Use of computational fluid dynamics for 3D fiber tract visualization on human high-thickness histological slices: histological mesh tractography

Abstract

Understanding the intricate three-dimensional relationship between fiber bundles and subcortical nuclei is not a simple task. It is of paramount importance in neurosciences, especially in the field of functional neurosurgery. The current methods for in vivo and post mortem fiber tract visualization have shortcomings and contributions to the field are welcome. Several tracts were chosen to implement a new technique to help visualization of white matter tracts, using high-thickness histology and dark field images. Our study describes the use of computational fluid dynamic simulations for visualization of 3D fiber tracts segmented from dark field microscopy in high-thickness histological slices (histological mesh tractography). A post mortem human brain was MRI scanned prior to skull extraction, histologically processed and serially cut at 430 µm thickness as previously described by our group. High-resolution dark field images were used to segment the outlines of the structures. These outlines served as basis for the construction of a 3D structured mesh, were a Finite Volume Method (FVM) simulation of water flow was performed to generate streamlines representing the geometry. The simulations were accomplished by an open source computer fluid dynamics software. The resulting simulation rendered a realistic 3D impression of the segmented anterior commissure, the left anterior limb of the internal capsule, the left uncinate fascicle, and the dentato-rubral tracts. The results are in line with clinical findings, diffusion MR imaging and anatomical dissection methods.

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Brain Structure and Function (2021) 226:323–333
https://doi.org/10.1007/s00429-020-02187-3
METHODS PAPER
Use ofcomputational fluid dynamics for3D fiber tract visualization
onhuman high‑thickness histological slices: histological mesh
tractography
EduardoJoaquimLopesAlho1,2,3 · ErichT.Fono2· AnaTerezaDiLorenzoAlho3· JózsefNagy4· HelmutHeinsen1,3
Received: 29 October 2019 / Accepted: 24 November 2020 / Published online: 3 January 2021
© Springer-Verlag GmbH Germany, part of Springer Nature 2021
Abstract
Understanding the intricate three-dimensional relationship between fiber bundles and subcortical nuclei is not a simple
task. It is of paramount importance in neurosciences, especially in the field of functional neurosurgery. The current methods
for invivo and post mortem fiber tract visualization have shortcomings and contributions to the field are welcome. Several
tracts were chosen to implement a new technique to help visualization of white matter tracts, using high-thickness histology
and dark field images. Our study describes the use of computational fluid dynamic simulations for visualization of 3D fiber
tracts segmented from dark field microscopy in high-thickness histological slices (histological mesh tractography). A post
mortem human brain was MRI scanned prior to skull extraction, histologically processed and serially cut at 430µm thickness
as previously described by our group. High-resolution dark field images were used to segment the outlines of the structures.
These outlines served as basis for the construction of a 3D structured mesh, were a Finite Volume Method (FVM) simulation
of water flow was performed to generate streamlines representing the geometry. The simulations were accomplished by an
open source computer fluid dynamics software. The resulting simulation rendered a realistic 3D impression of the segmented
anterior commissure, the left anterior limb of the internal capsule, the left uncinate fascicle, and the dentato-rubral tracts.
The results are in line with clinical findings, diffusion MR imaging and anatomical dissection methods.
Keywords Tractography· White matter· Histology· Human brain· Dentato-rubral tract· Diffusion tensor imaging
Introduction
Advances in neuroimaging and its rapid widespread for
multiple fields of the neurosciences require a better under-
standing of the intricate three-dimensional (3D) relation-
ship between white matter tracts, cortical grey matter and
subcortical nuclei. In the field of functional neurosurgery,
the refinement of stereotactic method based in individual-
ized neuroimaging studies have made possible to aim inter-
ventions at diminutive deep-seated nuclei or fiber tracts, as
therapeutic targets for successful treatment of various neu-
ropsychiatric disorders. Nowadays, it is of paramount impor-
tance, not only the origin and the aim point of a specific fiber
tract, but the topographic localization of the actual pathway
among other deep brain structures. In the field of deep brain
stimulation (DBS), newly designed electrodes with direc-
tional and multiple-contact leads highlight the possibility
of target compounds instead of a single one. The concept of
targeting trajectories instead of a single nucleus has upturned
the effects of DBS, increasing the complexity of stereotactic
interventions (Dos Santos Ghilardi etal. 2018). Such innova-
tions require detailed understanding and accurate maps of
the 3D microscopic neuroanatomy.
Current white matter tract visualization methods include
invivo and post mortem techniques. Diffusion tensor imag-
ing (DTI) and tractography, introduced in the early 1990s
(Pierpaoli etal. 1996; Mori etal. 1999), allow invivo
* Eduardo Joaquim Lopes Alho
eduardoalho@hotmail.com
1 Morphological Brain Research Unit, Department
ofPsychiatry, University ofWürzburg, Würzburg, Germany
2 Division ofFunctional Neurosurgery, Department
ofNeurology, University ofSão Paulo Medical School, Rua
Dr. Ovidio Pires de Campos, 785, SãoPaulo01060-970,
Brazil
3 Laboratory forMedical Investigations 44, Department
ofRadiology, São Paulo Medical School, SãoPaulo, Brazil
4 Eulerian-Solutions E.U, Linz, Austria
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