Atlas-guided Histology Reconstruction of Mouse Brain

Histology acquisition often introduces tissue distortions that prevent a smooth 3D reconstruction from being built. In this paper, we propose a method of atlas-guided optimization to the piecewise registration scheme we developed previously. It takes the information of several consecutive slices in a neighbourhood into account. In order to achieve an accurate anatomic presentation, we run the method iteratively with the assistance from a pre-segmented brain atlas. The registration parameters are optimized to accommodate different brain sub-regions, e.g. cerebellum, hippocampus, etc. The results are evaluated by both visual and quantitative approaches. The proposed method has been proved to be robust enough for reconstructing an accurate and smooth mouse brain volume.