Enabling Live-Cell 4D Super-Resolution Microscopy Guided by Artificial Intelligence

Project Information

SelfDriving4DSR

Grant agreement ID: 101001332

DOI

10.3030/101001332

EC signature date 11 February 2021

Start date 1 July 2021

End date 30 June 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 905,00

EU contribution

€ 1 999 905,00

Coordinated by

UNIVERSIDADE NOVA DE LISBOA
Portugal

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (16)

High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation

Author(s): 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
Published in: Nature Methods, 2023, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-02057-w

Democratising deep learning for microscopy with ZeroCostDL4Mic

Author(s): 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, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-22518-0

DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches

Author(s): 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: Communications Biology, 2022, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-022-03634-z

Avoiding a replication crisis in deep-learning-based bioimage analysis

Author(s): Romain F. Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet
Published in: Nature Methods, Issue 18, 2021, Page(s) 1136-1144, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-021-01284-3

CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data

Author(s): Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W. Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet
Published in: PLOS Biology, Issue 22, 2024, Page(s) e3002740, ISSN 1545-7885
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.pbio.3002740

Mapping molecular complexes with super-resolution microscopy and single-particle analysis

Author(s): Afonso Mendes; Hannah S. Heil; Simao Coelho; Christophe Leterrier; Ricardo Henriques
Published in: Open Biology, Issue 2, 2022, ISSN 2046-2441
Publisher: Royal Society Publishing
DOI: 10.1098/rsob.220079

Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy

Author(s): 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: ACS Omega, Issue 3, 2022, ISSN 2470-1343
Publisher: American Chemical Society omega
DOI: 10.1021/acsomega.2c05231

Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus

Author(s): Simon Schäper, António D. Brito, Bruno M. Saraiva, Georgia R. Squyres, Matthew J. Holmes, Ethan C. Garner, Zach Hensel, Ricardo Henriques, Mariana G. Pinho
Published in: Nature Microbiology, Issue 9, 2024, Page(s) 1049-1063, ISSN 2058-5276
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41564-024-01629-6

Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework

Author(s): Bruno M. Saraiva, Inês Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Published in: Nature Methods, Issue 22, 2025, Page(s) 283-286, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-024-02562-6

Fast4DReg: Fast registration of 4D microscopy datasets

Author(s): Joanna W Pylvänäinen; Romain F Laine; Bruno M.S. Saraiva; Sujan Ghimire; Gautier Follain; Ricardo Henriques; Guillaume Jacquemet
Published in: Journal of Cell Science, 2023, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.

The rise of data‐driven microscopy powered by machine learning

Author(s): Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Published in: Journal of Microscopy, Issue 295, 2024, Page(s) 85-92, ISSN 0022-2720
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jmi.13282

Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding.

Author(s): Yue Yuan; Caron Jacobs; Caron Jacobs; Isabel Llorente Garcia; Pedro M. Pereira; Pedro M. Pereira; Scott P. Lawrence; Romain F. Laine; Romain F. Laine; Mark Marsh; Ricardo Henriques; Ricardo Henriques; Ricardo Henriques
Published in: Viruses, Issue 1, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13010142

Expansion microscopy on Saccharomyces cerevisiae

Author(s): Artemis G. Korovesi, Leonor Morgado, Marco Fumasoni, Ricardo Henriques, Hannah Heil, Mario Del Rosario
Published in: microPublication Biology, 2022, ISSN 2578-9430
Publisher: microPublication Biology
DOI: 10.17912/micropub.biology.000566

Nanoscale Colocalization of NK Cell Activating and Inhibitory Receptors Controls Signal Integration

Author(s): David Tomaz; Pedro Matos Pereira; Nadia Guerra; Julian Dyson; Keith Gould; Ricardo Henriques
Published in: Frontiers in Immunology, 2022, ISSN 1664-3224
Publisher: Frontiers in immunology
DOI: 10.3389/fimmu.2022.868496

eHooke: A tool for automated image analysis of spherical bacteria based on cell cycle progression

Author(s): Bruno M. Saraiva, Ludwig Krippahl, Sérgio R. Filipe, Ricardo Henriques, Mariana G. Pinho
Published in: Biological Imaging, Issue 1, 2021, ISSN 2633-903X
Publisher: Cambridge University Press (CUP)
DOI: 10.1017/s2633903x21000027

Live-cell imaging in the deep learning era

Author(s): Joanna W Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Published in: Current opinion in cell biology, 2023, ISSN 1879-0410
Publisher: Current opinion in cell biology
DOI: 10.1016/j.ceb.2023.102271

Non-peer reviewed articles (8)

PhotoFiTT: A Quantitative Framework for Assessing Phototoxicity in Live-Cell Microscopy Experiments

Author(s): Mario Del Rosario, Estibaliz Gómez-de-Mariscal, Leonor Morgado, Raquel Portela, Guillaume Jacquemet, Pedro M. Pereira, Ricardo Henriques
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2024.07.16.603046

Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction

Author(s): Simon Schaeper, Antonio D Brito, Bruno M Saraiva, Georgia R Squyres, Matthew J Holmes, Ethan C Garner, Zach Hensel, Ricardo Henriques, Mariana G Pinho
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.06.29.547026

NanoPyx: super-fast bioimage analysis powered by adaptive machine learning

Author(s): Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.08.13.553080

Transertion and cell geometry organize the Escherichia coli nucleoid during rapid growth

Author(s): Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.10.16.562172

Roadmap on Deep Learning for Microscopy

Author(s): Volpe, Giovanni; Wählby, Carolina; Tian, Lei; Hecht, Michael; Yakimovich, Artur; Monakhova, Kristina; Waller, Laura; Sbalzarini, Ivo F.; Metzler, Christopher A.; Xie, Mingyang; Zhang, Kevin; Lenton, Isaac C. D.; Rubinsztein-Dunlop, Halina; Brunner, Daniel; Bai, Bijie; Ozcan, Aydogan; Midtvedt, Daniel; Wang, Hao; Sladoje, Nataša; Lindblad, Joakim; Smith, Jason T.; Ochoa, Marien; Barroso, Margarid
Published in: arXiv, 2023, ISSN 2331-8422
Publisher: arXiv
DOI: 10.48550/arxiv.2303.03793

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Author(s): Gómez-de-Mariscal, Estibaliz; Del Rosario, Mario; Pylvänäinen, Joanna W; Jacquemet, Guillaume; Henriques, Ricardo
Published in: arXiv, 2023, ISSN 2331-8422
Publisher: arXiv
DOI: 10.48550/arxiv.2308.04387

CLEM-Reg: An automated point cloud based registration algorithm for correlative light and volume electron microscopy

Author(s): Daniel Krentzel; Matouš Elphick; Marie-Charlotte Domart; Christopher J. Peddie; Romain F. Laine; Ricardo Henriques; Lucy M. Collinson; Martin L. Jones
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.05.11.540445

DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible

Author(s): Iván Hidalgo-Cenalmor, Joanna W Pylvänäinen, Mariana G Ferreira, Craig T Russell, Ignacio Arganda-Carreras, AI4Life Consortium, Guillaume Jacquemet, Ricardo Henriques, Estibaliz Gómez-de-Mariscal
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2023.11.19.567606