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FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain

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, nume...

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Autores principales: Reuter, Jan André, Matuschke, Felix, Menzel, Miriam, Schubert, Nicole, Ginsburger, Kévin, Poupon, Cyril, Amunts, Katrin, Axer, Markus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851223/
https://www.ncbi.nlm.nih.gov/pubmed/31401715
http://dx.doi.org/10.1007/s11548-019-02053-6
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author Reuter, Jan André
Matuschke, Felix
Menzel, Miriam
Schubert, Nicole
Ginsburger, Kévin
Poupon, Cyril
Amunts, Katrin
Axer, Markus
author_facet Reuter, Jan André
Matuschke, Felix
Menzel, Miriam
Schubert, Nicole
Ginsburger, Kévin
Poupon, Cyril
Amunts, Katrin
Axer, Markus
author_sort Reuter, Jan André
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11548-019-02053-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-68512232019-12-03 FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain Reuter, Jan André Matuschke, Felix Menzel, Miriam Schubert, Nicole Ginsburger, Kévin Poupon, Cyril Amunts, Katrin Axer, Markus Int J Comput Assist Radiol Surg Original Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11548-019-02053-6) contains supplementary material, which is available to authorized users. Springer International Publishing 2019-08-11 2019 /pmc/articles/PMC6851223/ /pubmed/31401715 http://dx.doi.org/10.1007/s11548-019-02053-6 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Reuter, Jan André
Matuschke, Felix
Menzel, Miriam
Schubert, Nicole
Ginsburger, Kévin
Poupon, Cyril
Amunts, Katrin
Axer, Markus
FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title_full FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title_fullStr FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title_full_unstemmed FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title_short FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
title_sort faconstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6851223/
https://www.ncbi.nlm.nih.gov/pubmed/31401715
http://dx.doi.org/10.1007/s11548-019-02053-6
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