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Short answer
Cryosectioning is the cutting of thin sections from frozen tissue inside a cryostat, a microtome housed in a refrigerated chamber. The sections are picked up on glass slides for staining or other analysis. What makes it a managed process rather than a single instrument task is that the result depends on several specified conditions: chamber and specimen temperature, block equilibration, freezing compound, blades, slides and cold slide storage.
Definition and scope
In the university core-facility protocols published by the University of Auckland and East Carolina University, cryosectioning starts from fresh frozen tissue embedded in a freezing medium and ends with sections mounted on slides and stored cold. The cutting instrument is the cryostat; the cutting mechanism is a microtome operating inside the cold chamber. The cryostat vs. microtome comparison covers how the two terms relate, so this page concentrates on the technique and what it requires.
The scope here is general information for researchers and lab or clinic staff. It is not a bench protocol, and the settings quoted below are examples of what individual facilities specify for their own instruments, not recommendations.
How cryosectioning is used in practice
The two protocols describe the same workflow in the same order: bring the cryostat to working temperature, prepare a frozen block on a specimen holder (chuck) using a freezing compound, trim into the tissue, cut sections, mount them on slides, store the slides cold, then clean the chamber and tools. For what happens to sections afterwards, see the CASRAI guide to immunohistochemistry protocol, controls and troubleshooting.
Where two core-facility protocols agree and differ
The table compares the University of Auckland Histology Laboratory protocol (Leica CM3050S cryostat) with the East Carolina University Anatomy and Cell Biology core protocol (Epredia HM525 NX cryostat). The values belong to those facilities and instruments.
| Topic | University of Auckland | East Carolina University |
|---|---|---|
| Warm-up or equilibration | Set up 30 minutes before sectioning for equilibration | Frozen blocks sit in the cryostat about 15 minutes (or longer) to reach sectioning temperature |
| Temperature setting | Chamber temperature 1 to 3 °C cooler than object (specimen) temperature | Temperature chosen for the tissue and section thickness; temperatures below -24 °C must be requested in advance |
| Trimming thickness | 30 µm | Usually 30 µm, then switch to the chosen section thickness |
| Room-temperature items | Materials left at room temperature while tools go inside the cryostat | Specimen holders must be at room temperature before use |
| Angle setting | Microtome angle at 5° | Blade angle set at 10° for the blade in use |
| Slide type | Superfrost Plus glass slides | Silane or poly-L-lysine treated slides, or positive-charge “Plus” slides |
| Slide storage | Chilled box | All slides stored between -20 and -80 °C; unfixed-tissue slides go in a slide box inside the cryostat |
| Blocks after cutting | Not specified | Wrapped in Parafilm and stored at -80 °C |
| Cryostat after use | Set to -15 °C; tissue not left in the cryostat overnight because of the defrost cycle | Not specified |
Two points stand out. Both facilities trim at 30 µm and both specify room-temperature specimen holders or materials; the equilibration times differ, 30 minutes of set-up at Auckland and about 15 minutes for frozen blocks at ECU. The angle values differ because they describe different settings on different instruments, which is why a protocol written for one cryostat does not transfer unchanged to another.
Related concepts
Cryosectioning sits between tissue handling and downstream analysis. Cold-storage practice for the finished slides and blocks is covered in -80 °C freezer management.
Where it matters for labs, clinics and supply decisions
A facility that offers cryosectioning has to keep a defined set of items on hand. The list below comes from the Auckland and ECU protocols and says nothing about brands, grades or quantities.
- Freezing and embedding: OCT or similar freezing compound (called “frozen section compound” in the Auckland protocol), cryomolds and specimen discs or chucks.
- Cutting: disposable blades (the Auckland protocol uses disposable knife blades; ECU notes razor blades may be kept at room temperature), an anti-roll plate, and artist brushes for handling sections and clearing debris.
- Mounting and storage: charged or treated slides and a slide box to hold slides with sections.
- Handling and cleaning: stainless-steel forceps, ethanol for wiping the chamber, diluted disinfectant for tools, and a sharps container for used blades.
- Protection: lab coat, safety glasses and gloves.
Operational points the protocols state explicitly: lock the hand wheel or handle whenever not sectioning, cover the exposed blade with the anti-roll plate, treat the blade as very sharp, and discard used blades to a sharps bin (see sharps disposal regulations for laboratories). Instrument time is also a managed resource: the Auckland protocol begins with reserving the cryostat in a record book, and ECU asks users who need temperatures below -24 °C to arrange it before the session.
Common misunderstandings
A cryostat is not a freezer for storing tissue
The Auckland protocol advises against leaving tissue in the cryostat overnight because of the defrost cycle. Long-term storage of blocks in the ECU protocol is at -80 °C, outside the cryostat.
One protocol does not fit every instrument
Settings such as angle, temperature range and trimming thickness are tied to the instrument, blade and facility. The table above shows two sets of values that are both correct for their own setting.
Room-temperature and cold items are both deliberate
ECU requires chucks at room temperature, brushes and microtome blades kept in the cryostat, and frozen blocks left in the cryostat to reach sectioning temperature.
FAQ
What is cryosectioning?
It is the cutting of thin sections from frozen tissue in a cryostat and mounting them on slides, as described in the University of Auckland and East Carolina University protocols.
Is a cryostat the same as a microtome?
No. A cryostat is a refrigerated chamber that contains a microtome. See the cryostat vs. microtome comparison.
What consumables does cryosectioning need?
The Auckland and ECU protocols list freezing compound (OCT), cryomolds, specimen discs or chucks, treated or positive-charge slides, blades, brushes, forceps, slide boxes and personal protective equipment.
How should the finished slides be stored?
The ECU protocol states that all slides should be stored between -20 and -80 °C. The Auckland protocol stores them in a chilled box.
Sources
- University of Auckland, School of Medical Sciences Histology Laboratory, “Cryostat Sectioning of Frozen Samples” (Leica CM3050S protocol), checked 29 October 2026: https://www.auckland.ac.nz/content/dam/uoa/auckland/fmhs/sms/anatomy/histology/Cryostat-sectioning-of-frozen-samples.pdf
- East Carolina University, Anatomy and Cell Biology, “General Frozen Sectioning Protocol, Epredia HM525 NX Cryostat”, checked 29 October 2026: https://anatomy-cellbiology.ecu.edu/wp-content/pv-uploads/sites/7/Frozen-Sectioning-Instructions-HM525-Cryostat.pdf
Both documents are institutional core-facility protocols, not consensus standards. Check the manual for your own instrument and your institution’s safety rules before setting up a cryostat.
