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In this paper, we present a versatile framework to enable autonomous flights of a Micro Aerial Vehicle (MAV) which has only slow, noisy, delayed and possibly arbitrarily scaled measurements available. Using such measurements directly for position control would be practically impossible as MAVs exhibit great agility in motion. In addition, these measurements often come from a selection of different onboard sensors, hence accurate calibration is crucial to the robustness of the estimation processes. Here, we address these problems using an EKF formulation which fuses these measurements with inertial sensors. We do not only estimate pose and velocity of the MAV, but also estimate sensor biases, scale of the position measurement and self (inter-sensor) calibration in real-time. Furthermore, we show that it is possible to obtain a yaw estimate from position measurements only. We demonstrate that the proposed framework is capable of running entirely onboard a MAV performing state prediction at the rate of 1 kHz. Our results illustrate that this approach is able to handle measurement delays (up to 500ms), noise (std. deviation up to 20 cm) and slow update rates (as low as 1 Hz) while dynamic maneuvers are still possible. We present a detailed quantitative performance evaluation of the real system under the influence of different disturbance parameters and different sensor setups to highlight the versatility of our approach.