Markus Axer

Markus Axer
Forschungszentrum Jülich
Jülich, Germany

Session: C. Neuroimaging I

Will talk about: 3D-Polarized light imaging – The structural connectome goes microscopic

Bio sketch:

Markus Axer is head of the group “Fiber Architecture” in the Institute of Neuroscience and Medicine (INM-1) at Forschungszentrum Jülich GmbH, member of the Helmholtz Association of German Research Centers, Germany. He is a physicist and oversees the development of 3D-Polarized Light Imaging (3D-PLI), which includes the design of polarimetric systems, image acquisition and big data analysis. This neuroimaging technique opens up new avenues to unravel the nerve fiber architecture in the brain at different levels of detail and establishes the so far missing link between the microscopic and the macroscopic characterization of the anatomical connectivity of the human brain. In 1999, Dr. Axer graduated from the RWTH Aachen University, and in 2003 received his awarded Ph.D. in Particle Physics from the RWTH Aachen University. After a two-years research fellowship at the European Organization for Nuclear Research CERN, Geneva (Switzerland), Dr. Axer joined the field of neuroscience at the INM.

Talk abstract:

3D-Polarized Light Imaging (3D-PLI) is a neuroimaging technique that has opened up new avenues to study the complex architecture of nerve fibers in postmortem brains. It combines the virtues of microscopic resolution with large area scan capabilities, thus enabling whole brain connectome analysis based on serial histological imaging. 3D-PLI requires no histological staining or labeling, because it utilizes intrinsic tissue properties able to modify the polarization state of the light: birefringence, the main polarization property of interest for biological  tissues, is caused by a difference in index of refraction that results in a phase shift between orthogonal polarization states, and is often exhibited by fibrous structures, such as nerve fibers. 3D-PLI capitalizes on the birefringence of myelinated and unmyelinated fibers in unstained histological sections to contrast fibers with nerve cell bodies or glial cells and to determine the spatial orientation (i.e., 3D-vectors) of single fibers at microscopic resolution. On the basis of non-linear registration of a substantial number of serial fiber orientation images, large-scale virtual 3D models of fiber structures are created. Such models are unique data sets to bridge between macroscopic and microscopic descriptions of the brain’s fiber architecture gained from diffusion MRI or other microscopic approaches, respectively. The key elements of the 3D-PLI methodology, such as the polarimetric setup, image processing algorithms and volume reconstruction techniques, are particularly developed to address whole human brain analysis at the micrometer scale, i.e., to handle terabyte to petabyte sized data sets. The presentation will demonstrate the key elements developed along the 3D-PLI processing pipeline from the measurement towards the reconstructed large-scale 3D fiber orientation brain models.