Quantifying morphological parameters of the terminal branching units in a mouse lung by phase contrast synchrotron radiation computed tomography

Airspace Diameter Map-A Quantitative Measurement of All Pulmonary Airspaces to Characterize Structural Lung Diseases

(1) Background: Stereological estimations significantly contributed to our understanding of lung anatomy and physiology. Taking stereology fully 3-dimensional facilitates the estimation of novel parameters. (2) Methods: We developed a protocol for the analysis of all airspaces of an entire lung. It includes (i) high-resolution synchrotron radiation-based X-ray tomographic microscopy, (ii) image segmentation using the free machine-learning tool Ilastik and ImageJ, and (iii) calculation of the airspace diameter distribution using a diameter map function. To evaluate the new pipeline, lungs from adult mice with cystic fibrosis (CF)-like lung disease (βENaC-transgenic mice) or mice with elastase-induced emphysema were compared to healthy controls. (3) Results: We were able to show the distribution of airspace diameters throughout the entire lung, as well as separately for the conducting airways and the gas exchange area. In the pathobiological context, we observed an irregular widening of parenchymal airspaces in mice with CF-like lung disease and elastase-induced emphysema. Comparable results were obtained when analyzing lungs imaged with μCT, sugges-ting that our pipeline is applicable to different kinds of imaging modalities. (4) Conclusions: We conclude that the airspace diameter map is well suited for a detailed analysis of unevenly distri-buted structural alterations in chronic muco-obstructive lung diseases such as cystic fibrosis and COPD.

Preclinical hyperpolarized 129 Xe MRI: ventilation and T2 * mapping in mouse lungs at 7 T using multi-echo flyback UTE

Fast apparent transverse relaxation (short T₂ *) is a common obstacle when attempting to perform quantitative ¹ H MRI of the lungs. While T₂ * times are longer for pulmonary hyperpolarized (HP) gas functional imaging (in particular for gaseous ¹²⁹ Xe), T₂ * can still lead to quantitative inaccuracies for sequences requiring longer echo times (such as diffusion weighted images) or longer readout duration (such as spiral sequences). This is especially true in preclinical studies, where high magnetic fields lead to shorter relaxation times than are typically seen in human studies. However, the T₂ * of HP ¹²⁹ Xe in the most common animal model of human disease (mice) has not been reported. Herein, we present a multi-echo radial flyback imaging sequence and use it to measure HP ¹²⁹ Xe T₂ * at 7 T under a variety of respiratory conditions. This sequence mitigates the impact of T₁ relaxation outside the animal by using multiple gradient-refocused echoes to acquire images at a number of effective echo times for each RF excitation. After validating the sequence using a phantom containing water doped with superparamagnetic iron oxide nanoparticles, we measured the ¹²⁹ Xe T₂ * in vivo for 10 healthy C57Bl/6 J mice and found T₂ * ~ 5 ms in the lung airspaces. Interestingly, T₂ * was relatively constant over all experimental conditions, and varied significantly with sex, but not age, mass, or the O₂ content of the inhaled gas mixture. These results are discussed in the context of T₂ * relaxation within porous media.

Micrometer-resolution X-ray tomographic full-volume reconstruction of an intact post-mortem juvenile rat lung

In this article, we present an X-ray tomographic imaging method that is well suited for pulmonary disease studies in animal models to resolve the full pathway from gas intake to gas exchange. Current state-of-the-art synchrotron-based tomographic phase-contrast imaging methods allow for three-dimensional microscopic imaging data to be acquired non-destructively in scan times of the order of seconds with good soft tissue contrast. However, when studying multi-scale hierarchically structured objects, such as the mammalian lung, the overall sample size typically exceeds the field of view illuminated by the X-rays in a single scan and the necessity for achieving a high spatial resolution conflicts with the need to image the whole sample. Several image stitching and calibration techniques to achieve extended high-resolution fields of view have been reported, but those approaches tend to fail when imaging non-stable samples, thus precluding tomographic measurements of large biological samples, which are prone to degradation and motion during extended scan times. In this work, we demonstrate a full-volume three-dimensional reconstruction of an intact rat lung under immediate post-mortem conditions and at an isotropic voxel size of (2.75 µm)³. We present the methodology for collecting multiple local tomographies with 360° extended field of view scans followed by locally non-rigid volumetric stitching. Applied to the lung, it allows to resolve the entire pulmonary structure from the trachea down to the parenchyma in a single dataset. The complete dataset is available online (https://doi.org/10.16907/7eb141d3-11f1-47a6-9d0e-76f8832ed1b2).

Three-dimensional visualization of microvasculature from few-projection data using a novel CT reconstruction algorithm for propagation-based X-ray phase-contrast imaging

Propagation-based X-ray phase-contrast imaging (PBI) is a powerful nondestructive imaging technique that can reveal the internal detailed structures in weakly absorbing samples. Extending PBI to CT (PBCT) enables high-resolution and high-contrast 3D visualization of microvasculature, which can be used for the understanding, diagnosis and therapy of diseases involving vasculopathy, such as cardiovascular disease, stroke and tumor. However, the long scan time for PBCT impedes its wider use in biomedical and preclinical microvascular studies. To address this issue, a novel CT reconstruction algorithm for PBCT is presented that aims at shortening the scan time for microvascular samples by reducing the number of projections while maintaining the high quality of reconstructed images. The proposed algorithm combines the filtered backprojection method into the iterative reconstruction framework, and a weighted guided image filtering approach (WGIF) is utilized to optimize the intermediate reconstructed images. Notably, the homogeneity assumption on the microvasculature sample is adopted as prior knowledge, and therefore, a prior image of microvasculature structures can be acquired by a k-means clustering approach. Then, the prior image is used as the guided image in the WGIF procedure to effectively suppress streaking artifacts and preserve microvasculature structures. To evaluate the effectiveness and capability of the proposed algorithm, simulation experiments on 3D microvasculature numerical phantom and real experiments with CT reconstruction on the microvasculature sample are performed. The results demonstrate that the proposed algorithm can, under noise-free and noisy conditions, significantly reduce the artifacts and effectively preserve the microvasculature structures on the reconstructed images and thus enables it to be used for clear and accurate 3D visualization of microvasculature from few-projection data. Therefore, for 3D visualization of microvasculature, the proposed algorithm can be considered an effective approach for reducing the scan time required by PBCT.

lapdMouse: associating lung anatomy with local particle deposition in mice

To facilitate computational toxicology, we developed an approach for generating high-resolution lung-anatomy and particle-deposition mouse models. Major processing steps of our method include mouse preparation, serial block-face cryomicrotome imaging, and highly automated image analysis for generating three-dimensional (3D) mesh-based models and volume-based models of lung anatomy (airways, lobes, sublobes, and near-acini structures) that are linked to local particle-deposition measurements. Analysis resulted in 34 mouse models covering 4 different mouse strains (B6C3F1: 8, BALB/C: 11, C57Bl/6: 8, and CD-1: 7) as well as both sexes (16 male and 18 female) and different particle sizes [2 μm (n = 15), 1 μm (n = 16), and 0.5 μm (n = 3)]. On average, resulting mouse airway models had 1,616.9 ± 298.1 segments, a centerline length of 597.6 ± 59.8 mm, and 1,968.9 ± 296.3 outlet regions. In addition to 3D geometric lung models, matching detailed relative particle-deposition measurements are provided. All data sets are available online in the lapdMouse archive for download. The presented approach enables linking relative particle deposition to anatomical structures like airways. This will in turn improve the understanding of site-specific airflows and how they affect drug, environmental, or biological aerosol deposition.NEW & NOTEWORTHY Computer simulations of particle deposition in mouse lungs play an important role in computational toxicology. Until now, a limiting factor was the lack of high-resolution mouse lung models and measured local particle-deposition information, which are required for developing accurate modeling approaches (e.g., computational fluid dynamics). With the developed imaging and analysis approach, we address this issue and provide all of the raw and processed data in a publicly accessible repository.

Alteration of lens and retina textures from mice embryos with folic acid deficiency: image processing analysis

PURPOSE

Folic acid (FA) is an essential vitamin for embryonic development. It plays particularly a critical role in RNA, DNA and protein synthesis. On the other hand, the collagen IV and laminin-1 are important proteins during embryonic development. This study was done to find if FA deficiency at a short and a long term in mothers could alter the tissue texture of retina and lens of the progeny.

METHODS

Collagen IV and laminin-1 were localized by immunohistochemistry in the lens and retina of the FA-deficient embryos. To carry out the image processing, texture segmentation was performed through canny edge detection and Fourier transform (FT). We defined a parameter, the grain size, to describe the texture of the lens and retina. A bootstrap method to estimate the distribution and confidence intervals of the mean, standard deviation, skewness and kurtosis of the grain size has been developed.

RESULTS

Analysis through image processing using Matlab showed changes in the grain size between control- and FA-deficient groups in both studied molecules. Measures of texture based on FT exhibited changes in the directionality and arrangements of type IV collagen and laminin-1.

CONCLUSIONS

Changes introduced by FA deficiency were visible in the short term (2 weeks) and evident in the long term (8 weeks) in both grain size and orientation of fibre structures in the tissues analysed (lens and retina). This is the first work devoted to study the effect of FA deficit in the texture of eye tissues using image processing techniques.

Remodeling of alveolar septa after murine pneumonectomy

In most mammals, removing one lung (pneumonectomy) results in the compensatory growth of the remaining lung. In mice, stereological observations have demonstrated an increase in the number of mature alveoli; however, anatomic evidence of the early phases of alveolar growth has remained elusive. To identify changes in the lung microstructure associated with neoalveolarization, we used tissue histology, electron microscopy, and synchrotron imaging to examine the configuration of the alveolar duct after murine pneumonectomy. Systematic histological examination of the cardiac lobe demonstrated no change in the relative frequency of dihedral angle components (Ends, Bends, and Junctions) (P > 0.05), but a significant decrease in the length of a subset of septal ends ("E"). Septal retraction, observed in 20-30% of the alveolar ducts, was maximal on day 3 after pneumonectomy (P < 0.01) and returned to baseline levels within 3 wk. Consistent with septal retraction, the postpneumonectomy alveolar duct diameter ratio (Dout:Din) was significantly lower 3 days after pneumonectomy compared to all controls except for the detergent-treated lung (P < 0.001). To identify clumped capillaries predicted by septal retraction, vascular casting, analyzed by both scanning electron microscopy and synchrotron imaging, demonstrated matted capillaries that were most prominent 3 days after pneumonectomy. Numerical simulations suggested that septal retraction could reflect increased surface tension within the alveolar duct, resulting in a new equilibrium at a higher total energy and lower surface area. The spatial and temporal association of these microstructural changes with postpneumonectomy lung growth suggests that these changes represent an early phase of alveolar duct remodeling.

3D angioarchitecture changes after spinal cord injury in rats using synchrotron radiation phase-contrast tomography

STUDY DESIGN

A basic experiment study.

OBJECTIVES

An understanding of the three-dimensional (3D) angioarchitecture changes that occur after SCI will improve our knowledge of the pathogenesis of SCI and aid in the development of valuable therapeutic strategies to improve its poor outcomes. Our aim was to visualize the normal and traumatized spinal angioarchitecture in 3D using a high-resolution synchrotron radiation phase-contrast tomography (SR-PCT) and evaluate its diagnostic capability.

SETTING

SCI Center of Xiangya Hospital of Central South University in China.

METHODS

SR-PCT was used as novel high-resolution imaging tool to detect 3D morphological alterations in spinal cord microvasculature after injury.

RESULTS

In a rat model, the morphology of the microvasculature on 2D digital slices was matched with histological findings in both the normal and injured spinal cord. 3D angioarchitecture changes after SCI were successfully obtained via SR-PCT without the use of a contrast agent. Quantitative analysis on 3D images of the injured spinal cord revealed a significant decrease in the number and volume of vascular networks. This was especially relevant to vessels with a diameter <50 μm.

CONCLUSION

The 3D local blood supply to the spinal cord was severely disrupted after the acute violent injury. Our results indicate that the use of SR-PCT may improve our understanding of the pathogenesis of SCI and provide a new approach to the morphological investigation of neurovascular diseases in preclinical research.

Emphysema early diagnosis using X-ray diffraction enhanced imaging at synchrotron light source

Background

Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and mortality worldwide, and emphysema is a common component of COPD. Currently, it is very difficult to detect early stage emphysema using conventional radiographic imaging without contrast agents, because the change in X-ray attenuation is not detectable with absorption-based radiography. Compared with the absorption-based CT, phase contrast imaging has more advantages in soft tissue imaging, because of its high spatial resolution and contrast.

Methods

In this article, we used diffraction enhanced imaging (DEI) method to get the images of early stage emphysematous and healthy samples, then extract X-ray absorption, refraction, and ultra-small-angle X-ray scattering (USAXS) information from DEI images using multiple image radiography (MIR). We combined the absorption image with the USAXS image by a scatter plot. The critical threshold in the scatter plot was calibrated using the linear discriminant function in the pattern recognition.

Results

USAXS image was sensitive to the change of tissue micro-structure, it could show the lesions which were invisible in the absorption image. Combined with the absorption-based image, the USAXS information enabled better discrimination between healthy and emphysematous lung tissue in a mouse model. The false-color images demonstrated that our method was capable of classifying healthy and emphysematous tissues.

Conclusion

Here we present USAXS images of early stage emphysematous and healthy samples, where the dependence of the USAXS signal on micro-structures of biomedical samples leads to improved diagnosis of emphysema in lung radiographs.

Role of Alveolar Topology on Acinar Flows and Convective Mixing

Due to experimental challenges, computational simulations are often sought to quantify inhaled aerosol transport in the pulmonary acinus. Commonly, these are performed using generic alveolar topologies, including spheres, toroids, and polyhedra, to mimic the complex acinar morphology. Yet, local acinar flows and ensuing particle transport are anticipated to be influenced by the specific morphological structures. We have assessed a range of acinar models under self-similar breathing conditions with respect to alveolar flow patterns, convective flow mixing, and deposition of fine particles (1.3 μm diameter). By tracking passive tracers over cumulative breathing cycles, we find that irreversible flow mixing correlates with the location and strength of the recirculating vortex inside the cavity. Such effects are strongest in proximal acinar generations where the ratio of alveolar to ductal flow rates is low and interalveolar disparities are most apparent. Our results for multi-alveolated acinar ducts highlight that fine 1 μm inhaled particles subject to alveolar flows are sensitive to the alveolar topology, underlining interalveolar disparities in particle deposition patterns. Despite the simplicity of the acinar models investigated, our findings suggest that alveolar topologies influence more significantly local flow patterns and deposition sites of fine particles for upper generations emphasizing the importance of the selected acinar model. In distal acinar generations, however, the alveolar geometry primarily needs to mimic the space-filling alveolar arrangement dictated by lung morphology.

In-line phase contrast imaging of hepatic portal vein embolization with radiolucent embolic agents in mice: a preliminary study

It is crucial to understand the distribution of embolic agents inside target liver during and after the hepatic portal vein embolization (PVE) procedure. For a long time, the problem has not been well solved due to the radiolucency of embolic agents and the resolution limitation of conventional radiography. In this study, we first reported use of fluorescent carboxyl microspheres (FCM) as radiolucent embolic agents for embolizing hepatic portal veins. The fluorescent characteristic of FCM could help to determine their approximate location easily. Additionally, the microspheres were found to be fairly good embolizing agents for PVE. After the livers were excised and fixed, they were imaged by in-line phase contrast imaging (PCI), which greatly improved the detection of the radiolucent embolic agents as compared to absorption contrast imaging (ACI). The preliminary study has for the first time shown that PCI has great potential in the pre-clinical investigation of PVE with radiolucent embolic agents.