Preliminary Steps: Before sectioning a sample in the cryostat, the user must prepare both the sample and the cryostat. Prepping the cryostat may consist of running a disinfection protocol and then setting the desired chamber temperature. While the chamber is cooling, the pathologist may then freeze the tissue sample. Tissue must be frozen immersed in a specialized solution to support its cellular morphology during sectioning; if its cellular structure crumbles, the tissue can't be stained and examined properly.
Microtomy: Once the sample is embedded and the chamber is at its set temperature, the pathologist can then mount the sample to its holder on the microtome and begin sectioning it. Sectioning may be performed manually with the handwheel on the side of the cryostat or, in the case of more sophisticated units, with a motorized microtome that sections automatically.
Cleanup: Microtomy can be messy; after sectioning a sample there may be small scraps littering the chamber. The user can sweep up the shavings manually or, if waste trays are installed, empty the trays. If one decides to remove the tray, they must allow the chamber temperature to equilibrate with the room's ambient temperature — otherwise, the tray will condensate when removed from the chamber and then freeze to the chamber once placed back in.