Research Team


Estibaliz Gómez de Mariscal

Estibaliz Gómez de Mariscal

Postdoc


Started in: October 2021

Funding: EMBO Installation Grant; EMBO Fellowship


Estibaliz is a 4th-year Postdoc in our research group. Worked on 10 publications. Contributed to 5 technologies. Raised 2 grants. Collaborates with 10 labs. Mentored 2 Software Engineers.

Overview: I'm interested in understanding cell-level biology using bioimage analysis. My research centers on facing the challenges when applying machine-learning techniques to microscopy images and on contributing to biological discoveries with it. Previously, I developed methods to process TEM images and phase-contrast time-lapse movies to contribute to the characterization of cancer cell motility. I have also conceived new biostatistical approaches to analyse big data. I'm also one of the creators of deepImageJ, an environment to bridge deep-learning to ImageJ. A crucial part of my work and dedication is to make computational tools accessible (open and user-friendly) and reusable, and train non-experts to benefit from them. As a postdoc in Ridardo's lab I'll be learning (a lot) of super-resolution microscopy, and building novel machine-learning methodologies applied to it.


In the news


Supervisees

Iván Hidalgo-Cenalmor

Iván Hidalgo-Cenalmor

Software Engineer
H2021 AI4Life Grant funded

Mariana Ferreira

Mariana Ferreira

Software Engineer
H2021 AI4Life Grant funded


Collaborations

Anna Kreshuk

Anna Kreshuk

EMBL
Heidelberg, Germany

Joint: 1 2

Arrate Muñoz-Barrutia

Arrate Muñoz-Barrutia

Universidad Carlos III de Madrid
Madrid, Spain

Joint: 2 1

Florian Jug

Florian Jug

Human Technopole
Milan, Italy

Joint: 3 1

Guillaume Jacquemet

Guillaume Jacquemet

Abo Akademi University
Turku, Finland

Joint: 16 1

Mariana Pinho

Mariana Pinho

ITQB NOVA
Oeiras, Portugal

Joint: 4 1 2

Mike Heilemann

Mike Heilemann

Goethe University
Frankfurt, Germany

Joint: 3 1

Pedro Matos Pereira

Pedro Matos Pereira

ITQB NOVA
Oeiras, Portugal

Joint: 20 3

Séamus Holden

Séamus Holden

Warwick University
Warwick, UK

Joint: 5

Wei Ouyang

Wei Ouyang

SciLifeLab
Stockholm, Sweden

Joint: 2 1

Yoav Shechtman

Yoav Shechtman

Technion - Israel Institute of Technology
Haifa, Israel

Joint: 4


Technologies

BioImage Model Zoo BioImage Model Zoo
CellTracksColab CellTracksColab
DeepBacs DeepBacs
DL4MicEverywhere DL4MicEverywhere
PhotoFiTT PhotoFiTT

Publications with our group (see more on Google Scholar)

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
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
CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data
Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet
Published in PLOS Biology, January 2024
Technologies: CARE, CellTracksColab and ZeroCostDL4Mic
DOI: 10.1371/journal.pbio.3002740
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
This microtubule does not exist - Super-resolution microscopy image generation by a diffusion model
Alon Saguy, Tav Nahimov, Maia Lehrman, Estibaliz Gómez-de-Mariscal, Iván Hidalgo-Cenalmor, Onit Alalouf, Ricardo Henriques, Yoav Shechtman
Preprint published in bioRxiv, January 2023
Technologies: CARE and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.07.06.548004
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
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
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
Bioimage model zoo - a community-driven resource for accessible deep learning in bioimage analysis
Wei Ouyang, Fynn Beuttenmueller, Estibaliz Gómez-de-Mariscal, Constantin Pape, Tom Burke, Carlos Garcia-López-de-Haro, Craig Russell, Lucía Moya-Sans, Cristina de-la-Torre-Gutiérrez, Deborah Schmidt, Dominik Kutra, Maksim Novikov, Martin Weigert, Uwe Schmidt, Peter Bankhead, Guillaume Jacquemet, Daniel Sage, Ricardo Henriques, Arrate Muñoz-Barrutia, Emma Lundberg, Florian Jug, Anna Kreshuk
Preprint published in BioRxiv, January 2022
Technologies: BioImage Model Zoo and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC and H2021
DOI: 10.1101/2022.06.07.495102

Funding with our group

SMALS - Smart Microscopy for Adaptative Live Super-resolution imaging to elucidate the initial steps of the HIV viral transmission
Estibaliz Gómez-de-Mariscal
Alias: SMALS
Funded by: FCT - CEEC Individual
Duration: April 2024 - March 2027
A transformative data-driven live-cell super-resolution microscopy development to elucidate the initial steps of effective viral transmission
Estibaliz Gómez-de-Mariscal
Funded by: EMBO - Postdoctoral Fellowships
Duration: July 2022 - June 2024
Publications: 8