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

Informazioni relative al progetto

SelfDriving4DSR

ID dell’accordo di sovvenzione: 101001332

DOI

10.3030/101001332

Data della firma CE 11 Febbraio 2021

Data di avvio 1 Luglio 2021

Data di completamento 30 Giugno 2026

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 999 905,00

Contributo UE

€ 1 999 905,00

Coordinato da

UNIVERSIDADE NOVA DE LISBOA
Portugal

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (16)

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

Autori: 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
Pubblicato in: Nature Methods, 2023, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-023-02057-w

Democratising deep learning for microscopy with ZeroCostDL4Mic

Autori: 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
Pubblicato in: Nature Communications, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-22518-0

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

Autori: 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
Pubblicato in: Communications Biology, 2022, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-022-03634-z

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

Autori: Romain F. Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet
Pubblicato in: Nature Methods, Numero 18, 2021, Pagina/e 1136-1144, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-021-01284-3

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

Autori: Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W. Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet
Pubblicato in: PLOS Biology, Numero 22, 2024, Pagina/e e3002740, ISSN 1545-7885
Editore: Public Library of Science (PLoS)
DOI: 10.1371/journal.pbio.3002740

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

Autori: Afonso Mendes; Hannah S. Heil; Simao Coelho; Christophe Leterrier; Ricardo Henriques
Pubblicato in: Open Biology, Numero 2, 2022, ISSN 2046-2441
Editore: Royal Society Publishing
DOI: 10.1098/rsob.220079

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

Autori: Daria Aristova; Roman Selin; Hannah Sophie Heil; Viktoriia Kosach; Yuriy Slominsky; Sergiy Yarmoluk; Vasyl Pekhnyo; Vladyslava Kovalska; Ricardo Henriques; Andriy Mokhir; Svitlana Chernii
Pubblicato in: ACS Omega, Numero 3, 2022, ISSN 2470-1343
Editore: American Chemical Society omega
DOI: 10.1021/acsomega.2c05231

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

Autori: Simon Schäper, António D. Brito, Bruno M. Saraiva, Georgia R. Squyres, Matthew J. Holmes, Ethan C. Garner, Zach Hensel, Ricardo Henriques, Mariana G. Pinho
Pubblicato in: Nature Microbiology, Numero 9, 2024, Pagina/e 1049-1063, ISSN 2058-5276
Editore: 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

Autori: Bruno M. Saraiva, Inês Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Pubblicato in: Nature Methods, Numero 22, 2025, Pagina/e 283-286, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-024-02562-6

Fast4DReg: Fast registration of 4D microscopy datasets

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

The rise of data‐driven microscopy powered by machine learning

Autori: Leonor Morgado, Estibaliz Gómez‐de‐Mariscal, Hannah S. Heil, Ricardo Henriques
Pubblicato in: Journal of Microscopy, Numero 295, 2024, Pagina/e 85-92, ISSN 0022-2720
Editore: Blackwell Publishing Inc.
DOI: 10.1111/jmi.13282

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

Autori: 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
Pubblicato in: Viruses, Numero 1, 2021, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13010142

Expansion microscopy on Saccharomyces cerevisiae

Autori: Artemis G. Korovesi, Leonor Morgado, Marco Fumasoni, Ricardo Henriques, Hannah Heil, Mario Del Rosario
Pubblicato in: microPublication Biology, 2022, ISSN 2578-9430
Editore: microPublication Biology
DOI: 10.17912/micropub.biology.000566

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

Autori: David Tomaz; Pedro Matos Pereira; Nadia Guerra; Julian Dyson; Keith Gould; Ricardo Henriques
Pubblicato in: Frontiers in Immunology, 2022, ISSN 1664-3224
Editore: Frontiers in immunology
DOI: 10.3389/fimmu.2022.868496

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

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

Live-cell imaging in the deep learning era

Autori: Joanna W Pylvänäinen, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Guillaume Jacquemet
Pubblicato in: Current opinion in cell biology, 2023, ISSN 1879-0410
Editore: 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

Autori: Mario Del Rosario, Estibaliz Gómez-de-Mariscal, Leonor Morgado, Raquel Portela, Guillaume Jacquemet, Pedro M. Pereira, Ricardo Henriques
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: 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

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

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

Autori: Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2023.08.13.553080

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

Autori: Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2023.10.16.562172

Roadmap on Deep Learning for Microscopy

Autori: 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
Pubblicato in: arXiv, 2023, ISSN 2331-8422
Editore: arXiv
DOI: 10.48550/arxiv.2303.03793

Harnessing Artificial Intelligence To Reduce Phototoxicity in Live Imaging

Autori: Gómez-de-Mariscal, Estibaliz; Del Rosario, Mario; Pylvänäinen, Joanna W; Jacquemet, Guillaume; Henriques, Ricardo
Pubblicato in: arXiv, 2023, ISSN 2331-8422
Editore: arXiv
DOI: 10.48550/arxiv.2308.04387

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

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

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

Autori: 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
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2023.11.19.567606