mesoscale multi-mode MRI of molecular targets

Project Information

MAGNIFISCENT

Grant agreement ID: 851919

DOI

10.3030/851919

Project closed

EC signature date 13 December 2019

Start date 1 January 2020

End date 31 December 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 946 250,00

EU contribution

€ 1 946 250,00

Coordinated by

TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Israel

Periodic Reporting for period 4 - MAGNIFISCENT (mesoscale multi-mode MRI of molecular targets)

Reporting period: 2024-07-01 to 2025-12-31

Summary of the context and overall objectives of the project

Non-invasive, brain-wide visualization of defined cellular populations remains a major unresolved challenge in neuroscience. Optical imaging approaches provide high spatial resolution but are limited by tissue penetration and invasiveness, while Magnetic Resonance Imaging (MRI) enables whole-brain coverage but lacks molecular specificity and sensitivity. A central barrier is the inability to efficiently deliver functional imaging agents across the blood–brain barrier (BBB) and achieve sufficient signal generation within defined cellular compartments. The MAGNIFISCENT project addresses these limitations by developing integrated molecular and delivery strategies that combine genetic targeting, chemical probe design, and advanced imaging modalities. Importantly, the work also aims to define the practical and physical constraints governing signal generation, probe distribution, and biological compatibility in the brain.

Why is it important for society? Achieving non-invasive, cell-specific imaging of the brain would provide transformative tools for understanding neurological and psychiatric disorders, including neurodegeneration, developmental disorders, and circuit dysfunction. Such capabilities would enable longitudinal studies of cellular dynamics across the entire brain, bridging a critical gap between cellular-resolution methods and whole-organ imaging. Beyond neuroscience, the development of strategies for targeted delivery and controlled signal generation has broader implications for drug delivery, gene therapy, and precision medicine. Establishing biologically compatible platforms that operate within realistic physiological constraints is essential for future clinical translation. The overall objective of the project is to establish a modular and biologically compatible framework for multimodal brain imaging, integrating genetic targeting, chemical probe development, and advanced imaging methods, while explicitly addressing feasibility, safety, and scalability. Specifically, the project aims to develop genetically encoded and chemically engineered reporters for multimodal imaging, delivery and targeting strategies for the brain, and signal amplification under physiological constraints.

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

During the reporting period, the project was implemented through a coordinated set of experimental, methodological, and analytical activities aimed at developing and validating multimodal imaging strategies for the brain. The work focused on three interconnected directions: (i) development of genetically encoded tools, (ii) chemical and hybrid probe design, and (iii) quantitative characterization of imaging constraints in brain tissue.
*Development of genetically encoded tools for spatially resolved signaling- A major effort was devoted to establishing genetically encoded systems capable of generating localized signals within defined subcellular compartments. This resulted in the development of split genetically encoded calcium indicators targeted to interorganellar junctions (PNAS, 2025), which demonstrated that functional signals can be restricted to nanoscale cellular domains.This work provides a key conceptual advance by showing that spatial confinement of signal generation can compensate for limitations in detection sensitivity, an important principle for multimodal imaging approaches. In parallel, a novel stop-codon–mediated polycistronic translation strategy (under review, 2026) was developed, enabling coordinated expression of multiple proteins from a single transcript in neurons in vivo. This platform establishes a foundation for implementing complex, multi-component imaging systems with precise stoichiometric control.
*Design and validation of multimodal chemical–genetic probes. The project advanced the development of hybrid imaging probes combining genetic targeting with chemical functionality. In particular, SNAP-tag-targeted MRI–fluorescent probes (ChemBioChem, 2023) demonstrated the feasibility of directing synthetic contrast agents to defined cellular targets using genetically encoded tags. This work establishes a modular strategy for linking molecular specificity with externally delivered probes, enabling flexible design of multimodal imaging systems.
*Quantitative characterization of imaging constraints in brain tissue. A central component of the project involved defining the physical and biological constraints governing imaging signal generation. The study “Revealing the MRI Contrast in Optically Cleared Brains” (Advanced Science, 2024) provided a systematic analysis of how tissue composition, probe distribution, and imaging parameters influence detectable contrast. This work yielded important insights into the limits of sensitivity and spatial resolution, informing the design of more realistic and effective imaging strategies. Complementary to this, the dataset on lipid content in optically cleared brains (Data in Brief, 2023) provides a quantitative resource for understanding how tissue composition affects imaging performance, supporting both experimental interpretation and computational modeling.
*Integration of findings and methodological advances. Across these activities, the project has established: Validated strategies for subcellularly confined signal generation, reducing reliance on bulk accumulation of probes; Modular chemical–genetic platforms for targeted probe delivery; Quantitative frameworks for understanding imaging constraints in brain tissue; New genetic tools enabling multiplexed and coordinated expression in neurons. Together, these advances significantly refine the conceptual and technical basis for multimodal brain imaging.

**Dissemination and exploitation of results. The results of the project have been actively disseminated through peer-reviewed publications in high-impact journals, including PNAS, Advanced Science, ChemBioChem, and Data in Brief, as well as through ongoing work currently under review. The tools and datasets generated in this project provide a foundation for future development of imaging technologies and molecular delivery systems, with potential applications in neuroscience research, drug delivery, and precision medicine. Briefly, genetically encoded systems developed here can be directly adopted by the neuroscience community. Multimodal probe strategies offer a platform for further technological innovation. Quantitative datasets support broader modeling and methodological development

Overall, the work performed during this period has successfully established key technological and conceptual building blocks, while also clarifying critical constraints that must be addressed in future developments. These findings provide a solid and realistic foundation for advancing toward robust, biologically compatible multimodal imaging approaches.

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)

Building on the above mentioned advances, the project is expected to deliver the following outcomes:
1. Fully integrated multimodal imaging systems: The project will establish combined genetic and chemical systems capable of targeting defined cellular populations, generating localized and tunable signals,integrating multiple imaging modalities within a single platform.These systems will be validated in biologically relevant contexts.
2. Experimentally validated design principles for signal generation: The project will provide a framework for optimizing signal generation under physiological constraints, including strategies based on spatial confinement and amplification, quantitative benchmarks for detectability, guidelines for balancing sensitivity, specificity, and biological compatibility.
3. Refined delivery and targeting strategies: Through iterative testing and validation, the project will define effective approaches for delivering functional components into brain tissue, constraints imposed by biological barriers, strategies for maintaining functionality while incorporating multiple features.
4. Open datasets and methodological frameworks the project will generate: datasets linking tissue composition to imaging performance, validated experimental protocols, tools that can be adopted by the broader research community.
5. Foundations for future translational applications. By addressing key challenges related to feasibility, safety, and integration, the project will lay the groundwork for next-generation imaging technologies, improved delivery platforms, broader applications in neuroscience and biomedical research.
Overall, the project is expected to shift the field from empirical, high-load approaches toward modular, quantitatively informed, and biologically compatible strategies for brain imaging.Rather than focusing solely on increasing probe concentration, the work establishes a new framework based on precision targeting, localized signal generation, and integration of complementary technologies.
This positions the project to make a significant and lasting contribution to the development of advanced imaging methodologies.

Ex vivo multimodal MRI-LM imaging of cleared brains