A sample vitrification system includes a capsule structure configured for carrying a biological sample within a compartment while the sample is subjected to ultra-rapid freezing by way of a cryogenic coolant jet, and while the sample is exposed to pulsed microwave radiation in a manner that disrupts water molecule pentamer formation and which disrupts initial ice crystal nucleation events within the compartment within tens of microseconds to provide a vitrification depth within the compartment of tens of microns or more. The sample can reside between a very high thermal conductivity substrate and a cover. The cryogenic coolant jet is applied to the substrate from beneath the sample. The cover can carry a set of microwave excitation elements configured for providing microwave radiation to internal portions of the compartment. Portions of the capsule structure's interior can be imaged during microwave assisted jet freezing, such as by way of an optical microscope.