Does anyone know how to do the run time calibration for MPU9250 ?

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    By that you mean finding the calibration matrix for each sensor? Like offsets, gains, hard iron corrections? – brtiberio Feb 18 '16 at 15:34

I used this script to calibrate the MPU6050, which is the same as the MPU9250 minus the digital compass. This guide explains how to calibrate the MPU9250's magnetometer.

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