A light-efficient microscope for fast volumetric imaging of photon starved samples

Project Information

LowLiteScope

Grant agreement ID: 101138041

DOI

10.3030/101138041

Project closed

EC signature date 20 September 2023

Start date 1 January 2024

End date 30 June 2025

Funded under

• European Research Council (ERC)

Total cost

No data

EU contribution

€ 150 000,00

Coordinated by

FUNDACIO INSTITUT DE CIENCIES FOTONIQUES
Spain

Periodic Reporting for period 1 - LowLiteScope (A light-efficient microscope for fast volumetric imaging of photon starved samples)

Reporting period: 2024-01-01 to 2025-06-30

Summary of the context and overall objectives of the project

Many important biological processes, such as brain activity or tissue development, happen quickly and in three dimensions, but observing them in living organisms has been very challenging. Traditional microscopes either take too long, use light that can disturb the sample, or fail to capture faint signals from bioluminescent proteins.

Our project developed the LowLiteScope, a new type of microscope combined with smart computer algorithms, that can capture 3D images of living cells and small organisms in a single snapshot, even when light is extremely limited. This allows us to track fast processes such as neural activity in freely moving worms or the way cells migrate in growing tissue spheroids. We also demonstrated that the system works with a new red-shifted bioluminescent neuronal activity indicator that accurately measures calcium ions with a near-infinite dynamic range, which could not previously be imaged.

By making this technology easier to use and faster than existing methods, our project opens the door to new discoveries in neuroscience, developmental biology, and regenerative medicine. The system is designed to be accessible to other researchers and has the potential for wider adoption and industrial application.

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 this Proof of Concept project, we developed and validated a new imaging platform that combines Fourier Light Field Microscopy (FLFM) with a dedicated deep learning reconstruction pipeline (LUCID) to overcome the long-standing barriers of speed and sensitivity in volumetric microscopy. On the hardware side, we built a multimodal FLFM optimized for photon-starved conditions, including bioluminescence, with extended depth of field and near-diffraction-limited resolution. This enabled single-exposure 3D imaging at sub-second timescales, a capability not possible with conventional approaches.

On the computational side, we created LUCID, an AI framework that integrates attention mechanisms and denoising directly into the reconstruction task. LUCID achieved two orders of magnitude faster reconstructions than classical Richardson–Lucy deconvolution while preserving fine details. Importantly, interpretability analyses confirmed that the network extracts biologically meaningful information rather than hallucinating structure.

We validated the platform across multiple biological systems. In stem cell–derived spheroids, we quantified tissue compaction and strain using fluorescent nuclei as fiducial markers. In freely moving C. elegans, we captured neuronal activity and tissue deformations in 3D at behavioral timescales, without disturbing natural behavior. Finally, we extended the system to bioluminescence imaging, where we achieved near single-cell resolution at short exposure times and successfully characterized a new red-shifted luciferase-based calcium sensor (CaMBI3), an experiment that would have been impossible with existing microscopes.

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 potential impact is twofold. Scientifically, the LowLiteScope opens new frontiers for studying fast, 3D biological processes that are currently invisible due to light sensitivity or photon limitations, spanning neuroscience, developmental biology, and regenerative medicine. Societally, it provides a non-invasive and quantitative imaging tool that can accelerate discovery in health and disease, with clear translational opportunities in drug development and functional tissue assays.

To ensure further uptake, several needs remain: (i) continued research and engineering to refine optical designs into compact, plug-and-play modules, (ii) IPR and business development to protect key innovations and engage with potential industry partners, (iii) demonstrations with end-users to validate

performance in real-world biological applications, and (iv) access to finance and commercialisation pathways to transition from lab prototypes to scalable, user-friendly products.

Overview of results: By the end of this project, we delivered a working prototype of the LowLiteScope and the LUCID pipeline, demonstrated high-speed volumetric imaging in challenging biological contexts, and validated a new bioluminescent calcium indicator. Together, these results establish both the technical feasibility and the scientific impact of the technology, while providing a clear roadmap for translation into broader research and commercial applications.