VP-CLEM-KIT - a pipeline for democratising volumetric visual proteomics
Agency: CZI
Type: Visual Proteomics Imaging
Principal Investigator: Lucy Collinson
Investigators: Lucy Collinson, Ricardo Henriques, Paul French
Start-date: December 2021
End-date: June 2024
Type: Visual Proteomics Imaging
Principal Investigator: Lucy Collinson
Investigators: Lucy Collinson, Ricardo Henriques, Paul French
Start-date: December 2021
End-date: June 2024
Technology explored
Supported publications
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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 Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1063/5.0240464 |
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ReScale4DL - Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation Mariana G. Ferreira, Bruno M. Saraiva, António D. Brito, Mariana G. Pinho, Ricardo Henriques, Estibaliz Gómez-de-Mariscal Preprint published in bioRxiv, April 2025 Technologies: BioImage Model Zoo, DeepBacs, DL4MicEverywhere, NanoPyx, Rescale4DL and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1101/2025.04.09.647871 |
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Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework Bruno M. Saraiva, Inês Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques Paper published in Nature Methods, January 2025 Technologies: Fast4DReg, NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL and NanoPyx Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 News: Tempo.pt, Nouvelles du monde and RTP DOI: 10.1038/s41592-024-02562-6 |
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VP-CLEM-Kit - An accessible pipeline for visual proteomics using super resolution volume correlative light and electron microscopy (SR-vCLEM) Dumisile Lumkwana, Jonathan Lightley, Arturo G Vesga, Joost de Folter, Marie-Charlotte Domart, Catherine Maclachlan, Sunil Kumar, James R Evans, Christopher Peddie, Alana Burrell, Azumi Yoshimura, Asandile Mangali, Nicola Vahrjmeijer, Meenal Bhaga, Catherine Smit, Benjamin Titze, Mathew H Horrocks, Lorian Cobra Straker, Edwin Garcia, Martin L Jones, Adam Mclean, Candice Roufosse, Ben Loos, Sonia Gandhi, Amy Strange, Ricardo Henriques, Paul M French, Lucy Collinson Preprint published in bioRxiv, January 2025 Technologies: NanoJ-SQUIRREL and NanoPyx Funded by: CZI, EMBO and ERC DOI: 10.1101/2025.04.08.647770 |
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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 Published in Small Methods, January 2025 Technologies: ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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Structural Repetition Detector - multi-scale quantitative mapping of molecular complexes through microscopy Afonso Mendes, Bruno M Saraiva, Guillaume Jacquemet, Joao I Mamede, Christophe Leterrier, Ricardo Henriques Preprint published in bioRxiv, September 2024 Technologies: Nuclear-Pores as references and SReD Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1101/2024.09.16.613204 |
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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 Preprint published in bioRxiv, July 2024 Technologies: DL4MicEverywhere, PhotoFiTT and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1101/2024.07.16.603046 |
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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-eSRRF, NanoJ-SQUIRREL, 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 Review published in Journal of Microscopy, January 2024 Technologies: NanoJ and NanoJ-Fluidics Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1111/jmi.13282 |
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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 Published in Small Methods, January 2024 Technologies: ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation Romain F. Laine, Hannah S. Heil, Simao Coelho, Jonathon Nixon-Abell, Angélique Jimenez, Theresa Wiesner, Damián Martínez, Tommaso Galgani, Louise Régnier, Aki Stubb, Gautier Follain, Samantha Webster, Jesse Goyette, Aurelien Dauphin, Audrey Salles, Siân Culley, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, Ricardo Henriques Paper published in Nature Methods, November 2023 Technologies: NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoPyx and Nuclear-Pores as references Funded by: CZI, EMBO, ERC, FCT, H2021, H2022, InnOValley and Wellcome Trust News: Photonics.com, The Science Times, Optics.org and Phys.org Blogs: Springer Nature Protocols and Methods Community DOI: 10.1038/s41592-023-02057-w |
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CLEM-Reg - An automated point cloud based registration algorithm for correlative light and volume electron microscopy Daniel Krentzel, Matouš Elphick, Marie-Charlotte Domart, Christopher J. Peddie, Romain F. Laine, Ricardo Henriques, Lucy M. Collinson, Martin L. Jones Preprint published in bioRxiv, May 2023 Technologies: BioImage Model Zoo, CLEM-Reg and ZeroCostDL4Mic Funded by: CZI and ERC DOI: 10.1101/2023.05.11.540445 |
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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, DeepBacs, Fast4DReg, NanoJ, NanoJ-eSRRF, NanoJ-Fluidics and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1016/j.ceb.2023.102271 |
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Fast4DReg–fast registration of 4D microscopy datasets Joanna W Pylvänäinen, Romain F Laine, Bruno MS Saraiva, Sujan Ghimire, Gautier Follain, Ricardo Henriques, Guillaume Jacquemet Paper published in Journal of Cell Science, January 2023 Technologies: CARE, Fast4DReg, NanoJ and ZeroCostDL4Mic Funded by: CZI and ERC DOI: 10.1242/jcs.260728 |
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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 Published in Small Methods, January 2023 Technologies: ZeroCostDL4Mic Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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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 and ZeroCostDL4Mic Funded by: CZI, ERC, FCT 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, CARE and ZeroCostDL4Mic Funded by: CZI, EMBO, ERC and H2021 DOI: 10.1101/2022.06.07.495102 |
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News
- 2025-02-28: News outlet EUTOPIA highlights Saraiva et al. Nature Methods 2025
- 2025-01-25: News outlet Tempo.pt highlights Saraiva et al. Nature Methods 2025
- 2025-01-09: News outlet Nouvelles du monde highlights Saraiva et al. Nature Methods 2025
- 2025-01-06: News outlet RTP highlights Saraiva et al. Nature Methods 2025
- 2023-11-27: News outlet Photonics.com highlights Laine et al. Nature Methods 2023
- 2023-11-20: News outlet The Science Times highlights Laine et al. Nature Methods 2023
- 2023-11-16: News outlet Optics.org highlights Laine et al. Nature Methods 2023
- 2023-11-14: Blog Springer Nature Protocols and Methods Community highlights Laine et al. Nature Methods 2023
- 2023-11-14: News outlet Phys.org highlights Laine et al. Nature Methods 2023