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3D reconstruction of the fiber connectivity of the rat brain at microscopicscale enables gaining detailed insight about the complex structuralorganization of the brain. We introduce a new method for registration and 3Dreconstruction of high- and ultra-high resolution (64 $\mu$m and 1.3 $\mu$mpixel size) histological images of a Wistar rat brain acquired by 3D polarizedlight imaging (3D-PLI). Our method exploits multi-scale and multi-modal 3D-PLIdata up to cellular resolution. We propose a new feature transform-basedsimilarity measure and a weighted regularization scheme for accurate and robustnon-rigid registration. To transform the 1.3 $\mu$m ultra-high resolution datato the reference blockface images a feature-based registration method followedby a non-rigid registration is proposed. Our approach has been successfullyapplied to 278 histological sections of a rat brain and the performance hasbeen quantitatively evaluated using manually placed landmarks by an expert.

Towards ultra-high resolution 3D reconstruction of a whole rat brain from 3D-PLI data