Research Team
Ricardo is a 12th-year Group Leader in our research group. Worked on 87 publications. Contributed to 28 technologies. Raised 29 grants. Collaborates with 27 labs. Mentored 13 PhD Students, 10 Postdocs, 2 Masters Students, 3 Postdoc (now PI)s, 1 Internship Student, 1 Lab Manager, 2 Software Engineers.
I am a trained Particle Physicist who developed an interest in Biological Physics shortly after completing my degree at the University of Lisbon in 2005. This led me to pursue a PhD in Biophysics, which I undertook jointly in the laboratories of Musa Mhlanga and Christophe Zimmer. My research was distributed across several institutions, including the Instituto de Medicina Molecular in Portugal, Institut Pasteur in France, the Council for Scientific and Industrial Research in South Africa, and Andor Technology in the UK and USA. It was during this period that I first entered the field of Super-Resolution Microscopy, a discipline in which I developed technologies to visualise cellular and viral structures with previously unattainable resolution. I completed my PhD in 2011, focusing on real-time super-resolution fluorescence microscopy, and subsequently conducted postdoctoral work at Institut Pasteur, applying these optical developments to investigate T-cell immunology and viral infection.
My path as a group leader
In 2013, I established my first independent research group at University College London (UCL) as an Associate Professor, with a dual focus on developing new imaging technologies and pursuing fundamental cell biology research. In 2017, I received an invitation to expand my research programme at the Francis Crick Institute, where I established a second laboratory. My work was recognised with a promotion to Full Professor at UCL in 2019. In 2020, I relocated my laboratory to Portugal, first at the Instituto Gulbenkian de Ciência, before accepting a position as a permanent Principal Investigator at the Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA) in 2024. I was also elected as an EMBO member in the same year. My research group continues to employ optical and computational biophysics to study cell biology and host-pathogen interactions. We develop technologies that permit the investigation of cellular structures and processes at the nanoscale and apply these methods to understand the molecular mechanisms of infection. Central to my philosophy is a commitment to open science, ensuring my research is reproducible, transparent, and that our tools are disseminated as open-source resources.
My research
My work has centred on generating new ideas, tools, and methodologies in super-resolution microscopy and computational imaging. A primary contribution has been the development of analytical methods that enable researchers to visualise dynamic cellular structures with nanoscale precision. One of the earliest examples of this was QuickPALM (Henriques et al., Nature Methods, 2010; DOI:10.1038/nmeth0510-339), which was the first open-source software for real-time, 3D single-molecule localization microscopy in living cells. This tool became widely adopted and helped set a standard for open analytical technologies in the field. This was followed by a comprehensive suite of open-source software tools integrated within the NanoJ framework (Laine et al., Journal of Physics D, 2019; DOI:10.1088/1361-6463/ab0261). Notable components include NanoJ-SRRF (Gustafsson et al., Nature Communications, 2016; DOI:10.1038/ncomms12471), an algorithm that enables super-resolution imaging on conventional microscopes, and NanoJ-SQUIRREL (Culley et al., Nature Methods, 2018; DOI:10.1038/nmeth.f.626), a method for quantifying and mapping artifacts in super-resolution images, reinforcing our commitment to data quality and reproducibility.
A significant evolution in our work has been the integration of machine learning and artificial intelligence into bioimage analysis. We observed that while deep learning offered transformative potential for microscopy, its adoption was hindered by requirements for specialised computational hardware and advanced coding skills. To address this, my group developed ZeroCostDL4Mic (von Chamier et al., Nature Communications, 2021; DOI:10.1038/s41467-021-22518-0), a platform that leverages free, cloud-based resources to make deep learning accessible to any researcher with a web browser. This initiative democratised access to state-of-the-art AI models for tasks such as segmentation, denoising, and object detection. We have since expanded on this with the DL4MicEverywhere platform (Hidalgo-Cenalmor et al., bioRxiv, 2023; DOI:10.1101/2023.11.19.567606), which allows these models to be executed on local computers, further simplifying their deployment. These platforms exemplify our focus on not only developing novel technologies but also ensuring they are accessible and usable by the broader scientific community.
The technologies we develop are purpose-driven, designed to generate new biological knowledge. For instance, we applied our super-resolution methods to map the nanoscale distribution of HIV cell receptors CD4 and CCR5 during viral binding (Yuan et al., Viruses, 2021; DOI:10.3390/v13010142) and to reveal the polarisation of the entry fusion complex of poxviruses (Gray et al., Nature Microbiology, 2019; DOI:10.1038/s41564-019-0488-4). Our tools have also been instrumental in deciphering the nanoscale mechanisms of ESCRT-III-mediated cell division in archaea (Risa et al., Science, 2020; DOI:10.1126/science.aaz2532; Harker-Kirschneck et al., PNAS, 2022; DOI:10.1073/pnas.2107763119) and in demonstrating how closed mitosis requires localised disassembly of the nuclear envelope (Dey et al., Nature, 2020; DOI:10.1038/s41586-020-2648-3). These discoveries, among over 67 publications, illustrate the direct impact of our technological contributions. This research has been supported by over €7 million in funding from agencies including the ERC, Horizon Europe, and the Wellcome Trust.
Giving back
Throughout my career, I have been dedicated to training and mentoring the next generation of scientists. I have directly supervised a diverse group of over 25 PhD students, postdoctoral researchers, Master's students, and software engineers. My mentorship approach focuses on providing hands-on guidance and creating opportunities for career progression, fostering skills across cell biology, optical physics, and computational biology. Many of my trainees have secured positions in academia and industry. I have also designed and taught specialised graduate courses at UCL and the Instituto Gulbenkian de Ciência and have organised numerous international workshops and training courses, through which we have trained over 300 researchers in advanced imaging and analysis techniques. My contribution to society is rooted in a commitment to open science. By developing and freely sharing our software and methodologies, we facilitate collaboration and accelerate knowledge exchange. I actively engage with the public and the scientific community through social media and participation in science festivals and public lectures, aiming to increase scientific literacy. My work also extends to the private sector through collaborations with industry partners, which helps translate our fundamental scientific discoveries into practical applications in healthcare, biotechnology, and imaging. This multifaceted approach ensures our research has a broad and tangible impact.
Latest news
- 2025-04-22: Blog BPoD - Biomedical Picture of the Day highlights Spahn et al. Nature Communications 2025 [external link]
- 2025-03-13: Invited Visiting Professor at the InFLAMES Flagship Programme - Ricardo Henriques [external link]
- 2025-03-11: Visiting Professor at InFLAMES
- 2025-02-28: News outlet EUTOPIA highlights Saraiva et al. Nature Methods 2025 [external link]
- 2025-01-25: News outlet Tempo.pt highlights Saraiva et al. Nature Methods 2025 [external link]
Show more news (61 additional items)
- 2025-01-09: News outlet Nouvelles du monde highlights Saraiva et al. Nature Methods 2025 [external link]
- 2025-01-06: News outlet RTP highlights Saraiva et al. Nature Methods 2025 [external link]
- 2024-10-22: News outlet Technology Networks highlights Spark et al. Nature Methods 2020 [external link]
- 2024-10-01: We're moving the Henriques lab to ITQB NOVA
- 2024-07-09: Ricardo Henriques elected as EMBO Member
- 2024-07-09: Ricardo Henriques elected as EMBO Member - Ricardo Henriques [external link]
- 2024-06-27: Funding CZI through the Essential Open Source Software for Science program - Ricardo Henriques [external link]
- 2024-06-02: News outlet Labonline highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-28: News outlet MSN highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-27: News outlet Aamuset Kaupunkimedia highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-17: Blog news-medical.net highlights Hidalgo-Cenalmor et al. Nature Methods 2024 [external link]
- 2024-05-13: News outlet Azooptics.com highlights Chamier et al. Biochemical Society Transactions 2019 [external link]
- 2024-03-26: Our ERC CoG SelfDriving4DSR project featured as example of frontier AI research
- 2024-03-26: Research in AI recognized in the "Mapping ERC Frontier Research" report - Ricardo Henriques [external link]
- 2023-12-28: Interviewed by RTP1 (national news channel in Portugal)
- 2023-12-11: Interviewed by RTP (Portuguese National TV) - Ricardo Henriques [external link]
- 2023-11-27: News outlet Photonics.com highlights Laine et al. Nature Methods 2023 [external link]
- 2023-11-20: News outlet The Science Times highlights Laine et al. Nature Methods 2023 [external link]
- 2023-11-16: News outlet Optics.org highlights Laine et al. Nature Methods 2023 [external link]
- 2023-11-14: Blog Springer Nature Protocols and Methods Community highlights Laine et al. Nature Methods 2023 [external link]
- 2023-11-14: News outlet Phys.org highlights Laine et al. Nature Methods 2023 [external link]
- 2023-02-09: Interviewed by 90 Segundos de Ciência (Portuguese news) - Ricardo Henriques [external link]
- 2022-11-15: News outlet Technology Times highlights Almada et al. Nature Communications 2019 [external link]
- 2022-09-01: Interviewed by The Microscopists Podcast - Ricardo Henriques [external link]
- 2022-06-18: News outlet MSN highlights Almada et al. Nature Communications 2019 [external link]
- 2022-05-17: News outlet Nanowerk highlights Whitley et al. Nature Communications 2021 [external link]
- 2021-11-03: Editorial in Nature Methods highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-10-05: News outlet La Razon (ESP) highlights Spark et al. Nature Methods 2020 [external link]
- 2021-07-14: News outlet Technology Networks highlights Weigert et al. Nature Methods 2018 [external link]
- 2021-05-07: News outlet Expresso highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-04-26: News outlet AZO Life Sciences highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-04-26: News outlet Drug Target Review highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-04-24: News outlet Nanotechnology Now highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-04-24: News outlet The Medical News highlights Chamier et al. Nature Communications 2021 [external link]
- 2021-04-16: Blog Microbiome Digest - Bik's Picks highlights Chamier et al. Nature Communications 2021 [external link]
- 2020-12-09: ERC CoG and EMBO IA awards highlighted by Publico (Portuguese news) - Ricardo Henriques [external link]
- 2020-11-08: News outlet ZAP highlights Spark et al. Nature Methods 2020 [external link]
- 2020-11-03: News outlet Medium US highlights Spark et al. Nature Methods 2020 [external link]
- 2020-10-27: News outlet Mirage News highlights Thevathasan et al. Nature Methods 2019 [external link]
- 2020-10-21: Blog Qubit highlights Spark et al. Nature Methods 2020 [external link]
- 2020-10-13: Blog Tech Explorist highlights Spark et al. Nature Methods 2020 [external link]
- 2020-10-12: Blog Whats New highlights Spark et al. Nature Methods 2020 [external link]
- 2020-09-12: News outlet NRK highlights Risa et al. Science 2020 [external link]
- 2020-09-02: News outlet Nature Asia highlights Dey et al. Nature 2020 [external link]
- 2020-08-31: News outlet Azom.com highlights Gustafsson et al. Nature Communications 2016 [external link]
- 2020-08-28: News outlet Scitech Daily highlights Risa et al. Science 2020 [external link]
- 2020-08-12: News outlet NCYT - Noticias de la Ciencia y la Technologia highlights Risa et al. Science 2020 [external link]
- 2020-08-06: News outlet UPI.com highlights Risa et al. Science 2020 [external link]
- 2020-07-01: News outlet ScienMag highlights Jacquemet et al. Journal of Cell Science 2020 [external link]
- 2020-04-21: Editorial in Nature highlights Chamier et al. Nature Communications 2021 [external link]
- 2019-08-19: News outlet This Week in Virology (TWiV) highlights Gray et al. Nature Microbiology 2019 [external link]
- 2019-07-10: Blog Nature Microbiology Community highlights Gray et al. Nature Microbiology 2019 [external link]
- 2018-12-10: News outlet VBIO highlights Weigert et al. Nature Methods 2018 [external link]
- 2018-12-07: News outlet Innovations Report highlights Weigert et al. Nature Methods 2018 [external link]
- 2018-07-01: Made Fellow of the Royal Microscopy Society - Ricardo Henriques
- 2018-06-30: News outlet The Times highlights the lab's research [external link]
- 2018-05-14: News outlet physicsworld.com highlights Culley et al. Nature Methods 2018 [external link]
- 2017-10-03: Lab highlighted as a reference case study for UCL-Consultancy - Ricardo Henriques [external link]
- 2017-01-11: News outlet Phys.org highlights Clough et al. PLOS Pathogens 2016 [external link]
- 2016-11-24: Blog The Toxoplasma Blog highlights Clough et al. PLOS Pathogens 2016 [external link]
- 2016-11-22: News outlet Bionity highlights Clough et al. PLOS Pathogens 2016 [external link]
Technologies
Show more technologies (22 additional items)
Latest Outreach
Latest publications with our group (see more on Google Scholar)
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Rxiv-Maker: an automated template engine for streamlined scientific publications Bruno M. Saraiva, Guillaume Jacquemet, Ricardo Henriques Preprint published in Zenodo, July 2025 Technologies: Rxiv-Maker () Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.5281/zenodo.15805470 |
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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: 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: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1038/s41467-025-60709-1 |
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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: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1063/5.0240464 |
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The nucleoid of rapidly growing Escherichia coli localizes close to the inner membrane and is organized by transcription, translation, and cell geometry Christoph Spahn, Stuart Middlemiss, Estibaliz Gómez-de-Mariscal, Ricardo Henriques, Helge B. Bode, Séamus Holden, Mike Heilemann Paper published in Nature Communications, April 2025 Technologies: CARE (), DeepBacs () and ZeroCostDL4Mic () Funded by: EMBO, ERC, H2021 and H2022 Blogs: BPoD - Biomedical Picture of the Day DOI: 10.1038/s41467-025-58723-4 |
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Show more publications (82 additional items)
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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 () 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 Paper published in Small Methods, January 2025 Technologies: CARE () and ZeroCostDL4Mic () Funded by: CZI, EMBO, ERC, H2021 and H2022 DOI: 10.1002/smtd.202400672 |
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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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DL4MicEverywhere - deep learning for microscopy made flexible, shareable and reproducible Iván Hidalgo-Cenalmor, Joanna W. Pylvänäinen, Mariana G. Ferreira, Craig T. Russell, Alon Saguy, Ignacio Arganda-Carreras, Yoav Shechtman, Guillaume Jacquemet, Ricardo Henriques, Estibaliz Gómez-de-Mariscal Paper published in Nature Methods, May 2024 Technologies: BioImage Model Zoo (), DL4MicEverywhere () and ZeroCostDL4Mic () Funded by: EMBO, ERC, H2021 and H2022 News: Labonline, MSN, AZoRobotics and Aamuset Kaupunkimedia Blogs: news-medical.net DOI: 10.1038/s41592-024-02295-6 |
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Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus Simon Schäper, António D. Brito, Bruno M. Saraiva, Georgia R. Squyres, Matthew J. Holmes, Ethan C. Garner, Zach Hensel, Ricardo Henriques, Mariana G. Pinho Paper published in Nature Microbiology, March 2024 Technologies: NanoJ () Funded by: EMBO and ERC DOI: 10.1038/s41564-024-01629-6 |
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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, March 2024 Technologies: NanoJ () and NanoJ-Fluidics () Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022 DOI: 10.1111/jmi.13282 |
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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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CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet Published in PLOS Biology, January 2024 Technologies: CARE (), CellTracksColab () and ZeroCostDL4Mic () DOI: 10.1371/journal.pbio.3002740 |
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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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Nano-org, a functional resource for single-molecule localisation microscopy data Sandeep Shirgill, Daniel J Nieves, Jeremy A Pike, Mohammad A Ahmed, Mohammed HH Baragilly, Kylie Savoye, Jonathan Worboys, Khodor Hazime, Adrian Garcia, David J Williamson, Ricardo Henriques, Steven F Lee, Dylan M Owen Preprint published in bioRxiv, January 2024 Technologies: nano-org Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1101/2024.08.06.606779 |
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Decoding life's inner workings - advances in quantitative bioimaging Ricardo Henriques, Christophe Leterrier, Aubrey Weigel Editorial published in Open Biology, November 2023 DOI: 10.1098/rsob.230329 |
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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: CARE (), NanoJ (), NanoJ-eSRRF (), NanoJ-SQUIRREL (), NanoJ-SRRF () 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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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 (), DeepAutoFocus (), DeepBacs () and ZeroCostDL4Mic () Funded by: EMBO, ERC, H2021 and H2022 DOI: 10.1101/2023.10.16.562172 |
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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 (), CARE (), 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 (), CARE (), DeepBacs (), Fast4DReg (), NanoJ (), 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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Processive movement of Staphylococcus aureus essential septal peptidoglycan synthases is independent of FtsZ treadmilling and drives cell constriction Simon Schaeper, Antonio D Brito, Bruno M Saraiva, Georgia R Squyres, Matthew J Holmes, Ethan C Garner, Zach Hensel, Ricardo Henriques, Mariana G Pinho Preprint published in bioRxiv, January 2023 Technologies: NanoJ () Funded by: EMBO and ERC DOI: 10.1101/2023.06.29.547026 |
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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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Mapping molecular complexes with super-resolution microscopy and single-particle analysis Afonso Mendes, Hannah S. Heil, Simao Coelho, Christophe Leterrier, Ricardo Henriques Review published in Open Biology, July 2022 Technologies: NanoJ-VirusMapper, Nuclear-Pores as references and ZeroCostDL4Mic () Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1098/rsob.220079 |
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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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The LEGO® brick road to open science and biotechnology Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C. Féral Review published in Trends in Biotechnology, March 2022 Technologies: NanoJ (), NanoJ-Fluidics () and NanoJ-SRRF () Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1016/j.tibtech.2022.02.003 |
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Physical mechanisms of ESCRT-III–driven cell division Lena Harker-Kirschneck, Anne E. Hafner, Tina Yao, Christian Vanhille-Campos, Xiuyun Jiang, Andre Pulschen, Fredrik Hurtig, Dawid Hryniuk, Siân Culley, Ricardo Henriques, Buzz Baum, Anđela Šarić Paper published in Proceedings of the National Academy of Sciences, January 2022 Funded by: Wellcome Trust DOI: 10.1073/pnas.2107763119 |
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Trimethine cyanine dyes as NA-sensitive probes for visualization of cell compartments in fluorescence microscopy Daria Aristova, Roman Selin, Hannah Sophie Heil, Viktoriia Kosach, Yuriy Slominsky, Sergiy Yarmoluk, Vasyl Pekhnyo, Vladyslava Kovalska, Ricardo Henriques, Andriy Mokhir Paper published in ACS omega, January 2022 Funded by: EMBO, ERC and H2021 DOI: 10.1021/acsomega.2c05231 |
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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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Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration David Tomaz, Pedro Matos Pereira, Nadia Guerra, Julian Dyson, Keith Gould, Ricardo Henriques Paper published in Frontiers in Immunology, January 2022 Technologies: NanoJ () and NanoJ-SQUIRREL () Funded by: BBSRC, EMBO and ERC DOI: 10.3389/fimmu.2022.868496 |
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eHooke - A tool for automated image analysis of spherical bacteria based on cell cycle progression Bruno M. Saraiva, Ludwig Krippahl, Sérgio R. Filipe, Ricardo Henriques, Mariana G. Pinho Paper published in Biological Imaging, September 2021 Funded by: ERC and Wellcome Trust DOI: 10.1017/s2633903x21000027 |
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FtsZ treadmilling is essential for Z-ring condensation and septal constriction initiation in Bacillus subtilis cell division Kevin D. Whitley, Calum Jukes, Nicholas Tregidgo, Eleni Karinou, Pedro Almada, Yann Cesbron, Ricardo Henriques, Cees Dekker, Séamus Holden Paper published in Nature Communications, April 2021 Technologies: DeepAutoFocus () Funded by: BBSRC and Wellcome Trust News: Nanowerk DOI: 10.1038/s41467-021-22526-0 |
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Democratising deep learning for microscopy with ZeroCostDL4Mic Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-Pérez, Pieta K. Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L. Jones, Loïc A. Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques Paper published in Nature Communications, April 2021 Technologies: CARE (), NanoJ (), NanoJ-SQUIRREL (), NanoJ-SRRF () and ZeroCostDL4Mic () Funded by: EMBO, ERC and Wellcome Trust News: AZO Life Sciences, Drug Target Review, Nanotechnology Now and The Medical News Blogs: Microbiome Digest - Bik's Picks DOI: 10.1038/s41467-021-22518-0 |
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Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication Emma Touizer, Christian Sieben, Ricardo Henriques, Mark Marsh, Romain F. Laine Review published in Viruses, February 2021 Technologies: NanoJ-VirusMapper and Super-Beacons Funded by: Wellcome Trust DOI: 10.3390/v13020233 |
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Single-Molecule Super-Resolution Imaging of T-Cell Plasma Membrane CD4 Redistribution upon HIV-1 Binding Yue Yuan, Caron A. Jacobs, Isabel Llorente Garcia, Pedro M. Pereira, Scott P. Lawrence, Romain F. Laine, Mark Marsh, Ricardo Henriques Paper published in Viruses, January 2021 Funded by: ERC DOI: 10.3390/v13010142 |
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Avoiding a replication crisis in deep-learning-based bioimage analysis Romain F Laine, Ignacio Arganda-Carreras, Ricardo Henriques, Guillaume Jacquemet Perspective published in Nature methods, January 2021 Technologies: CARE () Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1038/s41592-021-01284-3 |
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The field guide to 3D printing in microscopy Mario Del Rosario, Hannah S Heil, Afonso Mendes, Vittorio Saggiomo, Ricardo Henriques Review published in Adv. Biol., January 2021 Technologies: CARE (), NanoJ (), NanoJ-Fluidics () and NanoJ-SRRF () Funded by: EMBO, ERC and Wellcome Trust DOI: 10.1002/adbi.202100994 |
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vLUME - 3D virtual reality for single-molecule localization microscopy Alexander Spark, Alexandre Kitching, Daniel Esteban-Ferrer, Anoushka Handa, Alexander R. Carr, Lisa-Maria Needham, Aleks Ponjavic, Ana Mafalda Santos, James McColl, Christophe Leterrier, Simon J. Davis, Ricardo Henriques, Steven F. Lee Paper published in Nature Methods, October 2020 Technologies: Nuclear-Pores as references, QuickPALM and vLume Funded by: BBSRC and Wellcome Trust News: Technology Networks, La Razon (ESP), ZAP and Medium US Blogs: Qubit, , Tech Explorist and Whats New DOI: 10.1038/s41592-020-0962-1 |
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Closed mitosis requires local disassembly of the nuclear envelope Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum Paper published in Nature, August 2020 Technologies: CARE (), NanoJ (), NanoJ-SRRF () and Nuclear-Pores as references Funded by: BBSRC and Wellcome Trust News: Nature Asia DOI: 10.1038/s41586-020-2648-3 |
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The proteasome controls ESCRT-III–mediated cell division in an archaeon Gabriel Tarrason Risa, Fredrik Hurtig, Sian Bray, Anne E. Hafner, Lena Harker-Kirschneck, Peter Faull, Colin Davis, Dimitra Papatziamou, Delyan R. Mutavchiev, Catherine Fan, Leticia Meneguello, Andre Arashiro Pulschen, Gautam Dey, Siân Culley, Mairi Kilkenny, Diorge P. Souza, Luca Pellegrini, Robertus A. M. de Bruin, Ricardo Henriques, Ambrosius P. Snijders, Anđela Šarić, Ann-Christin Lindås, Nicholas P. Robinson, Buzz Baum Paper published in Science, August 2020 Technologies: NanoJ () and NanoJ-SRRF () News: NRK, Scitech Daily, NCYT - Noticias de la Ciencia y la Technologia and UPI.com DOI: 10.1126/science.aaz2532 |
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The cell biologist's guide to super-resolution microscopy Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, Ricardo Henriques, Christophe Leterrier Review published in Journal of Cell Science, June 2020 Technologies: CARE (), NanoJ (), NanoJ-Fluidics (), NanoJ-SRRF () and Nuclear-Pores as references Funded by: BBSRC and Wellcome Trust News: ScienMag and EurekAlert! DOI: 10.1242/jcs.240713 |
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Between life and death - strategies to reduce phototoxicity in super-resolution microscopy Kalina L Tosheva, Yue Yuan, Pedro Matos Pereira, Siân Culley, Ricardo Henriques Review published in Journal of Physics D - Applied Physics, January 2020 Technologies: CARE (), NanoJ (), NanoJ-Fluidics () and NanoJ-SRRF () Funded by: BBSRC and Wellcome Trust DOI: 10.1088/1361-6463/ab6b95 |
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An Introduction to Live-Cell Super-Resolution Imaging Siân Culley, Pedro Matos Pereira, Romain F Laine, Ricardo Henriques Book chapter published in Imaging from Cells to Animals In Vivo, January 2020 Technologies: CARE (), NanoJ (), NanoJ-Fluidics (), NanoJ-SQUIRREL () and QuickPALM DOI: 10.1201/9781315174662-4 |
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Super‐beacons - Open‐source probes with spontaneous tuneable blinking compatible with live‐cell super‐resolution microscopy Pedro M Pereira, Nils Gustafsson, Mark Marsh, Musa M Mhlanga, Ricardo Henriques Paper published in Traffic, January 2020 Technologies: NanoJ (), NanoJ-Fluidics (), NanoJ-SQUIRREL (), NanoJ-SRRF () and Super-Beacons Funded by: BBSRC and Wellcome Trust DOI: 10.1111/tra.12728 |
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Live imaging of a hyperthermophilic archaeon reveals distinct roles for two ESCRT-III homologs in ensuring a robust and symmetric division Andre Arashiro Pulschen, Delyan R Mutavchiev, Siân Culley, Kim Nadine Sebastian, Jacques Roubinet, Marc Roubinet, Gabriel Tarrason Risa, Marleen van Wolferen, Chantal Roubinet, Uwe Schmidt, Gautam Dey, Sonja-Verena Albers, Ricardo Henriques, Buzz Baum Paper published in Current Biology, January 2020 Technologies: Sulfoscope Funded by: Wellcome Trust DOI: 10.1016/j.cub.2020.05.021 |
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Fluctuation-based super-resolution traction force microscopy Aki Stubb, Romain F Laine, Mitro Miihkinen, Hellyeh Hamidi, Camilo Guzmán, Ricardo Henriques, Guillaume Jacquemet, Johanna Ivaska Paper published in Nano letters, January 2020 Technologies: FBSR-TFM, NanoJ (), NanoJ-SQUIRREL () and NanoJ-SRRF () Funded by: BBSRC DOI: 10.1021/acs.nanolett.9b04083 |
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Nuclear pores as versatile reference standards for quantitative superresolution microscopy Jervis Vermal Thevathasan, Maurice Kahnwald, Konstanty Cieśliński, Philipp Hoess, Sudheer Kumar Peneti, Manuel Reitberger, Daniel Heid, Krishna Chaitanya Kasuba, Sarah Janice Hoerner, Yiming Li, Yu-Le Wu, Markus Mund, Ulf Matti, Pedro Matos Pereira, Ricardo Henriques, Bianca Nijmeijer, Moritz Kueblbeck, Vilma Jimenez Sabinina, Jan Ellenberg, Jonas Ries Paper published in Nature Methods, September 2019 Technologies: CARE (), NanoJ (), NanoJ-SQUIRREL (), NanoJ-SRRF () and Nuclear-Pores as references Funded by: BBSRC and Wellcome Trust News: Mirage News DOI: 10.1038/s41592-019-0574-9 |
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Artificial intelligence for microscopy - what you should know Lucas von Chamier, Romain F. Laine, Ricardo Henriques Review published in Biochemical Society Transactions, July 2019 Technologies: CARE (), NanoJ (), NanoJ-Fluidics (), NanoJ-SQUIRREL () and NanoJ-SRRF () Funded by: BBSRC and Wellcome Trust News: Azooptics.com DOI: 10.1042/bst20180391 |
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Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion Robert D. M. Gray, David Albrecht, Corina Beerli, Moona Huttunen, Gary H. Cohen, Ian J. White, Jemima J. Burden, Ricardo Henriques, Jason Mercer Paper published in Nature Microbiology, July 2019 Technologies: NanoJ () and NanoJ-VirusMapper Funded by: BBSRC and Wellcome Trust Blogs: Nature Microbiology Community DOI: 10.1038/s41564-019-0488-4 |
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Super-resolution fight club - assessment of 2D and 3D single-molecule localization microscopy software Daniel Sage, Thanh-An Pham, Hazen Babcock, Tomas Lukes, Thomas Pengo, Jerry Chao, Ramraj Velmurugan, Alex Herbert, Anurag Agrawal, Silvia Colabrese, Ann Wheeler, Anna Archetti, Bernd Rieger, Raimund Ober, Guy M. Hagen, Jean-Baptiste Sibarita, Jonas Ries, Ricardo Henriques, Michael Unser, Seamus Holden Paper published in Nature Methods, April 2019 Technologies: QuickPALM Funded by: BBSRC DOI: 10.1038/s41592-019-0364-4 |
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Automating multimodal microscopy with NanoJ-Fluidics Pedro Almada, Pedro M. Pereira, Siân Culley, Ghislaine Caillol, Fanny Boroni-Rueda, Christina L. Dix, Guillaume Charras, Buzz Baum, Romain F. Laine, Christophe Leterrier, Ricardo Henriques Paper published in Nature Communications, March 2019 Technologies: NanoJ (), NanoJ-Fluidics (), NanoJ-SQUIRREL (), NanoJ-SRRF () and NanoJ-VirusMapper Funded by: BBSRC and Wellcome Trust News: Technology Times, MSN, DNYUZ and Express Informer DOI: 10.1038/s41467-019-09231-9 |
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NanoJ - a high-performance open-source super-resolution microscopy toolbox Romain F Laine, Kalina L Tosheva, Nils Gustafsson, Robert D M Gray, Pedro Almada, David Albrecht, Gabriel T Risa, Fredrik Hurtig, Ann-Christin Lindås, Buzz Baum, Jason Mercer, Christophe Leterrier, Pedro M Pereira, Siân Culley, Ricardo Henriques Paper published in Journal of Physics D - Applied Physics, January 2019 Technologies: CARE (), NanoJ (), NanoJ-SQUIRREL (), NanoJ-SRRF (), NanoJ-VirusMapper and QuickPALM Funded by: BBSRC and Wellcome Trust DOI: 10.1088/1361-6463/ab0261 |
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TMEM16F activation by Ca2+ triggers plasma membrane expansion and directs PD-1 trafficking Christopher Bricogne, Michael Fine, Pedro M. Pereira, Julia Sung, Maha Tijani, Youxue Wang, Ricardo Henriques, Mary K. Collins, Donald W. Hilgemann Paper published in Scientific Reports, January 2019 Funded by: BBSRC DOI: 10.1038/s41598-018-37056-x |
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Real time multi-modal super-resolution microscopy through Super-Resolution Radial Fluctuations (SRRF-Stream) Justin Cooper, Mark Browne, Hugh Gribben, Martin Catney, Colin Coates, Alan Mullan, Geraint Wilde, Ricardo Henriques Paper published in Single molecule spectroscopy and superresolution imaging XII, January 2019 Technologies: NanoJ-SRRF () DOI: 10.1117/12.2510761 |
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A hidden Markov model approach to characterizing the photo-switching behavior of fluorophores Lekha Patel, Nils Gustafsson, Yu Lin, Raimund Ober, Ricardo Henriques, Edward Cohen Published in The annals of applied statistics, January 2019 Funded by: BBSRC DOI: 10.1214/19-AOAS1240 |
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Fix your membrane receptor imaging - actin cytoskeleton and CD4 membrane organization disruption by chemical fixation Pedro M Pereira, David Albrecht, Siân Culley, Caron Jacobs, Mark Marsh, Jason Mercer, Ricardo Henriques Published in Frontiers in immunology, January 2019 Technologies: NanoJ (), NanoJ-Fluidics () and NanoJ-SQUIRREL () Funded by: BBSRC and Wellcome Trust DOI: 10.3389/fimmu.2019.00675 |
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Content-aware image restoration - pushing the limits of fluorescence microscopy Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Mauricio Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers Paper published in Nature Methods, November 2018 Technologies: CARE (), NanoJ-SQUIRREL () and NanoJ-SRRF () Funded by: BBSRC and Wellcome Trust News: Technology Networks, VBIO, Innovations Report and Informationsdienst Wissenschaft DOI: 10.1038/s41592-018-0216-7 |
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Heterogeneous localisation of membrane proteins in Staphylococcus aureus Felix Weihs, Katarzyna Wacnik, Robert D. Turner, Siân Culley, Ricardo Henriques, Simon J. Foster Paper published in Scientific Reports, February 2018 Technologies: NanoJ-SRRF () Funded by: BBSRC and Wellcome Trust DOI: 10.1038/s41598-018-21750-x |
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Quantitative mapping and minimization of super-resolution optical imaging artifacts Siân Culley, David Albrecht, Caron Jacobs, Pedro Matos Pereira, Christophe Leterrier, Jason Mercer, Ricardo Henriques Paper published in Nature Methods, February 2018 Technologies: NanoJ-SQUIRREL (), NanoJ-SRRF () and QuickPALM Funded by: BBSRC and Wellcome Trust News: physicsworld.com DOI: 10.1038/nmeth.4605 |
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SRRF - Universal live-cell super-resolution microscopy Siân Culley, Kalina L Tosheva, Pedro Matos Pereira, Ricardo Henriques Paper published in The international journal of biochemistry & cell biology, January 2018 Technologies: NanoJ-SQUIRREL () and NanoJ-SRRF () Funded by: BBSRC and Wellcome Trust DOI: 10.1016/j.biocel.2018.05.014 |
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The role of mitotic cell-substrate adhesion re-modeling in animal cell division Christina L Dix, Helen K Matthews, Marina Uroz, Susannah McLaren, Lucie Wolf, Nicholas Heatley, Zaw Win, Pedro Almada, Ricardo Henriques, Michael Boutros, Xavier Trepat, Buzz Baum Published in Developmental cell, January 2018 Funded by: BBSRC DOI: 10.1016/j.devcel.2018.03.009 |
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Septins recognize and entrap dividing bacterial cells for delivery to lysosomes Sina Krokowski, Damian Lobato-Marquez, Arnaud Chastanet, Pedro Matos Pereira, Dimitrios Angelis, Dieter Galea, Gerald Larrouy-Maumus, Ricardo Henriques, Elias T Spiliotis, Rut Carballido-Lopez, Serge Mostowy Published in Cell host & microbe, January 2018 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.1016/j.chom.2018.11.005 |
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Open-source single-particle analysis for super-resolution microscopy with VirusMapper Robert DM Gray, Jason Mercer, Ricardo Henriques Paper published in JoVE, January 2017 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.3791/55471 |
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K63-Linked Ubiquitination Targets Toxoplasma gondii for Endo-lysosomal Destruction in IFNγ-Stimulated Human Cells Barbara Clough, Joseph D. Wright, Pedro M. Pereira, Elizabeth M. Hirst, Ashleigh C. Johnston, Ricardo Henriques, Eva-Maria Frickel Paper published in PLOS Pathogens, November 2016 Funded by: BBSRC News: Phys.org and Bionity Blogs: The Toxoplasma Blog DOI: 10.1371/journal.ppat.1006027 |
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HIV-1 Nef Impairs the Formation of Calcium Membrane Territories Controlling the Signaling Nanoarchitecture at the Immunological Synapse Joana G. Silva, Nuno P. Martins, Ricardo Henriques, Helena Soares Paper published in The Journal of Immunology, October 2016 Funded by: BBSRC DOI: 10.4049/jimmunol.1601132 |
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Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations Nils Gustafsson, Siân Culley, George Ashdown, Dylan M. Owen, Pedro Matos Pereira, Ricardo Henriques Paper published in Nature Communications, August 2016 Technologies: NanoJ-SRRF () and QuickPALM Funded by: BBSRC News: Azom.com DOI: 10.1038/ncomms12471 |
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Infection Counter - Automated Quantification of in Vitro Virus Replication by Fluorescence Microscopy Siân Culley, Greg Towers, David Selwood, Ricardo Henriques, Joe Grove Paper published in Viruses, July 2016 Technologies: Infection-Counter () Funded by: BBSRC DOI: 10.3390/v8070201 |
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VirusMapper - open-source nanoscale mapping of viral architecture through super-resolution microscopy Robert DM Gray, Corina Beerli, Pedro Matos Pereira, Kathrin Maria Scherer, Jerzy Samolej, Christopher Karl Ernst Bleck, Jason Mercer, Ricardo Henriques Paper published in Scientific reports, January 2016 Technologies: NanoJ-VirusMapper Funded by: BBSRC DOI: 10.1038/srep29132 |
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Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti Janine Scholefield, Ricardo Henriques, Anca F Savulescu, Elisabeth Fontan, Alix Boucharlat, Emmanuel Laplantine, Asma Smahi, Alain Israël, Fabrice Agou, Musa M Mhlanga Paper published in Nature Communications, January 2016 Technologies: QuickPALM Funded by: BBSRC and FCT DOI: 10.1038/ncomms12629 |
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Mitochondria mediate septin cage assembly to promote autophagy of Shigella Andrea Sirianni, Sina Krokowski, Damián Lobato‐Márquez, Stephen Buranyi, Julia Pfanzelter, Dieter Galea, Alexandra Willis, Siân Culley, Ricardo Henriques, Gerald Larrouy‐Maumus, Michael Hollinshead, Vanessa Sancho‐Shimizu, Michael Way, Serge Mostowy Paper published in EMBO reports, January 2016 Funded by: BBSRC DOI: 10.15252/embr.201541832 |
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PALM and STORM - Into large fields and high-throughput microscopy with sCMOS detectors Pedro Almada, Siân Culley, Ricardo Henriques Review published in Methods, January 2015 Technologies: QuickPALM DOI: 10.1016/j.ymeth.2015.06.004 |
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High-content 3D multicolor super-resolution localization microscopy Pedro M Pereira, Pedro Almada, Ricardo Henriques Book chapter published in Methods in cell biology, January 2015 Technologies: QuickPALM DOI: 10.1016/bs.mcb.2014.10.004 |
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TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO–IKK supramolecular structures Nadine Tarantino, Jean-Yves Tinevez, Elizabeth Faris Crowell, Bertrand Boisson, Ricardo Henriques, Musa Mhlanga, Fabrice Agou, Alain Israël, Emmanuel Laplantine Paper published in Journal of Cell Biology, January 2014 DOI: 10.1083/jcb.201307172 |
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Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse Helena Soares, Ricardo Henriques, Martin Sachse, Leandro Ventimiglia, Miguel A Alonso, Christophe Zimmer, Maria-Isabel Thoulouze, Andrés Alcover Paper published in Journal of Experimental Medicine, January 2013 Technologies: QuickPALM DOI: 10.1084/jem.20130150 |
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Hierarchies of host factor dynamics at the entry site of Shigella flexneri during host cell invasion Soudeh Ehsani, José Carlos Santos, Cristina D Rodrigues, Ricardo Henriques, Laurent Audry, Christophe Zimmer, Philippe Sansonetti, Guy Tran Van Nhieu, Jost Enninga Paper published in Infection and immunity, January 2012 Technologies: QuickPALM DOI: 10.1128/IAI.06391-11 |
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Highly dynamic host actin reorganization around developing Plasmodium inside hepatocytes Carina SS Gomes-Santos, Maurice A Itoe, Cristina Afonso, Ricardo Henriques, Rui Gardner, Nuno Sepulveda, Pedro D Simoes, Helena Raquel, Antonio Paulo Almeida, Luis F Moita, Friedrich Frischknecht, Maria M Mota Paper published in PLoS One, January 2012 DOI: 10.1371/journal.pone.0029408 |
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Enhanced epifluorescence microscopy by uniform and intensity optimized illumination Sébastien Herbert, Ricardo Henriques Perspective published in Cytometry Part A, January 2012 DOI: 10.1002/cyto.a.21177 |
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Single-molecule localization super-resolution microscopy - deeper and faster Sébastien Herbert, Helena Soares, Christophe Zimmer, Ricardo Henriques Review published in Microscopy and microanalysis, January 2012 Technologies: QuickPALM DOI: 10.1017/S1431927612013347 |
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Superresolution imaging of HIV in infected cells with FlAsH-PALM Mickaël Lelek, Francesca Di Nunzio, Ricardo Henriques, Pierre Charneau, Nathalie Arhel, Christophe Zimmer Paper published in Proceedings of the National Academy of Sciences, January 2012 DOI: 10.1073/pnas.1013267109 |
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PALM and STORM - unlocking live‐cell super‐resolution Ricardo Henriques, Caron Griffiths, E Hesper Rego, Musa M Mhlanga Review published in Biopolymers, January 2011 Technologies: QuickPALM DOI: 10.1002/bip.21586 |
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QuickPALM - 3D real-time photoactivation nanoscopy image processing in ImageJ Ricardo Henriques, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga Paper published in Nature Methods, January 2010 Technologies: QuickPALM DOI: 10.1038/nmeth0510-339 |
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High-throughput SNP genotyping - combining tag SNPs and molecular beacons Luis B Barreiro, Ricardo Henriques, Musa M Mhlanga Book chapter published in Single Nucleotide Polymorphisms - Methods and Protocols, January 2009 DOI: 10.1007/978-1-60327-411-1_17 |
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Imaging host-pathogen interactions Friedrich Frischknecht, Spencer Shorte, Ulrike Engel, Keira Melican, Agneta Richter-Dahlfors, Petra Rohrbach, Miguel Prudêncio, Maik J Lehmann, Nicolas Chenouard, Alexandre Dufour, Jean-Christophe Olivo-Marin, Ricardo Henriques, Musa M Mhlanga, Matthias F Langhorst, Joerg Schaffer, Bernhard Goetze, Freddy Frischknecht, Matthias Gunzer, Simone Lepper Editorial published in Biotechnol. J, January 2009 DOI: 10.1002/biot.200900129 |
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PALM and STORM - what hides beyond the Rayleigh limit? Ricardo Henriques, Musa M Mhlanga Review published in Biotechnology Journal - Healthcare Nutrition Technology, January 2009 DOI: 10.1002/biot.200900024 |
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Frontiers in fluorescence microscopy José Rino, José Braga, Ricardo Henriques, Maria Carmo-Fonseca Review published in International Journal of Developmental Biology, January 2009 DOI: 10.1387/ijdb.072351jr |
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Latest funding with our group
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Quinoline-Derived Foldamers - A novel approach to combat antibiotic multiresistant and persistent Pedro M. Mateus, Pedro Matos Pereira, Ricardo Henriques Funded by: FCT - LS4Future Seed Funding Duration: March 2024 - September 2024 |
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Sub-cellular Metabolic Compartmentalization During Oocyte Development Zita Carvalho dos Santos, Ricardo Henriques, Jorge Carvalho Funded by: CZI - Measuring Metabolism Across Scales Duration: January 2024 - December 2026 |
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Cutting-edge super-resolution image analysis in napari through NanoJ Bruno Saraiva, Ricardo Henriques Funded by: CZI - Applications - napari Plugin Foundations grants Duration: January 2023 - December 2023 Publications: 4 |
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Real-Time high-content Super-Resolution Imaging of ES Cell States Eran Meshorer, Ricardo Henriques, Anna Kreshuk, Sandrine Lévêque-Fort, Nicolas Bourg, Genevieve Almouzni Alias: RT-SuperES Funded by: H2022 - EIC Pathfinder Open Duration: April 2022 - March 2027 Publications: 16 |
Show more funding (24 additional items)
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High-resolution single-molecule imaging via 3D printing Simao Coelho, Ricardo Henriques, Pedro Matos Pereira Funded by: InnOValley - Proof of Concept Duration: July 2022 - December 2023 Publications: 1 |
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VP-CLEM-KIT - a pipeline for democratising volumetric visual proteomics Lucy Collinson, Ricardo Henriques, Paul French Funded by: CZI - Visual Proteomics Imaging Duration: December 2021 - June 2024 Publications: 19 |
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Enabling Live-Cell 4D Super-Resolution Microscopy Guided by Artificial Intelligence Ricardo Henriques Alias: SelfDriving4DSR Funded by: ERC - Consolidator Duration: September 2021 - September 2026 Publications: 35 |
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Artificial Intelligence for Image Data Analysis in the Life Sciences Anna Kreshuk, Florian Jug, Ricardo Henriques, Wei Ouyang, Arrate Muñoz-Barrutia, Emma Lundberg, Matthew Hartley Alias: AI4Life Funded by: H2021 - INFRA Duration: September 2021 - August 2025 Publications: 20 |
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Optial Biology PhD programme Michael Hausser, Ricardo Henriques, Antonella Riccio Funded by: Wellcome Trust - 4-year PhD Programme in Science Duration: August 2021 - August 2025 |
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Investigating the mechanisms underpinning the interaction between autonomous immunity and intracellular S. aureus cell division and persistence Pedro Matos Pereira, João Paulo Santos Fadista, Mário José Ferreira, Moritz Sorg, Patricia Reed, Pedro Fernandes, Ricardo Henriques Funded by: FCT - R&D Projects Duration: March 2021 - February 2024 Publications: 3 |
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Unveiling live-cell viral replication at the nanoscale Ricardo Henriques Funded by: EMBO - Installation Grant Duration: January 2021 - January 2026 Publications: 28 |
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Benchtop, turnkey super-resolution microscopy for biology, biophysics and biotechnology Bart Hoogenboom, Philip Robinson, Graeme King, Stefan Howorka, Alan Lowe, Ricardo Henriques, Anthony Roberts, Kenth Gustafsson, Gary Parkinson, Franck Pichaud Funded by: BBSRC - Research Grant Duration: July 2020 - June 2021 |
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Beyond protein localization - monitoring molecular function with nanometer sensitivity Ricardo Henriques, Romain Laine, Takeharu Nagai, Kai Lu Funded by: UCL - Strategic Partner Fund - Establishing collaborative research between UCL and Osaka University Duration: September 2019 - August 2020 |
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4D Super-Resolution Proteomics Ricardo Henriques Funded by: UCL - Capital Equipment Fund Duration: June 2019 - May 2020 |
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Establishing collaborative research between UCL and Institut Curie Ricardo Henriques, Romain Laine, Bassam Hajj Funded by: UCL - Cities Partnership Programme Duration: June 2019 - June 2019 |
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High-speed 3D super-resolution microscopy Ricardo Henriques Funded by: UCL - Impact Acceleration Account Duration: April 2019 - September 2019 |
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Democratising Live-Cell Adaptive Super-Resolution Microscopy based on SRRF Ricardo Henriques, Buzz Baum Funded by: BBSRC - Tools and Resources Development Fund Duration: January 2019 - February 2020 Publications: 4 |
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Developing AI for Microscopy Ricardo Henriques Funded by: NVIDIA - NVIDIA Academic Hardware Grant Program Duration: December 2018 - December 2018 |
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Content Aware AI Driven Driven Super Resolution Microscopy Ricardo Henriques Funded by: BBSRC - Training Grant Duration: September 2018 - April 2024 Publications: 8 |
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An accessible framework to achieve multi-dimensional live-cell super-resolution high-content screening Ricardo Henriques, Robin Ketteler Funded by: BBSRC - Tools and Resources Development Fund Duration: December 2017 - December 2018 Publications: 12 |
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Enabling Live-Cell Super Resolution Imaging Through Lattice Light Sheet Microscopy Franck Pichaud, Karl Matter, Alan Lowe, Guillaume Charras, Ricardo Henriques, Buzz Baum Funded by: BBSRC - ALERT Duration: January 2017 - May 2018 Publications: 14 |
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Understanding cellular organisation - from archaea to eukaryotes Buzz Baum, Mohan Balasubramanian, Jan Löwe, Ricardo Henriques, Ann-Christin Lindas, Thijs Ettema, Ethan Garner Funded by: Wellcome Trust - Collaborative Award in Science Duration: December 2016 - December 2021 Publications: 28 |
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Super-Beacons and Beacon-STORM - a new generation of small tunable photoswitching probes and Super-Resolution approaches Ricardo Henriques Funded by: BBSRC - New Investigator Research Grant Duration: January 2016 - December 2018 Publications: 24 |
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Imaging the structure and dynamics of molecules and complexes in living organisms Nuno Moreno, Adan Guerrero Cardenas, Adriano Henriques, Antonio Jacinto, Beatriz García Fernández, Emilio José Gualda Manzano, Florence Janody, José Feijó, Lars Jansen, Mariana Pinho, Monica Bettencourt Carvalho Dias, Pedro Almada, Raquel Oliveira, Ricardo Henriques, Sérgio Filipe, Susana Gouveia, Teresa Costa Funded by: FCT - Projectos de IC&DT de Consolidação de Competências e Recursos em Investigação Duration: July 2013 - December 2016 |
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Enhancing single-molecule localization super-resolution microscopy Ricardo Henriques Funded by: Pasteur-Roux-Cantarini - Postdoctoral Fellowships Duration: January 2012 - August 2013 |
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Spatio-temporal tracking of gene expression in living cells via super-resolution microscopy Ricardo Henriques Funded by: FCT - PhD Fellowship Duration: January 2010 - October 2011 |
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Super-resolution imaging of gene expression and nuclear architecture Musa Mhlanga, Ricardo Henriques Funded by: FCT - R&D Projects Duration: January 2009 - December 2012 Publications: 1 |
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Identification and characterization of the supercomplexes from the bacterial aerobic respiratory chain of Escherichia coli and Bacillus subtilis Ana Margarida Carvalho Melo, Ana Paula Gonçalves Batista, Joao Nuno Carita, Ligia M Saraiva, Miguel Teixeira, Ricardo Henriques Funded by: FCT - R&D Projects Duration: January 2008 - December 2011 |