.2510761
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
Citations: 8
Technologies: NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF and Super-Beacons
Funded by: BBSRC and Wellcome Trust
DOI: 10.1111/tra.12728
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
Citations: 4
Technologies: NanoJ and NanoJ-SQUIRREL
Funded by: BBSRC, EMBO and ERC
DOI: 10.3389/fimmu.2022.868496
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
Citations: 3
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
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