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Fiber Architecture

The research group “Fiber Architecture” develops techniques to reconstruct the three-dimensional nerve fiber architecture in mouse, rat, monkey, and human brains at microscopic resolution. As a key technology, the neuroimaging technique Three-dimensional Polarized Light Imaging (3D-PLI) is used.

Saggital brain section of the human hippocampus measured with 3D Polarized Light Imaging

3D-PLI allows to map nerve fibers and fiber tracts in whole postmortem brains with a resolution of a few micrometers. The spatial orientations of the nerve fibers are derived by transmitting polarized light through unstained histological brain sections in a polarimeter and measuring their birefringence (optical anisotropy). 3D-PLI enables to investigate the pathways of long-range fiber bundles as well as single fibers and serves as a bridging technology between the macroscopic and the microscopic scale.

The “Fiber Architecture” group is in charge of developing the microscopy techniques, methods for signal analysis and image processing, as well as simulations.

MicroscopySignal & Image ProcessingTheory & Simulation
  • Hardware development
  • Automation
  • Polarimetry
  • High Performance Computing
  • Image segmentation & registration
  • Visualization
  • Modeling
  • Theoretical optics
  • Computational electrodynamics




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)

Selected Publications

  • Caspers, S., Axer, M. Decoding the microstructural correlate of diffusion MRI. NMR in Biomedicine. (2017); e3779.
  • Menzel, M.; Reckfort, J.; Weigand, D.; Köse, H.; Amunts, K.; Axer, M. Diattenuation of brain tissue and its impact on 3D polarized light imaging. Biomedical Optics Express 8 (2017) 7, 3163 – 3197.
  • Zeineh, M.; Palomero-Gallagher, N.; Axer, M.; Gräßel, D.; Goubran, M.; Wree, A.; Woods, R.; Amunts, K.; Zilles, K. Direct Visualization and Mapping of the Spatial Course of Fiber Tracts at Microscopic Resolution in the Human Hippocampus. Cerebral Cortex (2016).
  • Axer, M.; Strohmer, S.; Gräßel, D.; Bücker, O.; Dohmen, M.; Reckfort, J.; Zilles, K.; Amunts, K. Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging. Frontiers in Neuroanatomy 10 (2016) 40.
  • Caspers, S.; Axer, M.; Caspers, J.; Jockwitz, C.; Jutten, K.; Reckfort, J.; Gräßel, D.; Amunts, K.; Zilles, K. Target sites for transcallosal fibers in human visual cortex - A combined diffusion and polarized light imaging study. Cortex 72 (2015), 40-53.
  • Dohmen, M.; Menzel, M.; Wiese, H.; Reckfort, J.; Hanke, F.; Pietrzyk, U.; Zilles, K.; Amunts, K.; Axer, M. Understanding fiber mixture by simulation in 3D Polarized Light Imaging. NeuroImage 111 (2015), 464 – 475.
  • Menzel, M.; Michielsen, K.; De Raedt, H.; Reckfort, J.; Amunts, K.; Axer, M. A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue. Journal of the Royal Society Interface 12 (2015), 20150734.
  • Reckfort, J.; Wiese, H.; Pietrzyk, U.; Zilles, K.; Amunts, K.; Axer, M. A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI. Frontiers in Neuroanatomy 9 (2015), 118.
  • Zilles, K.; Palomero-Gallagher, N.; Gräßel, D.; Schlömer, Ph.; Cremer, M.; Woods, R.; Amunts, K.; Axer, M. High-Resolution Fiber and Fiber Tract Imaging Using Polarized Light Microscopy in the Human, Monkey, Rat, and Mouse Brain. In: Axon and Brain Architecture, Rockland, K. (ed.), pp. 369 – 389, Elsevier (2015).
  • Axer, M.; Amunts, K.; Gräßel, D.; Palm, C.; Dammers, J.; Axer, H.; Pietrzyk, U.; Zilles, K. A novel approach to the human connectome: Ultra-high resolution mapping of fiber tracts in the brain. 
NeuroImage 54 (2011), 1091 – 1101.
  • Axer, M.; Gräßel, D.; Kleiner, M.; Dammers, J.; Dickscheid, T.; Reckfort, J.; Hütz, T.; Eiben, B.; Pietrzyk, U.; Zilles, K.; Amunts, K.: High-resolution fiber tract resconstruction in the human brain by means of three-dimensional polarized light imaging. Frontiers in Neuroinformatics 5 (2011).


  • 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 (2017)
  • Schubert, 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 (2016)
  • Menzel, M.; JARA Best Master 2015: "Simulation and Modeling for the Reconstruction of Nerve Fibers in the Brain by 3D Polarized Light Imaging"
  • Menzel, 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 (2014)
  • Dohmen, M.; award granted by “Verein zur Förderung von Mathematik und Naturwissenschaften e.V. der Bergischen Universität Wuppertal“ for outstanding dissertation (2013).

Additional Information

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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


Stefanie Hennen

Building: 15.9, Room: 3021

+49 2461 61-2481
 +49-2461 61-3483

Janine Hucko

Building: 15.9, Room: 3020

+49 2461 61-6443
+49 2461 61-3483


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

Building: 15.9