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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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: EZInput () and NanoPyx () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO and ERC 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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