Search

link to homepage

Institute of Neuroscience and Medicine
(leer)

Navigation and service


Fiber Architecture

The research group “Fiber Architecture (FA)” develops the 3D Polarized Light Imaging (3D-PLI) technology to reveal the structural connectivity and fiber architecture in post mortem brains at microscopic resolution.

HippocampusSagittal section through the human hippocampus. Fibers are color-coded according to their spatial orientation.
Copyright: INM-1, Research Center Jülich

3D-PLI measures the birefringence of myelinated nerve fibers with polarization microscopy techniques. It gives contrast to distinct nerve fibers and their tracts, and makes estimations of their spatial courses possible. Moreover, its sensitivity to myelin makes 3D-PLI well suited to address pathological alterations of the brain’s fiber architecture.

To understand the brain’s connectivity patterns over different scales, we establish protocols and methods to integrate complementary imaging methods applicable to the same tissue samples in (inter)national collaborations, including Diffusion MRI, 3D-PLI, Two-Photon Fluorescence Microscopy, Mass Spectrometry Imaging, and X-ray Diffraction.

The introduction of instruments for automated imaging of entire brains and computational methods for handling the massive data sets has opened the door to neuroanatomical studies at an unprecedented scale. 3D-PLI combines research topics in a truly interdisciplinary manner: polarization microscopy technologies, modern signal and image processing algorithms, big data analytics, and cutting-edge simulation approaches, all based on high-performance computing.

Depiction of the Polarimetry process

Microscopy

Our expertise in the field of microscopy includes Polarimetry, Blockface Imaging, Hardware development and Automation

More: Microscopy …

Computational Workflow: This workflow describes the different steps, computing platform and output images of the 3D-PLI workflow.

Signal & Image Processing

The emphases of our Signal & Image Processing are Biophysical signal interpretation, Image segmentation, 3D reconstruction, Machine learning and Visualization

More: Signal & Image Processing …

Nerve fiber model and methods for simulating 3D-Polarized Light Imaging (3D-PLI)

Theory & Simulation

In the field of Theory & Simulation we use mainly approaches of Modeling, Theoretical optics and Computational electrodynamics

More: Theory & Simulation …

Projects and Collaborations

Outreach and Teaching Activities

Theses

Awards

2018Schlömer, P., „InnovationPlus” award for initiating of a cooperation with high innovation potential, funded by “Innovationsfonds der Helmholtz-Zentren”, Jülich, Germany
2017Wiese, H., award granted by “Verein zur Förderung von Mathematik und Naturwissenschaften e.V. der Bergischen Universität Wuppertal“ for outstanding dissertation, Wuppertal, Germany
Hänel, C., Demiralp, A.C., Axer, M., Gräßel, D., Hentschel, B., Kuhlen, T.W.; Honorable mention for best short paper; “Interactive Level-of-Detail Visualization of 3D Polarized Light Imaging Data Using Spherical Harmonics“, EuroVis, Spain
2016Schubert, N.; BVM prize 2016 for the best scientific talk: "Visualization of Vector Fields Derived from 3D Polarized Light Imaging", Bildverarbeitung für die Medizin (BVM), Berlin, Germany
2015Menzel, M.; JARA Best Master 2015: "Simulation and Modeling for the Reconstruction of Nerve Fibers in the Brain by 3D Polarized Light Imaging", Aachen, Germany
2014Menzel, M.; poster prize in the category "Computational Neuroscience": "Simulation and Modeling for the Reconstruction of Nerve Fibers in the Brain by 3D Polarized Light Imaging", NeuroVisionen 10, Jülich, Germany
2013Dohmen, M.; award granted by “Verein zur Förderung von Mathematik und Naturwissenschaften e.V. der Bergischen Universität Wuppertal“ for outstanding dissertation, Wuppertal, Germany

Impressions Fiber Architecture

Coronal section of a human brain measured with 3D Polarized Light Imaging (3D-PLI)
Coronal section of a vervet brain measured with 3D Polarized Light Imaging (3D-PLI)
Coronal section of a rat brain measured with 3D Polarized Light Imaging (3D-PLI)
Detail of a vervet coronal brain section measured with 3D Polarized Light Imaging (3D-PLI)
Lenticular fascicle in a human brain section measured with 3D Polarized Light Imaging (3D-PLI)
U-fibers in a human brain section measured with 3D Polarized Light Imaging (3D-PLI)
Cortical nerve fibers in a human brain section measured with 3D Polarized Light Imaging (3D-PLI)

Latest Publications

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Teaching NeuroImages: In vivo visualization of Edinger comb and Wilson pencils
Neurology 92(14), e1663 () [10.1212/WNL.0000000000007252]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
Ex vivo visualization of the trigeminal pathways in the human brainstem using 11.7T diffusion MRI combined with microscopy polarized light imaging
Brain structure & function 224(1), 159-170 () [10.1007/s00429-018-1767-1]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article
The hippocampus of birds in a view of evolutionary connectomics
Cortex 118, 165 () [10.1016/j.cortex.2018.09.025] 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
MEDUSA: A GPU-based tool to create realistic phantoms of the brain microstructure using tiny spheres
NeuroImage 193, 10-24 () [10.1016/j.neuroimage.2019.02.055] 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
Diattenuation Imaging reveals different brain tissue properties
() 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
Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging
Frontiers in neuroanatomy 12, 75 () [10.3389/fnana.2018.00075] 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
Rigid and non-rigid registration of polarized light imaging data for 3D reconstruction of the temporal lobe of the human brain at micrometer resolution
NeuroImage 181, 235-251 () [10.1016/j.neuroimage.2018.06.084] Embargoed 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
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
Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T
Brain structure & function 223(5), 2157–2179 () [10.1007/s00429-018-1617-1] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Additional Information

PLI Logo

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


Servicemeu

Homepage