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URPP Adaptive Brain Circuits in Development and Learning (AdaBD)

mesoSPIM Platform

Light-sheet microscopy platform

visualization of the benchtop mesospim
Visualization of the Benchtop mesoSPIM (

The project

The mesoSPIM microscopy platform offers to basic and clinical scientists three custom-built light-sheet microscopes that allow 3D imaging of chemically cleared samples that are too large for traditional microscopes, such as entire mouse brains or post-mortem human tissues. Images are taken through a laser scanning technique, without cutting the samples into slices, a process called light-sheet imaging.

Our platform offers a comprehensive range of services, including user training, consulting, customization of software and hardware. Further, we carry out our own research and development in light-sheet microscopy, further developing our microscopes as an open-source project, including video tutorialsand user meetings. In 2023, we reached a milestone by completing a new generation of mesoSPIM microscopes,  the Benchtop microscope, which is more compact, easier to build, portable and affordable.  Moreover, it has improved optics, higher resolution, and a larger field of view.

The mesoSPIM technology allows unprecedented analysis of brain circuits architecture, from embryo to adulthood. This facilitates research of several groups within our URPP and beyond, who investigate brain circuits during development in health and disease. 

Services of the platform

  • Onboarding of new users to light-sheet imaging with mesoSPIM
  • Training on basic processing of light-sheet data (interactive visualization, stitching, fusion)
  • Consulting of users on sample preparation, light-sheet imaging, and data processing
  • Customization of sample mounting: making holders for samples of unusual size or shape
  • Development and upgrade of acquisition software
  • Maintenance and troubleshooting of the mesoSPIM systems at the Brain Research Institute and the Center for Microscopy and Image Analysis (ZMB), UZH
  • Coordination of sample clearing with the ZMB tissue clearing platform, optimization of protocols
  • Organization of user meetings and outreach activities
  • R&D in light-sheet microscopy: novel mesoSPIM systems and applications



Nikita Vladimirov, PhD
Marco Garbelli, PhD



Vladimirov N, Voigt FF, Naert T, Araujo GR, Cai R, Reuss AM, Zhao S, Schmid p, Hildebrand S, Schaettin M, Groos D, Mateos JM, Bethge Ph, Yamamoto T, Aerne V, Roebroeck A, Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F (2024) The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples  Nature Communications 15, 2679

Diederich B, Müllenbroich C, Vladimirov N, Bowman R, Stirling J, Reynaud EG (2022) CAD we share? Publishing reproducible microscope hardware. Nature Methods 19, 1026–1030

Voigt FF, Kirschenbaum D, Platonova E, Pagès S, Campbell RAA, Kästli R, Schaettin M, Egolf L, van der Bourg A, Bethge Ph, Haenraets K, Frézel N, Topilko Th, Perin P, Hillier D, Hildebrand S, Schueth A, Roebroeck A, Roska B, Stoeckli E, Pizzala R, Renier N, Zeilhofer HU, Karayannis Th, Ziegler U, Batti L, Holtmaat A, Lüscher Ch, Aguzzi A, Helmchen F (2019)The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue.Nature Methods 16, 1105–1108



The mesoSPIM Initiative

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