Three dimensional Polarized Light Imaging (3D-PLI) is an optical technique which allows mapping the spatial fiber architecture of fibrous postmortem tissues, at sub-millimeter resolutions. Here, we propose an analytical and fast approach to compute the fiber orientation distribution (FOD) from high-resolution vector data provided by 3D-PLI. The FOD is modeled as a sum of K orientations/Diracs on the unit sphere, described on a spherical harmonics basis and analytically computed using the spherical Fourier transform. Experiments are performed on rich synthetic data which simulate the geometry of the neuronal fibers and on human brain data. Results indicate the analytical FOD is computationally efficient and very fast, and has high angular precision and angular resolution. Furthermore, investigations on the right occipital lobe illustrate that our strategy of FOD computation enables the bridging of spatial scales from microscopic 3D-PLI information to macro- or mesoscopic dimensions of diffusion Magnetic Resonance Imaging (MRI), while being a means to evaluate prospective resolution limits for diffusion MRI to reconstruct region-specific white matter tracts. These results demonstrate the interest and great potential of our analytical approach.
High spatio-angular resolution diffusion MRI (dMRI) has been shown to provide accurate identification of complex neuronal fiber configurations, albeit, at the cost of long acquisition times. We propose a method to recover intra-voxel fiber configurations at high spatio-angular resolution relying on a 3D kq-space under-sampling scheme to enable accelerated acquisitions. Simulations and real data analysis suggest that accurate FOD mapping can be achieved from severe kq-space under-sampling regimes potentially enabling high spatio-angular resolution dMRI in the clinical setting.
A novel method for automated assessment of directions of collagen fibers in soft tissues is presented. It is based on multiple rotated images obtained via polarized light microscope with perpendicular and inclined polarizers and thus it breaks the limitation of 90° periodicity of polarized light intensity and evaluates the fiber orientation over the whole 180° range accurately and quickly. After having verified the method, we used histological specimens of porcine Achilles tendon and aorta to validate the proposed algorithm and to lower the number of rotated images needed for evaluation. Our a…
Knowledge of appropriate local fiber architecture is necessary to simulate patient-specific electromechanics in the human heart. However, it is not yet possible to reliably measure in-vivo fiber directions, especially in human atria. Thus, we present a method which defines the fiber architecture in arbitrarily shaped atria using image registration and reorientation methods based on atlas atria with fibers predefined from detailed histological observations. Thereby, it is possible to generate detailed fiber families in every new patient-specific geometry in an automated, time-efficient process.…
3D scattered light imaging: extracting 3D fiber orientations from 1D line profiles in brain imaging
Forschungszentrum Juelich（于利希研究中心）；University of Wuppertal（伍珀塔尔大学）；University of Twente（特文特大学）；Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences（荷兰神经科学研究所，荷兰皇家艺术与科学院）
Pontificia Universidad Católica de Chile（智利天主教大学）；University of Graz（格拉茨大学）；Medical University of Graz（格拉茨医科大学）；University of Pennsylvania（宾夕法尼亚大学）；Università della Svizzera italiana（瑞士意大利语区大学）
We propose FiberNet, a method to estimate \emph{in-vivo} the cardiac fiber architecture of the human atria from multiple catheter recordings of the electrical activation. Cardiac fibers play a central role in the electro-mechanical function of the heart, yet they are difficult to determine in-vivo, and hence rarely truly patient-specific in existing cardiac models. FiberNet learns the fiber arrangement by solving an inverse problem with physics-informed neural networks. The inverse problem amounts to identifying the conduction velocity tensor of a cardiac propagation model from a set of sparse…
Fiber-like features are an important aspect of breast imaging. Vessels and ducts are present in all breast images, and spiculations radiating from a mass can indicate malignancy. Accordingly, fiber objects are one of the three types of signals used in the American College of Radiology digital mammography (ACR-DM) accreditation phantom. This work focuses on the image properties of fiber-like structures in digital breast tomosynthesis (DBT) and how image reconstruction can affect their appearance. The impact of DBT image reconstruction algorithm and regularization strength on the conspicuity of …
More children and adults under the age of 40 die of brain tumor than from any other cancer. Brain surgery constitutes the first and decisive step for the treatment of such tumors. It is extremely crucial to achieve complete tumor resection during surgery, however, this is a highly challenging task, as it is very difficult to visually differentiate tumorous cells from the surrounding healthy white matter. The nerve fiber bundles constitutive of the white matter are organized in such a way that they exhibit a certain degree of structural anisotropy and birefringence. The birefringence exhibited …
Diffusion tractography is routinely used to study white matter architecture and brain connectivity in vivo. A key step for successful tractography of neuronal tracts is the correct identification of tract directions in each voxel. Here we propose a fingerprinting-based methodology to identify these fiber directions in Orientation Distribution Functions, dubbed ODF-Fingerprinting (ODF-FP). In ODF-FP, fiber configurations are selected based on the similarity between measured ODFs and elements in a pre-computed library. In noisy ODFs, the library matching algorithm penalizes the more complex fibe…
Objective: Soft-tissue sarcoma spreads preferentially along muscle fibers. We explore the utility of deriving muscle fiber orientations from diffusion tensor MRI (DT-MRI) for defining the boundary of the clinical target volume in muscle tissue. Approach: We recruited eight healthy volunteers to acquire MR images of the left and right thigh. The imaging session consisted of (a) two MRI spin-echo-based scans, T1- and T2-weighted; (b) a diffusion weighted (DW) spin-echo-based scan using an echo planar acquisition with fat suppression. The thigh muscles were auto-segmented using CNN. DT-MRI data w…
Ground-truth effects in learning-based fiber orientation distribution estimation in neonatal brains
Signal Processing Laboratory (LTS5)（信号处理实验室）；École Polytechnique Fédérale de Lausanne (EPFL)（瑞士联邦理工学院洛桑分校）；Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL)（洛桑大学医院放射科及洛桑大学）；College of Electronic and Information Engineering, Tongji University（同济大学电子与信息学院）；CIBM Center for Biomedical Imaging（生物医学成像中心）；Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital and Harvard Medical School（波士顿儿童医院放射科计算放射实验室及哈佛医学院）；Department of Radiological Sciences, University of California Irvine（加州大学 Irvine 分校放射科学系）
Characterizing the properties and orientations of sub-voxel fiber populations, although essential to study white-matter architecture, microstructure and connectivity, remains one of the main challenges faced by the MRI microstructure community. While some progress has been made in overcoming this challenge using models, signal representations and tractography algorithms, these approaches are ultimately limited by their key assumptions or by the lack of specificity of the diffusion signal alone. In order to alleviate these limitations, we combine diffusion-relaxation MR acquisitions incorporati…
Previous simulation studies by Menzel et al. [Phys. Rev. X 10, 021002 (2020)] have shown that scattering patterns of light transmitted through artificial nerve fiber constellations contain valuable information about the tissue substructure such as the individual fiber orientations in regions with crossing nerve fibers. Here, we present a method that measures these scattering patterns in monkey and human brain tissue using coherent Fourier scatterometry with normally incident light. By transmitting a non-focused laser beam (wavelength of 633 nm) through unstained histological brain sections, we…
