Coherent Raman Imaging for the Molecular Study of the OrigiN of diseases

Project Information

CRIMSON

Grant agreement ID: 101016923

DOI

10.3030/101016923

Project closed

EC signature date 30 November 2020

Start date 1 December 2020

End date 31 May 2024

Funded under

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

Total cost

€ 5 132 801,25

EU contribution

€ 5 132 801,25

Coordinated by

POLITECNICO DI MILANO
Italy

Periodic Reporting for period 3 - CRIMSON (Coherent Raman Imaging for the Molecular Study of the OrigiN of diseases)

Reporting period: 2023-06-01 to 2024-05-31

Summary of the context and overall objectives of the project

CRIMSON aims to provide a next-generation bio-photonics imaging device based on vibrational spectroscopy, with the potential to revolutionise the study of the cellular origin of diseases allowing for novel approaches
towards personalised therapy. CRIMSON employed label-free broadband coherent Raman scattering (CRS) extended to the fingerprint region, in combination with artificial-intelligence spectroscopic data analysis, for fast cell/tissue classification with unprecedented biochemical sensitivity. The project consortium developed a hyperspectral CRS microscope for quantitative imaging of cells and tissue. High acquisition speed enabled the observation of intra- and inter-cellular dynamic changes by time-lapse imaging. Partners simulated future in-vivo studies, realizing an innovative CRS endoscope. CRIMSON relied on the development of new compact ultrafast lasers, innovative broadband CRS detection schemes and advanced spectral analysis routines.
To validate the CRS platform, CRIMSON has investigated three open biological questions related to cancer, as paradigmatic examples of the complexity and heterogeneity of cellular diseases.
CRIMSON brings together a multidisciplinary team of world-leading academic organizations, biomedical end users and innovative SMEs, with vertical integration of all required skills. CRIMSON contributed to bridge the gap between research and product development, increasing the TRL and making CRS a user-friendly, robust and cost-effective mainstream tool for a vast biological research community. CRIMSON project delivered almost all expected outputs and achieved most of the goals in line with the planned timelines and deadlines. We have made significant scientific and technological advancements, particularly in the field of coherent Raman Spectroscopy (CRS) and microscopy.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The CRIMSON project aimed to develop a new non-invasive microscopy and endoscopy tool using broadband coherent Raman scattering (CRS) for biomedical research.

Work Package 1 focused on advancing broadband CRS strategies. Three CRS setups were built and optimized for cell and tissue imaging at Polimi and IPHT. POLIMI developed a multiplex SRS microscope with an OPO for fingerprint region imaging, while CNRS-IF created a dual-color laser for CH2 and CH3 imaging. CRI produced a 38-channel lock-in amplifier, now commercially available. IF-CNRS demonstrated Fast-Fourier-Transform CARS and SRS imaging, with fast hyperspectral acquisition of Carbamazepine dihydrate. A comparative study of CRS techniques and an analysis of BCARS setups for cell identification were published.

Work Package 2 developed hardware tools for CRS imaging. AFS designed fibre lasers for SRS/CARS, integrated into CRIL and LIGHTCORE systems. CRIL built a CRS microscope offering real-time multiplex SRS imaging of cells and tissues. LIGHTCORE developed an endoscope for in-vivo imaging, demonstrating multimodal imaging and real-time capabilities with hand-held and helmet devices for imaging neurons and tissues.

Work Package 3 focused on advanced CRS data analysis. Machine learning and chemometric models were used for identifying biological samples. Two neural networks were developed for pre-processing CARS spectra, and deep learning models analyzed hyperspectral data to detect disease changes. Two publications addressed non-resonant background removal and biological variance in CRS data.

Work Package 4 completed ethical approvals, technical specifications, and photodamage studies. The advanced imaging technologies were validated in cancer research, focusing on autophagy in liver disease, cancer-immune cell interactions in head and neck cancer, and senescence in thyroid cancer, with potential for personalized cancer treatments.

In Work Package 5, dissemination activities engaged scientific and non-scientific audiences through publications, events, website, and social media.

Work Package 6 coordinated overall project management, meetings, budget, and IP.

Work Package 7 on ethics requirements was completed in the first reporting period.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The goal of the CRIMSON project was reched: the development of an innovative bio-photonic system for cell/tissue imaging which will be used in the near future as a research tool to understand the cellular origin of diseases. The selected imaging technique is broadband coherent Raman scattering (CRS), extended to the fingerprint region. Broadband CRS brings about several advantages, such as:

1. Label-free imaging, avoiding the use of exogenous or endogenous labels.
2. Living cell imaging capability.
3. High acquisition speed, enabling the observation of dynamic cellular processes by time-lapse imaging.
4. High biochemical sensitivity, thanks to the capability to acquire quantitative hyperspectral images allowing the identification of molecules by their unique vibrational spectrum.
5. The possibility to couple these advantages with endoscopy-based in vivo imaging.

Despite the potential of broadband CRS as a disruptive cell/tissue imaging method, several limitations have hindered the adoption of CRS microscopy by biologists as a standard research tool and the technology remains confined to low Technology Readiness Level (TRL) laboratory applications. Limitations comprise the costs and the need of regular alignment or maintenance, which make the technology not suitable for biomedical research laboratories and the lack of capability to provide rich chemical information and spectroscopic information in the fingerprint region.
With the aim of overcoming the limitations and contributing to making broadband CRS a mature technology used by biology laboratories in cellular diseases’ research, the CRIMSON project has delivered:

1. Two compact and turnkey laser system specifically optimised for broadband CRS.
2. A high-speed broadband CRS acquisition system.
3. Optimised microscopy and endoscopy platforms.
4. Advanced AI analysis tools, including chemometrics, machine- and deep-learning, provide a classification of cells and tissues, enabling the rich data sets obtained with CRS to be interpreted with high sensitivity and specificity.

We have validated the technology through the application to three case studies related to cancer, focusing on inter- and intra-cellular processes occurring in liver, head & neck and thyroid tumours.


CRIL has identified a new market opportunity, which is currently under exploration, expected to be valued at a multi-billion level. This consists in the tablet analysis for quality assessment in the drug manufacturing phase, through fast bro adband SRS imaging. Such an opportunity will be further investigated as a follow-up of CRIMSON. This result has been published in the EU portal “Horizon Result Platform” at the following link: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/opportunities/horizon-results-platform/78077

Finally, the data analysis software developed in WP3 has been published online and is now available to any potential user for free as a web-based cloud tool, see https://ramapp.io/. This has also been published in the EU portal “Horizon Result Platform” at the following link: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/opportunities/horizon-results-platform/78162

Infographics of the CRIMSON project