Periodic Reporting for period 2 - IMAGINE (Next generation imaging technologies to probe structure and function of biological specimen across scales in their natural context)
Okres sprawozdawczy: 2024-05-01 do 2025-10-31
IMAGINE develops the next generation of scale-crossing imaging technologies to enable an integrated investigation of structure and function of biological systems. It focuses on developing and integrating 4 major disruptive microscopy technologies (X-ray imaging, cryo-electron microscopy, cryo and dynamic super-resolution microscopy and large volume intravital light microscopy), also developing the AI-powered image analysis and data integration and sharing capabilities, that are needed to correlate these technologies and make their data widely available. To harness their power for some of the most pressing societal challenges, IMAGINE prepares its new imaging technologies to be deployed in the field so that the collection of environmental specimens in their natural context can be coupled with their study by highest resolution imaging technologies
The main objectives are to:
•develop innovative cross-scale imaging instrumentation, tools, and methods, which will advance the state-of-art of the six participating pan-European RIs and show their transformative operational potential for the Life Sciences to address major socio-economic challenges of human and planetary health;
•validate the newly developed imaging technologies for service readiness in RIs and integrate them across RIs, to provide new and improved services to a wider community of academic and industrial users;
•train RI staff in the operation and use of the newly developed imaging technologies; and
•create an effective Open Innovation ecosystem in the multi-stakeholder industry-academia technology development environment around RIs, to fully realize the innovative potential for industrial exploitation of new imaging technologies and rapidly place new products on the market.
The main objectives are to:
•develop innovative cross-scale imaging instrumentation, tools, and methods, which will advance the state-of-art of the six participating pan-European RIs and show their transformative operational potential for the Life Sciences to address major socio-economic challenges of human and planetary health;
•validate the newly developed imaging technologies for service readiness in RIs and integrate them across RIs, to provide new and improved services to a wider community of academic and industrial users;
•train RI staff in the operation and use of the newly developed imaging technologies; and
•create an effective Open Innovation ecosystem in the multi-stakeholder industry-academia technology development environment around RIs, to fully realize the innovative potential for industrial exploitation of new imaging technologies and rapidly place new products on the market.
X-ray Imaging
- HiTT established at EMBL P14 as a high-throughput 3D imaging service (since 2023).
- Automated workflows enable imaging of ~150 samples per session with broad sample compatibility.
- Imaging extended to larger specimens (up to 5 mm) and interoperable with cryo-ET.
- Robust cryo-FIB and liquid-phase imaging workflows established; support expanded to snap-frozen tissues.
Electron Microscopy
- Advanced vitrification methods (jet-based, high-pressure freezing) enable reliable preservation of thick tissues.
- New carriers and grids support correlative X-ray–cryo-EM workflows.
- Automated serial lift-out and ML-driven cryo-FIB enable scalable, high-throughput cryo-ET sample preparation.
Super-Resolution Microscopy
- Progress toward dynamic MINFLUX for real-time molecular tracking in living cells.
- Dual-color MINFLUX and improved fluorophore strategies developed.
- Cryo-SRM and cryo-SMLM advanced toward routine correlative cryo-CLEM workflows.
Intravital Imaging
- Multimodal mesoscopic imaging platforms (OCM, OPM) developed for high-speed, volumetric imaging.
- Portable OCM and optimized OPM enable long-term, high-resolution imaging in the field and lab.
- Progress toward fully correlative intravital–X-ray–EM pipelines.
Marine Imaging (Field Deployment)
- Image-enabled sorting workflows established for marine plankton with >90% classification accuracy.
- Field-deployable imaging and sorting pipelines validated.
- Scalable microfluidic and mesoscopic imaging platforms developed for larger specimens.
AI-based Image Analysis
- Advanced denoising, reconstruction, segmentation, and registration methods developed for multimodal microscopy.
- Automated pipelines align EM with spatial transcriptomics at scale.
- Unified multimodal data model implemented (RO-Crate) with web-based visualization tools.
- HiTT established at EMBL P14 as a high-throughput 3D imaging service (since 2023).
- Automated workflows enable imaging of ~150 samples per session with broad sample compatibility.
- Imaging extended to larger specimens (up to 5 mm) and interoperable with cryo-ET.
- Robust cryo-FIB and liquid-phase imaging workflows established; support expanded to snap-frozen tissues.
Electron Microscopy
- Advanced vitrification methods (jet-based, high-pressure freezing) enable reliable preservation of thick tissues.
- New carriers and grids support correlative X-ray–cryo-EM workflows.
- Automated serial lift-out and ML-driven cryo-FIB enable scalable, high-throughput cryo-ET sample preparation.
Super-Resolution Microscopy
- Progress toward dynamic MINFLUX for real-time molecular tracking in living cells.
- Dual-color MINFLUX and improved fluorophore strategies developed.
- Cryo-SRM and cryo-SMLM advanced toward routine correlative cryo-CLEM workflows.
Intravital Imaging
- Multimodal mesoscopic imaging platforms (OCM, OPM) developed for high-speed, volumetric imaging.
- Portable OCM and optimized OPM enable long-term, high-resolution imaging in the field and lab.
- Progress toward fully correlative intravital–X-ray–EM pipelines.
Marine Imaging (Field Deployment)
- Image-enabled sorting workflows established for marine plankton with >90% classification accuracy.
- Field-deployable imaging and sorting pipelines validated.
- Scalable microfluidic and mesoscopic imaging platforms developed for larger specimens.
AI-based Image Analysis
- Advanced denoising, reconstruction, segmentation, and registration methods developed for multimodal microscopy.
- Automated pipelines align EM with spatial transcriptomics at scale.
- Unified multimodal data model implemented (RO-Crate) with web-based visualization tools.
Further research and commercialisation efforts are being prepared, but have not been concluded yet.