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The influence of short-term microwave irradiation on the process of seed extraction from Scots pine cones was investigated in this study. Cones from the Brzesko Forest District (near Kraków, southern Poland) were collected in 2015. The size and changes in the mass of cones during the process of seed extraction, as well as the relations between these parameters, were analyzed. Changes in water content and drying rate of cones were modeled using suitable mathematical equations. The thermal balance of the whole process of seeds extraction was calculated, and the heat necessary to extract the seeds was determined. Cones were initially exposed to 2.45 GHz microwaves with a power of 800 W for either 5 or 15 seconds. Subsequently, cones were placed in a circulating air oven and seeds extracted under convective drying at a constant temperature of 50 ± 0.1 °C. We found that seeds from cones subjected to 15-seconds microwave radiation were dramatically damaged, while no significant difference were found in germination and quality of seeds between cones subjected to the 5-seconds microwave pre-treatment and control cones, both yielding first-class quality seeds (mean germination capacity > 90%). The results of this study could help developing microwave-dryer control algorithms to support the automated process of cone seed extraction in large-capacity extraction plants. [ABSTRACT FROM AUTHOR]