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Markus Axer

Prof. Dr. Markus Axer


Deputy Director of INM-1

Research Group Fibre architecture

Member of the JuDocs Council at FZJ

Professor at the Bergische Universität Wuppertal (Computer Simulation in Science, Physik)

Research Topics

The main goal of my research is to reveal and understand the brain’s nerve fiber architecture and the resulting structural connectivity. My work includes the design of polarimetric microscopes, the implementation of image processing algorithms, as well as big data analytics utilizing high-performance computing amongst others. I’m absolutely convinced that simulation approaches are required to fundamentally complement the experimental data and crucially help to understand and utilize underlying physical principles in the imaging processes. The combined usage of these interdisciplinary topics will finally enable the generation of unique atlases of different species, such as rodents, birds, pinnipeds, non-human and human primates.

Methods and Tools

  • 3D Polarized Light Imaging (engineering of polarizing microscopes, high-throughput imaging, process automation, brain preparation)
  • Correlative, multimodal imaging using Diffusion MRI, Two-Photon Fluorescence Microscopy, Mass Spectrometry, X-ray Scattering, Light Scattering
  • High performance computing (software parallelization for CPU/GPU usage, workflow implementation)
  • photomicrographic image processing and visualization (large-scale): segmentation, registration, independent component analysis, stitching
  • Simulation of the interaction of light with brain tissue and simulation of polarimetric measurements (geometric optics, electrodynamics)


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


Phone: +49 2461 61-6314
Fax: +49 2461 61-2820