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

  • Sharib AliEmail author
  • Martin Schober
  • Philipp Schlömer
  • Katrin Amunts
  • Markus Axer
  • Karl Rohr
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11083)


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.



This project was funded by the Helmholtz Association through the Helmholtz Portfolio theme “Supercomputing and Modeling for the Human Brain” and by the European Union through the Horizon 2020 Research and Innovation Programme under Grant Agreement No. 7202070 (Human Brain Project SGA1).


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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  • Sharib Ali
    • 1
    Email author
  • Martin Schober
    • 2
  • Philipp Schlömer
    • 2
  • Katrin Amunts
    • 2
    • 3
  • Markus Axer
    • 2
  • Karl Rohr
    • 1
  1. 1.Department of Bioinformatics, Biomedical Computer Vision Group, BIOQUANT, IPMB, DKFZUniversity of HeidelbergHeidelbergGermany
  2. 2.Research Centre JülichInstitute of Neuroscience and Medicine 1JülichGermany
  3. 3.Cécile and Oskar Vogt Institute of Brain ResearchHeinrich Heine University Düsseldorf, University Hospital DüsseldorfDüsseldorfGermany

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