Microscopy Innovation Platform
Microscopy Innovation Platform
The project
The microscopy innovation platform (MIP), formerly mesoSPIM platform, carries out innovation projects in light microscopy pushing the boundaries of brain imaging.
It continuously further develops its custom-built light-sheet microscopes (mesoSPIM) as an open-source project. mesoSPIM microscopes 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. 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.
In addition, the platform aims at driving cutting-edge innovation across a wider range of light microscopy technologies. For example, it focuses on advancing the Schmidt two-photon microscope. The Schmidt Objective enables large field-of-view imaging with submicron resolution, bridging the gap between mesoscopic and cellular scales. Our developments allow unprecedented analysis of brain circuits architecture, from embryo to adulthood, at affordable prices and with the flexibility of custom-made instruments. The platform actively contributes to several research projects within the URPP and beyond.
Besides Research & Development, our platform offers a comprehensive range of services, including user training, consulting, customization of software and hardware, video tutorials and user meetings. Another focus is on tissue clearing and samples preparation.
Services of the platform
- Research&Development in light microscopy: novel systems and applications
- 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
- Tissue clearing and samples preparation, optimization of protocols
- Organization of user meetings and outreach activities
Staff
Nikita Vladimirov, PhD
Marco Garbelli, PhD
Angeliki Vavladeli, PhD
Publications
Noble AR, Masek M, Hofmann C, Cuoco A, Rusterholz TDS, Ozkoc H, Greter NR, Phelps IG, Vladimirov N, Kollmorgen S, Stoeckli E, Bachmann-Gagescu R (2024)
Shared and unique consequences of Joubert Syndrome gene dysfunction on the zebrafish central nervous system
Biol Open 13(11): bio060421
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
Voigt FF, Reuss AM, Naert T, Hildebrand S, Schaettin M, Hotz AL, Whitehead L, Bahl A, Neuhauss SC, Roebroeck A, Stoeckli ET, Lienkamp SS, Aguzzi A, Helmchen F (2024)Reflective multi-immersion microscope objectives inspired by the Schmidt telescope. Nature Biotechnology, 42(1), pp.65-71
Baum S, …, Vladimirov N, Walsworth RL, Watanabe H (2023) Mineral detection of neutrinos and dark matter. A whitepaper
Physics of the Dark Universe 41: 101245
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