Democratizing Deep Learning for Microscopists with DL4MicEverywhere
Agency: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust
Type: Essential Open Source Software for Science (Cycle 6)
Principal Investigator: Ricardo Henriques
Investigators: Ricardo Henriques, Guillaume Jacquemet, Caron Jacobs
Start-date: August 2025
End-date: July 2027
Grant Code: 313383/Z/24/Z; EOSS6-0000000260
Type: Essential Open Source Software for Science (Cycle 6)
Principal Investigator: Ricardo Henriques
Investigators: Ricardo Henriques, Guillaume Jacquemet, Caron Jacobs
Start-date: August 2025
End-date: July 2027
Grant Code: 313383/Z/24/Z; EOSS6-0000000260
Technology explored
Supported publications
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AI-Driven Cell-Fate Prediction in Microscopy Rita Carlota, Mario Del Rosario, Inês Cunha, Juliette Griffié, Guillaume Jacquemet, Ricardo Henriques Preprint published in preprints.org, July 2026 Technologies: mAIcrobe () and PhotoFiTT () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2022 and La Caixa Foundation DOI: 10.20944/preprints202607.1414.v1 |
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AI4Life Open Calls and Public Challenges: why, how, and what we have learned Vera Galinova, Mehdi Seifi, Beatriz Serrano Solano, Kristína Lidayová, Damian Dalle Nogare, Agustín Andrés Corbat, Joshua Talks, Edoardo Giacomello, Estibaliz Gómez-de-Mariscal, Mariana G. Ferreira, Caterina Fuster-Barceló, Juan Manuel Battagliotti, Carlos García-López-de-Haro, Benjamin Salmon, Melisande Croft, Si Young Yie, Guillermo Rey-Paniagua, Xiaotian Hu, Sungjun Cho, Aagam Sheth, Chhayansh Porwal, Xiaomeng Li, AI4Life Consortium, Ricardo Henriques, Xinyang Li, Alexander Krull, Anna Klemm, Arrate Muñoz Barrutia, Anna Kreshuk, Wei Ouyang, Florian Jug, Joran Deschamps Preprint published in bioRxiv, July 2026 Technologies: BioImage Model Zoo (), CARE (), DL4MicEverywhere (), mAIcrobe (), Nuclear-Pores as references and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, ERC, H2021, H2022 and La Caixa Foundation DOI: 10.64898/2026.07.21.739486 |
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VLab4Mic: prediction of structural resolvability in super-resolution microscopy Damián Martínez, Bruno M. Saraiva, Tayla Shakespeare, Mark Bates, Dylan M. Owen, Christophe Leterrier, Mario Del Rosario, Ricardo Henriques Preprint published in bioRxiv, June 2026 Technologies: EZInput (), mAIcrobe (), nano-org, NanoJ (), NanoJ-SQUIRREL (), Nuclear-Pores as references and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2022 and La Caixa Foundation DOI: 10.64898/2026.06.02.729521 |
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Packaging Jupyter notebooks as installable desktop apps using LabConstrictor Iván Hidalgo-Cenalmor, Marcela Xiomara Rivera Pineda, Bruno M Saraiva, Ricardo Henriques, Guillaume Jacquemet Preprint published in arXiv, March 2026 Technologies: CARE (), CellTracksColab (), DL4MicEverywhere (), mAIcrobe () and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, EMBO, ERC, H2022 and La Caixa Foundation DOI: 10.48550/arXiv.2603.10704 |
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EZInput: A Cross-Environment Python Library for Easy UI Generation in Scientific Computing Bruno M Saraiva, Iván Hidalgo-Cenalmor, António D Brito, Damián Martínez, Tayla Shakespeare, Guillaume Jacquemet, Ricardo Henriques Preprint published in arXiv, January 2026 Technologies: DL4MicEverywhere (), mAIcrobe (), NanoJ-eSRRF (), NanoPyx () and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2021 and H2022 DOI: 10.48550/arXiv.2601.08859 |
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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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Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues Dominik Kylies, Hannah S. Heil, Arturo G. Vesga, Mario Del Rosario, Maria Schwerk, Malte Kuehl, Milagros N. Wong, Victor G. Puelles, Ricardo Henriques Paper published in Nature Protocols, July 2025 Technologies: NanoJ (), NanoJ-eSRRF (), NanoJ-SQUIRREL (), NanoJ-SRRF (), NanoPyx () and Nuclear-Pores as references Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1038/s41596-025-01178-0 |
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Structural Repetition Detector for multi-scale quantitative mapping of molecular complexes through microscopy Afonso Mendes, Bruno M. Saraiva, Guillaume Jacquemet, João I. Mamede, Christophe Leterrier, Ricardo Henriques Paper published in Nature Communications, July 2025 Technologies: Nuclear-Pores as references and SReD () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1038/s41467-025-60709-1 |
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Rxiv-Maker: An Automated Template Engine for Streamlined Scientific Publications Bruno M Saraiva, Guillaume Jaquemet, Ricardo Henriques Preprint published in arXiv, June 2025 Technologies: DL4MicEverywhere () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2021 and H2022 DOI: 10.48550/arXiv.2508.00836 |
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Nanoscale imaging of biological systems via expansion and super-resolution microscopy Daria Aristova, Dominik Kylies, Mario Del Rosario, Hannah S. Heil, Maria Schwerk, Malte Kuehl, Milagros N. Wong, Ricardo Henriques, Victor G. Puelles Paper published in Applied Physics Reviews, April 2025 Technologies: NanoJ-eSRRF () and NanoJ-SRRF () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1063/5.0240464 |
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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, Ashwin Balakrishnan, Mike Heilemann, Ricardo Henriques, Yoav Shechtman Paper published in Small Methods, January 2025 Technologies: CARE () and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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Non-synaptic exocytosis along the axon shaft and its regulation by the submembrane periodic skeleton Theresa Wiesner, Christopher Louis Parperis, Fanny Boroni-Rueda, Nicolas Jullien, Afonso Mendes, Léa Marie, Louisa Mezache, Marie-Jeanne Papandréou, Ricardo Henriques, Christophe Leterrier Preprint published in bioRxiv, January 2025 Technologies: CARE () and SReD () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, EMBO and ERC DOI: 10.1101/2025.09.17.676728 |
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