Research Team

Ricardo Henriques

Ricardo Henriques

Group Leader

Started in: September 2013

Funding: ITQB NOVA


Ricardo is a 12th-year Group Leader in our research group. Worked on 84 publications. Contributed to 26 technologies. Raised 29 grants. Collaborates with 26 labs. Mentored 13 PhD Students, 10 Postdocs, 2 Masters Students, 3 Postdoc (now PI)s, 1 Internship Student, 1 Lab Manager, 2 Software Engineers.

By training, I am a Particle Physicist that fell in love with Biological Physics shortly after graduating. I did my PhD in both the Musa Mhlanga and Christophe Zimmer laboratories, carrying out research between iMM (Portugal), Institut Pasteur (France), CSIR (South Africa) and Andor Technology (UK and USA). During this time, I entered the field of Super-Resolution Microscopy, developing technologies that enable imaging of cellular and viral structures at unprecedented resolution. During my PhD and postdoc, I applied the methods I developed to study Cell Signalling, T-cell Immunology and Viral Infection. In 2013 I established my first research group at UCL, with a dual emphasis on Developing new Imaging Technologies and Cell Biology research. In 2017 I was further invited to extend my group into the Francis Crick Institute, where I established a second small laboratory. In 2019 I was promoted to full Professor at UCL. In 2020, I returned to Portugal, moving my laboratory to Instituto Gulbenkian de Ciência. In 2024, I was invited to join Instituto de Tecnologia Química e Biológica António Xavier as a permanent Principal Investigator. My research group uses optical and computational biophysics to study cell biology and host-pathogen interactions. We develop technologies that enable the study of cellular structures and processes at the nanoscale, and apply these methods to study the molecular mechanisms of infection. My group has a strong emphasis on open science, developing open-source software and hardware that enable researchers worldwide to carry out advanced imaging experiments. My technological developments are widely disseminated to the Cell Biology and Biomedical research community. My algorithms QuickPALM, NanoJ, SRRF and SQUIRREL are among the most used and cited analytical methods in the Super-Resolution Microscopy field. My core philosophy has been to make my research reproducible, transparent and open-source.

Talks biosketch

Prof. Ricardo Henriques is a Principal Investigator at ITQB NOVA (Instituto de Tecnologia Química e Biológica António Xavier). He is a distinguished researcher who has contributed to cell biology, super-resolution microscopy, and computational imaging. He obtained his Physics Diploma from the University of Lisbon in 2005 and earned his Biophysics PhD in 2011, specialising in real-time super-resolution fluorescence microscopy. Between 2011 and 2013, Ricardo completed postdoctoral work at Institut Pasteur in Paris, applying his optical developments to study cell biology and viral infection. In 2013, he joined the MRC LMCB (Laboratory for Molecular Cell Biology) at UCL as an Associate Professor. During his tenure at UCL, he led a research group pushing the boundaries of optical microscopy, machine learning, and the study of cell mechanisms. The recognition of his research led to a dual role at the Francis Crick Institute in 2017 and a promotion to Full Professor at UCL in 2019. Since 2020, Ricardo has returned to Portugal, first joining IGC (Instituto Gulbenkian de Ciência) and later in 2024, moving to ITQB NOVA (Instituto de Tecnologia Química e Biológica António Xavier). He became an EMBO member in 2024. His group uses optical and computational biophysics to study cell biology and host-pathogen interactions. He has developed open-source software methods that have become gold standards in super-resolution microscopy, enabling researchers worldwide to visualise cellular structures at nanoscale resolution. Ricardo's commitment to open science and reproducibility has made his research accessible and impactful.

Contributions to the Generation of New Ideas, Tools, Methodologies or Knowledge

Ricardo Henriques has made significant contributions to the fields of super-resolution microscopy, computational imaging, and cell biology. He has pioneered innovative technologies, methodologies, and knowledge that highlight the significance of his work and its broad-reaching implications for the scientific community and beyond.

His work in super-resolution microscopy has positively impacted the field, enabling researchers to visualise dynamic cellular structures at nansocale resolution and precision. One of his notable contributions is the development of QuickPALM (Henriques et al., Nature Methods, 2010; DOI:10.1038/nmeth0510-339), the first open-source software for single-molecule localization microscopy. This approach enables real-time 3D nanoscale imaging in living cells. Since its inception, QuickPALM has become a gold standard in the single-molecule microscopy field, setting a standard for imaging technologies worldwide.

In addition to QuickPALM, Ricardo has introduced a suite of critical open-source software tools, including the large NanoJ toolbox (Laine et al., Journal of Physics, 2019; DOI:10.1088/1361-6463/ab0261). This toolbox encompasses NanoJ-SQUIRREL (Culley et al., Nature Methods, 2018; DOI:10.1088/1361-6463/ab0261) and NanoJ-SRRF (Gustafsson et al., Nature Communications, 2016; DOI:10.1038/ncomms12471), among others, which have been key in analysing super-resolution data, facilitating image reconstruction, artifact reduction, and complex dataset interpretation.

Ricardo's pioneering work extends beyond technology development. He has integrated machine learning into advanced bioimaging, exemplified by his development of ZeroCostDL4Mic (von Chamier et al., Nature Communications, 2021; DOI:10.1038/s41467-021-22518-0) and DL4MicEverywhere platforms (Hidalgo-Cenalmor at al., bioRxiv, 2023:10.1101/2023.11.19.567606). These platforms democratise access to deep learning for microscopy, enabling enhanced analysis and interpretation of imaging data. Ricardo Henriques has made significant contributions in the field of biomedical imaging technology, which he has used to generate new biological knowledge. In his lab, super-resolution microscopy was used to understand the nanoscale distribution and dynamics of HIV cell receptors CD4 and CCR5 during viral binding (Yuan et al., Viruses, 2021; DOI:10.3390/v13010142). Henriques's technology was also used to identify the polarization of the entry fusion complex of poxviruses (Gray et al., Nature Microbiology, 2019; 10.1038/s41564-019-0488-4). To further decipher the nanoscale mechanisms of ESCRT-III-mediated cell division of archaeons (Risa et al., Science, 2020; DOI:10.1126/science.aaz2532 and Harker-Kirschneck et al., PNAS, 2022; DOI:10.1073/pnas.2107763119). In addition, his technology was key in uncovering how closed mitosis requires local disassembly of the nuclear envelope (Dey et al., Nature, 2020; DOI:10.1038/s41586-020-2648-3).

His contributions have been widely disseminated through high-impact publications, with over 67 publications to his name. Over his career, Ricardo has also secured 7 million euros in funding from agencies such as ERC Consolidator, Horizon Europe, and Wellcome Trust, reflecting his global scientific impact and sustained excellence in research, training, and leadership.

Contributions to the Training and Mentoring of Students and Early Career Researchers

Throughout his career, Ricardo Henriques has mentored and supervised numerous researchers with diverse backgrounds, including 14 PhD students, 12 postdocs, 2 Master's students, 1 internship student, and 2 software engineers. He has provided hands-on mentorship and created opportunities for their career progression, supporting their skill development in cell biology, optical physics, and computational biology. His trainees have gone on to secure positions in academia and industry, demonstrating the impact of his mentorship.

Ricardo has also taught specialised graduate courses in cell biology, super-resolution microscopy, and machine learning at University College London and Instituto Gulbenkian de Ciência. He has organized international workshops and training courses, training over 300 researchers worldwide in advanced imaging techniques. Through these activities, he has built an extensive network and provided key skills to accelerate careers.

Contributions to Society

Ricardo has significantly impacted society through innovative research and a dedication to open science. He champions open research practices, facilitating collaboration and knowledge exchange. Ricardo's dedication to public engagement and outreach is impressive, with a large social media following and active participation in science festivals, lectures, and workshops. He contributes to increasing scientific literacy and appreciation for research by sharing findings and explaining complex concepts. Ricardo's work extends to the private sector, facilitating the translation of scientific discoveries into practical applications. He has contributed to developing new technologies and tools in healthcare, biotechnology, and imaging through collaborations with industry partners. His commitment to society and his passion for making science accessible and impactful have earned him a well-deserved reputation as a leader in his field.

In the news

Technologies

CLEM-Reg CLEM-Reg Newest update: 2024-12-05
SReD SReD Newest update: 2024-11-30
BioImage Model Zoo BioImage Model Zoo Newest update: 2024-11-26
DL4MicEverywhere DL4MicEverywhere Newest update: 2024-11-11
ZeroCostDL4Mic ZeroCostDL4Mic Newest update: 2024-11-11
Fast4DReg Fast4DReg Newest update: 2024-10-25
CellTracksColab CellTracksColab Newest update: 2024-10-23
CARE CARE Newest update: 2024-10-05
PhotoFiTT PhotoFiTT Newest update: 2024-07-17
DeepAutoFocus DeepAutoFocus Newest update: 2024-07-15
NanoPyx NanoPyx Newest update: 2024-07-11
NanoJ NanoJ Newest update: 2024-03-22
NanoJ-eSRRF NanoJ-eSRRF Newest update: 2024-03-22
NanoJ-SRRF NanoJ-SRRF Newest update: 2024-03-22
nano-org nano-org Newest update: 2024-01-01
DeepBacs DeepBacs Newest update: 2022-05-11
NanoJ-SQUIRREL NanoJ-SQUIRREL Newest update: 2020-09-10
FBSR-TFM FBSR-TFM Newest update: 2020-01-01
Sulfoscope Sulfoscope Newest update: 2020-01-01
Super-Beacons Super-Beacons Newest update: 2020-01-01
vLume vLume Newest update: 2020-01-01
NanoJ-Fluidics NanoJ-Fluidics Newest update: 2019-04-04
Nuclear-Pores as references Nuclear-Pores as references Newest update: 2019-01-01
Infection-Counter Infection-Counter Newest update: 2016-04-05
NanoJ-VirusMapper NanoJ-VirusMapper Newest update: 2016-01-01
QuickPALM QuickPALM Newest update: 2010-01-01

Publications with our group (see more on Google Scholar)

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, January 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
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
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, January 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
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, January 2024
Technologies: Nuclear-Pores as references and SReD
Funded by: CZI, EMBO, ERC, H2021 and H2022
DOI: 10.1101/2024.09.16.613204
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
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, January 2024
Technologies: DL4MicEverywhere, PhotoFiTT and ZeroCostDL4Mic
Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022
DOI: 10.1101/2024.07.16.603046
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, January 2024
Technologies: NanoJ
Funded by: EMBO and ERC
DOI: 10.1038/s41564-024-01629-6
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
Decoding life's inner workings - advances in quantitative bioimaging
Ricardo Henriques, Christophe Leterrier, Aubrey Weigel
Editorial published in Open Biology, January 2023
DOI: 10.1098/rsob.230329
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, January 2023
Technologies: BioImage Model Zoo, CLEM-Reg and ZeroCostDL4Mic
Funded by: CZI and ERC
DOI: 10.1101/2023.05.11.540445
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, January 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
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
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
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
NanoPyx - super-fast bioimage analysis powered by adaptive machine learning
Bruno M. Saraiva, Inês M. Cunha, António D. Brito, Gautier Follain, Raquel Portela, Robert Haase, Pedro M. Pereira, Guillaume Jacquemet, Ricardo Henriques
Preprint published in bioRxiv, January 2023
Technologies: NanoJ, NanoJ-eSRRF, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and NanoPyx
Funded by: CZI, EMBO, ERC, FCT, H2021 and H2022
DOI: 10.1101/2023.08.13.553080
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
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, January 2023
Technologies: CARE, DeepAutoFocus, DeepBacs and ZeroCostDL4Mic
Funded by: EMBO, ERC, H2021 and H2022
DOI: 10.1101/2023.10.16.562172
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
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
The LEGO® brick road to open science and biotechnology
Etienne Boulter, Julien Colombelli, Ricardo Henriques, Chloé C. Féral
Review published in Trends in Biotechnology, January 2022
Technologies: NanoJ and NanoJ-Fluidics
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1016/j.tibtech.2022.02.003
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
Expansion Microscopy on Saccharomyces cerevisiae
AG Korovesi, L Morgado, M Fumasoni, R Henriques, HS Heil, M Del Rosario
Paper published in microPublication Biology, January 2022
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.17912/micropub.biology.000566
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, January 2022
Technologies: NanoJ-VirusMapper, Nuclear-Pores as references and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1098/rsob.220079
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
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, January 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
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
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, January 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
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: BioImage Model Zoo and ZeroCostDL4Mic
Funded by: EMBO, ERC and Wellcome Trust
DOI: 10.1038/s41592-021-01284-3
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
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, January 2021
Funded by: ERC and Wellcome Trust
DOI: 10.1017/s2633903x21000027
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, January 2021
Technologies: NanoJ-VirusMapper, Super-Beacons and ZeroCostDL4Mic
Funded by: Wellcome Trust
DOI: 10.3390/v13020233
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, January 2021
Technologies: DeepAutoFocus
Funded by: BBSRC and Wellcome Trust
News: Nanowerk
DOI: 10.1038/s41467-021-22526-0
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
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
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, January 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
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, January 2020
Technologies: NanoJ, NanoJ-Fluidics and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
News: ScienMag and EurekAlert!
DOI: 10.1242/jcs.240713
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
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
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, January 2020
Technologies: NanoJ
News: NRK, Scitech Daily, NCYT - Noticias de la Ciencia y la Technologia and UPI.com
DOI: 10.1126/science.aaz2532
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, January 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
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
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 and NanoJ-Fluidics
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab6b95
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, January 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
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
Artificial intelligence for microscopy - what you should know
Lucas von Chamier, Romain F. Laine, Ricardo Henriques
Review published in Biochemical Society Transactions, January 2019
Technologies: CARE, NanoJ, NanoJ-Fluidics, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
News: Azooptics.com
DOI: 10.1042/bst20180391
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 and NanoJ-SRRF
DOI: 10.1117/12.2510761
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, January 2019
Technologies: NanoJ and NanoJ-VirusMapper
Funded by: BBSRC and Wellcome Trust
Blogs: Nature Microbiology Community
DOI: 10.1038/s41564-019-0488-4
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-Fluidics, NanoJ-SQUIRREL, NanoJ-SRRF, NanoJ-VirusMapper and QuickPALM
Funded by: BBSRC and Wellcome Trust
DOI: 10.1088/1361-6463/ab0261
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
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
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, January 2019
Technologies: QuickPALM
Funded by: BBSRC
DOI: 10.1038/s41592-019-0364-4
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, January 2019
Technologies: 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
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, January 2018
Technologies: NanoJ, NanoJ-SQUIRREL and QuickPALM
Funded by: BBSRC and Wellcome Trust
News: physicsworld.com
DOI: 10.1038/nmeth.4605
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, NanoJ-SQUIRREL and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1016/j.biocel.2018.05.014
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
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
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, January 2018
Technologies: CARE and NanoJ-SQUIRREL
Funded by: BBSRC and Wellcome Trust
News: Technology Networks, VBIO, Innovations Report and Informationsdienst Wissenschaft
DOI: 10.1038/s41592-018-0216-7
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, January 2018
Technologies: NanoJ and NanoJ-SRRF
Funded by: BBSRC and Wellcome Trust
DOI: 10.1038/s41598-018-21750-x
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
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, January 2016
Funded by: BBSRC
News: Phys.org and Bionity
Blogs: The Toxoplasma Blog
DOI: 10.1371/journal.ppat.1006027
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, January 2016
Technologies: Infection-Counter
Funded by: BBSRC
DOI: 10.3390/v8070201
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
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, January 2016
Technologies: NanoJ-SRRF and QuickPALM
Funded by: BBSRC
News: Azom.com
DOI: 10.1038/ncomms12471
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
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, January 2016
Funded by: BBSRC
DOI: 10.4049/jimmunol.1601132
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
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
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
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
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
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
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
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
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
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
PALM and STORM - a super-resolution molecular view into living cells
C Griffiths, R Henriques, MM Mhlanga
Review published in Biotechnology International, January 2011
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
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
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
Chronic arthritis directly induces quantitative and qualitative bone disturbances leading to compromised biomechanical properties
J Caetano-Lopes, AM Nery, R Henriques, H Canhão, J Duarte, PM Amaral, M Vale, R Moura, PA Pereira, P Weinmann, S Abdulghani, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, M Viana Queiroz, YT Konttinen, L Graça, MF Vaz, JE Fonseca
Paper published in Clinical & Experimental Rheumatology, January 2009
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
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
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
Degradation of bone biomechanical properties secondary to quantitative and qualitative bone disturbances induced by arthritis in SKG mice
J Caetano-Lopes, AM Nery, R Henriques, H Canhao, J Duarte, P Amaral, M Vale, R Moura, PA Pereira, P Weinmann, M Souto-Carneiro, P Rego, J Monteiro, S Sakagushi, L Graca, M Viana Queiroz, MF Vaz, JE Fonseca
Paper published in Calcified Tissue International, January 2008

Funding with our group

Democratizing Deep Learning for Microscopists with DL4MicEverywhere
Ricardo Henriques, Guillaume Jacquemet, Caron Jacobs
Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust - Essential Open Source Software for Science (Cycle 6)
Duration: July 2024 - June 2026
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
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
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: 3
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
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: 10
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: 13
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: 28
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: 14
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
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
Unveiling live-cell viral replication at the nanoscale
Ricardo Henriques
Funded by: EMBO - Installation Grant
Duration: January 2021 - January 2026
Publications: 21
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
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
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
4D Super-Resolution Proteomics
Ricardo Henriques
Funded by: UCL - Capital Equipment Fund
Duration: June 2019 - May 2020
High-speed 3D super-resolution microscopy
Ricardo Henriques
Funded by: UCL - Impact Acceleration Account
Duration: April 2019 - September 2019
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
Developing AI for Microscopy
Ricardo Henriques
Funded by: NVIDIA - NVIDIA Academic Hardware Grant Program
Duration: December 2018 - December 2018
Content Aware AI Driven Driven Super Resolution Microscopy
Ricardo Henriques
Funded by: BBSRC - Training Grant
Duration: September 2018 - April 2024
Publications: 8
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
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
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
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
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
Enhancing single-molecule localization super-resolution microscopy
Ricardo Henriques
Funded by: Pasteur-Roux-Cantarini - Postdoctoral Fellowships
Duration: January 2012 - August 2013
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
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
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