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2018 | OriginalPaper | Chapter

Towards Ultra-High Resolution 3D Reconstruction of a Whole Rat Brain from 3D-PLI Data

Authors : Sharib Ali, Martin Schober, Philipp Schlömer, Katrin Amunts, Markus Axer, Karl Rohr

Published in: Connectomics in NeuroImaging

Publisher: Springer International Publishing

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Abstract

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 \(\upmu \)m and 1.3 \(\upmu \)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 \(\upmu \)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.

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next chapter FOD-Based Registration for Susceptibility Distortion Correction in Connectome Imaging
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Metadata
Title
Towards Ultra-High Resolution 3D Reconstruction of a Whole Rat Brain from 3D-PLI Data
Authors
Sharib Ali
Martin Schober
Philipp Schlömer
Katrin Amunts
Markus Axer
Karl Rohr
Copyright Year
2018
Book
Connectomics in NeuroImaging

Print ISBN: 978-3-030-00754-6

Electronic ISBN: 978-3-030-00755-3

Copyright Year: 2018

DOI
https://doi.org/10.1007/978-3-030-00755-3_1

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