Immunohistochemistry (IHC)

Immunohistochemistry (or IHC) is a technique that utilizes antibodies (primary and secondary) conjugated to proteins to help visualize and localize those specific proteins in a tissue sample. This process is typically done using thin tissue sections. Immunohistochemistry can be completed in a few steps. First, the tissue sample must be “fixed” or preserved using chemicals like paraformaldehyde or formalin. Fixed tissue stabilizes the structural integrity of cells and proteins, preventing them from deteriorating or changing during the rest of the IHC process. Tissue samples must then be sectioned to get very thin slices, typically 5µm to 50µm thick. Primary antibodies against the target protein are added to tissue slices, followed by secondary antibodies. The secondary antibodies may have a fluorophore to allow for visualization of the specific protein during imaging.

Because immunohistochemistry requires thin sections of tissue, it is crucial to be able to obtain consistent, reliable tissue slices of uniform thickness. Getting such slices can be done using vibrating microtomes (vibratomes) and rotary microtomes.

Common problems with tissue slices for immunohistochemistry

Tissue slice with coarse surface chatter

A few problems can be encountered with making thin tissue slices for immunohistochemistry. First, the most commonly encountered problem is getting “thick-and-thin” sections while slicing fixed tissue. This means that you get one thin tissue slice (or none at all), followed by a thicker tissue slice. Therefore, your tissue slices have inconsistent thicknesses which can alter the accurate visualization of proteins through IHC. 

A second common problem is getting chattermarks on tissue slices. This means you see cutting artifacts on the surface of sections that can interfere with IHC protein staining.

Making better tissue slices for immunohistochemistry

Compresstome® Vibrating Microtome

The quality of your experiments will depend on the quality of your tissue slices. The Compresstome® vibrating microtome has been scientifically demonstrated to create more consistent and reliable thin tissue sections for immunohistochemistry compared to other vibratomes. How does the Compresstome® do this? Our vibrating microtome produces tissue slices of consistent thicknesses without chattermarks by:

    • Stabilizing the brain tissue during the cutting process through 360-degree agarose embedding
    • Allowing for faster slicing, which helps save time for serial sectioning
    • Utilizing a high-frequency vibrating mechanism to reduce or eliminate chattermarks
    • Reducing chattermarks by eliminating the Z-axis deflection of the cutting blade using our patented Auto Zero-Z technology

Comparison of tissue slices sectioned with a Compresstome® vibrating microtome vs. another leading market vibratome.


Here, you can see the significant reduction in chattermarks in tissues slices produced with our Compresstome® tissue slicer versus sections (A, C). Slices made at the same cutting speed and oscillation on another market vibratome produces chattermarks on the surface of tissue slices.

Rotary Microtome

Rotary microtomes are used extensively for cutting fixed tissue samples, typically embedded in paraffin wax or resin. Our rotary microtomes have a specimen head that firmly holds tissue sample cassettes, allowing for stability during cutting. This helps reduce chattermarks and allows for sectioning of tissue slices down to 1µm thickness. The speed of cutting on a rotary microtome also allows you to obtain “ribbons” of consecutive tissue slices, making it easier for plating onto glass slides.

Real lab examples of our microtomes for immunohistochemistry

“3D” use of animal tissues in experimental design

Have you wondered how one mouse brain may be used for multiple experiments? Come discover the strategy behind using animal tissues for multi-use research experiments, so that your tissue samples can go further. Dr. Yiying Zhang from Harvard Medical School and Massachusetts General Hospital is our guest webinar speaker. For this Precisionary webinar, Dr. Zhang will discuss a “3D” use of animal tissues in planning experimental designs in academic research.

References and Protocols

Microtomes from Precisionary Instruments have been used by labs around the world, and cited in hundreds of peer-reviewed publications. Explore these references by experiment, animal model, and organ system. For convenience, we also put together key experimental protocols to help you.