A transformative data-driven live-cell super-resolution microscopy development to elucidate the initial steps of effective viral transmission


Funding Image
Agency: EMBO
Type: Postdoctoral Fellowships
Principal Investigator: Estibaliz Gómez-de-Mariscal
Start-date: July 2022
End-date: June 2024

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


ZeroCostDL4Mic ZeroCostDL4Mic Newest update: 2024-10-19
CARE CARE Newest update: 2024-10-05
NanoJ NanoJ Newest update: 2024-03-22
DeepBacs DeepBacs Newest update: 2022-05-11
NanoJ-Fluidics NanoJ-Fluidics Newest update: 2019-04-04

Supported publications


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
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
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
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
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