The project aims to generate an atlas of the human brain similar to the Morel’s stereotactic atlas of human thalamus and basal ganglia [1], which belongs to the best atlases. The combination of the Morel atlas with the data acquired and treated will provide a comprehensive generic dataset of the human brain to be used first for minimally invasive, MR-guided focused ultrasound therapies at the Children’s University Hospital in Zürich.

The multimodal data acquisition includes first the MRI of the brain of a body donated to the University of Basel post mortem but still in the cranium. After extraction from cranium the brain will be scanned again to determine the expected global and local shrinkage as the result of formalin penetration and fixation. Subsequently, the brain will be divided into blocs for high-resolution synchrotron radiation-based micro computed tomography in phase and absorption contrast mode. Preliminary results indicate that grating interferometry provides superior contrast even for the thalamus. The thalamus exhibits almost no absorption contrast and is, therefore, one of the most ambitious challenges in X-ray tomography. Finally, the blocs will be cryo-sectioned and stained for histological imaging as established in the Department of Neurosurgery at the University Hospital in Zürich.

The obtained data of GB-size will be rigidly and non-rigidly registered in order to correct the shrinkage and the local deformations generated by the preparation procedure necessary for the high-resolution imaging down to the cellular level. Special attention will be drawn to the registration of the set of histological 2D slices with the 3D SRµCT data, which is necessary because of the numerous degrees of freedom.

The comprehensive generic brain atlas with a spatial resolution down to sub-micrometer level, which is expected to closely resemble to the in vivo situation, should be made available for educational purposes and, more important, to support the successful planning of non-invasive patient treatments in the field of neurosurgery.