This title appears in the Scientific Report : 2014 

Advanced image processing for 3D-PLI: revealing fiber architecture in cortial areas
Wiese, Hendrik (Corresponding author)
Pietrzyk, Uwe / Amunts, Katrin / Axer, Markus
Strukturelle und funktionelle Organisation des Gehirns; INM-1
Physik der Medizinischen Bildgebung; INM-4
20th Annual Meeting of the Organization for Human Brain Mapping, Hamburg (Germany), 2014-06-08 - 2014-06-12
Theory, modelling and simulation
Supercomputing and Modelling for the Human Brain
Imaging the Living Brain
Introduction:Polarized Light Imaging (PLI) has been shown to be a valuable tool for mapping nerve fibers and analyzing structural connectivity in unstained histological sections of post-mortem brains (Axer et al. 2011a). In their study Axer et al. demonstrated, how to infer the out of plane fiber orientation in white matter regions from the birefringence signals of myelinated axons at the resolution level of a tenth of a millimeter. So far, however, a comprehensive analysis of fiber pathways within the gray matter, including the cerebral cortex, was impeded by weak signals caused by a low fiber density.Here, we introduce a new analysis method, which accounts for variances in the degree of birefringence, by utilizing additional data gained through a tiltable specimen stage. This technique significantly enhances the information in gray matter regions enabling new insights at a resolution level of 64x64μm².Materials and Methods:We employed the in-house developed polarimetric setup, i.e. the large-area polarimeter as introduced by Axer et al. (2011b), that is capable of measuring birefringent human brain tissue with a section thickness of 70μm. The built-in biaxial specimen stage enabled to tilt the sample by 8° into an arbitrary direction, making studies of the fiber architecture from different perspectives feasible. Using this setup, an unstained coronal section of a complete hemisphere of a human brain through the occipital lobe was tilted by 8° into 72 different directions distributed equally over 360°. For each step data acquisition and analysis was performed as described by Axer et al. (2011a). Since the obtained images were initially afflicted with parallax aberrations induced by the different camera angles, co-registration had to be applied using a projective linear transformation. This enabled a pixelwise Fourier analysis of these 72 data points to determine the 3D fiber orientations independently from the local fiber density.The derived fiber orientations were then compared to those computed with the original PLI methodology (Axer et al., 2011b).Results and Discussion:We observed a significant improvement of the fiber orientation reconstruction in cortical areas. In Figure 1 (bottom left) it is shown, that previous image processing algorithms interpret the weak birefringence information in cortical areas as fibers oriented out-of-plane, while the weak birefringence is actually related to the low fiber density. With the new analysis method we were able to separate fiber orientation and fiber density, which enabled the tracing of fiber paths from deep white matter regions into cortical areas (bottom right). Hence, it is demonstrated that fibers, which were in the past interpreted as being orthogonal with respect to the sectioning plane, are in fact oriented in the lateral direction (Figure 1 bottom right, arrows).Fiber architecture studies in the cerebral cortex were so far restricted to microscopic PLI (cf. Axer et al. 2011b), for which data acquisition and processing with previously employed methods was extensive and time-consuming. However, this new advancement significantly increased information gain on the macroscopic scale, extending the applicability of large-area PLI.