Most tornadoes have their winds estimated based on damage, on some occasions Doppler Radar used to measure wind speed when it is possible. The scientists send a beam of microwaves from the radar dish towards the tornado. The microwaves reflect off of the debris, dirt, and other items swirling around inside of it. Another method is a wind anemometer. The cups spin on top of the device, and measure wind speed. Direct intercepts with instruments are rare, however.
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