Tractography from Serial Optical Coherence Tomography: How and Why?
- 1Université de Sherbrooke
Abstract
To disentangle complex fiber configurations that remain challenging for diffusion MRI tractography, insights might be gained from microscopy tractography. Indeed, by precisely following small white matter (WM) fascicles, invisible at the resolution of diffusion MRI, microscopy tractography can help explain how fiber populations are organized at the finest scales. Due to its high resolution and its 3D nature, serial optical coherence tomography (S-OCT) offers promise for studying WM at the microscale. However, whether the reflectivity contrast from S-OCT supports tractography at the microscale remains unknown. Furthermore, there is a gap in the literature regarding how an ideal microscopy tractography algorithm should behave with respect to the choice of tractography algorithm, tracking maps definition and microscale orientation distribution functions (ODF) estimation. In this work, we describe a tailored approach to reconstruct WM fascicles at the microscale from S-OCT acquisitions. We validate our approach on a simulated microscopy-like FiberCup dataset, and show that multiscale Frangi filters outperforms structure tensor analysis for estimating ODF. We also show that anatomically-constrained particle filtering tractography enables targetted, region-to-region tractography, and outperforms standard deterministic or probabilistic tracking approaches. We further demonstrate our method on a whole mouse brain S-OCT reconstruction at 10 m by reconstructing thalamocortical WM projections. Overall, our results show that S-OCT tractography recovers fine white matter fascicles that are supported by viral tracing experiments from the Allen Mouse Brain Connectivity Atlas. Moreover, this work shows the first ODF estimation and fully-3D probabilistic particle filtering tractography of the mouse brain from S-OCT reconstructions at 10 m isotropic resolution.
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BibTeX
@misc{poirier2026tractography,
title = {{Tractography from Serial Optical Coherence Tomography: How and Why?}},
author = {C. Poirier and L. Petit and J. Lefebvre and M. Descoteaux},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.14.744847},
url = {https://www.biorxiv.org/content/10.64898/2026.08.14.744847v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Tractography from Serial Optical Coherence Tomography: How and Why?
AU - C. Poirier
AU - L. Petit
AU - J. Lefebvre
AU - M. Descoteaux
PY - 2026
DA - 2026/08/14
PB - bioRxiv
DO - 10.64898/2026.08.14.744847
UR - https://www.biorxiv.org/content/10.64898/2026.08.14.744847v2
AB - To disentangle complex fiber configurations that remain challenging for diffusion MRI tractography, insights might be gained from microscopy tractography. Indeed, by precisely following small white matter (WM) fascicles, invisible at the resolution of diffusion MRI, microscopy tractography can help explain how fiber populations are organized at the finest scales. Due to its high resolution and its 3D nature, serial optical coherence tomography (S-OCT) offers promise for studying WM at the microscale. However, whether the reflectivity contrast from S-OCT supports tractography at the microscale remains unknown. Furthermore, there is a gap in the literature regarding how an ideal microscopy tractography algorithm should behave with respect to the choice of tractography algorithm, tracking maps definition and microscale orientation distribution functions (ODF) estimation. In this work, we describe a tailored approach to reconstruct WM fascicles at the microscale from S-OCT acquisitions. We validate our approach on a simulated microscopy-like FiberCup dataset, and show that multiscale Frangi filters outperforms structure tensor analysis for estimating ODF. We also show that anatomically-constrained particle filtering tractography enables targetted, region-to-region tractography, and outperforms standard deterministic or probabilistic tracking approaches. We further demonstrate our method on a whole mouse brain S-OCT reconstruction at 10 m by reconstructing thalamocortical WM projections. Overall, our results show that S-OCT tractography recovers fine white matter fascicles that are supported by viral tracing experiments from the Allen Mouse Brain Connectivity Atlas. Moreover, this work shows the first ODF estimation and fully-3D probabilistic particle filtering tractography of the mouse brain from S-OCT reconstructions at 10 m isotropic resolution.
ER -