Periodic Reporting for period 1 - IMAGINE (Next generation imaging technologies to probe structure and function of biological specimen across scales in their natural context)
Okres sprawozdawczy: 2023-05-01 do 2024-04-30
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/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 specimen 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 6 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 realise 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 6 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 realise the innovative potential for industrial exploitation of new imaging technologies and rapidly place new products on the market.
IMAGINE aims to advance 6 key areas of scale crossing imaging technologies, integrate them into correlative multi-modal workflows and create technologies to deploy them in the field in 6 WPs:
1) X-ray Imaging
- Proof of concept stage of the development of a pipeline for high-throughput medium-resolution room temperature tomography (HiTT) was completed
- The feasibility of HiTT to be used as targeting tool for volume electron microscopy as well as using HiTT to study plant morphology has been demonstrated
- The HiTT pipeline was opened for project proposals, resulting 14 proposals received and 147 shifts of beamtime allocated
- Pilot experiments on Toxoplasma gondii infected cells, vitrification with EasyGrid and data-collection on ID16A have been carried out
- Establishment of collaboration with industry for the production of new silicon nitride (SiN) windows compatible with autogrids
- Characteristics of the respective sample mounting systems and sample exposure stage have been compiled, a set of mechanical mounting systems is currently being designed; and new sample mounting base is currently being manufactured
- Data on a sample mounted on the SLS OMNY-pin have been collected to ultimately link X-ray imaging with light microscopy techniques
2) Electron Microscopy
- The EasyGrid, a device for automated preparation and quality control of Cryo-EM samples has been used to prepare adherent cells grown on EM grids and cells in suspension
- Initial vitrification tests of cells grown on SiN chips that are compatible with both X-ray cryo-nanoimaging and cryo-FIB-SEM techniques have been conducted
- Protocols for best practices on different cryo-CLEM workflows are currently established
- Initial assessment of the use of plasma sources for high-throughput removal of biological material has been performed
- Collaborative projects to test commercial pFIB platforms have been initiated and the proof-of-principle experiments were completed
- Demonstration of whole cell preservation by liquid ethane/propane jet freezing has been conducted
3) Super Resolution Light Microscopy
- Relevant photophysical parameters for MINFLUX imaging were identified, reversibly switchable fluorescent proteins have been screened and characterised for their photon emission rates and on/off switching kinetics
- Correlative cryo-SRM EM approaches have been tested and proof-of concept has been completed
- Establishment of cryo-fluorosensce spectroscopy for fluorophore screening and characterisation has been conducted
4) Intravital Microscopy
- Advancements in multi-modal volume imaging of living organism by oblique plane microscope (OPM) have been tested and characterised on fluorescent bead samples and Nematostella polyps and Hydra
- Label-free optical coherence (OCM) has been applied on various marine organisms and substantial progress has been made on miniaturising the OCM system for mobile services and deployment in the field
- Applicability of OCM has been demonstrated during conferences and courses
- The preparatory work for development of correlative intravital imaging strategies has been finalised
5) Deployment in the field: Marine Imaging
- Workflows on high-speed image-enabled flow cytometric for sorting microscopic plankton collected in the field have been tested: feedback microscopy, image collection, and image-based sorting
- Development and implementation of mesoscopic image-based sorting of marine organisms by the compact version of OCM has been deployed in the field
- Feedback microscopy, Complex Object Parametric Analyzer and Sorter (COPAS), and OCM have been demonstrated through lectures/practicals
6) AI-based Image Analysis
- Preliminary investigation on AI-based analysis of morphology for screening, sorting, and registration has been performed mostly on Optical Projection Tomography (OPT) and OCM
- An algorithm for image decomposition for fluorescence microscopy has been developed to allow use of less fluorescence channels in fluorescence microscopy
- Preliminary investigation on image analysis to enable 3D targeting for CLEM of multi/cellular samples has been performed
- The introduction and integration of OME-NGFF files into BioImage Archive was evaluated and planned. Testing of storage in multiple back-end systems was conducted, and prototypes of basic visualisation have been implemented in a common frame of reference
1) X-ray Imaging
- Proof of concept stage of the development of a pipeline for high-throughput medium-resolution room temperature tomography (HiTT) was completed
- The feasibility of HiTT to be used as targeting tool for volume electron microscopy as well as using HiTT to study plant morphology has been demonstrated
- The HiTT pipeline was opened for project proposals, resulting 14 proposals received and 147 shifts of beamtime allocated
- Pilot experiments on Toxoplasma gondii infected cells, vitrification with EasyGrid and data-collection on ID16A have been carried out
- Establishment of collaboration with industry for the production of new silicon nitride (SiN) windows compatible with autogrids
- Characteristics of the respective sample mounting systems and sample exposure stage have been compiled, a set of mechanical mounting systems is currently being designed; and new sample mounting base is currently being manufactured
- Data on a sample mounted on the SLS OMNY-pin have been collected to ultimately link X-ray imaging with light microscopy techniques
2) Electron Microscopy
- The EasyGrid, a device for automated preparation and quality control of Cryo-EM samples has been used to prepare adherent cells grown on EM grids and cells in suspension
- Initial vitrification tests of cells grown on SiN chips that are compatible with both X-ray cryo-nanoimaging and cryo-FIB-SEM techniques have been conducted
- Protocols for best practices on different cryo-CLEM workflows are currently established
- Initial assessment of the use of plasma sources for high-throughput removal of biological material has been performed
- Collaborative projects to test commercial pFIB platforms have been initiated and the proof-of-principle experiments were completed
- Demonstration of whole cell preservation by liquid ethane/propane jet freezing has been conducted
3) Super Resolution Light Microscopy
- Relevant photophysical parameters for MINFLUX imaging were identified, reversibly switchable fluorescent proteins have been screened and characterised for their photon emission rates and on/off switching kinetics
- Correlative cryo-SRM EM approaches have been tested and proof-of concept has been completed
- Establishment of cryo-fluorosensce spectroscopy for fluorophore screening and characterisation has been conducted
4) Intravital Microscopy
- Advancements in multi-modal volume imaging of living organism by oblique plane microscope (OPM) have been tested and characterised on fluorescent bead samples and Nematostella polyps and Hydra
- Label-free optical coherence (OCM) has been applied on various marine organisms and substantial progress has been made on miniaturising the OCM system for mobile services and deployment in the field
- Applicability of OCM has been demonstrated during conferences and courses
- The preparatory work for development of correlative intravital imaging strategies has been finalised
5) Deployment in the field: Marine Imaging
- Workflows on high-speed image-enabled flow cytometric for sorting microscopic plankton collected in the field have been tested: feedback microscopy, image collection, and image-based sorting
- Development and implementation of mesoscopic image-based sorting of marine organisms by the compact version of OCM has been deployed in the field
- Feedback microscopy, Complex Object Parametric Analyzer and Sorter (COPAS), and OCM have been demonstrated through lectures/practicals
6) AI-based Image Analysis
- Preliminary investigation on AI-based analysis of morphology for screening, sorting, and registration has been performed mostly on Optical Projection Tomography (OPT) and OCM
- An algorithm for image decomposition for fluorescence microscopy has been developed to allow use of less fluorescence channels in fluorescence microscopy
- Preliminary investigation on image analysis to enable 3D targeting for CLEM of multi/cellular samples has been performed
- The introduction and integration of OME-NGFF files into BioImage Archive was evaluated and planned. Testing of storage in multiple back-end systems was conducted, and prototypes of basic visualisation have been implemented in a common frame of reference
Further research and commercialisation efforts are being prepared, but have not been concluded yet.