EMBL Imaging Centre

Open access to cutting-edge electron and light microscopy

We provide researchers from Europe and beyond with a synergistic portfolio of imaging services including cryo-EM, super-resolution and intravital microscopy to enable new ground-breaking research that crosses the scales of biology.

Innovation & Research

Technology Development as an integral part to drive the best service

The development of advanced imaging technologies continues a long and successful tradition at EMBL, with many inventions and patents in light and electron microscopy. Constant improvement and development of new imaging and correlative technologies is also an inherent part of the EMBL Imaging Centre, jointly by EMBL Imaging Centre service with EMBL research staff, as well as with industrial partners.

Open Innovation – Technology development jointly with industrial partners

EMBL has a long successful history in technology development in collaboration with industrial partners. Technology development in context of the EMBL Imaging Centre aims to drive industrial early-stage next generation technologies by biological applications based on the needs of the user community. This novel concept of collaboration between academia and industry is underpinned by longer term partnerships and agreements. In such an “open innovation” environment, technology development is done side by side with users testing new technologies for applicability in their research. Partner companies can thus feed these experiences directly back into their R&D, to make sure new products deliver what users need to accomplish their research goals. Inherent to this concept is a great opportunity to mobilise funding for such public-private partnerships.

The EMBL Imaging Centre is grateful to call four leading companies in microscopy technology founding technology partners – Abberior Instruments, Leica Microsystems, Thermo Fisher Scientific and Zeiss Microscopy.

We remain however open to work with additional companies in complementary technology areas. If you are interested in such collaboration please contact Stephanie Alexander.

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Partnership on MINFLUX nanoscopy

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Research within EMBL Units

Mattei team

The Mattei research team is affiliated with the Structural and Computational Biology Unit at EMBL Heidelberg. The team membersdevelop methods and software supporting high-throughput and fully automated pipelines to tackle the current challenges in cryo-EM sample preparation and screening.

Credit: Simone Mattei/EMBL.
To address some of the major rate-limiting steps that currently affect the throughput and the success rate of cryo-EM projects we will develop high-throughput and fully automated pipelines to enable large-scale cryo-EM sample preparation and screening. Our pipeline will integrate specimen handling, sparse-matrix screening, and biochemical characterisation workflows to explore sample stability within a wide range of buffer conditions. The produced screening conditions will be applied to a range of cryo-EM supports by newly developed vitrification devices able to provide controlled and efficient preparation of cryo-grids. We will integrate the existing imaging routines with machine learning based applications to establish a fully automated pipeline that will cover all the imaging steps required for large-scale cryo-EM sample screening. Our pipeline will provide full tracking of the samples throughout the entire process thanks to a dedicated data management system.

Zimmermann team

The Zimmermann research team is affiliated with the Cell Biology and Biophysics Unit at EMBL Heidelberg. The team is interested in method development in the areas of super-resolution microscopy and cryo-fluorescence microscopy. A specific focus lies on a better understanding of intermittent darkstates of fluorescent molecules (“blinking”) and how these states are populated at different light intensities (as found in point scanning and widefield imaging) and temperatures.

Credit: Timo Zimmermann/EMBL
In addition to returning to the ground state by the emission of a fluorescence photon, an excited fluorophore can transition to additional longer lived states like the triplet state. These states will not emit a fluorescence photon and can be considered „dark“. While these states are not efficiently populated at low illumination intensities, the high intensities in point scanning microscopy methods can lead to the buildup of significant populations of transient dark states which will return to the ground state after the scanning beam passed on. Different beam scanning speeds can accordingly affect the brightness of the collected emission signal and can be used to probe transient darkstate behaviour.