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

3D reconstruction of the fiber connectivity of the rat brain at microscopic scale enables gaining detailed insight about the complex structural organization of the brain. We introduce a new method for registration and 3D reconstruction of high- and ultra-high resolution (64 $\mu$m and 1.3 $\mu$m pixel size) histological images of a Wistar rat brain acquired by 3D polarized light imaging (3D-PLI). Our method exploits multi-scale and multi-modal 3D-PLI data up to cellular resolution. We propose a new feature transform-based similarity measure and a weighted regularization scheme for accurate and robust non-rigid registration. To transform the 1.3 $\mu$m ultra-high resolution data to the reference blockface images a feature-based registration method followed by a non-rigid registration is proposed. Our approach has been successfully applied to 278 histological sections of a rat brain and the performance has been quantitatively evaluated using manually placed landmarks by an expert.Comment: 9 pages, Accepted at 2nd International Workshop on Connectomics in NeuroImaging (CNI), MICCAI'201

ELASTIC REGISTRATION OF HIGH-RESOLUTION 3D PLI DATA OF THE HUMAN BRAIN

We introduce a new approach for the elastic registration ofhigh-resolution 3D polarized light imaging (3D PLI) data ofhistological sections of the human brain. For accurate regis-tration of different types of 3D PLI modalities, we proposea novel intensity similarity measure that is based on a least-squares formulation of normalized cross-correlation. More-over, we present a fully automatic registration pipeline forrigid and elastic registration of high-resolution 3D PLI imageswith a blockface reference including a preprocessing step. Wehave successfully evaluated our approach using manually ob-tained ground truth for five sections of a human brain and ex-perimentally compared it with previous approaches. We alsopresent experimental results for 60 brain sections