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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

  • 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) 10.1093/cercor/bhw010
  • 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)
  • Palm, C.; Axer, M.; Gräßel, D.; Dammers, J.; Lindemeyer, J.; Zilles, K.; Pietrzyk, U.; Amunts, K.
 Towards ultra-high resolution fibre tract mapping of the human brain – registration of polarised light images and reorientation of fibre vectors
. Frontiers in Human Neuroscience, 4 (2010) 9, 1 – 16

Additional Information


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: 3020

+49 2461 61-9167
 +49-2461 61-3483

Julia Scheuvens

Building: 15.9, Room: 3021

+49 2461 61-2481
+49 2461 61-3483


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

Building: 15.9