The ‘mesoscale selective plane illumination microscopy’ (mesoSPIM) initiative aims to provide the imaging community with open-source light-sheet microscopes for large cleared samples. On the one hand, it is aimed at neuroscientists and developmental biologists seeking high-quality anatomical data from cleared samples, on the other hand, it strives to provide instrumentation developers with imaging platforms that can be tailored towards specific needs – i.e. to accommodate uncommonly large samples or different illumination schemes.

In addition, we foster interactions between the developers of clearing methods, instrumentation designers and users by organizing meetings and workshops.


In late 2015, the mesoSPIM project started as a tiny side project for Fabian Voigt when
Adriano Aguzzi (University Hospital Zurich) approached Fritjof Helmchen (Brain Research Institute, University of Zurich) with a request for help in the selection of a light-sheet microscope for CLARITY-cleared mouse brains. After some unsatisfactory tests of existing commercial setups, we decided to build our own. For more about the mesoSPIM history visit the mesoSPIM wiki and check Fritjof’s Helmchen talk.

In May 2018 mesoSPIM became a facility instrument at the Center for Microscopy and Data Analysis (ZMB/UZH).

In June 2021 mesoSPIM became a technology platform of URPP Adaptive Brain Circuits in Development and Learning (AdaBD).


image-leftNikita Vladimirov’s expertise is light-sheet microscopy, programming, and computational neuroscience. He did his PhD in computational biology at Heidelberg University and a postdoc in computational neuroscience at IBM Research. Interest in neuroscience led him to zebrafish brain imaging at HHMI Janelia Research Center. He then joined the BIMSB/MDC institute in Berlin where he received a Marie-Curie fellowship for his innovative project in light-sheet microscopy with adaptive optics. Tinkering with a mesoSPIM setup at the BIMSB Systems Biology Imaging core grew into a long-term commitment to this open-science project. In summer 2021 he joined the URPP Adaptive Brain Circuits in Development and Learning (AdaBD), Helmchen Lab and the ZMB at UZH to lead future development of mesoSPIM project.

image-leftFabian F. Voigt is a postdoc in the laboratory of Florian Engert at Harvard University, Department of Molecular and Cellular Biology. Fabian started the mesoSPIM initiative as a PhD student in the laboratory of Fritjof Helmchen at the Brain Research Institute, University of Zurich. As a BSc student in Interdisciplinary Science, Fabian started out building light-sheet endoscopes for in vivo calcium imaging in mice (miniSPIM). In his BSc thesis, he used electrically tunable lenses (ETL) for fast 3D two-photon imaging and later brought the technology to the lab of Jan Huisken at MPI-CBG in Dresden which resulted in the ETL-SPIM, a fast volume scanning light-sheet microscope. In his MSc studies at ETH Zurich, he designed two-photon mesoscopes.

image-leftFritjof Helmchen is Professor of Neuroscience and Co-Director of the Brain Research Institute. His research is focused on the development and application of optical methods, in particular two-photon microscopy, to study neural activity on the subcellular, cellular, and circuit level. His group has pioneered several microscopy techniques, including 3D, high-speed, and multi-area in vivo two-photon imaging, and has contributed to recent advancements in the study of cortical microcircuits. Fritjof Helmchen is currently director of the Neuroscience Center Zurich and co-director of URPP AdaBD.


This open-source project is made possible by the long-term support of our sponsors:

2015 - present: Helmchen Lab, UZH

2018 - present: Center for Microscopy and Data Analysis (ZMB), UZH

2021 - present: URPP Adaptive Brain Circuits in Development and Learning (AdaBD)

URPP logo


University of Zurich & ETH Zurich

Evgenia Platonova, Rahel Kästli, Martina Schättin, Philipp Bethge, Alexander van der Bourg Ladan Egolf, Martin Wieckhorst, Dubravka Göckeritz-Dujmovic, Karen Haenraets, Noémie Frézel, Esther Stöckli, Urs Ziegler, Hanns Ulrich Zeilhofer, Theofanis Karayannis

University Hospital Zurich

Daniel Kirschenbaum, Adriano Aguzzi

Wyss Center for Bio- and Neuroengineering

Stéphane Pagès, Laura Batti

University of Geneva

Anthony Holtmaat, Christian Lüscher

Sainsbury Wellcome Centre for Neural Circuits and Behaviour, London

Robert A. A. Campbell

University of Pavia

Paola Perin, Roberto Pizzala

ICM - Brain & Spine Institute, Paris

Thomas Topilko, Nicolas Renier

Hungarian Academy of Sciences Research Centre for Natural Sciences & Faculty of Information Technology and Bionics, Pazmany Peter Catholic University

Daniel Hillier

Friedrich Miescher Institute Basel

Botond Roska

Maastricht University

Sven Hildebrand, Anna Schueth, Alard Roebroeck

Contact and requests

Nikita Vladimirov
URPP Adaptive Brain Circuits in Development and Learning (AdaBD)
Brain Research Institute | Center for microcroscopy and data analysis
University of Zurich
Winterthurerstrasse 190
CH-8057 Switzerland