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Theory and Simulation

To better understand the physics behind light-matter interactions in brain tissue and develop general concepts of how the measurement and signal analysis of 3D Polarized Light Imaging (3D-PLI) can be improved, two complementary simulation approaches are pursued: a linear optics approach (Menzel et al. 2015) and an electrodynamics approach (Menzel et al. 2016). For the simulations, highly-dense nerve fiber models are generated (Ginsburger et al. 2018), reflecting the nerve fiber architecture of the brain. The simulations are performed on supercomputers in cooperation with the Jülich Supercomputing Centre (JSC).

Nerve fiber model and methods for simulating 3D-Polarized Light Imaging (3D-PLI)adapted from Menzel et al. 2016
Copyright: Springer Nature (2016)

The simulations reproduce the entire 3D-PLI measurement, starting from synthetic nerve fiber arrangements and ending with measurement-like tissue images. The simulations can be used to test hypotheses on the underlying fiber structure of brain tissue.
The simulation approach based on linear optics models the birefringence of brain tissue samples. A comparison of the known underlying fiber model with the fiber orientations derived in a standard 3D-PLI measurement helps to identify possible misinterpretations in the fiber reconstruction process (Dohmen et al. 2015).

Comparison of a 3D-PLI measurement and linear optics simulations for the optic chiasm of a hooded seal (nerve fiber crossing)adapted from Dohmen et al. 2015
Copyright: Elsevier (2015)

The simulation approach based on electrodynamics allows to study more complex light-matter interactions like scattering and interference of light, enabling to model e.g. the intensity of light transmitted through a brain sample (Menzel et al. 2018, 2019).

Comparison of a transmission microscopy measurement and electrodynamics simulations for regions with flat and steep nerve fiber bundlesadapted from Menzel et al. 2018
Copyright: Miriam Menzel, Forschungszentrum Jülich GmbH

Selected Publications

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Preprint
Dense Fiber Modeling for 3D-Polarized Light Imaging Simulations
OpenAccess  Download fulltext Files  Download fulltextFulltext by arXiv.org Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Diattenuation Imaging reveals different brain tissue properties
Scientific reports 9(1), 1939 () [10.1038/s41598-019-38506-w] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Preprint
Finite-Difference Time-Domain simulations of transmission microscopy enable a better interpretation of 3D nerve fiber architectures in the brain
() OpenAccess  Download fulltext Files  Download fulltextFulltext Download fulltextFulltext by arXiv.org Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Improving the Realism of White Matter Numerical Phantoms: A Step toward a Better Understanding of the Influence of Structural Disorders in Diffusion MRI
Frontiers in physics 6, 12 () [10.3389/fphy.2018.00012] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Diattenuation of Brain Tissue and its Impact on 3D Polarized Light Imaging
Biomedical optics express 8(7), 3163-3197 () [10.1364/BOE.8.003163] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Contribution to a conference proceedings/Contribution to a book
Finite-Difference Time-Domain Simulation for Three-dimensional Polarized Light Imaging
Brain-Inspired Computing
International Workshop on Brain-Inspired Computing, BrainComp 2015, CetraroCetraro, Italy, 6 Jul 2015 - 10 Jul 20152015-07-062015-07-10
Luxemburg : Springer, Lecture Notes in Computer Science 10087, 73-85 () [10.1007/978-3-319-50862-7_6]   Download fulltextFulltext BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging
Frontiers in neuroanatomy 10, 40 () [10.3389/fnana.2016.00040] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue
Interface 12(111), 20150734 () [10.1098/rsif.2015.0734]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Understanding fiber mixture by simulation in 3D Polarized Light Imaging
NeuroImage 111, 464–475 () [10.1016/j.neuroimage.2015.02.020]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

Additional Information

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Groupleader

Dr. rer. nat. Markus Axer

Building: 15.9, Room: 3029

Institute of Neuroscience and Medicine (INM-1)
Forschungszentrum Jülich
52425 Jülich

Tel.: +49 2461 61-6314
Fax: +49 2461 61-2820
E-Mail: m.axer@fz-juelich.de

Management

Stefanie Hennen

Building: 15.9, Room: 3021

+49 2461 61-2481
 +49-2461 61-3483
s.hennen@fz-juelich.de

Janine Hucko

Building: 15.9, Room: 3020

+49 2461 61-6443
+49 2461 61-3483
j.hucko@fz-juelich.de

Address

Institut für Neurowissenschaften und Medizin (INM-1)
Forschungszentrum Jülich
52425 Jülich

Building: 15.9


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