X-ray phase-contrast CT of a pancreatic ductal adenocarcinoma mouse model

Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach

The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.

Three-dimensional analysis of human pancreatic cancer specimens by phase-contrast based X-ray tomography - the next dimension of diagnosis

BACKGROUND

The worldwide increase of pancreatic ductal adenocarcinoma (PDAC), which still has one of the lowest survival rates, requires novel imaging tools to improve early detection and to refine diagnosis. Therefore, the aim of this study was to assess the feasibility of propagation-based phase-contrast X-ray computed tomography of already paraffin-embedded and unlabeled human pancreatic tumor tissue to achieve a detailed three-dimensional (3D) view of the tumor sample in its entirety.

METHODS

Punch biopsies of areas of particular interest were taken from paraffin blocks after initial histological analysis of hematoxylin and eosin stained tumor sections. To cover the entire 3.5 mm diameter of the punch biopsy, nine individual tomograms with overlapping regions were acquired in a synchrotron parallel beam configuration and stitched together after data reconstruction. Due to the intrinsic contrast based on electron density differences of tissue components and a voxel size of 1.3 μm achieved PDAC and its precursors were clearly identified.

RESULTS

Characteristic tissue structures for PDAC and its precursors, such as dilated pancreatic ducts, altered ductal epithelium, diffuse immune cell infiltrations, increased occurrence of tumor stroma and perineural invasion were clearly identified. Certain structures of interest were visualized in three dimensions throughout the tissue punch. Pancreatic duct ectasia of different caliber and atypical shape as well as perineural infiltration could be contiguously traced by viewing serial tomographic slices and by applying semi-automatic segmentation. Histological validation of corresponding sections confirmed the former identified PDAC features.

CONCLUSION

In conclusion, virtual 3D histology via phase-contrast X-ray tomography visualizes diagnostically relevant tissue structures of PDAC in their entirety, preserving tissue integrity in label-free, paraffin embedded tissue biopsies. In the future, this will not only enable a more comprehensive diagnosis but also a possible identification of new 3D imaging tumor markers.

Quantitative X-ray phase contrast computed tomography with grating interferometry : Biomedical applications of quantitative X-ray grating-based phase contrast computed tomography

The ability of biomedical imaging data to be of quantitative nature is getting increasingly important with the ongoing developments in data science. In contrast to conventional attenuation-based X-ray imaging, grating-based phase contrast computed tomography (GBPC-CT) is a phase contrast micro-CT imaging technique that can provide high soft tissue contrast at high spatial resolution. While there is a variety of different phase contrast imaging techniques, GBPC-CT can be applied with laboratory X-ray sources and enables quantitative determination of electron density and effective atomic number. In this review article, we present quantitative GBPC-CT with the focus on biomedical applications.

Dosimetric assessment of the exposure of radiotherapy patients due to cone-beam CT procedures

Cone-beam computed tomography (CBCT) is widely used for pre-treatment verification and patient setup in image-guided radiation therapy (IGRT). CBCT imaging is employed daily and several times per patient, resulting in potentially high cumulative imaging doses to healthy tissues that surround exposed target organs. Computed tomography dose index (CTDI) is the parameter used by CBCT equipment as indication of the radiation output to patients. This study aimed to increase the knowledge on the relation between CBCT organ doses and weighted CTDI (CTDI_W) for a thorax scanning protocol. A CBCT system was modelled using the Monte Carlo (MC) radiation transport program MCNPX2.7.0. Simulation results were validated against half-value layer (HVL), axial beam profile, patient skin dose (PSD) and CTDI measurements. For organ dose calculations, a male voxel phantom ("Golem") was implemented with the CBCT scanner computational model. After a successful MC model validation with measurements, a systematic comparison was performed between organ doses (and their distribution) and CTDI dosimetry concepts [CTDI_W and cumulative dose quantities f₁₀₀(150) and [Formula: see text]]. The results obtained show that CBCT organ doses vary between 1.2 ± 0.1 mGy and 3.3 ± 0.2 mGy for organs located within the primary beam. It was also verified that CTDI_W allows prediction of absorbed doses to tissues at distances of about 5 cm from the isocentre of the CBCT system, whereas f₁₀₀(150) allows prediction of organ doses at distances of about 10 cm from the isocentre, independently from its location. This study demonstrates that these dosimetric concepts are suitable methods that easily allow a good approximation of the additional CBCT imaging doses during a typical lung cancer IGRT treatment.

Qualitative and Quantitative Imaging Evaluation of Renal Cell Carcinoma Subtypes with Grating-based X-ray Phase-contrast CT

Current clinical imaging methods face limitations in the detection and correct characterization of different subtypes of renal cell carcinoma (RCC), while these are important for therapy and prognosis. The present study evaluates the potential of grating-based X-ray phase-contrast computed tomography (gbPC-CT) for visualization and characterization of human RCC subtypes. The imaging results for 23 ex vivo formalin-fixed human kidney specimens obtained with phase-contrast CT were compared to the results of the absorption-based CT (gbCT), clinical CT and a 3T MRI and validated using histology. Regions of interest were placed on each specimen for quantitative evaluation. Qualitative and quantitative gbPC-CT imaging could significantly discriminate between normal kidney cortex (54 ± 4 HUp) and clear cell (42 ± 10), papillary (43 ± 6) and chromophobe RCCs (39 ± 7), p < 0.05 respectively. The sensitivity for detection of tumor areas was 100%, 50% and 40% for gbPC-CT, gbCT and clinical CT, respectively. RCC architecture like fibrous strands, pseudocapsules, necrosis or hyalinization was depicted clearly in gbPC-CT and was not equally well visualized in gbCT, clinical CT and MRI. The results show that gbPC-CT enables improved discrimination of normal kidney parenchyma and tumorous tissues as well as different soft-tissue components of RCCs without the use of contrast media.

Nondestructive imaging of the internal microstructure of vessels and nerve fibers in rat spinal cord using phase-contrast synchrotron radiation microtomography

The spinal cord is the primary neurological link between the brain and other parts of the body, but unlike those of the brain, advances in spinal cord imaging have been challenged by the more complicated and inhomogeneous anatomy of the spine. Fortunately with the advancement of high technology, phase-contrast synchrotron radiation microtomography has become widespread in scientific research because of its ability to generate high-quality and high-resolution images. In this study, this method has been employed for nondestructive imaging of the internal microstructure of rat spinal cord. Furthermore, digital virtual slices based on phase-contrast synchrotron radiation were compared with conventional histological sections. The three-dimensional internal microstructure of the intramedullary arteries and nerve fibers was vividly detected within the same spinal cord specimen without the application of a stain or contrast agent or sectioning. With the aid of image post-processing, an optimization of vessel and nerve fiber images was obtained. The findings indicated that phase-contrast synchrotron radiation microtomography is unique in the field of three-dimensional imaging and sets novel standards for pathophysiological investigations in various neurovascular diseases.

Mass Density Measurement of Mineralized Tissue with Grating-Based X-Ray Phase Tomography

Establishing the mineral content distribution in highly mineralized tissues, such as bones and teeth, is fundamental in understanding a variety of structural questions ranging from studies of the mechanical properties to improved pathological investigations. However, non-destructive, volumetric and quantitative density measurements of mineralized samples, some of which may extend several mm in size, remain challenging. Here, we demonstrate the potential of grating-based x-ray phase tomography to gain insight into the three-dimensional mass density distribution of tooth tissues in a non-destructive way and with a sensitivity of 85 mg/cm³. Density gradients of 13 − 19% over 1 − 2 mm within typical samples are detected, and local variations in density of 0.4 g/cm³ on a length scale of 0.1 mm are revealed. This method proves to be an excellent quantitative tool for investigations of subtle differences in mineral content of mineralized tissues that can change following treatment or during ageing and healing.

In Vivo Microcomputed Tomography of Nanocrystal-Doped Tissue Engineered Scaffolds

Tissue engineered scaffolds (TES) hold promise for improving the outcome of cell-based therapeutic strategies for a variety of biomedical scenarios, including musculoskeletal injuries, soft tissue repair, and spinal cord injury. Key to TES research and development, and clinical use, is the ability to longitudinally monitor TES location, orientation, integrity, and microstructure following implantation. Here, we describe a strategy for using microcomputed tomography (microCT) to visualize TES following implantation into mice. TES were doped with highly radiopaque gadolinium oxide nanocrystals and were implanted into the hind limbs of mice. Mice underwent serial microCT over 23 weeks. TES were clearly visible over the entire time course. Alginate scaffolds underwent a 20% volume reduction over the first 6 weeks, stabilizing over the next 17 weeks. Agarose scaffold volumes were unchanged. TES attenuation was also unchanged over the entire time course, indicating a lack of nanocrystal dissolution or leakage. Histology at the implant site showed the presence of very mild inflammation, typical for a mild foreign body reaction. Blood work indicated marked elevation in liver enzymes, and hematology measured significant reduction in white blood cell counts. While extrapolation of the X-ray induced effects on hematopoiesis in these mice to humans is not straightforward, clearly this is an area for careful monitoring. Taken together, these data lend strong support that doping TES with radiopaque nanocrystals and performing microCT imaging, represents a possible strategy for enabling serial in vivo monitoring of TES.

Increasing the field of view in grating based X-ray phase contrast imaging using stitched gratings

Grating based X-ray differential phase contrast imaging (DPCI) allows for high contrast imaging of materials with similar absorption characteristics. In the last years' publications, small animals or parts of the human body like breast, hand, joints or blood vessels have been studied. Larger objects could not be investigated due to the restricted field of view limited by the available grating area. In this paper, we report on a new stitching method to increase the grating area significantly: individual gratings are merged on a carrier substrate. Whereas the grating fabrication process is based on the LIGA technology (X-ray lithography and electroplating) different cutting and joining methods have been evaluated. First imaging results using a 2×2 stitched analyzer grating in a Talbot-Lau interferometer have been generated using a conventional polychromatic X-ray source. The image quality and analysis confirm the high potential of the stitching method to increase the field of view considerably.

Assessment of fibrotic tissue and microvascular architecture by in-line phase-contrast imaging in a mouse model of liver fibrosis

PURPOSE

To explore the value of in-line phase-contrast imaging with computed tomography (ILPCI-CT) by synchrotron radiation (SR) for liver fibrosis.

MATERIALS AND METHODS

Liver fibrosis models were set up in 13 BALB/c mice by peritoneal injections of thioacetamide and evaluated by ILPCI-CT. Histological staging was used to categorize liver fibrosis into normal, mild fibrosis and advanced fibrosis groups. Microvessel density (MVD), the ratio of total vessel length to volume (L/V), the ratio of total number of branching points to liver volume (P/V) and the distribution of vessel diameter were assessed.

RESULTS

The CT images showed slightly high-density shadows around the portal tracts in the fibrosis group. Three-dimensional reconstruction can detect vascular and nodular changes on the surface of fibrotic livers. The MVDs between the three groups were significantly different (P = 0.024). L/V was significantly different between the three groups (P = 0.014). There was a positive correlation between MVD and P/V.

CONCLUSION

Fibrous material can be detected by ILPCI-CT even in the early stage of fibrosis. MVD, L/V, P/V and the distribution of vessel diameter were consistent with fibrosis-related angiogenesis progress. Three-dimensional reconstruction is a promising method to visualize morphological changes of the fibrotic liver.

KEY POINTS

• ILPCI-CT can detect fibrous material even in the early stage of liver fibrosis. • MVD, L/V, P/V, and the distribution of vascular diameter reflect pathological angiogenesis. • 3D reconstruction could be a promising approach for detecting liver fibrosis.

High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography

Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds’ internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory.

Statistical iterative reconstruction algorithm for X-ray phase-contrast CT

Grating-based phase-contrast computed tomography (PCCT) is a promising imaging tool on the horizon for pre-clinical and clinical applications. Until now PCCT has been plagued by strong artifacts when dense materials like bones are present. In this paper, we present a new statistical iterative reconstruction algorithm which overcomes this limitation. It makes use of the fact that an X-ray interferometer provides a conventional absorption as well as a dark-field signal in addition to the phase-contrast signal. The method is based on a statistical iterative reconstruction algorithm utilizing maximum-a-posteriori principles and integrating the statistical properties of the raw data as well as information of dense objects gained from the absorption signal. Reconstruction of a pre-clinical mouse scan illustrates that artifacts caused by bones are significantly reduced and image quality is improved when employing our approach. Especially small structures, which are usually lost because of streaks, are recovered in our results. In comparison with the current state-of-the-art algorithms our approach provides significantly improved image quality with respect to quantitative and qualitative results. In summary, we expect that our new statistical iterative reconstruction method to increase the general usability of PCCT imaging for medical diagnosis apart from applications focused solely on soft tissue visualization.

Microcomputed tomography: approaches and applications in bioengineering

Microcomputed tomography (microCT) has become a standard and essential tool for quantifying structure-function relationships, disease progression, and regeneration in preclinical models and has facilitated numerous scientific and bioengineering advancements over the past 30 years. In this article, we recount the early events that led to the initial development of microCT and review microCT approaches for quantitative evaluation of bone, cartilage, and cardiovascular structures, with applications in fundamental structure-function analysis, disease, tissue engineering, and numerical modeling. Finally, we address several next-generation approaches under active investigation to improve spatial resolution, acquisition time, tissue contrast, radiation dose, and functional and molecular information.

Quantitative electron density characterization of soft tissue substitute plastic materials using grating-based x-ray phase-contrast imaging

Many scientific research areas rely on accurate electron density characterization of various materials. For instance in X-ray optics and radiation therapy, there is a need for a fast and reliable technique to quantitatively characterize samples for electron density. We present how a precise measurement of electron density can be performed using an X-ray phase-contrast grating interferometer in a radiographic mode of a homogenous sample in a controlled geometry. A batch of various plastic materials was characterized quantitatively and compared with calculated results. We found that the measured electron densities closely match theoretical values. The technique yields comparable results between a monochromatic and a polychromatic X-ray source. Measured electron densities can be further used to design dedicated X-ray phase contrast phantoms and the additional information on small angle scattering should be taken into account in order to exclude unsuitable materials.

Micro-CT of rodents: state-of-the-art and future perspectives

Micron-scale computed tomography (micro-CT) is an essential tool for phenotyping and for elucidating diseases and their therapies. This work is focused on preclinical micro-CT imaging, reviewing relevant principles, technologies, and applications. Commonly, micro-CT provides high-resolution anatomic information, either on its own or in conjunction with lower-resolution functional imaging modalities such as positron emission tomography (PET) and single-photon emission computed tomography (SPECT). More recently, however, advanced applications of micro-CT produce functional information by translating clinical applications to model systems (e.g., measuring cardiac functional metrics) and by pioneering new ones (e.g. measuring tumor vascular permeability with nanoparticle contrast agents). The primary limitations of micro-CT imaging are the associated radiation dose and relatively poor soft tissue contrast. We review several image reconstruction strategies based on iterative, statistical, and gradient sparsity regularization, demonstrating that high image quality is achievable with low radiation dose given ever more powerful computational resources. We also review two contrast mechanisms under intense development. The first is spectral contrast for quantitative material discrimination in combination with passive or actively targeted nanoparticle contrast agents. The second is phase contrast which measures refraction in biological tissues for improved contrast and potentially reduced radiation dose relative to standard absorption imaging. These technological advancements promise to develop micro-CT into a commonplace, functional and even molecular imaging modality.

Phase-contrast CT: qualitative and quantitative evaluation of atherosclerotic carotid artery plaque

PURPOSE

To evaluate the potential of phase-contrast computed tomography (CT) for atherosclerotic plaque imaging in human carotid arteries in an experimental ex vivo study.

MATERIALS AND METHODS

The study was approved by the institutional review board, and informed consent was obtained from the patients' relatives. Seven postmortem human carotid artery specimens were imaged at a laboratory setup by using a conventional x-ray tube and grating interferometer. After histologic processing, phase-contrast imaging and histopathologic data were matched. Characteristics of the necrotic core (NC) covered by a fibrous cap (FC), intraplaque hemorrhage (IPH), and calcifications (CAs) were established, and sensitivity, specificity, and accuracy of phase-contrast CT for plaque detection and the potential for accurate quantification were assessed. The Cohen κ and Pearson correlation coefficient R were used to determine the agreement between phase-contrast imaging and histopathologic findings for plaque characterization and correlation of quantitative plaque measurements, respectively. A difference with a P value of less than .05 was considered significant.

RESULTS

Characteristic criteria were found in all analyzed plaque components. Applying these criteria, phase-contrast CT had a good sensitivity for the detection of the FC and NC, IPH, and CAs (all, >80%) and excellent specificity and accuracy (all, >90%), with good interreader agreement (κ ≥ 0.72, P < .0001). There were excellent correlations for quantitative measurements of FC, NC, and CAs between phase-contrast imaging and histopathologic findings (R ≥ 0.92). Interreader reproducibility was excellent, with an intraclass correlation coefficient of 0.98 or higher for all measurements.

CONCLUSION

The results of this study indicate that ex vivo phase-contrast CT can help identify and quantify atherosclerotic plaque components, with excellent correlation to histopathologic findings. Although not yet applicable in vivo, phase-contrast CT may become a valuable tool to monitor atherosclerotic disease process noninvasively.

Helical differential X-ray phase-contrast computed tomography

We report on the first experimental results of helical differential phase-contrast computed tomography (helical DPC-CT) with a laboratory X-ray tube source and a Talbot-Lau grating interferometer. The results experimentally verify the feasibility of helical data acquisition and reconstruction in phase-contrast imaging, in analogy to its use in clinical CT systems. This allows fast and continuous volumetric scans for long objects with lengths exceeding the dimension of the detector. Since helical CT revolutionized the field of medical CT several years ago, we anticipate that this method will bring the same significant impact on the future medical and industrial applications of X-ray DPC-CT.

High energy x-ray phase contrast CT using glancing-angle grating interferometers

PURPOSE

The authors present initial progress toward a clinically compatible x-ray phase contrast CT system, using glancing-angle x-ray grating interferometry to provide high contrast soft tissue images at estimated by computer simulation dose levels comparable to conventional absorption based CT.

METHODS

DPC-CT scans of a joint phantom and of soft tissues were performed in order to answer several important questions from a clinical setup point of view. A comparison between high and low fringe visibility systems is presented. The standard phase stepping method was compared with sliding window interlaced scanning. Using estimated dose values obtained with a Monte-Carlo code the authors studied the dependence of the phase image contrast on exposure time and dose.

RESULTS

Using a glancing angle interferometer at high x-ray energy (∼ 45 keV mean value) in combination with a conventional x-ray tube the authors achieved fringe visibility values of nearly 50%, never reported before. High fringe visibility is shown to be an indispensable parameter for a potential clinical scanner. Sliding window interlaced scanning proved to have higher SNRs and CNRs in a region of interest and to also be a crucial part of a low dose CT system. DPC-CT images of a soft tissue phantom at exposures in the range typical for absorption based CT of musculoskeletal extremities were obtained. Assuming a human knee as the CT target, good soft tissue phase contrast could be obtained at an estimated absorbed dose level around 8 mGy, similar to conventional CT.

CONCLUSIONS

DPC-CT with glancing-angle interferometers provides improved soft tissue contrast over absorption CT even at clinically compatible dose levels (estimated by a Monte-Carlo computer simulation). Further steps in image processing, data reconstruction, and spectral matching could make the technique fully clinically compatible. Nevertheless, due to its increased scan time and complexity the technique should be thought of not as replacing, but as complimentary to conventional CT, to be used in specific applications.