Compact Cell-Imaging Device to provide insight into the cellular origins of diseases and to aid in the development of novel therapeutics

Project Information

CoCID

Grant agreement ID: 101017116

DOI

10.3030/101017116

Project closed

EC signature date 4 December 2020

Start date 1 January 2021

End date 31 May 2025

Funded under

• INDUSTRIAL LEADERSHIP - Leadership in enabling and industrial technologies - Information and Communication Technologies (ICT)

Total cost

€ 5 686 215,00

EU contribution

€ 5 686 215,00

Coordinated by

UNIVERSITY COLLEGE DUBLIN, NATIONAL UNIVERSITY OF IRELAND, DUBLIN
Ireland

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Open Research Data Pilot (6)

Imaging of HEV-infected ex vivo porcine precision cut liver slices
Structural differences in HEV-infected pig and human cell lines
Correlation of the kinetics normal cell homeostasis of viral antigen and genomic RNA with restoration of

Correlation of the kinetics of viral antigen and genomic RNA with restoration of normal cell homeostasis

3D model of infected lung epithelial cell
Calibration table of x-ray absorption coefficient for adherent cells.

The table will provide calibration value to translated x-ray linear absorption coefficient obtained with lab-based SXM with respect to the synchrotron source for EM grid sample holders and limited angle tomography.

Calibration table of x-ray absorption coefficient for suspended cells.

The table will provide calibration value to translated x-ray linear absorption coefficient obtained with lab-based SXM with respect to the synchrotron source for cells in suspension and full rotation tomography.

Demonstrators, pilots, prototypes (1)

Fully tested in-line FM

Fully validated FM as indicated through bench tests and inline imaging of fluorescent nanospheres

Publications

Peer reviewed articles (32)

Gap junctions and connexin hemichannels both contribute to the electrical properties of retinal pigment epithelium

Author(s): Julia Fadjukov, Sophia Wienbar, Satu Hakanen, Vesa Aho, Maija Vihinen-Ranta, Teemu O. Ihalainen, Gregory W. Schwartz, Soile Nymark
Published in: Journal of General Physiology, Issue 154, 2023, ISSN 0022-1295
Publisher: Rockefeller University Press
DOI: 10.1085/jgp.202112916

Lipid monitoring of Chlorella vulgaris using non-invasive near-infrared spectral imaging

Author(s): Salli Pääkkönen, Ilkka Pölönen, Marco Calderini, Aliisa Yli-Tuomola, Visa Ruokolainen, Maija Vihinen-Ranta, Pauliina Salmi
Published in: Journal of Applied Phycology, Issue 37, 2025, Page(s) 205-219, ISSN 0921-8971
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10811-024-03397-6

Soft X-Ray Tomography Has Evolved into a Powerful Tool for Revealing Cell Structures

Author(s): Venera Weinhardt, Carolyn Larabell
Published in: Annual Review of Analytical Chemistry, 2025, ISSN 1936-1327
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-anchem-071124-093849

Three-Dimensional Remodeling of SARS-CoV2-Infected Cells Revealed by Cryogenic Soft X-ray Tomography

Author(s): Victoria Castro, Ana Joaquina Pérez-Berna, Gema Calvo, Eva Pereiro*, and Pablo Gastaminza
Published in: ACS Nano, Issue 2023, 17, 22, 2023, Page(s) 22708–22721, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.3c07265

Iterative immunostaining combined with expansion microscopy and image processing reveals nanoscopic network organization of nuclear lamina

Author(s): Elina Mäntylä, Toni Montonen, Lucio Azzari, Salla Mattola, Markus Hannula, Maija Vihinen-Ranta, Jari Hyttinen, Minnamari Vippola, Alessandro Foi, Soile Nymark, Teemu O. Ihalainen
Published in: Molecular Biology of the Cell, Issue 34, 2023, ISSN 1059-1524
Publisher: American Society for Cell Biology
DOI: 10.1091/mbc.e22-09-0448

Creation of ordered 3D tubes out of DNA origami lattices

Author(s): Johannes M. Parikka, Heini Järvinen, Karolina Sokołowska, Visa Ruokolainen, Nemanja Markešević, Ashwin K. Natarajan, Maija Vihinen-Ranta, Anton Kuzyk, Kosti Tapio, J. Jussi Toppari
Published in: Nanoscale, Issue 15, 2024, Page(s) 7772-7780, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2nr06001a

Hepatitis C virus‐induced differential transcriptional traits in host cells after persistent infection elimination by direct‐acting antivirals in cell culture

Author(s): Victoria Castro, Gema Calvo, Juan Carlos Oliveros, Sofía Pérez‐del‐Pulgar, Pablo Gastaminza
Published in: Journal of Medical Virology, Issue 96, 2024, ISSN 0146-6615
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/jmv.29787

Herpesvirus-Induced Manipulation of the Nucleolus

Author(s): Simon Leclerc, Sergey Kapishnikov, Visa Ruokolainen, Inka Huusko, Salla Mattola, David Rogers, Stephen O´Connor, Vesa Aho, Kenneth Fahy, M Vihinen-Ranta
Published in: Microscopy and Microanalysis, Issue 30, 2024, ISSN 1431-9276
Publisher: Cambridge University Press
DOI: 10.1093/mam/ozae044.1050

Monitoring reversion of hepatitis C virus-induced cellular alterations by direct-acting antivirals using cryo soft X-ray tomography and infrared microscopy

Author(s): Ana J. Pérez-Berná; Nuria Benseny-Cases; María José Cubillas Rodríguez; Ricardo Valcárcel; José L. Carrascosa; Pablo Gastaminza; Eva Pereiro
Published in: Acta Crystallographica Section D: Structural Biology, Issue 1, 2021, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321009955

Infection-induced chromatin modifications facilitate translocation of herpes simplex virus capsids to the inner nuclear membrane

Author(s): Vesa Aho ,Sami Salminen, Salla Mattola, Alka Gupta, Felix Flomm, Beate Sodeik, Jens B. Bosse, Maija Vihinen-Ranta
Published in: PLOS PATHOGENS, 2021, ISSN 1553-7366
Publisher: Public Library of Science
DOI: 10.1371/journal.ppat.1010132

A coronavirus assembly inhibitor that targets the viral membrane protein

Author(s): Manon Laporte, Dirk Jochmans, Dorothée Bardiot, Lowiese Desmarets, Oliver J. Debski-Antoniak, Giulia Mizzon, Rana Abdelnabi, Pieter Leyssen, Winston Chiu, Zhikuan Zhang, Norimichi Nomura, Sandro Boland, Umeharu Ohto, Yannick Stahl, Jurgen Wuyts, Steven De Jonghe, Annelies Stevaert, Martijn J. van Hemert, Brenda W. Bontes, Patrick Wanningen, G. J. Mirjam Groenewold, Aneta Zegar, Katarzyna Owczarek
Published in: Nature, Issue 640, 2025, Page(s) 514-523, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-025-08773-x

Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells

Author(s): Jian-Hua Chen,Bieke Vanslembrouck, Axel Ekman, Vesa Aho, Carolyn A. Larabell, Mark A. Le Gros, Maija Vihinen-Ranta, Venera Weinhardt
Published in: Viruses, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14122651

Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion

Author(s): Anthoula Chatzimpinou, Anne Diehl, A. Tobias Harhoff, Kristina Driller, Bieke Vanslembrouck, Jian-Hua Chen, Kristaps Kairišs, Valentina Loconte, Mark A. Le Gros, Carolyn Larabell, Kürşad Turgay, Hartmut Oschkinat, Venera Weinhardt
Published in: npj Biofilms and Microbiomes, Issue 11, 2025, ISSN 2055-5008
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41522-025-00659-0

Compact Cell Imaging Device (CoCID) to provide insights into the cellular origins of viral infections

Author(s): Kenneth Fahy, Venera Weinhardt, Maija Vihinen-Ranta, Nicola Fletcher, Dunja Skoko, Eva Pereiro, Pablo Gastaminza, Ralf Bartenschlager, Dimitri Scholz, Axel Ekman, Tony McEnroe
Published in: Journal of Physics: Photonics, 2021, ISSN 2515-7647
Publisher: IOP Publishing
DOI: 10.1088/2515-7647/abfc5a

Progression of herpesvirus infection is inhibited by calcium reporter.

Author(s): Kunnas, Kari; Vihinen-Ranta, Maija; Leclerc, Simon
Published in: microPublication biology, Issue 11, 2024, ISSN 2578-9430
Publisher: Caltech Library

A protocol for full-rotation soft X-ray tomography of single cells

Author(s): Jian-Hua Chen, Bieke Vanslembrouck, Valentina Loconte, Axel Ekman, Mirko Cortese, Ralf Bartenschlager, Gerry McDermott, Carolyn A. Larabell, Mark A. Le Gros, and Venera Weinhardt
Published in: STAR Protocols, 2022, ISSN 2666-1667
Publisher: Elsevier
DOI: 10.1016/j.xpro.2022.101176

Functional roles of the membrane-associated AAV protein MAAP

Author(s): Lionel Galibert, Amira Hyvönen, Reetta A. E. Eriksson, Salla Mattola, Vesa Aho, Sami Salminen, Justin D. Albers, Sanna K. Peltola, Saija Weman, Tiina Nieminen, Seppo Ylä-Herttuala, Hanna P. Lesch, Maija Vihinen-Ranta, Kari J. Airenne
Published in: Scientific Reports, Issue 11, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-01220-7

Parvovirus nonstructural protein 2 interacts with chromatin-regulating cellular proteins

Author(s): Salla Mattola, Kari Salokas, Vesa Aho, Elina Mäntylä, Sami Salminen, Satu Hakanen, Einari A. Niskanen, Julija Svirskaite, Teemu O. Ihalainen, Kari J. Airenne, Minna Kaikkonen-Määttä, Colin R. Parrish, Markku Varjosalo, Maija Vihinen-Ranta
Published in: PLOS Pathogens, Issue 18, 2022, Page(s) e1010353, ISSN 1553-7374
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.ppat.1010353

<scp>CELS</scp>‐<scp>3D</scp>—Cutting edge light source for exciting fluorescence in microtome‐based <scp>3D</scp> microscopy and targeted correlative microscopy

Author(s): Vladyslav Denyshchenko, Christopher Evans, Tiina O'Neill, Jakub Krstev, Emilia Filipczak, Silas O'Toole, Vladimir Lobaskin, Dimitri Scholz
Published in: Journal of Anatomy, Issue 246, 2025, Page(s) 782-797, ISSN 0021-8782
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/joa.14164

Enhanced hepatitis E virus infection of polarised hepatocytes in vitro

Author(s): Hannah M. Brown, Julien Marlet, Nancy León-Janampa, Denys Brand, Nicola F. Fletcher
Published in: Scientific Reports, Issue 15, 2025, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-025-92164-9

Using soft X-ray tomography for rapid whole-cell quantitative imaging of SARS-CoV-2-infected cells.

Author(s): Valentina Loconte; Valentina Loconte; Jian-Hua Chen; Jian-Hua Chen; Mirko Cortese; Axel Ekman; Mark A. Le Gros; Mark A. Le Gros; Carolyn A. Larabell; Carolyn A. Larabell; Ralf Bartenschlager; Ralf Bartenschlager; Venera Weinhardt; Venera Weinhardt
Published in: Cell Reports Methods, Issue 2, 2021, ISSN 2667-2375
Publisher: Cell Press
DOI: 10.1016/j.crmeth.2021.100117

Automated 3D cytoplasm segmentation in soft X-ray tomography

Author(s): Ayse Erozan, Philipp D. Lösel, Vincent Heuveline, Venera Weinhardt
Published in: iScience, Issue 27, 2025, Page(s) 109856, ISSN 2589-0042
Publisher: Elsevier BV
DOI: 10.1016/j.isci.2024.109856

Dehydration as alternative sample preparation for soft X‐ray tomography

Author(s): Anthoula Chatzimpinou, Charlotta Funaya, David Rogers, Stephen O'Connor, Sergey Kapishnikov, Paul Sheridan, Kenneth Fahy, Venera Weinhardt
Published in: Journal of Microscopy, Issue 291, 2023, Page(s) 248-255, ISSN 0022-2720
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jmi.13214

Nuclear entry and egress of parvoviruses

Author(s): Salla Mattola, Vesa Aho, Luisa F. Bustamante‐Jaramillo, Edoardo Pizzioli, Michael Kann, Maija Vihinen‐Ranta
Published in: Molecular Microbiology, Issue 118, 2023, Page(s) 295-308, ISSN 0950-382X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mmi.14974

Extending Imaging Volume in Soft X‐Ray Tomography

Author(s): Axel Ekman, Jian-Hua Chen, Bieke Vanslembrouck, Valentina Loconte, Carolyn A. Larabell, Mark A. Le Gros, Venera Weinhardt
Published in: Advanced Photonics Research, Issue 4, 2024, ISSN 2699-9293
Publisher: Wiley
DOI: 10.1002/adpr.202200142

Imaging of Virus-Infected Cells with Soft X-ray Tomography

Author(s): Damià Garriga, Francisco Javier Chichón, Bárbara M. Calisto, Diego S. Ferrero, Pablo Gastaminza, Eva Pereiro and Ana Joaquina Pérez-Berna
Published in: Viruses, Issue Monthly, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13112109

Persistence of Human Bocavirus 1 in Tonsillar Germinal Centers and Antibody-Dependent Enhancement of Infection

Author(s): Man Xu, Maria Fernanda Perdomo, Salla Mattola, Lari Pyöriä, Mari Toppinen, Jianming Qiu, Maija Vihinen-Ranta, Klaus Hedman, Johanna Nokso-Koivisto, Leena-Maija Aaltonen, Maria Söderlund-Venermo
Published in: mBio, Issue 12, 2023, ISSN 2161-2129
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03132-20

Mitochondrial Reorganization in Herpesvirus-Infected Cells

Author(s): S Leclerc, K Kunnas, A Ekman, E Pereiro, K Fahy, C Larabell, V Aho, V Weinhardt, M Vihinen-Ranta
Published in: Microscopy and Microanalysis, Issue 29, 2023, Page(s) 1153-1154, ISSN 1431-9276
Publisher: Cambridge University Press
DOI: 10.1093/micmic/ozad067.589

Rapid hepatitis C virus replication machinery removal after antiviral treatment with DAA monitored by multimodal imaging

Author(s): Victoria Castro, Gema Calvo, Ana J. Pérez-Berná, Kevin Mamprin, Sergey Kapishnikov, David Rogers, Stephen O'Connor, Paul Sheridan, Kenneth Fahy, Eva Pereiro, Pablo Gastaminza
Published in: Structure, 2025, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2025.05.015

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Author(s): Simon Leclerc, Alka Gupta, Visa Ruokolainen, Jian-Hua Chen, Kari Kunnas, Axel A. Ekman, Henri Niskanen, Ilya Belevich, Helena Vihinen, Paula Turkki, Ana J. Perez-Berna, Sergey Kapishnikov, Elina Mäntylä, Maria Harkiolaki, Eric Dufour, Vesa Hytönen, Eva Pereiro, Tony McEnroe, Kenneth Fahy, Minna U. Kaikkonen, Eija Jokitalo, Carolyn A. Larabell, Venera Weinhardt, Salla Mattola, Vesa Aho, Maija Vi
Published in: PLOS Pathogens, Issue 20, 2024, Page(s) e1011829, ISSN 1553-7374
Publisher: Public Library of Science (PLoS)
DOI: 10.1371/journal.ppat.1011829

G2/M checkpoint regulation and apoptosis facilitate the nuclear egress of parvoviral capsids

Author(s): Salla Mattola, Elina Mäntylä, Vesa Aho, Sami Salminen, Simon Leclerc, Mikko Oittinen, Kari Salokas, Jani Järvensivu, Satu Hakanen, Teemu O Ihalainen, Keijo Viiri, Maija Vihinen-Ranta
Published in: Frontiers in Cell and Developmental Biology, Issue 10, 2022, ISSN 2296-634X
Publisher: Frontiers Media SA
DOI: 10.3389/fcell.2022.1070599

Concepts to Reveal Parvovirus–Nucleus Interactions

Author(s): Salla Mattola, Satu Hakanen, Sami Salminen, Vesa Aho, Elina Mäntylä, Teemu O. Ihalainen, Michael Kann, Maija Vihinen-Ranta
Published in: Viruses, Issue 13, 2025, Page(s) 1306, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13071306

Other (2)

Alternative cell entry mechanisms for SARS-CoV-2 and multiple animal viruses

Author(s): Ravi Ojha, Anmin Jiang, Elina Mäntylä, Naphak Modhira, Robert Witte, Arnaud Gaudin, Lisa De Zanetti, Rachel Gormal, Maija Vihinen-Ranta, Jason Mercer, Maarit Suomalainen, Urs F. Greber, Yohei Yamauchi, Pierre Yves-Lozach, Ari Helenius, Olli Vapalahti, Paul Young, Daniel Watterson, Frédéric A. Meunier, Merja Joensuu, Giuseppe Balistreri
Published in: bioRxiv, 2023
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.02.547368

Demonstrating Soft X-Ray Tomography in the lab for correlative cryogenic biological imaging using X-rays and light microscopy

Author(s): Stephen O’Connor, David Rogers, Maryna Kobylynska, James Geraets, Katja Thaysen, Jacob Marcus Egebjerg, Madeleen C. Brink, Louisa Herbsleb, Michaela Salakova, Leon Fuchs, Frauke Alves, Claus Feldmann, Axel Ekman, Paul Sheridan, William Fyans, Tony McEnroe, Fergal O’Reily, Kenneth Fahy, Roland A. Fleck, Daniel Wüstner, Jeremy C. Simpson, Andreas Walter, Sergey Kapishnikov
Published in: bioRxiv, 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.12.23.629889

Book chapters (1)

Laboratory based correlative cryo-soft X-ray tomography and cryo-fluorescence microscopy

Author(s): Kenneth Fahy, Sergey Kapishnikov, Martina Donnellan, Tony McEnroe, Fergal O'Reilly, William Fyans, Paul Sheridan
Published in: Methods in Cell Biology, Correlative Light and Electron Microscopy V, 2024, Page(s) 293-320
Publisher: Elsevier
DOI: 10.1016/bs.mcb.2024.02.033