Democratizing Deep Learning for Microscopists with DL4MicEverywhere

Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust logo
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

Technology explored

DL4MicEverywhere DL4MicEverywhere Newest update: 2026-08-17

Supported publications

Word cloud of AI-Driven Cell-Fate Prediction in Microscopy 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
Word cloud of AI4Life Open Calls and Public Challenges: why, how, and what we have learned 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
Word cloud of VLab4Mic: prediction of structural resolvability in super-resolution microscopy 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
Word cloud of Packaging Jupyter notebooks as installable desktop apps using LabConstrictor 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
Word cloud of EZInput: A Cross-Environment Python Library for Easy UI Generation in Scientific Computing 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
Word cloud of PhotoFiTT: a quantitative framework for assessing phototoxicity in live-cell microscopy experiments 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
Word cloud of Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues 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
Word cloud of Structural Repetition Detector for multi-scale quantitative mapping of molecular complexes through microscopy 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
Word cloud of Nanoscale imaging of biological systems via expansion and super-resolution microscopy 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
Word cloud of This Microtubule Does Not Exist: Super‐Resolution Microscopy Image Generation by a Diffusion Model 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
Word cloud of Non-synaptic exocytosis along the axon shaft and its regulation by the submembrane periodic skeleton 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