Research Team
Estibaliz is a 3rd-year Postdoc in our research group. Worked on 8 publications. Contributed to 3 technologies. Raised 2 grants. Collaborates with 9 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
- 2024-02-27: Interviewed by FocalPlane - Estibaliz Gómez-de-Mariscal [link]
Supervisees
Collaborations
Guillaume Jacquemet
Abo Akademi University
Turku, Finland
Joint:
13
Séamus Holden
Warwick University
Warwick, UK
Joint:
5
Technologies
Publications with our group (see more on Google Scholar)
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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-SRRF and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1242/jcs.261545 |
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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 Preprint published in arXiv, January 2024 Technologies: BioImage Model Zoo, DL4MicEverywhere, NanoJ, NanoJ-Fluidics and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.48550/arXiv.2401.05282 |
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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, Ignacio Arganda-Carreras, AI4Life Consortium, Guillaume Jacquemet, Ricardo Henriques, Estibaliz Gómez-de-Mariscal Preprint published in bioRxiv, November 2023 Technologies: BioImage Model Zoo, DeepBacs, DL4MicEverywhere and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1101/2023.11.19.567606 |
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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, 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-eSRRF, NanoJ-Fluidics, NanoJ-SRRF and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1016/j.ceb.2023.102271 |
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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 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 |
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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 and Wellcome Trust DOI: 10.1038/s42003-022-03634-z |
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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 |
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Funding with our group
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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 |
