VirusAwareScopes: Machine Learning-Driven Adaptive Microscopy for Long-Term Viral Infection Studies

Alias: VirusAwareScopes
Agency: La Caixa Foundation
Type: Health Research
Principal Investigator: Ricardo Henriques
Start-date: November 2025
End-date: October 2028
Grant Code: HR25-00453

VirusAwareScopes addresses a fundamental challenge in viral research: high-resolution imaging inherently damages living cells, preventing long-term observation of infection dynamics. This project develops an intelligent microscopy platform that adapts imaging conditions in real-time using machine learning, enabling sustained nanoscale imaging while preserving cell viability. By combining multiple super-resolution modalities with AI-driven adaptive optics and PhotoFiTT technology to predict phototoxicity, the system achieves observation periods of 24+ hours while maintaining sub-120nm resolution. The platform will initially map complete HIV-1 infection cycles whilst remaining deployable to standard microscopy setups through integration with established frameworks.

Technology explored

mAIcrobe Newest update: 2026-08-01

1 10 10 3

BioImage Model Zoo Newest update: 2026-07-29

32 12 12 4

NanoPyx Newest update: 2026-06-08

7 105 105 15

ZeroCostDL4Mic Newest update: 2026-03-29

624 649 649 144

DL4MicEverywhere Newest update: 2026-03-28

8 86 86 17

CellTracksColab Newest update: 2026-02-02

0 50 50 5

CARE Newest update: 2025-12-08

952 336 336 87

CLEM-Reg Newest update: 2025-10-22

9 22 22 6

SReD Newest update: 2025-09-29

4 4 4 0

NanoJ-eSRRF Newest update: 2025-05-30

80 25 25 1

PhotoFiTT Newest update: 2025-03-13

2 11 11 0

NanoJ Newest update: 2024-03-22

364 17 17 3

NanoJ-SRRF Newest update: 2024-03-22

618 28 28 3

nano-org Newest update: 2024-01-01

0

vLume Newest update: 2020-10-12

80

Nuclear-Pores as references Newest update: 2019-09-27

752

NanoJ-Fluidics Newest update: 2019-04-04

86 53 53 8

NanoJ-VirusMapper Newest update: 2016-01-01

49

QuickPALM Newest update: 2010-01-01

470

Supported publications

VLab4Mic: prediction of structural resolvability in super-resolution microscopy Damián Martínez, Bruno M. Saraiva, Tayla Shakespeare, Mark Bates, Dylan M. Owen, Christophe Leterrier, Mario Del Rosario, Ricardo Henriques Preprint published in bioRxiv, June 2026 Technologies: EZInput (), mAIcrobe (), nano-org, NanoJ (), NanoJ-SQUIRREL (), Nuclear-Pores as references and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, CZI, EMBO, ERC, H2022 and La Caixa Foundation DOI: 10.64898/2026.06.02.729521

Packaging Jupyter notebooks as installable desktop apps using LabConstrictor Iván Hidalgo-Cenalmor, Marcela Xiomara Rivera Pineda, Bruno M Saraiva, Ricardo Henriques, Guillaume Jacquemet Preprint published in arXiv, March 2026 Technologies: CARE (), CellTracksColab (), DL4MicEverywhere (), mAIcrobe () and ZeroCostDL4Mic () Funded by: Chan Zuckerberg Initiative (CZI), The Kavli Foundation, and The Wellcome Trust, EMBO, ERC, H2022 and La Caixa Foundation DOI: 10.48550/arXiv.2603.10704