3D scattered light imaging: extracting 3D fiber orientations from 1D line profiles in brain imaging
Abstract
Understanding the 3D fiber architecture of the brain at the microscopic scale is essential for revealing its structural connectivity and function. Polarization-based optical imaging (3D-PLI) techniques enable high-fidelity reconstruction of single nerve fiber orientations but struggle to resolve fiber crossings, which are critical for recovering the full connectome. Scattering-based imaging provides access to the structure factor of three-dimensionally oriented fibers. By probing a fixed scattering angle under multiple azimuthal illumination angles, in-plane fiber orientations and crossings can be recovered using computational scattered light imaging (SLI). However, despite containing 3D information, a theoretical framework to extract full 3D orientations has been lacking. In this talk, a simple analogical approximation of Rayleigh-Gans scattering theory is introduced to extract the 3D orientation of nerve fibers from one-dimensional SLI measurements. The theory is validated using tilted microscopic glass phantoms consisting of 2 um-thick rod lattices fabricated by two-photon lithography. Finally, the method is applied to brain tissue samples and compared with 3D-PLI.
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BibTeX
@misc{scheidt2026scattered,
title = {{3D scattered light imaging: extracting 3D fiber orientations from 1D line profiles in brain imaging}},
author = {Dennis Scheidt and Charlotte Voß and Cristian Rosero Arias and Santiago Saavedra Castano and Felix Matuschke and Roxana Koojimans and Katrin Amunts and Arturo Susarrey-Arce and Markus Axer},
howpublished = {arXiv},
year = {2026},
month = sep,
doi = {10.48550/arxiv.2609.03764},
eprint = {2609.03764},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2609.03764},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - 3D scattered light imaging: extracting 3D fiber orientations from 1D line profiles in brain imaging
AU - Dennis Scheidt
AU - Charlotte Voß
AU - Cristian Rosero Arias
AU - Santiago Saavedra Castano
AU - Felix Matuschke
AU - Roxana Koojimans
AU - Katrin Amunts
AU - Arturo Susarrey-Arce
AU - Markus Axer
PY - 2026
DA - 2026/09/03
PB - arXiv
DO - 10.48550/arxiv.2609.03764
UR - https://arxiv.org/abs/2609.03764
AB - Understanding the 3D fiber architecture of the brain at the microscopic scale is essential for revealing its structural connectivity and function. Polarization-based optical imaging (3D-PLI) techniques enable high-fidelity reconstruction of single nerve fiber orientations but struggle to resolve fiber crossings, which are critical for recovering the full connectome. Scattering-based imaging provides access to the structure factor of three-dimensionally oriented fibers. By probing a fixed scattering angle under multiple azimuthal illumination angles, in-plane fiber orientations and crossings can be recovered using computational scattered light imaging (SLI). However, despite containing 3D information, a theoretical framework to extract full 3D orientations has been lacking. In this talk, a simple analogical approximation of Rayleigh-Gans scattering theory is introduced to extract the 3D orientation of nerve fibers from one-dimensional SLI measurements. The theory is validated using tilted microscopic glass phantoms consisting of 2 um-thick rod lattices fabricated by two-photon lithography. Finally, the method is applied to brain tissue samples and compared with 3D-PLI.
ER -