Understanding how cells are organized and how their molecular components interact in a coordinated and cooperative manner is a central goal of modern life sciences. To answer these questions, researchers need to observe many structures inside the same cell at once and map how they are arranged and interact. This requires "multiplexed super-resolution microscopy" – an advanced imaging approach that reveals cellular details far beyond the limits of conventional light microscopes. However, existing methods are often technically demanding, difficult to reproduce, and not well suited for fragile biological samples. An international research team led by the University of Göttingen, together with the University Medical Center Göttingen (UMG), as part of the Göttingen Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), set out to overcome these limitations. The team developed a dedicated microfluidics system that makes multiplexed super-resolution microscopy easier, more reproducible, and accessible to a broader community. The work was published in the journal ACS Nano.
To truly understand how a cell functions, scientists must visualize not just one component at a time, but many proteins and specialized structures simultaneously and see how they interact inside the cell. In addition, these experiments become increasingly complex and sensitive to small variations, which can limit reproducibility. The new microfluidics system precisely injects and removes solutions from the sample chamber, replacing manual pipetting with controlled and reproducible fluid handling. "The system we have developed means we can maintain high image quality throughout long imaging cycles," says Dr Samrat Basak, joint first author and Postdoctoral researcher now based at LMU Munich. "By keeping conditions consistent across the different labelling and washing steps, the microfluidics platform allows information from different targets to be directly mapped, making it possible to image proteins, specialized structures and complex interactions within the cell." The researchers demonstrated this technique in human cancer cells, revealing the organization of protein filaments inside the cell. The team also applied the method to isolated specialized muscle cells from the ventricles of a mouse heart. "The fragile, specialized muscle cells of the heart are particularly challenging to image," explains joint first author Kim-Chi Vu, UMG and MBExC. "The microfluidics system was essential to complete the imaging without deforming the cells or detaching them from the surface."
The new machine can be operated in manual or automated modes and is compatible with a wide range of imaging systems. "The core idea was to develop a system which is cost-efficient, adaptable, and can be redesigned according to specific imaging needs of complex biological systems," explains Dr Roman Tsukanov, senior Postdoctoral researcher at Göttingen University. "By automating fluid exchange, we removed a major source of variability and made complex imaging protocols much more user-friendly."
"This approach will help standardize multiplexed super-resolution imaging and make it broadly accessible, benefiting both research and medical applications," adds Professor Jörg Enderlein at Göttingen University's Physics Faculty.
Original publication: Basak, S.; Vu, K.C.; Mougios, N. et al "Versatile Microfluidics Platform for Enhanced Multitarget Super-Resolution Microscopy. ACS Nano (2026). DoI: 10.1021/acsnano.5c18697
