A transformative data-driven live-cell super-resolution microscopy development to elucidate the initial steps of effective viral transmission
Agency: EMBO
Type: Postdoctoral Fellowships
Principal Investigator: Estibaliz Gómez-de-Mariscal
Start-date: July 2022
End-date: June 2024
Grant Code: ALTF 174-2022
Type: Postdoctoral Fellowships
Principal Investigator: Estibaliz Gómez-de-Mariscal
Start-date: July 2022
End-date: June 2024
Grant Code: ALTF 174-2022
The project aims to combine live-cell imaging, super-resolution microscopy, and sophisticated bioimage analysis to build a bespoke technology that enables the simultaneous observation of several cells with viral nanoparticle resolution. The technology will be used to study the spatiotemporal dynamics of the competition between HIV-1 and the host's immune system, with the goal of identifying new biological processes during pathogen transmission.
Technology explored
Supported publications
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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 Paper published in Journal of Physics: Photonics, January 2026 Technologies: BioImage Model Zoo (), CARE (), mAIcrobe () and ZeroCostDL4Mic () Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1088/2515-7647/ae0fd1 |
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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 Paper published in Nature Communications, December 2025 Technologies: mAIcrobe (), PhotoFiTT () and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1038/s41467-025-66209-6 |
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The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann Paper published in Nature Communications, April 2025 Technologies: CARE (), DeepBacs () and ZeroCostDL4Mic () Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1038/s41467-025-58723-4 |
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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 DOI: 10.1038/s41592-024-02295-6 |
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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 |
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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-eSRRF (), NanoJ-SQUIRREL (), NanoJ-SRRF () and ZeroCostDL4Mic () Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1242/jcs.261545 |
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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 (), DeepAutoFocus (), DeepBacs () and ZeroCostDL4Mic () Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1101/2023.10.16.562172 |
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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-Fluidics () and ZeroCostDL4Mic () Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1016/j.ceb.2023.102271 |
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News
- 2025-04-22: Blog BPoD - Biomedical Picture of the Day highlights Spahn et al. Nature Communications 2025 [external link]
- 2024-06-02: News outlet Labonline highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-28: News outlet MSN highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-28: News outlet AZoRobotics highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-27: News outlet Aamuset Kaupunkimedia highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-17: Blog news-medical.net highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]