Wordcloud of Publications
publications wordcloud

Our primary focus is on optical cell biology, where we deploy open-technology we prototype to address standing biological problems. To do so, we focus on the development of novel optical imaging technologies and their application to the study of biological systems. We are particularly interested in the development of super-resolution microscopy methods and their application to the study of host-pathogen interactions, cell signaling, and immunology. Additionally, we are exploring the use of machine learning methods for the analysis of biological images. Our research lines touch the themes:

  • Super-resolution microscopy: The lab has developed methods and algorithms for super-resolution microscopy such as SRRF, QuickPALM, NanoJ, and SQUIRREL. These are widely used analytical tools in the field.

  • Cell biology: Several projects apply super-resolution microscopy to study cell signaling, T-cell immunology, and viral infection.

  • Structural biology: The lab deploys super-resolution microscopy to study the structure of biological systems, such as viruses and the cytoskeleton.

  • Image analysis: The lab develops tools like ZeroCostDL4Mic for analysis and quantification of complex 3D fluorescence microscopy data.

  • Technology development: A core focus is developing new imaging technologies and making them accessible and open-source for the research community.

  • Interdisciplinary research: Collaborations span areas like biotechnology, immunology, virology, and structural biology.

Current Projects

SMALS - Smart Microscopy for Adaptative Live Super-resolution imaging to elucidate the initial steps of the HIV viral transmission
Estibaliz Gómez-de-Mariscal
Alias: SMALS
Funded by: FCT - CEEC Individual
Duration: April 2024 - March 2027
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
3D Nanoscope - a highly accessible, high-performance device for live cell nanoscopy
Arturo G. Vesga
Alias: 3DNanoScope4All
Funded by: Marie Curie - HORIZON TMA MSCA Postdoctoral Fellowships
Duration: March 2024 - February 2026
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
How does membrane topology influence T-cell activation and HIV infection?
Simao Coelho
Funded by: FCT - Exploratory Research Projects
Duration: March 2023 - September 2024
A transformative data-driven live-cell super-resolution microscopy development to elucidate the initial steps of effective viral transmission
Estibaliz Gómez-de-Mariscal
Funded by: EMBO - Postdoctoral Fellowships
Duration: July 2022 - June 2024
Publications: 5
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: 6
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: 11
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: 23
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: 10
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
Mapping HIV-1 infection by 4D Super-Resolution Microscopy
Hannah Heil
Funded by: FCT - CEEC Individual
Duration: July 2021 - June 2027
Publications: 2
Unveiling live-cell viral replication at the nanoscale
Ricardo Henriques
Funded by: EMBO - Installation Grant
Duration: January 2021 - January 2026
Publications: 16
Content Aware AI Driven Driven Super Resolution Microscopy
Ricardo Henriques
Funded by: BBSRC - Training Grant
Duration: September 2018 - April 2024
Publications: 8

Past Projects

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: 2
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
Mapping the early stages of HIV-1 infection by live-cell 4D Super-Resolution Microscopy
Hannah Heil
Funded by: EMBO - Postdoctoral Fellowships
Duration: September 2021 - August 2023
Publications: 5
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
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
Applying advanced microscopy techniques to decipher functional and structural organisation of life at multiple scale
Romain Laine
Funded by: MRC - Skills Development Research Fellow
Duration: April 2019 - March 2021
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
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
Minimal Model of Poxvirus Infection
David Albrecht
Funded by: Marie Curie - Postdoctoral Fellowships
Duration: September 2017 - August 2019
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
Understanding virus cell entry
Caron Jacobs
Funded by: UK-SA Commonwealth Commission - PhD Scholarship
Duration: January 2014 - December 2018
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
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