Longitudinal Chinese Population Structural Fetal Brain Atlases Construction: toward precise fetal brain segmentation.

In magnetic resonance imaging (MRI) studies of fetal brain development, structural brain atlases usually serve as essential references for the fetal population. Individual images are spatially normalized into a common or standard atlas space to extract regional information on volumetric or morphological brain variations. However, the existing fetal brain atlases are mostly based on MR images obtained from Caucasian populations and thus are not ideal for the characterization of the brains of the Chinese population due to neuroanatomical differences related to genetic factors. In this paper, we use an unbiased template construction algorithm to create a set of age-specific Chinese fetal atlases between 21-35 weeks of gestation from 115 normally developing fetal brains. Based on the 4D spatiotemporal atlas, the morphologically developmental patterns, e.g., cortical thickness, sulcal and gyral patterns, were quantified from in utero MRI. Additionally, after applying the Chinese fetal atlases and Caucasian fetal atlases to an independent Chinese pediatric dataset, we find that the Chinese fetal atlases result in significantly higher accuracy than the Caucasian fetal atlases in guiding brain tissue segmentation. These results suggest that the Chinese fetal brain atlases are necessary for quantitative analysis of the typical and atypical development of the Chinese fetal population in the future.

Age-specific structural fetal brain atlases construction and cortical development quantification for chinese population.

In magnetic resonance imaging (MRI) studies of fetal brain development, structural brain atlases usually serve as essential references for the fetal population. Individual images are usually normalized into a common or standard space for analysis. However, the existing fetal brain atlases are mostly based on MR images obtained from Caucasian populations and thus are not ideal for the characterization of the fetal Chinese population due to neuroanatomical differences related to genetic factors. In this paper, we use an unbiased template construction algorithm to create a set of age-specific Chinese fetal atlases between 21-35 weeks of gestation from 115 normal fetal brains. Based on the 4D spatiotemporal atlas, the morphological development patterns, e.g., cortical thickness, cortical surface area, sulcal and gyral patterns, were quantified. The fetal brain abnormalities were detected when referencing the age-specific template. Additionally, a direct comparison of the Chinese fetal atlases and Caucasian fetal atlases reveals dramatic anatomical differences, mainly in the medial frontal and temporal regions. After applying the Chinese and Caucasian fetal atlases separately to an independent Chinese fetal brain dataset, we find that the Chinese fetal atlases result in significantly higher accuracy than the Caucasian fetal atlases in guiding brain tissue segmentation. These results suggest that the Chinese fetal brain atlases are necessary for quantitative analysis of the typical and atypical development of the Chinese fetal population in the future. The atlases with their parcellations are now publicly available at https://github.com/DeepBMI/FBA-Chinese.

HybraPD atlas: Towards precise subcortical nuclei segmentation using multimodality medical images in patients with Parkinson disease.

Human brain atlases are essential for research and surgical treatment of Parkinson's disease (PD). For example, deep brain stimulation for PD often requires human brain atlases for brain structure identification. However, few atlases can provide disease-specific subcortical structures for PD, and most of them are based on T1w and T2w images. In this work, we construct a HybraPD atlas using fused quantitative susceptibility mapping (QSM) and T1w images from 87 patients with PD. The constructed HybraPD atlas provides a series of templates, that is, T1w, GRE magnitude, QSM, R2*, and brain tissue probabilistic maps. Then, we manually delineate a parcellation map with 12 bilateral subcortical nuclei, which are highly related to PD pathology, such as sub-regions in globus pallidus and substantia nigra. Furthermore, we build a whole-brain parcellation map by combining existing cortical parcellation and white-matter segmentation with the proposed subcortical nuclei map. Considering the multimodality of the HybraPD atlas, the segmentation accuracy of each nucleus is evaluated using T1w and QSM templates, respectively. The results show that the HybraPD atlas provides more accurate segmentation than existing atlases. Moreover, we analyze the metabolic difference in subcortical nuclei between PD patients and healthy control subjects by applying the HybraPD atlas to calculate uptake values of contrast agents on positron emission tomography (PET) images. The atlas-based analysis generates accurate disease-related brain nuclei segmentation on PET images. The newly developed HybraPD atlas could serve as an efficient template to study brain pathological alterations in subcortical regions for PD research.

Quantification of the bone lacunocanalicular network from 3D X-ray phase nanotomography images.

There is a growing interest in developing 3D microscopy for the exploration of thick biological tissues. Recently, 3D X-ray nanocomputerised tomography has proven to be a suitable technique for imaging the bone lacunocanalicular network. This interconnected structure is hosting the osteocytes which play a major role in maintaining bone quality through remodelling processes. 3D images have the potential to reveal the architecture of cellular networks, but their quantitative analysis remains a challenge due to the density and complexity of nanometre sized structures and the need to handle and process large datasets, for example, 20483 voxels corresponding to 32 GB per individual image in our case. In this work, we propose an efficient image processing approach for the segmentation of the network and the extraction of characteristic parameters describing the 3D structure. These parameters include the density of lacunae, the porosity of lacunae and canaliculi, and morphological features of lacunae (volume, surface area, lengths, anisotropy etc.). We also introduce additional parameters describing the local environment of each lacuna and its canaliculi. The method is applied to analyse eight human femoral cortical bone samples imaged by magnified X-ray phase nanotomography with a voxel size of 120 nm, which was found to be a good compromise to resolve canaliculi while keeping a sufficiently large field of view of 246 µm in 3D. The analysis was performed on a total of 2077 lacunae showing an average length, width and depth of 17.1 µm × 9.2 µm × 4.4 µm, with an average number of 58.2 canaliculi per lacuna and a total lacuno-canalicular porosity of 1.12%. The reported descriptive parameters provide information on the 3D organisation of the lacuno-canalicular network in human bones.

Assessment of the human bone lacuno-canalicular network at the nanoscale and impact of spatial resolution.

Recently, increasing attention has been given to the study of osteocytes, the cells that are thought to play an important role in bone remodeling and in the mechanisms of bone fragility. The interconnected osteocyte system is deeply embedded inside the mineralized bone matrix and lies within a closely fitted porosity known as the lacuno-canalicular network. However, quantitative data on human samples remain scarce, mostly measured in 2D, and there are gaps to be filled in terms of spatial resolution. In this work, we present data on femoral samples from female donors imaged with isotropic 3D spatial resolution by magnified X-ray phase nano computerized-tomography. We report quantitative results on the 3D structure of canaliculi in human femoral bone imaged with a voxel size of 30 nm. We found that the lacuno-canalicular porosity occupies on average 1.45% of the total tissue volume, the ratio of the canalicular versus lacunar porosity is about 37.7%, and the primary number of canaliculi stemming from each lacuna is 79 on average. The examination of this number at different distances from the surface of the lacunae demonstrates branching in the canaliculi network. We analyzed the impact of spatial resolution on quantification by comparing parameters extracted from the same samples imaged with 120 nm and 30 nm voxel sizes. To avoid any bias related to the analysis region, the volumes at 120 nm and 30 nm were registered and cropped to the same field of view. Our results show that the measurements at 120 and 30 nm are strongly correlated in our data set but that the highest spatial resolution provides more accurate information on the canaliculi network and its branching properties.

Anisotropic elastic properties of human femoral cortical bone and relationships with composition and microstructure in elderly.

The strong dependence between cortical bone elasticity at the millimetre-scale (mesoscale) and cortical porosity has been evidenced by previous studies. However, bone is an anisotropic composite material made by mineral, proteins and water assembled in a hierarchical structure. Whether the variations of structural and compositional properties of bone affect the different elastic coefficients at the mesoscale is not clear. Aiming to understand the relationships between bone elastic properties and compositions and microstructure, we applied state-of-the-art experimental modalities to assess these aspects of bone characteristics. All elastic coefficients (stiffness tensor of the transverse isotropic bone material), structure of the vascular pore network, collagen and mineral properties were measured in 52 specimens from the femoral diaphysis of 26 elderly donors. Statistical analyses and micromechanical modeling showed that vascular pore volume fraction and the degree of mineralization of bone are the most important determinants of cortical bone anisotropic mesoscopic elasticity. Though significant correlations were observed between collagen properties and elasticity, their effects in bone mesoscopic elasticity were minor in our data. This work also provides a unique set of data exhibiting a range of variations of compositional and microstructural cortical bone properties in the elderly and gives strong experimental evidence and basis for further development of biomechanical models for human cortical bone. STATEMENT OF SIGNIFICANCE: This study reports the relationships between microstructure, composition and the mesoscale anisotropic elastic properties of human femoral cortical bone in elderly. For the first time, we provide data covering the complete anisotropic elastic tensor, the microstructure of cortical vascular porosity, mineral and collagen characteristics obtained from the same or adjacent samples in each donor. The results revealed that cortical vascular porosity and degree of mineralization of bone are the most important determinants of bone anisotropic stiffness at the mesoscale. The presented data gives strong experimental evidence and basis for further development of biomechanical models for human cortical bone.

Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue.

X-ray phase contrast imaging offers higher sensitivity compared to conventional X-ray attenuation imaging and can be simply implemented by propagation when using a partially coherent synchrotron beam. We address the phase retrieval in in-line phase nano-CT using multiple propagation distances. We derive a method which extends Paganin's single distance method and compare it to the contrast transfer function (CTF) approach in the case of a homogeneous object. The methods are applied to phase nano-CT data acquired at the voxel size of 30 nm (ID16A, ESRF, Grenoble, France). Our results show a gain in image quality in terms of the signal-to-noise ratio and spatial resolution when using four distances instead of one. The extended Paganin's method followed by an iterative refinement step provides the best reconstructions while the homogeneous CTF method delivers quasi comparable results for our data, even without refinement step.