Elastic registration of high-resolution 3D PLI data of the human brain

We introduce a new approach for the elastic registration of high-resolution 3D polarized light imaging (3D PLI) data of histological sections of the human brain. For accurate registration of different types of 3D PLI modalities, we propose a novel intensity similarity measure that is based on a least-squares formulation of normalized cross-correlation. Moreover, we present a fully automatic registration pipeline for rigid and elastic registration of high-resolution 3D PLI images with a blockface reference including a preprocessing step. We have successfully evaluated our approach using manually obtained ground truth for five sections of a human brain and experimentally compared it with previous approaches. We also present experimental results for 60 brain sections.