Software
Team members:
Kalina Tosheva
MRC-LMCB
Tchyn Lang Laure Ho
BBSRC LiDO iCASE
Hannah Heil
EMBO Postdoctoral Fellowship
Mario Del Rosario
IGC Core Funded
Bruno M. Saraiva
ERC Funded
Afonso Mendes
IGC IBB
Estibaliz Gómez de Mariscal
EMBO Funded
Simão Coelho
ERC Funded
Leonor Morgado
IGC-Abbelight Partnership
Ines Cunha
EMBO Installation Grant funded
Pedro Almada
Alumni
Pedro Matos Pereira
Alumni
Siân Culley
Alumni
Caron Jacobs
Alumni
Nils Gustafsson
Alumni
Jerzy Samolej
Alumni
Robert Gray
Alumni
David Albrecht
Alumni
Lucas Von Chamier
Alumni
Romain F. Laine
Alumni
Daniel Krentzel
Crick Sandwich Student
Alumni
Cheng-Yu Huang
Alumni
Christoph Spahn
EMBO Short-Term Fellow
Alumni
Collaborators:
Anna Kreshuk
Alan Lowe
Andela Šarić
Buzz Baum
Bassam Hajj
Christophe Leterrier
Ed Cohen
Florian Jug
Guillaume Jacquemet
Isabel Llorente-García
Joe Grove
Johanna Ivaska
Jason Mercer
Jonas Ries
Lucy Collinson
Loïc Royer
Mike Heilemann
Mariana Pinho
Martin Weigert
Musa Mhlanga
Seamus Holden
Steven Lee
Uwe Schmidt
Publications:
 | Fast4DReg: Fast registration of 4D microscopy datasets Joanna W Pylvänäinen, *Romain F Laine*, Sujan Ghimire, Gautier Follain, *Ricardo Henriques*, Guillaume Jacquemet Published in bioRxiv, August 2022 (see preprint) Research themes: New Methods, Software Type: Preprint |
 | Mapping molecular complexes with Super-Resolution Microscopy and Single-Particle Analysis *Afonso Mendes*, *Hannah S. Heil*, *Simao Coelho*, Christophe Leterrier, *Ricardo Henriques* Published in Open Biology, July 2022 (see publication) Research themes: Structural Biology, New Methods, Software Type: Review, Corresponding author |
 | 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* Published in Nature Communications Biology, July 2022 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
| | 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 Published in bioRxiv, June 2022 (see preprint) Research themes: New Methods, Software Type: Preprint |
| | 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, Tommaso Galgani, Aki Stubb, Gautier Follain, *Siân Culley*, Guillaume Jacquemet, Bassam Hajj, Christophe Leterrier, *Ricardo Henriques* Published in bioRxiv, April 2022 (see preprint) Research themes: New Methods, Software Type: Preprint, Corresponding author |
 | Avoiding a replication crisis in deep-learning-based bioimage analysis *Romain F Laine*, Ignacio Arganda-Carreras, *Ricardo Henriques*, Guillaume Jacquemet Published in Nature methods, October 2021 (see publication) Research themes: New Methods, Software Type: Paper |
 | 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 Published in Biological Imaging, September 2021 (see publication) Research themes: New Methods, Software Type: Paper |
 | The Field Guide to 3D Printing in Optical Microscopy for Life Sciences *Mario Del Rosario*, *Hannah S. Heil*, *Afonso Mendes*, Vittorio Saggiomo, *Ricardo Henriques* Published in Advanced Biology, May 2021 (see publication) Research themes: New Methods, Software, Hardware Type: Review, Corresponding author |
 | 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 Published in Nature communications, April 2021 (see publication or preprint) Research themes: Microbiology, New Methods, Software, Hardware Type: Paper |
| | 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* Published in Nature communications, April 2021 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
| | 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, Mafalda Da Cunha Santos, James McColl, Christophe Leterrier, Simon J Davis, *Ricardo Henriques*, Steven F Lee Published in Nature methods, October 2020 (see publication or preprint) Research themes: New Methods, Software Type: Paper |
 | The cell biologist’s guide to super-resolution microscopy Guillaume Jacquemet, Alexandre F. Carisey, Hellyeh Hamidi, *Ricardo Henriques*, Christophe Leterrier Published in Journal of Cell Science, June 2020 (see publication) Research themes: New Methods, Software, Hardware Type: Review, Corresponding author |
 | Fluctuation-Based Super-Resolution Traction Force Microscopy Aki Stubb, *Romain F Laine*, Camilo Guzmán, *Ricardo Henriques*, Guillaume Jacquemet, Johanna Ivaska Published in Nano Letters, March 2020 (see publication) Research themes: New Methods, Software Type: Paper |
 | 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, September 2019 (see publication) Research themes: New Methods, Software Type: Paper |
 | Artificial intelligence for microscopy: what you should know *Lucas von Chamier*, *Romain F Laine*, *Ricardo Henriques* Published in Biochemical Society Transactions, August 2019 (see publication) Research themes: New Methods, Software Type: Review, Corresponding author |
| | 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 Published in Nature methods, May 2019 (see publication) Research themes: New Methods, Software Type: Paper |
 | NanoJ: a high-performance open-source super-resolution microscopy toolbox *Romain F Laine*, *Kalina L Tosheva*, *Nils Gustafsson*, *Robert DM 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* Published in Journal of Physics D: Applied Physics, February 2019 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
| | 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 Published in Nature methods, December 2018 (see publication) Research themes: New Methods, Software Type: Paper |
 | SRRF: Universal live-cell super-resolution microscopy *Siân Culley*, *Kalina L Tosheva*, *Pedro Matos Pereira*, *Ricardo Henriques* Published in The international journal of biochemistry & cell biology, August 2018 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
| | 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* Published in Nature methods, April 2018 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
 | Open-source single-particle analysis for super-resolution microscopy with VirusMapper *Robert DM Gray*, Jason Mercer, *Ricardo Henriques* Published in JoVE (Journal of Visualized Experiments), April 2017 (see publication) Research themes: Microbiology, Structural Biology, New Methods, Software Type: Paper, Corresponding author |
| | 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* Published in Nature communications, August 2016 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
 | 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* Published in Scientific reports, July 2016 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |
 | Infection counter: automated quantification of in vitro virus replication by fluorescence microscopy *Siân Culley*, Greg J Towers, David L Selwood, *Ricardo Henriques*, Joe Grove Published in Viruses, July 2016 (see publication) Research themes: New Methods, Software Type: Paper |
| | QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ *Ricardo Henriques*, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga Published in Nature methods, May 2010 (see publication) Research themes: New Methods, Software Type: Paper, Corresponding author |