Research
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 |
|
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 |
|
|
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 |