The Optical Microscopy and Tomography Laboratory develops optical imaging methods and instruments to study biological processes, from bioparticles and individual cells to intact organisms. Its work combines optical design, photonics hardware development and quantitative image analysis to tailor imaging workflows to specific samples and biological questions.

Light sheet microscopy for extracellular vesicles, cells and organisms

Light-sheet microscopy enables rapid 3D fluorescence imaging while limiting photobleaching and phototoxicity. The laboratory develops compact optofluidic systems that combine light-sheet illumination with continuous sample delivery for automated, high-throughput imaging of individual cells and tissues. The same technology is used for high-throughput characterization of extracellular vesicles (EVs), enabling the analysis of large numbers of vesicles in a single experiment.

Federico Sala, Michele Castriotta, Petra Paiè, Andrea Farina, Sarah D’Annunzio, Alessio Zippo, Roberto Osellame, Francesca Bragheri, Andrea Bassi High-throughput 3D imaging of single cells with light-sheet fluorescence microscopy on chip Biomedical Optics Express, 2020, 11(8), 4397–4407.

Adaptive optics

In thick and heterogeneous samples, aberrations limit image quality across the field of view. The laboratory develops adaptive-optics microscopy using deformable optics and remote focusing to correct these aberrations while preserving the performance of high-numerical-aperture objectives. This enables high-resolution 3D imaging across larger fields and depths, with correction strategies designed and validated for the specimen and imaging geometry.

Paolo Pozzi, Vipin Balan, Alessia Candeo, Alessia Brix, Anna Silvia Pistocchi, Cosimo D’Andrea, Gianluca Valentini, Andrea Bassi Full-aperture extended-depth oblique plane microscopy through dynamic remote focusing Journal of Biomedical Optics, 2024, 29(3), 036502.

Photonics Integrated Circuits for microscopy

Photonic integrated circuits (PICs) generate and control light directly on a chip, opening up new possibilities for compact microscope systems. The laboratory develops PIC-based approaches for optical microscopy, including structured illumination. Its work spans optical design, illumination control, integration of the chip with the microscope, and experimental characterization.

Paolo Maran, Abhiram Rajan, Francesco Ceccarelli, Roberto Osellame, Petra Paiè, Alessia Candeo, Francesca Bragheri, Andrea Bassi Amplitude- and Phase-Programmable Dual-Color Photonic Chip for High-Contrast Structured Illumination MicroscopyACS Photonics, 2026, 13(4), 1129–1138.

Functional imaging with fluorescent sensors

The laboratory develops fluorescence-imaging systems to monitor physiological signals and processes in large biological samples. Fluorescent sensors can detect parameters such as Ca²⁺, pH, ATP and redox state, tracking their changes in real time under near-physiological conditions. In plants, these systems make it possible to observe responses across leaves, stems and roots, as well as the long-distance propagation of signals. Optical configurations and acquisition strategies are tailored to sample geometry, the region of interest and the dynamics of the process under study.

Giorgia Tortora, Bianca Maria Orlando Marchesano, Stefano Buratti, Laura Luoni, Matteo Grenzi, Keiko Yoshioka, Valeria Contartese, Alessia Candeo, Alex Costa, Andrea Bassi MAcro Plant Projection Imaging (MAPPI): An open, scalable platform for whole-plant fluorescence real-time imagingScience Advances, 2026, 12(4), eaea4466.