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Non-rigid landmark-based large-scale image registration in 3-D reconstruction of mouse and rat kidney nephrons.

Authors
  • Zhang, Yan-Ling1
  • Chang, Shi-Jie2
  • Zhai, Xiao-Yue3
  • Thomsen, Jesper Skovhus4
  • Christensen, Erik I5
  • Andreasen, Arne6
  • 1 Department of Rheumatology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China(1); Department of Biomedicine - Anatomy, Aarhus University, Aarhus, Denmark. Electronic address: [email protected] , (China)
  • 2 Department of Biomedical Engineering, China Medical University, Shenyang, China. Electronic address: [email protected] , (China)
  • 3 China Medical University, Department of Histology and Embryology, China Medical University, Shenyang, China. Electronic address: [email protected] , (China)
  • 4 Department of Biomedicine - Anatomy, Aarhus University, Aarhus, Denmark. Electronic address: [email protected] , (Denmark)
  • 5 Department of Biomedicine - Anatomy, Aarhus University, Aarhus, Denmark. Electronic address: [email protected] , (Denmark)
  • 6 Department of Biomedicine - Anatomy, Aarhus University, Aarhus, Denmark. Electronic address: [email protected] , (Denmark)
Type
Published Article
Journal
Micron (Oxford, England : 1993)
Publication Date
Jan 01, 2015
Volume
68
Pages
122–129
Identifiers
DOI: 10.1016/j.micron.2014.10.002
PMID: 25464150
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Serial histological sections are suffering from mechanical distortions that disturb the reconstruction of 3-D objects. We have corrected such artifacts with a non-rigid landmark-based method that respects the original geometry in the tissue block. The method is exemplified on a large scale in the registration of semi-thin serial sections of the mouse and rat kidneys, and has been tested on FFPE-sections. In this study of mouse and rat kidneys, we have measured and characterized the deformations introduced in the preparation of 2.5-μm-thick Epon sections and then eliminated them by a landmark-based non-rigid transformation (NRT). We obtained 2.5-μm-thick serial Epon sections from three mouse kidneys and three rat kidneys for 3-D reconstruction of the nephron tubules. First, the images from 3000 serial mouse and 13,000 serial rat sections underwent a classic rigid registration (CRR), and the distortions were measured and indexed. The section images underwent a further NRT in order to compensate for the deformations. The NRT used is a classic interactive landmark-based approach. The quality of the NRT was verified by comparing the geometry of the transformed images with corresponding block images. After CRR, the 2.5-μm-thick sections had a linear deformation of up to 2%, the tubular lengths were overestimated with up to 1.5×, and it was most difficult to trace the tubules from section to section. After the additional NRT, the geometry of the images reflected the original geometry in the block, the tubular lengths were no longer overestimated, and the NRT highly facilitated the tracing of the tubular system. NRT has facilitated the tracing of the tubular system in kidneys, a tracing, which would otherwise have been most difficult to perform. NRT has yielded substantial new knowledge to segmental and spatial nephron organization in the mouse and rat kidneys. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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