New Microscope Reveals Stunning Detail

Fabian Voigt at the Brain Research Institute of UZH has developed a novel light-sheet microscope that allows high-throughput imaging of large volumes of cleared biological tissue. This mesoscale selective plane illumination microscope (mesoSPIM) is now published in Nature Methods as an open-source resource for the community, providing detailed information on how to build a mesoSPIM.

The first time you see a well-cleared tissue sample is a magic moment: after several chemical processing steps, a highly scattering object turns perfectly transparent. For example, a mouse brain, in which light microscopes normally cannot even look deeper than a fraction of a millimeter, becomes so clear that you can see all the way through. This is the power of so-called ‘clearing techniques’, a class of tissue processing methods that reduce the scattering of light in fixed samples. One of the most common approaches is to remove lipids from the sample: The high lipid content in the brain makes it opaque and gives it a greyish tint. If the majority of lipids can be extracted from the sample without damaging its anatomy, for example by using organic solvents, a see-through brain results. Using tissue clearing, researchers can do away with traditional tissue sectioning and image a sample in its entirety. To image cleared samples, a technique known as light-sheet microscopy can be used: Instead of cutting the sample with a knife, a thin sheet of light illuminates an ‘optical section’ which is recorded by a camera. Digital reconstruction of the sample is then a matter of minutes compared to tissue slicing which can take hours.

Unsatisfied with commercial microscope options

Four years ago, Fabian Voigt and Daniel Kirschenbaum (USZ), PhD students in the laboratories of Fritjof Helmchen (UZH) and Adriano Aguzzi (USZ) were looking for a commercial microscope that could image cleared mouse brains. They tested various instruments, but none proved satisfactory: Some had insufficient resolution, some lacked ergonomics when handling samples, others were too slow. To address these issues, Fabian Voigt started to develop a custom light-sheet microscope that would allow imaging a whole mouse brain with 6.5 µm resolution within 8 minutes. The first prototypes of this instrument were installed at the Brain Research Institute and Institute of Neuropathology (USZ) in 2017. After showing the setup to colleagues, the team realized that many research groups faced the same problems: Tissue clearing techniques steadily improved, but microscope companies were too slow to innovate and provide the community with up-to-date instrumentation.

A world-wide initiative

Therefore, Voigt and colleagues started the mesoSPIM initiative ( An open-source resource that allows interested research groups to build highly capable microscopes for imaging cleared samples themselves. In their publication, the team describes the capabilities of the instrument and demonstrates imaging samples ranging from fruit flies, mouse brains, to human neocortex, the outer layer of the human brain. As of today, many institutions have decided to install a mesoSPIM instrument. Thanks to the spirit of open science, the mesoSPIM initiative has thus evolved into a world-wide collaboration.

Microscopes are now in operation at

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

For stunning videos and images go to the

Image: Vascular network of the mouse brain, as represented by the mesoSPIM