Multi-Mounted X-Ray Computed Tomography

Most existing X-ray computed tomography (CT) techniques work in single-mounted mode and need to scan the inspected objects one by one. It is time-consuming and not acceptable for the inspection in a large scale. In this paper, we report a multi-mounted CT method and its first engineering implementation. It consists of a multi-mounted scanning geometry and the corresponding algebraic iterative reconstruction algorithm. This approach permits the CT rotation scanning of multiple objects simultaneously without the increase of penetration thickness and the signal crosstalk. Compared with the conventional single-mounted methods, it has the potential to improve the imaging efficiency and suppress the artifacts from the beam hardening and the scatter. This work comprises a numerical study of the method and its experimental verification using a dataset measured with a developed multi-mounted X-ray CT prototype system. We believe that this technique is of particular interest for pushing the engineering applications of X-ray CT.     

Effects of X-Ray Dose On Rhizosphere Studies Using X-Ray Computed Tomography

X-ray Computed Tomography (CT) is a non-destructive imaging technique originally designed for diagnostic medicine, which was adopted for rhizosphere and soil science applications in the early 1980s. X-ray CT enables researchers to simultaneously visualise and quantify the heterogeneous soil matrix of mineral grains, organic matter, air-filled pores and water-filled pores. Additionally, X-ray CT allows visualisation of plant roots in situ without the need for traditional invasive methods such as root washing. However, one routinely unreported aspect of X-ray CT is the potential effect of X-ray dose on the soil-borne microorganisms and plants in rhizosphere investigations. Here we aimed to i) highlight the need for more consistent reporting of X-ray CT parameters for dose to sample, ii) to provide an overview of previously reported impacts of X-rays on soil microorganisms and plant roots and iii) present new data investigating the response of plant roots and microbial communities to X-ray exposure. Fewer than 5% of the 126 publications included in the literature review contained sufficient information to calculate dose and only 2.4% of the publications explicitly state an estimate of dose received by each sample. We conducted a study involving rice roots growing in soil, observing no significant difference between the numbers of root tips, root volume and total root length in scanned versus unscanned samples. In parallel, a soil microbe experiment scanning samples over a total of 24 weeks observed no significant difference between the scanned and unscanned microbial biomass values. We conclude from the literature review and our own experiments that X-ray CT does not impact plant growth or soil microbial populations when employing a low level of dose (<30 Gy). However, the call for higher throughput X-ray CT means that doses that biological samples receive are likely to increase and thus should be closely monitored.     

Structural Stabilization of Tissue for Embryo Phenotyping Using Micro-CT with Iodine Staining

The International Mouse Phenotyping Consortium has been established to conduct large-scale phenotyping of the approximately 23,000 single-gene knockout mice generated by the International Knockout Mouse Consortium to investigate the role of each gene in the mouse genome. Of the generated mouse lines, 30% are predicted to be embryonic lethal, requiring the implementation of imaging techniques and analysis tools specific to late gestation mouse embryo phenotyping. A well-adopted technique combines the use of iodinated contrast solutions and micro-computed tomography imaging. This simple iodine immersion technique provides superior soft-tissue contrast enhancement, however, the hypertonic nature of iodine promotes dehydration causing moderate to severe tissue deformation. Here, we combine the stabilizing properties of a hydrogel mesh with the enhanced contrast properties of iodine. The protocol promotes cross linking of tissue through formaldehyde fixation and the linking of hydrogel monomers to biomolecules. As a result, the hydrogel supports tissue structure and preserves its conformation taking advantage of iodine-enhanced soft tissue contrast to produce high quality mouse embryo images with minimal tissue distortion. Hydrogel stabilization substantially reduces intersample anatomical variation of mature mouse embryos subjected to iodine preparation protocols. A 20% and 50% reduction in intersample variation of normalized brain and lung volume is achieved through hydrogel stabilization, as well as a 20% reduction in variation in overall embryo anatomy as measured through image registration methods. This increases the sensitivity of computer automated analysis to reveal significant anatomical differences between mutant and wild-type mice.     

Silver Staining of Nerve Fibers in Cardiac Tissue

Fresh hearts of dog were perfused through the coronary vessels with 1000 ml. of fixative (chloral hydrate, 5 g. per 100 ml. of 70% ethyl alcohol) and blocks of tissue 2 × 5 mm. from epicardium to endocardium fixed 48 hours in the same fixative. The blocks were placed in 95% alcohol containing 0.3% addition of strong ammonia for 4 hours, followed by 2 changes of plain 95% alcohol of 1 hour each, then cleared and infiltrated with paraffin. Mounted sections 12-15 µ thick were incubated in 1% silver proteinate (obtained from Serumvertrieb, Marburg, Germany)² at 38° C. for 48 hours in the presence of 10 g. of 15 gauge copper wire per 200 ml. of solution. The slides were rinsed gently in 3 changes of distilled water for 2 minutes, 1 minute and 1 minute, respectively, and reduced in 1% hydroquinone and 5% sodium sulfite for 5 minutes. They were washed 5 minutes in tap water and 5 minutes in 2 changes of distilled water and toned 3-5 minutes in 0.25% gold chloride, rinsed in distilled water 10 seconds, reduced 10 seconds in 1 % oxalic acid, rinsed 1 minute, fixed in 5% sodium thiosulfate 5 minutes, washed in tap water through 3 changes, dehydrated, cleared and covered. All solutions were made with distilled water except where otherwise specified. The results gave good impregnation of fine nerve fibers without the usual confusing staining of reticular tissue.     

Characterization of Scattered X-Ray Photons in Dental Cone-Beam Computed Tomography

Purpose

Scatter is a very important artifact causing factor in dental cone-beam CT (CBCT), which has a major influence on the detectability of details within images. This work aimed to improve the image quality of dental CBCT through scatter correction.

Methods

Scatter was estimated in the projection domain from the low frequency component of the difference between the raw CBCT projection and the projection obtained by extrapolating the model fitted to the raw projections acquired with 2 different sizes of axial field-of-view (FOV). The function for curve fitting was optimized by using Monte Carlo simulation. To validate the proposed method, an anthropomorphic phantom and a water-filled cylindrical phantom with rod inserts simulating different tissue materials were scanned using 120 kVp, 5 mA and 9-second scanning time covering an axial FOV of 4 cm and 13 cm. The detectability of the CT image was evaluated by calculating the contrast-to-noise ratio (CNR).

Results

Beam hardening and cupping artifacts were observed in CBCT images without scatter correction, especially in those acquired with 13 cm FOV. These artifacts were reduced in CBCT images corrected by the proposed method, demonstrating its efficacy on scatter correction. After scatter correction, the image quality of CBCT was improved in terms of target detectability which was quantified as the CNR for rod inserts in the cylindrical phantom.

Conclusions

Hopefully the calculations performed in this work can provide a route to reach a high level of diagnostic image quality for CBCT imaging used in oral and maxillofacial structures whilst ensuring patient dose as low as reasonably achievable, which may ultimately make CBCT scan a reliable and safe tool in clinical practice.     

Constrained Total Generalized p-Variation Minimization for Few-View X-Ray Computed Tomography Image Reconstruction

Total generalized variation (TGV)-based computed tomography (CT) image reconstruction, which utilizes high-order image derivatives, is superior to total variation-based methods in terms of the preservation of edge information and the suppression of unfavorable staircase effects. However, conventional TGV regularization employs l₁-based form, which is not the most direct method for maximizing sparsity prior. In this study, we propose a total generalized p-variation (TGpV) regularization model to improve the sparsity exploitation of TGV and offer efficient solutions to few-view CT image reconstruction problems. To solve the nonconvex optimization problem of the TGpV minimization model, we then present an efficient iterative algorithm based on the alternating minimization of augmented Lagrangian function. All of the resulting subproblems decoupled by variable splitting admit explicit solutions by applying alternating minimization method and generalized p-shrinkage mapping. In addition, approximate solutions that can be easily performed and quickly calculated through fast Fourier transform are derived using the proximal point method to reduce the cost of inner subproblems. The accuracy and efficiency of the simulated and real data are qualitatively and quantitatively evaluated to validate the efficiency and feasibility of the proposed method. Overall, the proposed method exhibits reasonable performance and outperforms the original TGV-based method when applied to few-view problems.     

3D Algebraic Iterative Reconstruction for Cone-Beam X-Ray Differential Phase-Contrast Computed Tomography

Due to the potential of compact imaging systems with magnified spatial resolution and contrast, cone-beam x-ray differential phase-contrast computed tomography (DPC-CT) has attracted significant interest. The current proposed FDK reconstruction algorithm with the Hilbert imaginary filter will induce severe cone-beam artifacts when the cone-beam angle becomes large. In this paper, we propose an algebraic iterative reconstruction (AIR) method for cone-beam DPC-CT and report its experiment results. This approach considers the reconstruction process as the optimization of a discrete representation of the object function to satisfy a system of equations that describes the cone-beam DPC-CT imaging modality. Unlike the conventional iterative algorithms for absorption-based CT, it involves the derivative operation to the forward projections of the reconstructed intermediate image to take into account the differential nature of the DPC projections. This method is based on the algebraic reconstruction technique, reconstructs the image ray by ray, and is expected to provide better derivative estimates in iterations. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured with a three-grating interferometer and a mini-focus x-ray tube source. It is shown that the proposed method can reduce the cone-beam artifacts and performs better than FDK under large cone-beam angles. This algorithm is of interest for future cone-beam DPC-CT applications.     

In Vitro Validation of an Artefact Suppression Algorithm in X-Ray Phase-Contrast Computed Tomography

X-ray phase-contrast tomography can significantly increase the contrast-resolution of conventional attenuation-contrast imaging, especially for soft-tissue structures that have very similar attenuation. Just as in attenuation-based tomography, phase contrast tomography requires a linear dependence of aggregate beam direction on the incremental direction alteration caused by individual voxels along the path of the X-ray beam. Dense objects such as calcifications in biological specimens violate this condition. There are extensive beam deflection artefacts in the vicinity of such structures because they result in large distortion of wave front due to the large difference of refractive index; for such large changes in beam direction, the transmittance of the silicon analyzer crystal saturates and is no longer linearly dependent on the angle of refraction. This paper describes a method by which these effects can be overcome and excellent soft-tissue contrast of phase tomography can be preserved in the vicinity of such artefact-producing structures.     

Tuberculosis Contact Investigation Using Interferon-Gamma Release Assay with Chest X-Ray and Computed Tomography

Between September 2009 and January 2010, 6 members of the Japanese Eastern Army, who had completed the same training program, were diagnosed with active tuberculosis (TB) on different occasions. The Ministry of Defense conducted a contact investigation of all members who had come into contact with the infected members. The purpose of this study was to verify the efficacy of the TB screening protocol used in this investigation. A total of 884 subjects underwent interferon-gamma release assay (IGRA) and chest X-ray. The 132 subjects who were IGRA positive or with X-ray findings suggestive of TB subsequently underwent chest computer tomography (CT). Chest CT was performed for 132 subjects. Based on CT findings, 24 (2.7%) subjects were classified into the active TB group, 107 (12.1%) into the latent tuberculosis infection (LTBI) group, and 753 (85.2%) into the non-TB group. The first 2 groups underwent anti-TB therapy, and all 3 groups were followed for 2 years after treatment. Although one subject in the active TB group experienced relapse during the follow-up period, no patient in the LTBI or non-TB groups developed TB. IGRA and chest X-ray, followed by chest CT for those IGRA positive or with suspicious X-ray findings, appears to be an effective means of TB contact screening and infection prevention.     

Development and Validation of Computed Tomography Derived Anthropometric Regression Equations for Estimating Abdominal Adipose Tissue Distribution

The purpose of this study was twofold: (1) to develop multiple regression equations for predicting computed tomography (CT) derived intra-abdominal (IAF), subcutaneous (SCF), and total (TOTF= IAF+SCF) abdominal adipose tissue areas from anthropometric measures in adult white males with a large range of age (18–71 years) and percent body fat (2.0–40.6); and (2) to validate the new and existing equations that used similar Hounsfield Units (HU) for determining IAF for estimating these fat depots. One hundred fifty-one white male subjects had IAF, SCF, and TOTF determined by a single CT scan, skinfold and circumference measures taken and body density determined. Linear intra-correlations and factor analysis procedures were used to identify variables for inclusion in stepwise multiple regression solutions. IAF was estimated from age, waist circumference, the sum of mid-thigh and lower thigh circumferences, and vertical abdominal skinfold. SCF was estimated from age, umbilicus circumference, chest and suprailiac skinfolds. TOTF was estimated from age, body mass index (BMI), chest skinfold, and umbilicus circumference. R² for IAF, SCF, and TOTF was .73, .77, and .86 respectively. The existing and the new equations were validated on an independent sub-sample of 51 subjects. The only existing equation that met validation criteria had a validation R² = .67 for IAF. All three new equations met validation criteria with R ² validations of .75, .79, and .85 for IAF, SCF, and TOTF respectively. It is concluded that the new equations might be used as an inexpensive estimation of IAF, SCF, and TOTF in adult white males varying greatly in age and percent body fat.     

System Matrix Analysis for Computed Tomography Imaging

In practical applications of computed tomography imaging (CT), it is often the case that the set of projection data is incomplete owing to the physical conditions of the data acquisition process. On the other hand, the high radiation dose imposed on patients is also undesired. These issues demand that high quality CT images can be reconstructed from limited projection data. For this reason, iterative methods of image reconstruction have become a topic of increased research interest. Several algorithms have been proposed for few-view CT. We consider that the accurate solution of the reconstruction problem also depends on the system matrix that simulates the scanning process. In this work, we analyze the application of the Siddon method to generate elements of the matrix and we present results based on real projection data.     

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs

To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial ‘design of experiments’ approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.     

Ninhydrin Staining of Tissue Sections

This method represents a considerable improvement over earlier ninhydrin procedures. Celloidin sections were stained after mounting in a medium which clears with incubation at 55 °C. There appears to be no reason why paraffin section cannot be used. The sections were not placed in a large volume of ninhydrin (0.25% triketohydrindene hydrate in n-butanol) but only a small volume was sprayed onto the slide. Distortion resulting from heating in boiling water to develop the color was avoided by a slower treatment of 3 days' incubation at 55 °C. The use of water as a solvent in staining is also avoided, thus minimizing the possibility of color migration and insuring against the development of the intensely colored products of the ninhydrin reaction that occur in aqueous solution. Slides need not be observed upon the day of preparation, since the color was stable for about a week after its formation.     

Human Brown Adipose Tissue Depots Automatically Segmented by Positron Emission Tomography/Computed Tomography and Registered Magnetic Resonance Images

Reliably differentiating brown adipose tissue (BAT) from other tissues using a non-invasive imaging method is an important step toward studying BAT in humans. Detecting BAT is typically confirmed by the uptake of the injected radioactive tracer ¹⁸F-Fluorodeoxyglucose (¹⁸F-FDG) into adipose tissue depots, as measured by positron emission tomography/computed tomography (PET-CT) scans after exposing the subject to cold stimulus. Fat-water separated magnetic resonance imaging (MRI) has the ability to distinguish BAT without the use of a radioactive tracer. To date, MRI of BAT in adult humans has not been co-registered with cold-activated PET-CT. Therefore, this protocol uses ¹⁸F-FDG PET-CT scans to automatically generate a BAT mask, which is then applied to co-registered MRI scans of the same subject. This approach enables measurement of quantitative MRI properties of BAT without manual segmentation. BAT masks are created from two PET-CT scans: after exposure for 2 hr to either thermoneutral (TN) (24 °C) or cold-activated (CA) (17 °C) conditions. The TN and CA PET-CT scans are registered, and the PET standardized uptake and CT Hounsfield values are used to create a mask containing only BAT. CA and TN MRI scans are also acquired on the same subject and registered to the PET-CT scans in order to establish quantitative MRI properties within the automatically defined BAT mask. An advantage of this approach is that the segmentation is completely automated and is based on widely accepted methods for identification of activated BAT (PET-CT). The quantitative MRI properties of BAT established using this protocol can serve as the basis for an MRI-only BAT examination that avoids the radiation associated with PET-CT.     

Implementation of a Phase Detection Algorithm for Dynamic Cardiac Computed Tomography Analysis Based on Time Dependent Contrast Agent Distribution

This paper presents a phase detection algorithm for four-dimensional (4D) cardiac computed tomography (CT) analysis. The algorithm detects a phase, i.e. a specific three-dimensional (3D) image out of several time-distributed 3D images, with high contrast in the left ventricle and low contrast in the right ventricle. The purpose is to use the automatically detected phase in an existing algorithm that automatically aligns the images along the heart axis. Decision making is based on the contrast agent distribution over time. It was implemented in KardioPerfusion – a software framework currently being developed for 4D CT myocardial perfusion analysis. Agreement of the phase detection algorithm with two reference readers was 97% (95% CI: 82–100%). Mean duration for detection was 0.020 s (95% CI: 0.018–0.022 s), which was times less than the readers needed (s, ). Thus, this algorithm is an accurate and fast tool that can improve work flow of clinical examinations.     

A Spectrophotometry Analysis of Tissue Staining

By comparing spectral absorption curves of representative staining solutions and of substances stained with these solutions it is shown that information may be obtained regarding chemical changes associated with the staining process. The stains used in these determinations were acid fuchsin, anilin blue, azo-carmine G, basic fuchsin, eosin Y, orange G, picric acid and Sudan IV. The substrates stained were gelatin, tendon, blood plasma, thymus gland and fat.

Aqueous basic fuchsin and fuchsin-sulfurous reagent to which formalin was added (Setoff reaction) are different stains. The spectral absorption curves for staining solutions and substances stained with the solutions were comparable. Within the limitations of the spectrophotometry methods and stains employed, there was no evidence of significant chemical alteration in the chromophore radicals of the stains associated with the process of tissue staining.     

Phloxine-Methylene Blue Staining of Formalin-Fixed Tissue

It is at present difficult to obtain a good phloxine-metbylene blue stain on formalin-fixed tissue. When phloxine has been used, it is washed out in the process of staining with methylene blue and differentiating with colophony (rosin). In the original technic of Mallory, Zenker's fixation is used. The tissue is first stained with a 2.5% aqueous solution of phloxine, then with a solution of 1% methylene blue plus 1% azure II and differentiated in colophony.¹     

X-Ray Phase-Contrast Tomography of Renal Ischemia-Reperfusion Damage

Purpose

The aim of the study was to investigate microstructural changes occurring in unilateral renal ischemia-reperfusion injury in a murine animal model using synchrotron radiation.

Material and Methods

The effects of renal ischemia-reperfusion were investigated in a murine animal model of unilateral ischemia. Kidney samples were harvested on day 18. Grating-Based Phase-Contrast Imaging (GB-PCI) of the paraffin-embedded kidney samples was performed at a Synchrotron Radiation Facility (beam energy of 19 keV). To obtain phase information, a two-grating Talbot interferometer was used applying the phase stepping technique. The imaging system provided an effective pixel size of 7.5 µm. The resulting attenuation and differential phase projections were tomographically reconstructed using filtered back-projection. Semi-automated segmentation and volumetry and correlation to histopathology were performed.

Results

GB-PCI provided good discrimination of the cortex, outer and inner medulla in non-ischemic control kidneys. Post-ischemic kidneys showed a reduced compartmental differentiation, particularly of the outer stripe of the outer medulla, which could not be differentiated from the inner stripe. Compared to the contralateral kidney, after ischemia a volume loss was detected, while the inner medulla mainly retained its volume (ratio 0.94). Post-ischemic kidneys exhibited severe tissue damage as evidenced by tubular atrophy and dilatation, moderate inflammatory infiltration, loss of brush borders and tubular protein cylinders.

Conclusion

In conclusion GB-PCI with synchrotron radiation allows for non-destructive microstructural assessment of parenchymal kidney disease and vessel architecture. If translation to lab-based approaches generates sufficient density resolution, and with a time-optimized image analysis protocol, GB-PCI may ultimately serve as a non-invasive, non-enhanced alternative for imaging of pathological changes of the kidney.     

Accelerating an Ordered-Subset Low-Dose X-Ray Cone Beam Computed Tomography Image Reconstruction with a Power Factor and Total Variation Minimization

In recent years, there has been increased interest in low-dose X-ray cone beam computed tomography (CBCT) in many fields, including dentistry, guided radiotherapy and small animal imaging. Despite reducing the radiation dose, low-dose CBCT has not gained widespread acceptance in routine clinical practice. In addition to performing more evaluation studies, developing a fast and high-quality reconstruction algorithm is required. In this work, we propose an iterative reconstruction method that accelerates ordered-subsets (OS) reconstruction using a power factor. Furthermore, we combine it with the total-variation (TV) minimization method. Both simulation and phantom studies were conducted to evaluate the performance of the proposed method. Results show that the proposed method can accelerate conventional OS methods, greatly increase the convergence speed in early iterations. Moreover, applying the TV minimization to the power acceleration scheme can further improve the image quality while preserving the fast convergence rate.