A computer implemented medical method of calibrating a medical instrument is presented. In particular, this method calculates a position of the instrument tip model (13) within the indentation model (23), associated with an estimated position of the instrument tip (11) within the indentation (21) and calibrates the medical instrument (10), thereby using the determined position of the instrument tip model (13). One technical effect of the invention is that the position of any arbitrary medical instrument tip, in particular in an indentation of a calibration device, can be estimated. This is an improvement of accuracy in view of the generic approach of using the same reference point of the indentation of the calibration device for any arbitrary medical instrument tip. For this purpose a virtual model of a shape of a medical instrument, in particular the instrument tip, is matched onto a virtual model of a shape of a calibration device, in particular an indentation of the calibration device.
