Tractography from Serial Optical Coherence Tomography: How and Why?

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. Serial optical coherence tomography (S-OCT) is an imaging modality relying on the intrinsic contrast of a sample. When applied to brain tissues, the S-OCT contrast is primarily driven by the myelin reflectivity. Due to its high resolution, on the order of microns, and its 3D nature, S-OCT offers promise for studying WM connections at the microscale. However, while other microscopy imaging modalities have been shown to enable tractography, whether the reflectivity contrast from S-OCT supports the reconstruction of long-range WM fascicles 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 improve microscale orientation distribution functions (ODF) estimation by implementing a sliding-window formulation allowing the estimation of ODF at S-OCT resolution, and use apodized Dirac delta functions for reducing unwanted interference. We validate our approach on a simulated microscopy-like FiberCup dataset, and show that using multiscale Frangi filters for estimating ODF outperforms structure tensor analysis. We also show that particle filtering tractography with anatomical constraints 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 the thalamocortical white-matter projections. Overall, our results show that S-OCT tractography recovers fine white matter fascicles visible at the microscale, and that these connections 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.