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This work deals with the calibration of industrial robots operating at sub-micrometric precision. We demonstrate that the cutting-forces generated by the robot manufacturing process cause a significant deformation of the robot geometry, lo- wering its absolute accuracy. Then, we propose a way of studying and modeling such deformations, in order to compen- sate them during the robot usage. We have taken the micro electro-discharge machining process on the robot Agietron micro-nano as a case study and we have used an ultra high-precision measuring system to evaluate the deformations due to cutting-forces. Finally, we have built a mathematical model of the robot physical behavior and we have implemented it in the robot controller, in order to compensate the deformations in real-time.