Humanitas inaugurates CLEM: a laboratory that integrates optical, electron, and cryogenic microscopy technologies with data processing using Artificial Intelligence

A new advanced imaging platform, combining the vision of optical microscopy with the magnification power of electron microscopy – known as Correlative Light-Electron Microscopy (CLEM) – has been inaugurated on the Humanitas University campus, just a few tens of meters from the laboratories and hospital departments of Humanitas Research Hospital. This infrastructure allows for exploration across all scales, from tissues to subcellular and molecular structures, obtaining high-definition 3D images. It’s a kind of “cellular CT scan,” available for the first time in Italy at a Research Hospital.

The laboratory, located within the Roberto Rocca Innovation Building, is among the first in Europe to be installed within a Research Hospital. The goal is to apply the technological power of CLEM – which originated in materials science and the study of the chemical-physical structure of molecules – to research for the treatment of diseases. This innovative approach aims to find answers to the complex questions arising from hospital departments and research laboratories. It’s based on the understanding that what happens at the micro level – subcellularly within tissues – has macro effects: the symptoms of disease.

Leading this ambitious transformation, in collaboration with Humanitas doctors and researchers, is Edoardo D’Imprima, who returned from the European Molecular Biology Laboratory (EMBL) in Heidelberg specifically to launch Humanitas’s new CLEM laboratory.

“Humanitas has a clear mission: to develop diagnostic and therapeutic solutions to improve patients’ lives,” states Prof. Luigi Maria Terracciano – Scientific Director of Humanitas Research Hospital and Rector of Humanitas University. “Combining the experience of our research doctors with advanced technologies is the best way to achieve this goal. The CLEM platform, along with existing technologies and expertise – such as proteomics, metabolomics, and computational biology – will allow us to deeply explore the structures and biological mechanisms underlying diseases. It therefore represents a cross-cutting resource for cutting-edge research.”

CLEM technology for the study of biological processes in 4 dimensions

CLEM (Correlative Light and Electron Microscopy) is a technology designed to combine two complementary approaches to studying biology: on one hand, fluorescence optical microscopy, which allows for observing dynamic events in living tissues; on the other hand, electron microscopy, which offers nanometric resolution to analyse the structure of cellular components.

Here lies another novel aspect of the Humanitas project: traditional electron microscopy views images in 2D; the Pieve Emanuele laboratory uses a technology – called Volume EM – that allows for viewing data in 3 dimensions at nanometric resolution (a nanometer is one-millionth of a millimeter). It’s like observing a city street, moving from the perspective of a flat, overhead street map to the viewpoint of a pedestrian walking on that street: a three-dimensional, hyper-detailed vision.

Another key element has been the introduction of cryo-microscopy techniques, which are based on the instantaneous “freezing” of biological samples using high-pressure liquid nitrogen. This prevents ice formation and thus preserves their structural integrity. Thanks to this combination, it is now possible to observe a biological event live, precisely localise it, and then freeze it in time to analyse it in minute detail and in 3D. It’s a kind of cellular CT scan in four dimensions, also accounting for the temporal dimension. (See in-depth sheet).

“CLEM represents a new frontier for Biology and Medicine because it allows us to connect function and structure, macro and micro,” explains Edoardo D’Imprima. “In an era where precision medicine requires an increasingly deep and detailed understanding of highly complex biological processes, CLEM combines the ‘film’ of cellular dynamics with a snapshot of the molecular detail of the involved structures. All this in three dimensions and translated into numbers, thanks to Artificial Intelligence and computing power, to provide doctors with data – a quantitative response – not just images.”

The large-scale application of CLEM technology entails another fundamental challenge: managing the enormous amount of data generated by the instruments. To address this need, Humanitas University has enhanced its high-performance computing (HPC) center. This advanced system not only allows for storing the collected data but also for analysing it in real-time to extract quantitative information, crucial for supporting the work of Humanitas’s clinical and translational research groups.

Examples of ongoing research: neurosciences, bacteria, and fighting infections

Among the first researchers to initiate collaborations with the new CLEM laboratory is Roberto Rusconi – Associate Professor at Humanitas University and head of the Applied Biophysics and Microfluidics Laboratory. He studies how different types of surfaces can change bacterial adhesion and the risk of infection in medical prostheses, without the use of antibiotics.

Subsequently, other researchers have also begun to explore the potential of this technology. These include Davide Pozzi – Associate Professor at Humanitas University and researcher of the Neuroscience program directed by Prof. Michela Matteoli, who wants to use the new microscopes to observe if and how inflammation can alter the structure of synapses – the connection points between neurons that represent a crucial node in the origin of neurodegenerative diseases. Sara Carloni – Assistant Professor of Microbiology and Clinical Microbiology at Humanitas University and researcher at the laboratory directed by Prof. Maria Rescigno, studies the molecular tools by which microbiota bacteria communicate with the host and with each other, exchanging information and capabilities, including antibiotic resistance.

Other technologies empowering Humanitas Research

CLEM complements the technologies already present in the Humanitas University Innovation Building, including the 3D Innovation Lab, a clinical platform that combines 3D modeling, printing, and biofabrication. This is further enhanced by the introduction of new clinical imaging technologies – including photon-counting CT and a latest-generation 3 Tesla MRI – which allow for an unprecedented understanding of cardiological, neurological, oncological, and pulmonary pathologies. Both instruments mark a record-breaking advance: while the former machine is the third of its kind to be installed in Italy, the MRI is an absolute first in Italian hospitals, with only a few other installations underway worldwide. Purchased by Humanitas University thanks to funds from the Anthem Project – financed by the National Complementary Plan to the PNRR instituted by the Italian Ministry of University and Research – both machines will be entirely dedicated to the frontier clinical research projects promoted by Anthem.

Within this interdisciplinary ecosystem, Humanitas aims to be a hub of attraction for researchers, doctors, and engineers from all over the world, with the goal of developing increasingly precise, predictive, and personalised medicine.