In functional neurosurgery, there is a need for accurate localisation of the functional targets. One example is given by Parkinson's disease. The surgical intervention is based on the introduction of electrodes in the subthalamic nucleus. This nucleus is targeted on pre-operative stereotactic MR acquisitions. But MR imaging of the basal ganglia is intrinsically limited, first by image resolution, and second by the relationship between the measured MR signal and the real anatomy, not clearly understood. On the other hand, detailed and accurate cartography of the basal ganglia can be performed on post mortem histological serial sections. Indeed, histology overcomes the limitations of MR imaging. Moreover, staining of histological sections allows to recover functional information. But histology is by nature two-dimensional. An histological data set consists in a series of disorganized serial sections, as three dimensional shape information was lost during sectioning. Therefore, the first step toward the integration of histological and MR information is to perform a reliable three dimensional reconstruction of the histological volume. Acquisition of photographs during sectioning, showing the histological sections before sectioning, as well as fiducial landmarks, allows to reconstruct a volume with three dimensional integrity, and is further used to register each histological section with its corresponding optical section.