Journal Article

FZJ-2019-04297

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain

Reuter, J. A. (Corresponding author)FZJ* ; Matuschke, F.FZJ* ; Menzel, M.FZJ* ; Schubert, N.FZJ* ; Ginsburger, K. ; Poupon, C. ; Amunts, K.FZJ* ; Axer, M.FZJ*

2019
Springer Heidelberg [u.a.]

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Please use a persistent id in citations: http://hdl.handle.net/2128/23368  doi:10.1007/s11548-019-02053-6

Abstract: PURPOSE: The technique 3D polarized light imaging (3D-PLI) allows to reconstruct nerve fiber orientations of postmortem brains with ultra-high resolution. To better understand the physical principles behind 3D-PLI and improve the accuracy and reliability of the reconstructed fiber orientations, numerical simulations are employed which use synthetic nerve fiber models as input. As the generation of fiber models can be challenging and very time-consuming, we have developed the open source FAConstructor tool which enables a fast and efficient generation of synthetic fiber models for 3D-PLI simulations. METHODS: The program was developed as an interactive tool, allowing the user to define fiber pathways with interpolation methods or parametric functions and providing visual feedback.RESULTS: Performance tests showed that most processes scale almost linearly with the amount of fiber points in FAConstructor. Fiber models consisting of < 1.6 million data points retain a frame rate of more than 30 frames per second, which guarantees a stable and fluent workflow. The applicability of FAConstructor was demonstrated on a well-defined fiber model (Fiber Cup phantom) for two different simulation approaches, reproducing effects known from 3D-PLI measurements.CONCLUSION: We have implemented a user-friendly and efficient tool that enables an interactive and fast generation of synthetic nerve fiber configurations for 3D-PLI simulations. Already existing fiber models can easily be modified, allowing to simulate many different fiber models in a reasonable amount of time.

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Contributing Institute(s):

1. Strukturelle und funktionelle Organisation des Gehirns (INM-1)
2. JARA - HPC (JARA-HPC)

Research Program(s):

1. 574 - Theory, modelling and simulation (POF3-574) (POF3-574)
2. 571 - Connectivity and Activity (POF3-571) (POF3-571)
3. HBP SGA2 - Human Brain Project Specific Grant Agreement 2 (785907) (785907)
4. Simulations for a better Understanding of the Impact of Different Brain Tissue Components on 3D Polarized Light Imaging (jjsc43_20181101) (jjsc43_20181101)
5. 3D Reconstruction of Nerve Fibers in the Human, the Monkey, the Rodent, and the Pigeon Brain (jinm11_20181101) (jinm11_20181101)

Appears in the scientific report 2019

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Database coverage:
; ; ; Clarivate Analytics Master Journal List ; Current Contents - Clinical Medicine ; IF < 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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