This title appears in the Scientific Report :
2018
Please use the identifier:
http://dx.doi.org/10.1016/j.neuroimage.2018.06.084 in citations.
Please use the identifier: http://hdl.handle.net/2128/19686 in citations.
Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution
Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution
To understand the spatial organization as well as long- and short-range connections of the human brain at microscopic resolution, 3D reconstruction of histological sections is important. We approach this challenge by reconstructing series of unstained histological sections of multi-scale (1:3 μm and...
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Personal Name(s): | Ali, Sharib (Corresponding author) |
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Wörz, Stefan / Amunts, Katrin / Eils, Roland / Axer, Markus / Rohr, Karl (Last author) | |
Contributing Institute: |
JARA - HPC; JARA-HPC Strukturelle und funktionelle Organisation des Gehirns; INM-1 |
Published in: | NeuroImage, 181 (2018) S. 235-251 |
Imprint: |
Orlando, Fla.
Academic Press
2018
|
DOI: |
10.1016/j.neuroimage.2018.06.084 |
PubMed ID: |
30018015 |
Document Type: |
Journal Article |
Research Program: |
3D Reconstruction of Nerve Fibers in the Human, the Monkey and the Rodent Brain Supercomputing and Modelling for the Human Brain Human Brain Project Specific Grant Agreement 2 Connectivity and Activity |
Subject (ZB): | |
Link: |
Restricted Restricted Published on 2018-11-01. Available in OpenAccess from 2019-11-01. Published on 2018-11-01. Available in OpenAccess from 2019-11-01. |
Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/19686 in citations.
To understand the spatial organization as well as long- and short-range connections of the human brain at microscopic resolution, 3D reconstruction of histological sections is important. We approach this challenge by reconstructing series of unstained histological sections of multi-scale (1:3 μm and 64 μm) and multi-modal 3D polarized light imaging (3D-PLI) data. Since spatial coherence is lost during the sectioning procedure, image registration is the major step in 3D reconstruction. We propose a non-rigid registration method which comprises of a novel multi-modal similarity metric and an improved regularization scheme to cope with deformations inevitably introduced during the sectioning procedure, as well as a rigid registration approach using a robust similarity metric for improved initial alignment. We also introduce a multi-scale feature-based localization and registration approach for mapping of 1:3 μm sections to 64 μm sections and a scale-adaptive method that can handle challenging sections with large semi-global deformations due to tissue splits. We have applied our registration method to 126 consecutive sections of the temporal lobe of the human brain with 64 μm and 1:3 μm resolution. Each step of the registration method was quantitatively evaluated using 10 different sections and manually determined ground truth, and a quantitative comparison with previous methods was performed. Visual assessment of the reconstructed volumes and comparison with reference volumes confirmed the high quality of the registration result. |