What are Vibrating Microtomes?

Before the tissue slicers, scientists had to manually cut biological materials with their tools, which required meticulous work for great precision. With the invention of the tissue slicers, mainly the microtomes (from the Greek mikros, meaning “small,” and temnein, meaning “to cut”), biological specimens such as sensitive tissues, brain slices, and thin layers of bones were easily cut into extremely thin sections. Therefore, today, microtomes are widely used cutting tools in preclinical laboratories to produce extremely thin slices of the materials.

Microtomes vary depending on the requirements of the experiment and the appropriate application for slicing tissue, and these can be classified into manual, automatic, and semi-automatic[1]. Even though there are a variety of microtomes such as vibrating, rotary, cryostat, sledge, and laser, they all have the fundamental parts: microtome body, knife attachment, blade, and material or tissue holder.

In most microtomes, the knife remains stationary, and a section is sliced by advancing the material holder towards the blade. The section can be cut vertically or horizontally, and the advanced mechanism ensures joint cutting. Therefore, the material holder moves the exact distance that selected scale on the microtome body[1][2].

This article will investigate vibrating microtomes that are used to slice tissues with a vibrating blade. Vibrating microtomes have a vibrating blade that does the cutting procedure instead of a stationary blade which requires more pressure. Thus, the researcher can arrange the amplitude of vibration by increasing or decreasing the electrical voltage imposed on the knife[1][2].

Applications of Vibrating Microtomes

The vibrating microtome accurately cuts tissue under physiological conditions without freezing or embedding. These precise instruments maintain cell morphology, enzyme activity, as well as cell viability of the tissue.

The other useful feature of the vibrating microtome is that scientists can section fresh biological materials without additional processing, fixating, or freezing[2]. Generally, specimens must be fixated chemically and/or embedded in paraffin, wax, or epoxy and/or frozen using the cooling chamber before the slicing procedure[3]. Other microtome types require hardening the tissue by freezing or paraffin embedding.

We can list the other advantages of using vibrating microtomes as:

  • Not fracturing cell membranes (freezing frequently does that); cytosol remains in cells
  • Having sharper stains with no cytosol in the extracellular tissue
  • Keeping cells alive (tissue may be oxygenated under media during cutting)
  • Have a quick setup, and glue tissue to the platform. Thus no encapsulation is required/

Vibrating microtomes’ capability to sustain the viability of the tissue, enzyme activity, and structure of the cell, makes these slicing tools one of the most preferable and used tools in enzyme histochemistry and rodent neuroscientific research.

Examples of Vibrating Microtomes in Preclinical Research

As stated above, vibrating microtomes are widely used in histochemistry. In a study where researchers investigated the histochemical reactions, the sections were sliced at 10 μm by microtome for light microscopy. Later on, the diencephalon and mesencephalon of the mice’s brain was cut at 70 μm via a vibrating microtome for the electron microscopy[4].

In another study that used electron microscopy, experimenters perfused adult mice for 10 minutes and kept mice brains at 4°C overnight to investigate different brain sections. Then, brain sections were sliced 50 μm thick by a vibrating microtome. Subsequently, anesthetized mice brains’ were sliced with a vibrating microtome[5].

Apart from histochemistry, neuroscientific research in rodents also use vibrating microtomes for different brain sections. For example, a rodent neuroscientific research investigated brain sections that were cut from substantia nigra and striatum 50 μm thick by vibrating microtome[6].

Another research included anesthetized mice’s sagittal brain sections that were cut 50 μm thick with a vibrating microtome[7]. (In this research[7], experimenters also uses vibrating microtome for investigating 400 μm thick acute slices on an upright fluorescence microscope.)

In another study that explores the early-life neonatal inflammation in rodents, anesthetized and perfused mice brains are fixed and coronally cut 40 μm by a vibrating microtome to be stained with toluidine blue.

To perform electrophysiological analysis of tissue, the slices containing basolateral amygdala and coronal brain sections are cut 400 μm thick using the vibrating microtome in ice-cold oxygenated artificial cerebrospinal fluid.

In addition, the brains of anesthetized mice are decapitated, and a 400 μm thick coronal section is cut with a vibrating microtome to record the whole cell[8]. In a different study where female mice brains were cut via vibrating microtome 400 μm thick in coronal sections through the nucleus accumbens and ventral tegmental area[9].

In another rodent model setting, mice brains were exposed to transcardial perfusion overnight and immersion-fixation, and were sectioned with 50 μm with a vibrating microtome. When the polymerization process of the resin was completed, 60 nm cuts from interesting areas were obtained, separated from flat-embedded vibrating microtome, and exposed to a re-embedding procedure to be stained and examined at transmission electron microscopy[10].


Various studies, as listed above, have shown that vibrating microtomes are extremely useful tools for slicing biological materials accurately and efficiently with no requirement for additional processes. These cutting tools are used efficiently without distorting and contaminating the tissue structure in rodent research, where precise slicing of the tissue matters the most.


  1. Mastering the Microtome https://conductscience.com/mastering-the-microtome/
  2. Mohammed, F., Arishiya, T. F., & Mohamed, S. (2012). Microtomes and microtome knives. Annals of Dentistry University of Malaya19(2), 43-50.
  3. Sousa, A. L., .., Tranfield, E. M. (2021). The Histo-CLEM Workflow for tissues of model organisms. In Methods in Cell Biology, 162, 13-37.
  4. Cardy, J. D., & Firth, J. A. (1993). Adenosine triphosphate-lead histochemical reactions in ependymal epithelia of murine brains do not represent calcium transport adenosine triphosphatase. The Histochemical Journal25(4), 319-324.
  5. Carstens, K. E., .., & Dudek, S. M. (2016). Perineuronal nets suppress plasticity of excitatory synapses on CA2 pyramidal neurons. Journal of Neuroscience36(23), 6312-6320.
  6. Jones, I. W., Bolam, J. P., & Wonnacott, S. (2001). Presynaptic localisation of the nicotinic acetylcholine receptor β2 subunit immunoreactivity in rat nigrostriatal dopaminergic neurons. Journal of Comparative Neurology439(2), 235-247.
  7. Chuhma, N., …, & Rayport, S. (2011). Functional connectome of the striatal medium spiny neuron. Journal of Neuroscience31(4), 1183-1192.
  8. Zhong, H., …, & Zhou, R. (2022). Neonatal inflammation via persistent TGF-β1 downregulation decreases GABAAR expression in basolateral amygdala leading to the imbalance of the local excitation-inhibition circuits and anxiety-like phenotype in adult mice. Neurobiology of Disease169, 105745.
  9. Cordeira, J. W., …, & Rios, M. (2010). Brain-derived neurotrophic factor regulates hedonic feeding by acting on the mesolimbic dopamine system. Journal of neuroscience30(7), 2533-2541.
  10. Polavarapu, R., .., & Yepes, M. (2005). Tumor necrosis factor-like weak inducer of apoptosis increases the permeability of the neurovascular unit through nuclear factor-κB pathway activation. Journal of Neuroscience25(44), 10094-10100.