Periodic Reporting for period 2 - DynAMic (Dynamic adaptive microscopy for label-free multi-parametric imaging in biology and medicine)
Okres sprawozdawczy: 2021-09-01 do 2023-06-30
Optical microscopy constitutes one of the most fundamental paradigms in biological and medical imaging. However, significant challenges remain regarding the application of optical microscopy to in vivo interrogations. First, the diffusing nature of light propagation in tissue due to random variations of the refractive index limits in vivo microscopy to superficial depths; within only a few mean free paths (<1mm). Second, the invasive nature of fluorescent proteins and probes allows monitoring of only 1-5 events by spectrally multiplexing different fluorochromes, i.e. performance that is highly incompatible with functional genomics and proteomics targets.
The long-term vision and ambition of DynAMic is to revolutionize microscopic imaging by breaking i) the depth-to-resolution ratio and ii) the limited number of labels visualized, offering non-invasive, real-time, high resolution, multiparametric in vivo imaging, across length scales, deep in biological complex media.
The new optical imaging ability delivered in DynAMic will be applied to a first target application of ophthalmic imaging, also used as a window to the brain and nervous disease detection, defining the next generation ophthalmology and neurology sensing of devastating diseases, disrupting the modus operandi of retinal and neuronal imaging without disturbing the modus agendi of the end-users.
The long-term vision and ambition of DynAMic is to revolutionize microscopic imaging by breaking i) the depth-to-resolution ratio and ii) the limited number of labels visualized, offering non-invasive, real-time, high resolution, multiparametric in vivo imaging, across length scales, deep in biological complex media.
The new optical imaging ability delivered in DynAMic will be applied to a first target application of ophthalmic imaging, also used as a window to the brain and nervous disease detection, defining the next generation ophthalmology and neurology sensing of devastating diseases, disrupting the modus operandi of retinal and neuronal imaging without disturbing the modus agendi of the end-users.
Within the 1st reporting period, several research tracks were followed in parallel and in conjunction with specific goals within the overall timeline and targets of the project.
A highly significant initial effort was dedicated synergistically by all partners to define the user needs, and the most appropriate technologies within the consortium to target the most relevant, significant, and feasible to detect biomarkers. An exhaustive literature research was performed and from this, a subset of the most relevant, significant, and feasible to detect markers was selected as our prime targets. We believe that this effort and the produced detailed, concentrated and filtered information can be beneficial for the consortium but also for the greater scientific community.
Τhe first deliverables and milestones were completed in time, related to the webpage and logo of the project, the Consortium Agreement and the Data Management Plan
To facilitate a smooth operation and efficiency in progressing the work, despite the pandemic effects, the consortium has defined Technical Task Groups per WP that meet regularly over virtual meetings to advance common research and development in a focused, problem solving, and monitoring fashion. This has led to the definition of strategies and tasks for the development, implementation and testing of our technologies:
i. Non-diffraction and speckle illumination methods and adaptation to the microscopes
ii. PSF and k-vector engineering with appropriate model scattering media
iii. Designing adaptive optics modules to be integrated into the microscope
iv. Optimization algorithms for wavefront shaping and the relevant specifications of our ultrafast, real-time theoretical methods
v. Integration of electronics and software in a unified platform with appropriate operational characteristics
vi. Designing and developing the 1st prototype of a new high-performance Deformable Mirror
vii. Developing and implementing the stand-alone test be technologies before full integration
viii. Frequency domain optoacoustic microscopy as a stand-alone technology to be implemented in the final prototype
This effort provided the developments that made it possible to complete all deliverables on time and produce some new publications and conference presentations by the partners.
The approach defined within an amended and consolidated flowchart of the project consisted of developing and optimising our technologies as stand-alone before completing the puzzle by integrating everything in the 1st prototype system. Then an iteration procedure will solve any unforeseen problems and optimise operational characteristics in experimental measurements of relevant specimens such as excised ocular and retinal tissues, model organisms such as C. Elegans that provide an ideal test bed and engineered living materials, such as organoids that can simulate challenges imposed by real tissue. This has been initially performed in stand-alone microscopy systems.
In addition, the project partners outlined and defined the strategy for achieving effective communication, dissemination, and exploitation of DynAMic foreground results with an evolving Exploitation Plan.
Finally, three amendments to the GA were completed to include Linked Third Partied to CNRS and extend the duration of the project by 18 (18) months due to the pandemic and equipment acquiring delays.
A highly significant initial effort was dedicated synergistically by all partners to define the user needs, and the most appropriate technologies within the consortium to target the most relevant, significant, and feasible to detect biomarkers. An exhaustive literature research was performed and from this, a subset of the most relevant, significant, and feasible to detect markers was selected as our prime targets. We believe that this effort and the produced detailed, concentrated and filtered information can be beneficial for the consortium but also for the greater scientific community.
Τhe first deliverables and milestones were completed in time, related to the webpage and logo of the project, the Consortium Agreement and the Data Management Plan
To facilitate a smooth operation and efficiency in progressing the work, despite the pandemic effects, the consortium has defined Technical Task Groups per WP that meet regularly over virtual meetings to advance common research and development in a focused, problem solving, and monitoring fashion. This has led to the definition of strategies and tasks for the development, implementation and testing of our technologies:
i. Non-diffraction and speckle illumination methods and adaptation to the microscopes
ii. PSF and k-vector engineering with appropriate model scattering media
iii. Designing adaptive optics modules to be integrated into the microscope
iv. Optimization algorithms for wavefront shaping and the relevant specifications of our ultrafast, real-time theoretical methods
v. Integration of electronics and software in a unified platform with appropriate operational characteristics
vi. Designing and developing the 1st prototype of a new high-performance Deformable Mirror
vii. Developing and implementing the stand-alone test be technologies before full integration
viii. Frequency domain optoacoustic microscopy as a stand-alone technology to be implemented in the final prototype
This effort provided the developments that made it possible to complete all deliverables on time and produce some new publications and conference presentations by the partners.
The approach defined within an amended and consolidated flowchart of the project consisted of developing and optimising our technologies as stand-alone before completing the puzzle by integrating everything in the 1st prototype system. Then an iteration procedure will solve any unforeseen problems and optimise operational characteristics in experimental measurements of relevant specimens such as excised ocular and retinal tissues, model organisms such as C. Elegans that provide an ideal test bed and engineered living materials, such as organoids that can simulate challenges imposed by real tissue. This has been initially performed in stand-alone microscopy systems.
In addition, the project partners outlined and defined the strategy for achieving effective communication, dissemination, and exploitation of DynAMic foreground results with an evolving Exploitation Plan.
Finally, three amendments to the GA were completed to include Linked Third Partied to CNRS and extend the duration of the project by 18 (18) months due to the pandemic and equipment acquiring delays.
The long-term vision and ambition of DynAMic is to revolutionize microscopic imaging by breaking i) the depth-to-resolution ratio and ii) the limited number of labels visualized, offering non-invasive, real-time, high resolution, multiparametric in vivo imaging, across length scales, deep in biological complex media.
DynAMic proposes a radically new concept for optical imaging of tissue based on:
• Developing real-time wavefront-shaping adaptive optics to enhance microscopic imaging performance and for the first time in coherent Raman microscopy.
• Reaching tenfold deeper in tissue than conventional optical microscopy by compensating for the refractive index variations and retrieving scrambled coherent properties of transmitted light
• Utilizing advanced image formation to improve the sensitivity and utilization of Raman scattering for multi-parametric label-free contrast that radically expands at least tenfold the number of labels concurrently retrieved from living systems, linking optical observation to functional proteomic requirements.
To achieve this we are working on producing some new line of research and technology with a wider impact on science and society. Even at this early stage of the project timeline, we have identified innovations that potentially can impact the field of microscopy with spillover effects in many areas of biology research and clinical practice.
A prime goal is of course the complete DynAMic microscope that will create a totally new microscopy environment, but in the process of navigating towards that unified achievement we have identifies the following innovations that synergistically between partners can create impactful new technology:
- A new deformable mirror with operational and commercial characteristics suitable for microscopy systems routinely used in biology. This is now commercially available from 2022.
- A next generation “Wavesim” platform again optimised for microscopic imaging with wavefront shaping and optimised operational characteristics
- A k-vector engineering and adaptive optics Light Sheet Fluorescence Microscopy system. The system is now a prototype and new enterprise is starting up.
- A frequency domain optoacoustic microscopy modality that can be transferred to the DynAMic microscope, reducing costs and bill of materials as well as enhancing and widening applicability.
- Engineering of model scattering media to control light diffusion
DynAMic proposes a radically new concept for optical imaging of tissue based on:
• Developing real-time wavefront-shaping adaptive optics to enhance microscopic imaging performance and for the first time in coherent Raman microscopy.
• Reaching tenfold deeper in tissue than conventional optical microscopy by compensating for the refractive index variations and retrieving scrambled coherent properties of transmitted light
• Utilizing advanced image formation to improve the sensitivity and utilization of Raman scattering for multi-parametric label-free contrast that radically expands at least tenfold the number of labels concurrently retrieved from living systems, linking optical observation to functional proteomic requirements.
To achieve this we are working on producing some new line of research and technology with a wider impact on science and society. Even at this early stage of the project timeline, we have identified innovations that potentially can impact the field of microscopy with spillover effects in many areas of biology research and clinical practice.
A prime goal is of course the complete DynAMic microscope that will create a totally new microscopy environment, but in the process of navigating towards that unified achievement we have identifies the following innovations that synergistically between partners can create impactful new technology:
- A new deformable mirror with operational and commercial characteristics suitable for microscopy systems routinely used in biology. This is now commercially available from 2022.
- A next generation “Wavesim” platform again optimised for microscopic imaging with wavefront shaping and optimised operational characteristics
- A k-vector engineering and adaptive optics Light Sheet Fluorescence Microscopy system. The system is now a prototype and new enterprise is starting up.
- A frequency domain optoacoustic microscopy modality that can be transferred to the DynAMic microscope, reducing costs and bill of materials as well as enhancing and widening applicability.
- Engineering of model scattering media to control light diffusion