Publications

2024

High-speed scattering polarimetry for correlative nerve fiber imaging and multi-modal analysis Franca auf der Heiden, Markus Axer, Katrin Amunts, Miriam Menzel arXiv:2412.08499 (2024)
Deciphering Structural Complexity of Brain, Joint, and Muscle Tissues Using Fourier Ptychographic Scattered Light Microscopy Simon E. van Staalduine, Vittorio Bianco, Pietro Ferraro, Miriam Menzel bioRxiv 2024.11.28.625428 (2024)
Micron-resolution fiber mapping in histology independent of sample preparation Marios Georgiadis, Franca auf der Heiden, Hamed Abbasi, Loes Ettema, Jeffrey Nirschl, Hossein Moein Taghavi, Moe Wakatsuki, Andy Liu, William Hai Dang Ho, Mackenzie Carlon, Michail Doukas, Sjors A. Koppes, Stijn Keereweer, Raymond A. Sobel, Kawin Setsompop, Congyu Liao, Katrin Amunts, Markus Axer, Michael Zeineh, Miriam Menzel bioRxiv 2024.03.26.58674 (2024)
Towards high-speed computational scattered light imaging by introducing compressed sensing for optimized illumination Franca auf der Heiden, Oliver Münzer, Simon van Staalduine, Katrin Amunts, Markus Axer, Miriam Menzel Proc. SPIE 12853, High-Speed Biomedical Imaging and Spectroscopy IX, 1285303 (2024)

Reconstruction of nerve fiber orientations in cell-body stained histological brain sections using Computational Scattered Light Imaging Franca auf der Heiden, Marios Georgiadis, Michael Zeineh, Katrin Amunts, Markus Axer, Miriam Menzel Optics in the Life Sciences 2023, Technical Digest Series (Optica Publishing Group, 2023), paper BW1B.3 (2023)
Enhanced determination of nerve fiber orientations by introducing iterative thresholds in Computational Scattered Light Imaging Jan André Reuter, David Gräßel, Katrin Amunts, Markus Axer, Miriam Menzel Biophotonics Congress: Optics in the Life Sciences 2023, Technical Digest Series (Optica Publishing Group, 2023), paper BW1B.6 (2023)
Using light and X-ray scattering to untangle complex neuronal orientations and validate diffusion MRI Miriam Menzel, David Gräßel, Ivan Rajkovic, Michael M. Zeineh, Marios Georgiadis eLife 12, e84024 (2023)
Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering Marios Georgiadis, Miriam Menzel, Jan A. Reuter, Donald Born, Sophie Kovacevich, Dario Alvarez, Zirui Gao, Manuel Guizar-Sicairos, Thomas M. Weiss, Markus Axer, Ivan Rajkovic, Michael M. Zeineh Acta Biomaterialia (2023)

Combined Scattered Light and X-ray Imaging Reveals Complex White Matter Architecture Miriam Menzel, Marios Georgiadis, Ivan Rajkovic, David Gräßel, Michael Zeineh Biophotonics Congress, Technical Digest Series (Optica Publishing Group, 2022), paper BW2C.3 (2022)
Automated computation of nerve fibre inclinations from 3D polarised light imaging measurements of brain tissue Miriam Menzel, Jan A. Reuter, David Gräßel, Irene Costantini, Katrin Amunts, Markus Axer Scientific Reports 12, 4328 (2022)
GORDA: Graph-Based Orientation Distribution Analysis of SLI Scatterometry Patterns of Nerve Fibres Esteban Vaca, Miriam Menzel, Katrin Amunts, Markus Axer, Timo Dickscheid IEEE International Symposium on Biomedical Imaging 1–5 (2022)

Scatterometry Measurements with Scattered Light Imaging Enable New Insights into the Nerve Fiber Architecture of the Brain Miriam Menzel, Marouan Ritzkowski, Jan A. Reuter, David Gräßel, Katrin Amunts, Markus Axer Frontiers in Neuroanatomy 15, 767233 (2021)
Scattered Light Imaging: Resolving the substructure of nerve fiber crossings in whole brain sections with micrometer resolution Miriam Menzel, Jan A. Reuter, David Gräßel, Mike Huwer, Philipp Schlömer, Katrin Amunts, Markus Axer NeuroImage 233, 117952 (2021)
Scatterometry on whole brain sections using Scattered Light Imaging Miriam Menzel, Marouan Ritzskowski, David Gräßel, Philipp Schlömer, Katrin Amunts, Markus Axer Biophotonics Congress, OSA Technical Digest (Optica Publishing Group, 2021), paper BTu1B.2 (2021)

Coherent Fourier scatterometry reveals nerve fiber crossings in the brain Miriam Menzel, Silvania F. Pereira Biomedical Optics Express 11, 4735–4758 (2020)
Toward a High-resolution Reconstruction of 3D Nerve Fiber Architectures and Crossings in the Brain Using Light Scattering Measurements and Finite-Difference Time-Domain Simulations Miriam Menzel, Markus Axer, Hans De Raedt, Irene Costantini, Ludovico Silvestri, Francesco S. Pavone, Katrin Amunts, Kristel Michielsen Physical Review X 10, 021002 (2020)
Light Scattering Measurements Enable an Improved Reconstruction of Nerve Fiber Crossings Miriam Menzel, Mike Huwer, Philipp Schlömer, Katrin Amunts, Markus Axer Biophotonics Congress, OSA Technical Digest (Optica Publishing Group, 2020), paper BW2C.3 (2020)
SLIX: A Python package for fully automated evaluation of Scattered Light Imaging measurements on brain tissue Jan A. Reuter, Miriam Menzel Journal of Open Source Software 5, 4 2675 (2020)

FAConstructor: an interactive tool for geometric modeling of nerve fiber architectures in the brain Jan A. Reuter, Felix Matuschke, Miriam Menzel, Nicole Schubert, Kevin Ginsburger, Cyril Poupon, Markus Axer International Journal of Computer Assisted Radiology and Surgery 14, 11 1881–1889 (2019)
Diattenuation Imaging reveals different brain tissue properties Miriam Menzel, Markus Axer, Katrin Amunts, Hans De Raedt, Katrin Michielsen Scientific Reports 9, 1939 (2019)
Transmittance and Diattenuation Measurements Reveal Different Properties of Brain Tissue Miriam Menzel, Markus Axer, Katrin Amunts, Hans De Raedt, Kristel Michielsen Biophotonics Congress, OSA Technical Digest (Optica Publishing Group, 2019), paper BW4A.7 (2019)

Transmittance assisted interpretation of nerve fiber orientations Miriam Menzel, Markus Axer, Hans De Raedt, Irene Costantini, Ludovico Silvestri, Francesco S. Pavone, Katrin Amunts, Kristel Michielsen arXiv:1806.07157v1 (2018)
Finite-difference time-domain simulations assisting to reconstruct the brain's nerve fiber architecture by 3D polarized light imaging Miriam Menzel Schriften des Forschungszentrums Jülich 188, (2018)

Diattenuation of brain tissue and its impact on 3D polarized light imaging Miriam Menzel, Markus Axer, Katrin Amunts, Hans De Raedt, Kristel Michielsen Biomedical Optics Express 8, 3163–3197 (2017)

Finite-Difference Time-Domain Simulation for Three-Dimensional Polarized Light Imaging Miriam Menzel, Markus Axer, Hans De Raedt, Kristel Michielsen Lecture Notes in Computer Science, Springer 10087, 73–85 (2016)

Understanding Fiber Mixture by Simulation in 3D Polarized Light Imaging Melanie Dohmen, Miriam Menzel, Hendrik Wiese, Julia Reckfort, Frederike Hanke, Uwe Pietrzyk, Karl Zilles, Katrin Amunts, Markus Axer NeuroImage 111, 464–475 (2015)
Simulation-Based Validation of the Physical Model in 3D Polarized Light Imaging Miriam Menzel, Melanie Dohmen, Hans De Raedt, Kristel Michielsen, Katrin Amunts, Markus Axer Optics and the Life Sciences Congress, OSA Technical Digest (online), paper JT3A.33 (2015)
A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue Miriam Menzel, Kristel Michielsen, Hans De Raedt, Julia Reckfort, Katrin Amunts, Markus Axer Journal of the Royal Society Interface 12, 20150734 (2015)