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Safely imaging cleared tissues

05 May 2020

Researchers and engineers develop a reusable imaging chamber that is compatible with organic solvents.

Acquiring microscopic images through large tissues is limited by the opaqueness of these samples. In order to penetrate many layers of cells and see deep inside tissues, researchers have come up with various ways to create a uniform refractive index throughout the sample, rendering it virtually transparent. These methods, known as tissue clearing, made it possible to image large and complex 3D structures with unprecedented depth and resolution.

One such method was developed by scientists at the IMP - Research Institute of Molecular Pathology, together with colleagues at IMBA - Institute of Molecular Biotechnology (Masselink et al., 2019). The protocol is easy to apply and can be used to clear a wide range of tissues in several species, including Drosophila melanogaster, zebrafish, axolotl and Xenopus laevis. What sets it apart from other methods that are based on organic solvents is its use of the non-toxic substance ethyl cinnamate as clearing agent.

While a powerful method, this procedure still provides several challenges. Organic solvents can be dangerous to equipment and personnel. Another concern is that for the existing clearing methods there are only few available dishes compatible with the reagents used. These disposable plastic dishes provide insufficient protection and they constitute a significant ecological footprint that goes against the declared aim to reduce lab-waste. 

A group of researchers and engineers at the IMP has now taken the development one step further. Postdoc Wouter Masselink from the Tanaka-lab teamed up with scientific workshop leader Martin Colombini and microscopy specialist Pawel Pasierbeck to devise a safe and reusable imaging chamber that would make shared microscope facilities more accepting of allowing cleared tissue samples on their scopes.

In a technical report published in the current issue of Microscopy, Colombini et al. describe the development of a sample chamber that is resistant to all commonly used organic solvents. Furthermore, the universal system is compatible with a wide range of equipment due to universal microscope mounts. The chamber is easy to assemble and significantly improves the working environment in a central microscopy unit. To encourage the use of these chambers, the design is publicly available for download. The Austrian Science Fund FWF supported the work.


Martin Colombini, Pawel Pasierbek, and Wouter Masselink. A safe and reusable imaging chamber compatible with organic solvents. Microscopy, 25 April 2020

Wouter Masselink, Daniel Reumann, Prayag Murawala, Pawel Pasierbek, Yuka Taniguchi, François Bonnay, Katharina Meixner, Jürgen A. Knoblich and Elly M. Tanaka. Broad applicability of a streamlined ethyl cinnamate-based clearing procedure. Development (2019) 146.


STP files of the chamber design