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When transmitting polarised light through histological brain sections, different types of diattenuation (polarisation-dependent attenuation of light) can be observed: In some brain regions, the light is minimally attenuated when it is…

Medical Physics · Physics 2019-02-22 Miriam Menzel , Markus Axer , Katrin Amunts , Hans De Raedt , Kristel Michielsen

3D-Polarized Light Imaging (3D-PLI) is a neuroimaging technique used to study the structural connectivity of the human brain at the meso- and microscale. In 3D-PLI, the complex nerve fiber architecture of the brain is characterized by 3D…

Computational Physics · Physics 2020-12-21 Felix Matuschke , Kévin Ginsburger , Cyril Poupon , Katrin Amunts , Markus Axer

The method 3D polarised light imaging (3D-PLI) measures the birefringence of histological brain sections to determine the spatial course of nerve fibres (myelinated axons). While the in-plane fibre directions can be determined with high…

Biological Physics · Physics 2022-04-12 Miriam Menzel , Jan A. Reuter , David Gräßel , Irene Costantini , Katrin Amunts , Markus Axer

For developing a detailed network model of the brain based on image reconstructions, it is necessary to spatially resolve crossing nerve fibers. The accuracy hereby depends on many factors, including the spatial resolution of the imaging…

In many laboratories, conventional bright-field transmission microscopes are available to study the structure and organization principles of fibrous tissue samples, but they usually provide only 2D information. To access the third…

Three-dimensional Polarized Light Imaging (3D-PLI) is a promising technique to reconstruct the nerve fiber architecture of human post-mortem brains from birefringence measurements of histological brain sections with micrometer resolution.…

Medical Physics · Physics 2017-03-17 Miriam Menzel , Markus Axer , Hans De Raedt , Kristel Michielsen

Mapping the intricate network of nerve fibers is crucial for understanding brain function. Three-Dimensional Polarized Light Imaging (3D-PLI) and Computational Scattered Light Imaging (ComSLI) map dense nerve fibers in brain sections with…

Medical Physics · Physics 2025-06-03 Franca auf der Heiden , Markus Axer , Katrin Amunts , Miriam Menzel

Understanding the cortical organization of the human brain requires interpretable descriptors for distinct structural and functional imaging data. 3D polarized light imaging (3D-PLI) is an imaging modality for visualizing fiber architecture…

Computer Vision and Pattern Recognition · Computer Science 2024-09-04 Alexander Oberstrass , Jordan DeKraker , Nicola Palomero-Gallagher , Sascha E. A. Muenzing , Alan C. Evans , Markus Axer , Katrin Amunts , Timo Dickscheid

A comprehensive understanding of the organizational principles in the human brain requires, among other factors, well-quantifiable descriptors of nerve fiber architecture. Three-dimensional polarized light imaging (3D-PLI) is a microscopic…

Computer Vision and Pattern Recognition · Computer Science 2025-05-19 Alexander Oberstrass , Sascha E. A. Muenzing , Meiqi Niu , Nicola Palomero-Gallagher , Christian Schiffer , Markus Axer , Katrin Amunts , Timo Dickscheid

The neuroimaging technique three-dimensional polarized light imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements…

Medical Physics · Physics 2015-10-12 Miriam Menzel , Kristel Michielsen , Hans De Raedt , Julia Reckfort , Katrin Amunts , Markus Axer

The correct reconstruction of individual (crossing) nerve fibers is a prerequisite when constructing a detailed network model of the brain. The recently developed technique Scattered Light Imaging (SLI) allows the reconstruction of crossing…

Biological Physics · Physics 2021-11-30 Miriam Menzel , Marouan Ritzkowski , Jan André Reuter , David Gräßel , Katrin Amunts , Markus Axer

Comprehensive assessment of the various aspects of the brain's microstructure requires the use of complementary imaging techniques. This includes measuring the spatial distribution of cell bodies (cytoarchitecture) and nerve fibers…

3D reconstruction of the fiber connectivity of the rat brain at microscopic scale enables gaining detailed insight about the complex structural organization of the brain. We introduce a new method for registration and 3D reconstruction of…

Computer Vision and Pattern Recognition · Computer Science 2018-07-31 Sharib Ali , Martin Schober , Philipp Schlöme , Katrin Amunts , Markus Axer , Karl Rohr

Scattered Light Imaging (SLI) is a novel approach for microscopically revealing the fibre architecture of unstained brain sections. The measurements are obtained by illuminating brain sections from different angles and measuring the…

Image and Video Processing · Electrical Eng. & Systems 2022-04-13 Esteban Vaca , Miriam Menzel , Katrin Amunts , Markus Axer , Timo Dickscheid

Monitoring diseases that affect the brain's structural integrity requires automated analysis of magnetic resonance (MR) images, e.g., for the evaluation of volumetric changes. However, many of the evaluation tools are optimized for…

Neuropathological analyses benefit from spatially precise volumetric reconstructions that enhance anatomical delineation and improve morphometric accuracy. Our prior work has shown the feasibility of reconstructing 3D brain volumes from 2D…

Developing advanced technologies for sensing and imaging biological samples is crucial for medical applications, making quantum-enhanced methods particularly valuable, as they promise significant benefits over classical techniques. An…

Quantum Physics · Physics 2025-08-21 Cristofero Oglialoro , Enno Giese

More children and adults under the age of 40 die of brain tumor than from any other cancer. Brain surgery constitutes the first and decisive step for the treatment of such tumors. It is extremely crucial to achieve complete tumor resection…

High resolution optical microscopy is essential in neuroscience but suffers from scattering in biological tissues. It therefore grants access to superficial layers only. Recently developed techniques use scattered photons for imaging by…

Diffusion tensor imaging (DTI) plays a key role in analyzing the physical structures of biological tissues, particularly in reconstructing fiber tracts of the human brain in vivo. On the one hand, eigenvalues of diffusion tensors (DTs)…

Applications · Statistics 2013-04-18 Tao Yu , Chunming Zhang , Andrew L. Alexander , Richard J. Davidson
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