Research Projects



“Imaging and Analysis Techniques to Construct a Cell Census Atlas of the Human Brain”

Starting date: 22-08-2018
End date: 31-05-2023

This project is funded by National Institutes of Health from United States in the context of the Brain Initiative Cell Census Network ( and proposes to create a multi-scale atlas for the human brain to map hemisphere-wide networks and also zoom in to see individual, labeled cells at micron resolution. This advance will be made possible through multiple imaging technologies, including light-sheet microscopy, tissue clearing, immunohistochemistry, magnetic resonance imaging, and newly-developed techniques in Optical Coherence Tomography. The ability to probe the cellular properties and multi-scale networks of specific areas in the human brain could evolve to an automated system for visualizing across the entire human brain in health and disease.
The project team is coordinated by the Massachuset General Hospital (PIs Bruce Fischl and David Boas) and supported by Icahn School of Medicine at Mount Sinai (co-PI Patrick Hof) and by European Laboratory of Non Linear Spectroscopy (co-PI Francesco Pavone).

Project Website


ERC - BrainBIT

“All-optical brain-to-brain behaviour and information transfer”

Starting date: 01-12-2016
End date: 31-05-2022

Exchange of information between different brains usually takes place through the interaction between bodies and the external environment. The ultimate goal of this project is to establish a novel paradigm of brain-to-brain communication based on direct full-optical recording and controlled stimulation of neuronal activity in different subjects. To pursue this challenging objective, we propose to develop optical technologies well beyond the state of the art for simultaneous neuronal “reading” and “writing” across large volumes and with high spatial and temporal resolution, targeted to the transfer of advantageous behaviour in physiological and pathological conditions.
We will perform whole-brain high-resolution imaging in zebrafish larvae to disentangle the activity patterns related to different tasks. We will then use these patterns as stimulation templates in other larvae to investigate spatio-temporal subject-invariant signatures of specific behavioural states. This ‘pump and probe’ strategy will allow gaining deep insights into the complex relationship between neuronal activity and subject behaviour.
To move towards clinics-oriented studies on brain stimulation therapies, we will complement whole-brain experiments in zebrafish with large area functional imaging and optostimulation in mammals. We will investigate all-optical brain-to-brain information transfer to boost an advantageous behaviour, i.e. motor recovery, in a mouse model of stroke. Mice showing more effective responses to rehabilitation will provide neuronal activity templates to be elicited in other animals, in order to increase rehabilitation efficiency. We strongly believe that the implementation of new technologies for all-optical transfer of behaviour between different subjects will offer unprecedented views of neuronal activity in healthy and injured brain, paving the way to more effective brain stimulation therapies.

Project funded by EC H2020 programme.
BrainBIT on Cordis


“Human Brain Project - Specific Grant Agreement 3”

Starting date: 01-04-2020
End date: 31-03-2023

The overall aim of the Human Brain Project (HBP) is to put in place a cutting-edge, ICT-based scientific research infrastructure, that will permit scientific and industrial researchers to advance our knowledge in the fields of neuroscience, computing and brain-related medicine.
In the Specific Grant Agreement 3 (SGA3), the HBP will further develop the EBRAINS platform build in the preceding Specific Grant Agreement 2 (SGA2).
The group led by Francesco Saverio Pavone will provide further structural and functional imaging data aimed to further populate experimental data enriching the Mouse and Human Brain Atlases and to validate simulated mouse brain models.

Here below two videos related to main activities performed at LENS during the previous Specific Grant Agreement (SGA1), ended in March 2018:
Anna Letizia Allegra Mascaro - Multi-scale investigation of brain machinery with correlative microscopy

Giacomo Mazzamuto - Mazzamuto Giacomo - A software pipeline for efficient processing of 3D high-resolution microscopy images on large-brain samples

The two videos are realized by the HBP Education Programme Office in the context of HBP Student Conferences.

Project funded by EC H2020 programme.

Project Website

Laserlab-JRA ALTIS

Starting date: 01-12-2019
End date: 30-11-2023

The Joint Research Activity (JRA) ALTIS (Advanced Laser-based Techniques for Imaging and biomedicine) addresses the needs of new and innovative workstations, methodologies and platforms for advanced imaging and spectroscopy in, for example biomedicine, bio- and nano-materials and environmental science.
This JRA is based on four interconnected and strategic objectives, jointly pursued by 20 partners:
• Advanced Nano, Microscopic Imaging and Spectroscopy
• Advanced Meso- and Macroscopic Imaging and Spectroscopy
• Ultrafast Spectroscopy from THz to XUV develops ultrafast, pump-probe instrumentation and techniques
• Advanced spectroscopic methods for atmospheric pollutants and microplastics
LENS is involved in the first three objectives .

Project Website


Advanced Light Microscopy Italian Node - ERIC EuroBioimaging

Starting date: 2011

The European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences (Euro-BioImaging, EuBI or EuBI ERIC) provides open physical user access to a broad range of state-of-the-art technologies in biological and biomedical imaging for life scientists. In addition, EuBI will offer image data support and training for infrastructure users and providers. The EuBI consists of a set of 29 geographically distributed Node Candidates (specialised imaging facilities) that can grant access to scientists from all European countries and beyond. Currently, researchers can apply to use some of 36 imaging technologies offered through Euro-BioImaging. LENS is part of the Advanced Light Microscopy Italian Node.

Project Website

MIMIC - All-optical brain imaging and control in freely moving rodents

Starting date: 01-01-2018
End date: 31-12-2022

The goal of the present project is to develop innovative optical methods for imaging, control, and, ultimately, the transfer of neural activity patterns in freely moving rodents. Current methods for monitoring and controlling neural activity across large areas of the cerebral cortex are based on conventional microscopy techniques and require head-fixation of the rodent.
This precludes the study of neural dynamics associated to complex behaviors such as spatial exploration and the social interactions. We want to overcome the state of the art by developing a miniaturized, wide-field optical system to be mounted on the head of the animal, to monitor and control neural activity (MIMIC). For imaging purposes we will explore two strategies: one based on a lens-free system with OLED illumination and sCMOS image sensors; the other based on a miniaturization of an optical microscope with lenses. The imaging system will be integrated with an array of optical fibers coupled with microprisms for multispot optogenetic stimulation. Each MIMIC will be mounted on the head of mice that express fluorescent indicators of neural activity and photosensitive channels for the optogenetic stimulation, the goal beeing to study the relationship between neural activity and behavior in freely moving animals. The behavioral tasks will be performed in an virtual reality (VR)-based arena, in which the action of the subject determines a specific sensitive stimulation. Said VR arena will be developed combining touchscreen technologies and an immersive environment, in which we will study how cortical activity correlates with two domains of animal behavior, i.e., motor control and social interactions.
The potentials of MIMIC in monitoring and controlling neural activity will be exploited to transfer pattern of neural activity between freely behaving mice, with the ambitious goal of transferring pattern associated with optimal behavioral performances. This revolutionary approach will be employed to explore the possibility of improving rehabilitation in a mouse model of cortical stroke, with the idea of transferring activity pattern from subjects who show a positive response to rehabilitation training to less responsive mice. In conclusion, we believe that the approach proposed here for monitoring and control of neural activity could have a great impact in the fields of photonics and neurosciences. The results of our project could allow to drastically increase, in quantitative terms, the output of experimental data, to contribute to the study of the central nervous system in more naturalistic contexts, to advance technologies for the communication between nervous systems, and lastly to lay the ground for more effective neurorehabilitative strategies.

Project funded by Italian Ministry of Research (MIUR) under the FARE programme.



Past Projects

Quantitative measurement and imaging of drug-uptake by bacteria with antimicrobial resistance

Nuove tecnologie ottiche per la diagnosi istopatologica di tumori solidi, funded by Ente Cassa di Risparmio di Firenze

Imaging multispettrale nel THz e nel Medio Infrarosso per la diagnosi istopatologica, funded by Ente Cassa di Risparmio di Firenze

Caratterizzazione delle cascate di segnalazione e di trascrizione indotte dall’interazione membrane-amiloide

Sistemi innovativi di imaging ottico e analisi dell’immagine per la caratterizzazione di network neuronali alterati in pazienti pediatrici affetti da malformazioni focali dello sviluppo corticale

Diagnostic technology for the post-operative monitoring of pediatric brain tumors, funded by Ente Cassa di Risparmio di Pisa

Cardiac arrhythmias: from genes to improved management of patients, funded by EC FP7

Sviluppo di una piattaforma per lo studio della meccanotrasduzione: dalla singola molecola alla cellula vivente, funded by Italian Ministry of Research Futuro in Ricerca

Polarized cell structures in metastasis: coordination of the plasma, membrane, cytoskeleton and organelles. Funded by the Fondazione Italiana per la Ricerca sul Cancro (FIRC).

Proteomica/genomica/metabolomica per l’individuazione di biomarcatori e lo sviluppo d una piattaforma di rivelazione ultrasensibile in fluidi corporei periferici: applicazione al glioblastoma multiforme

FLAGSHIP Human Brain Project Ramp-Up-Phase (RUP) - FP7

FLAGSHIP Human Brain Project - Specific Grant Agreement 1 (SGA1) and Specific Grant Agreement 2 (SGA2) - H2020

Development of advanced laser imaging techniques for the anterior and posterior eye, funded by ERANET Biophotonics+

Led Technology in Photo Haemostasis, funded by ERANET Biophotonics+

Nose to Brain Delivery of BIIB033 via the Olfactory Region for the Regenerative treatment of Multiple Sclerosis Using Novel Multi-functional Biomaterials Combined with a Medical Device

Multimodal highly-sensitive PhotonICs endoscope for improved in-vivo COLOn Cancer Diagnosis and clinical decision support

Automated digital scanning and diagnosis of tissues using multimodal non-linear optical microscopy

Stem Cells
New Animal Model, Nanotechnologies and Neuroimaging to Study Interactions and Homing of Human Neural Stem Cells in Stroke. Funded by the Italian Ministry of Health

Monitoraggio e prevenzione delle morti improvvise cardiache giovanili in Toscana