X-ray Phase-contrast CT Research Articles

Establishing sample-preparation protocols for X-ray phase-contrast CT of rodent spinal cords: Aldehyde fixations and osmium impregnation

BackgroundDense and unbiased cellular-resolution representations of extended volumetric central nervous system soft-tissue anatomy are difficult to obtain, even in experimental post-mortem settings. Interestingly, X-ray phase-contrast computed tomography (X-PCI-CT), an emerging soft-tissue-sensitive volumetric imaging technique, can provide multiscale organ- to cellular-level morphological visualizations of neuroanatomical structure. New MethodHere, we tested different nervous-tissue fixation procedures, conventionally used for transmission electron microscopy, to better establish X-PCI-CT-specific sample-preparation protocols. Extracted rat spinal medullas were alternatively fixed with a standard paraformaldehyde-only aldehyde-based protocol, or in combination with glutaraldehyde. Some specimens were additionally post-fixed with osmium tetroxide. Multiscale X-PCI-CT datasets were collected at several synchrotron radiation facilities, using state-of-the-art setups with effective image voxel sizes of 3.03 to 0.33 μm3, and compared to high-field magnetic resonance imaging, histology and vascular fluorescence microscopy data. ResultsMultiscale X-PCI-CT of aldehyde-fixed spinal cord specimens resulted in dense histology-like volumetric representations and quantifications of extended deep spinal micro-vascular networks and of intra-medullary cell populations. Osmium post-fixation increased intra-medullary contrast between white and gray-matter tissues, and enhanced delineation of intra-medullary cellular structure, e.g. axon fibers and motor neuron perikarya. Comparison with Existing MethodsVolumetric X-PCI-CT provides complementary contrast and higher spatial resolution compared to 9.4 T MRI. X-PCI-CT’s advantage over planar histology is the volumetric nature of the cellular-level data obtained, using samples much larger than those fit for volumetric vascular fluorescence microscopy. ConclusionsDeliberately choosing (post-)fixation protocols tailored for optimal nervous-tissue structural preservation is of paramount importance in achieving effective and targeted neuroimaging via the X-PCI-CT technique.

Visualization of internal 3D structure of small live seed on germination by laboratory-based X-ray microscopy with phase contrast computed tomography

BackgroundThe visualization of internal 3D-structure of tissues at micron resolutions without staining by contrast reagents is desirable in plant researches, and it can be achieved by an X-ray computed tomography (CT) with a phase-retrieval technique. Recently, a laboratory-based X-ray microscope adopting the phase contrast CT was developed as a powerful tool for the observation of weakly absorbing biological samples. Here we report the observation of unstained pansy seeds using the laboratory-based X-ray phase-contrast CT.ResultsA live pansy seed within 2 mm in size was simply mounted inside a plastic tube and irradiated by in-house X-rays to collect projection images using a laboratory-based X-ray microscope. The phase-retrieval technique was applied to enhance contrasts in the projection images. In addition to a dry seed, wet seeds on germination with the poorer contrasts were tried. The phase-retrieved tomograms from both the dry and the wet seeds revealed a cellular level of spatial resolutions that were enough to resolve cells in the seeds, and provided enough contrasts to delineate the boundary of embryos manually. The manual segmentation allowed a 3D rendering of embryos at three different stages in the germination, which visualized an overall morphological change of the embryo upon germination as well as a spatial arrangement of cells inside the embryo.ConclusionsOur results confirmed an availability of the laboratory-based X-ray phase-contrast CT for a 3D-structural study on the development of small seeds. The present method may provide a unique way to observe live plant tissues at micron resolutions without structural perturbations due to the sample preparation.

X-ray phase-contrast dynamic CT for the analysis of local deformation of articular cartilage

X-ray phase-contrast dynamic CT for the analysis of local deformation of articular cartilage

Model-Based Iterative Reconstruction for Propagation-Based Phase-Contrast X-Ray CT including Models for the Source and the Detector.

Propagation-based phase-contrast X-ray computed tomography is a valuable tool for high-resolution visualization of biological samples, giving distinct improvements in terms of contrast and dose requirements compared to conventional attenuation-based computed tomography. Due to its ease of implementation and advances in laboratory X-ray sources, this imaging technique is increasingly being transferred from synchrotron facilities to laboratory environments. This however poses additional challenges, such as the limited spatial coherence and flux of laboratory sources, resulting in worse resolution and higher noise levels. Here we extend a previously developed iterative reconstruction algorithm for this imaging technique to include models for the reduced spatial coherence and the signal spreading of efficient scintillator-based detectors directly into the physical forward model. Furthermore, we employ a noise model which accounts for the full covariance statistics of the image formation process. In addition, we extend the model describing the interference effects such that it now matches the formalism of the widely-used single-material phase-retrieval algorithm, which is based on the sample-homogeneity assumption. We perform a simulation study as well as an experimental study at a laboratory inverse Compton source and compare our approach to the conventional analytical approaches. We find that the modeling of the source and the detector inside the physical forward model can tremendously improve the resolution at matched noise levels and that the modeling of the covariance statistics reduces overshoots (i.e. incorrect increase / decrease in sample properties) at the sample edges significantly.

Medical and Industrial Applications of X-ray Phase-contrast Imaging Using Synchrotron Radiation

BL-14 at the Photon Factory, Japan is a characteristic synchrotron radiation beamline where one can use a vertically polarized synchrotron radiation beam from a superconducting vertical wiggler with a field strength of 5 Tesla. One of the experimental stations, BL-14C, is dedicated to x-ray imaging such as x-ray phase-contrast CT using a large x-ray interferometer, x-ray diffraction enhanced imaging (DEI), DEI-CT and x-ray dark field imaging (DFI). The phase-contrast CT using an x-ray interferometer is sufficiently sensitive to evaluate small density differences in soft tissues and soft materials. Recent results on medical and industrial applications of phase-contrast CT using the large x-ray interferometer are reported by five papers in this special issue.

Assessment of intraductal carcinoma in situ (DCIS) using grating-based X-ray phase-contrast CT at conventional X-ray sources: An experimental ex-vivo study.

BackgroundThe extent of intraductal carcinoma in situ (DCIS) is commonly underestimated due to the discontinuous growth and lack of microcalcifications. Specimen radiography has been established to reduce the rate of re-excision. However, the predictive value for margin assessment with conventional specimen radiography for DCIS is low. In this study we assessed the potential of grating-based phase-contrast computed tomography (GBPC-CT) at conventional X-ray sources for specimen tomography of DCIS containing samples.Materials and methodsGBPC-CT was performed on four ex-vivo breast specimens containing DCIS and invasive carcinoma of non-specific type. Phase-contrast and absorption-based datasets were manually matched with corresponding histological slices as the standard of reference.ResultsMatching of CT images and histology was successful. GBPC-CT showed an improved soft tissue contrast compared to absorption-based images revealing more histological details in the same sections. Non-calcifying DCIS exceeding the invasive tumor could be correlated to areas of dilated bright ducts around the tumor.ConclusionsGBPC-CT imaging at conventional X-ray sources offers improved depiction quality for the imaging of breast tissue samples compared to absorption-based imaging, allows the identification of diagnostically relevant tissue details, and provides full three-dimensional assessment of sample margins.

Deformation analysis of articular cartilage by X-ray phase-contrast dynamic CT

Deformation analysis of articular cartilage by X-ray phase-contrast dynamic CT

Dynamic phase contrast X-ray CT of articular cartilage under repetitive compression

Dynamic phase contrast X-ray CT of articular cartilage under repetitive compression

Direct quantitative material decomposition employing grating-based X-ray phase-contrast CT

Dual-energy CT has opened up a new level of quantitative X-ray imaging for many diagnostic applications. The energy dependence of the X-ray attenuation is the key to quantitative material decomposition of the volume under investigation. This material decomposition allows the calculation of virtual native images in contrast enhanced angiography, virtual monoenergetic images for beam-hardening artifact reduction and quantitative material maps, among others. These visualizations have been proven beneficial for various diagnostic questions. Here, we demonstrate a new method of ‘virtual dual-energy CT’ employing grating-based phase-contrast for quantitative material decomposition. Analogue to the measurement at two different energies, the applied phase-contrast measurement approach yields dual information in form of a phase-shift and an attenuation image. Based on these two image channels, all known dual-energy applications can be demonstrated with our technique. While still in a preclinical state, the method features the important advantages of direct access to the electron density via the phase image, simultaneous availability of the conventional attenuation image at the full energy spectrum and therefore inherently registered image channels. The transfer of this signal extraction approach to phase-contrast data multiplies the diagnostic information gained within a single CT acquisition. The method is demonstrated with a phantom consisting of exemplary solid and fluid materials as well as a chicken heart with an iodine filled tube simulating a vessel. For this first demonstration all measurements have been conducted at a compact laser-undulator synchrotron X-ray source with a tunable X-ray energy and a narrow spectral bandwidth, to validate the quantitativeness of the processing approach.

High resolution laboratory grating-based X-ray phase-contrast CT

The conventional form of computed tomography using X-ray attenuation without any contrast agents is of limited use for the characterization of soft tissue in many fields of medical and biological studies. Grating-based phase-contrast computed tomography (gbPC-CT) is a promising alternative imaging method solving the low soft tissue contrast without the need of any contrast agent. While highly sensitive measurements are possible using conventional X-ray sources the spatial resolution does often not fulfill the requirements for specific imaging tasks, such as visualization of pathologies. The focus of this study is the increase in spatial resolution without loss of sensitivity. To overcome this limitation a super-resolution reconstruction based on sub-pixel shifts involving a deconvolution of the image data during each iteration is applied. In our study we achieve an effective pixel size of 28 μm with a conventional rotating anode tube and a photon-counting detector. We also demonstrate that the method can upgrade existing setups to measure tomographies with higher resolution. The results show the increase in resolution at high sensitivity and with the ability to make quantitative measurements. The combination of sparse sampling and statistical iterative reconstruction may be used to reduce the total measurement time. In conclusion, we present high-quality and high-resolution tomographic images of biological samples to demonstrate the experimental feasibility of super-resolution reconstruction.

In situ phase contrast X-ray brain CT

Phase contrast X-ray imaging (PCXI) is an emerging imaging modality that has the potential to greatly improve radiography for medical imaging and materials analysis. PCXI makes it possible to visualise soft-tissue structures that are otherwise unresolved with conventional CT by rendering phase gradients in the X-ray wavefield visible. This can improve the contrast resolution of soft tissues structures, like the lungs and brain, by orders of magnitude. Phase retrieval suppresses noise, revealing weakly-attenuating soft tissue structures, however it does not remove the artefacts from the highly attenuating bone of the skull and from imperfections in the imaging system that can obscure those structures. The primary causes of these artefacts are investigated and a simple method to visualise the features they obstruct is proposed, which can easily be implemented for preclinical animal studies. We show that phase contrast X-ray CT (PCXI-CT) can resolve the soft tissues of the brain in situ without a need for contrast agents at a dose ~400 times lower than would be required by standard absorption contrast CT. We generalise a well-known phase retrieval algorithm for multiple-material samples specifically for CT, validate its use for brain CT, and demonstrate its high stability in the presence of noise.

Revising the lower statistical limit of x-ray grating-based phase-contrast computed tomography.

Phase-contrast x-ray computed tomography (PCCT) is currently investigated as an interesting extension of conventional CT, providing high soft-tissue contrast even if examining weakly absorbing specimen. Until now, the potential for dose reduction was thought to be limited compared to attenuation CT, since meaningful phase retrieval fails for scans with very low photon counts when using the conventional phase retrieval method via phase stepping. In this work, we examine the statistical behaviour of the reverse projection method, an alternative phase retrieval approach and compare the results to the conventional phase retrieval technique. We investigate the noise levels in the projections as well as the image quality and quantitative accuracy of the reconstructed tomographic volumes. The results of our study show that this method performs better in a low-dose scenario than the conventional phase retrieval approach, resulting in lower noise levels, enhanced image quality and more accurate quantitative values. Overall, we demonstrate that the lower statistical limit of the phase stepping procedure as proposed by recent literature does not apply to this alternative phase retrieval technique. However, further development is necessary to overcome experimental challenges posed by this method which would enable mainstream or even clinical application of PCCT.

On the relative performance of edge illumination x-ray phase-contrast CT and conventional, attenuation-based CT.

This article is aimed at comparing edge illumination (EI) x-ray phase contrast computed tomography (PCT) and conventional (attenuation-based) computed tomography (CT), based on their respective contrast and noise transfer. The noise in raw projections obtained with EI PCT is propagated through every step of the data processing, including phase retrieval and tomographic reconstruction, leading to a description of the noise in the reconstructed phase tomograms. This is compared to the noise in corresponding attenuation tomograms obtained with CT. Specifically, a formula is derived that allows evaluating the relative performance of both modalities on the basis of their contrast-to-noise ratio (CNR), for a variety of experimental parameters. The noise power spectra of phase tomograms are shifted towards lower spatial frequencies, leading to a fundamentally different noise texture. The relative performance of EI PCT and CT, in terms of their CNR, is linked to spatial resolution: the CNR in phase tomograms is generally superior to that in attenuation tomograms for higher spatial resolutions (tens to hundreds of μm), but inferior for lower spatial resolutions (hundreds of μm to mm). These results imply that EI PCT could outperform CT in applications for which high spatial resolutions are key, e.g., small animal or specimen imaging.

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.

Grating based X-ray phase contrast CT imaging with iterative reconstruction algorithm

Grating based X-ray imaging technology is a coherent imaging technique that bears tremendous potential in three-dimensional tomographic imaging of weak absorption contrast specimens. Three kinds of contrast information including absorption, phase and scattering can be retrieved separately based on a single set of raw projections. However, the grating based X-ray imaging with the conventional phase-retrieval method using the conventional phase-stepping approach and filtered back projection (FBP) reconstruction algorithm require large amounts of raw data, so that long exposure time and large amounts of radiation dose is accepted by the sample. According to the traditional grating based X-ray imaging system, we propose a low dose, fast, multi-contrast CT reconstruction approach based on the iterative reconstruction algorithm that optimizes dose efficiency but does not share the main limitations of other reported methods. Prior to reconstruction, firstly, the projections are acquired with the phase stepping approach and multi-contrast projections are retrieved from the raw data by conventional retrieval algorithm. Then the rotational variable differential phase projections are converted to rotational invariable projections by means of decomposing the differential phase projections into the rotational invariable projections in two mutually perpendicular derivative directions via the transformation of coordinates. Finally, the absorption, phase and scattering information are reconstructed with the iterative reconstruction algorithm and the phase is retrieved based on the fast Fourier transform (FFT). We validated and assessed the phase reconstruction approach with a numerical simulation on a phase Shepp-Logan phantom. The experiment was performed at the X-ray imaging and biomedical application beam line (BL-13W) in the Shanghai Synchrotron Radiation Facility (SSRF) where 20 keV X-ray from a Si(111) monochromator is emitted. The X-ray interferometer was positioned at 34 m from the Wiggler source. The images were recorded with a scintillator/lens-coupled CCD camera with 2048 pixel2048 pixel resolution and an effective pixel size of 9 m. The numerical tests and the experimental results demonstrate that, for the small radiation dose deposited in the sample, the iterative reconstruction algorithm provides phase reconstructions of better quality and higher signal to noise ratio than the conventional FBP reconstruction algorithm, and also provides the multi-contrast 3D images, including absorption image, phase image and scattering image. This development is of particular interest for applications where the samples need inspecting under low dose and high speed conditions, and will play an important role in the nondestructive and quantitative imaging in the industry, biomedical and medical diagnosis fields.

Fast 3D reconstruction method for differential phase contrast X-ray CT.

We present a fast algorithm for fully 3D regularized X-ray tomography reconstruction for both traditional and differential phase contrast measurements. In many applications, it is critical to reduce the X-ray dose while producing high-quality reconstructions. Regularization is an excellent way to do this, but in the differential phase contrast case it is usually applied in a slice-by-slice manner. We propose using fully 3D regularization to improve the dose/quality trade-off beyond what is possible using slice-by-slice regularization. To make this computationally feasible, we show that the two computational bottlenecks of our iterative optimization process can be expressed as discrete convolutions; the resulting algorithms for computation of the X-ray adjoint and normal operator are fast and simple alternatives to regridding. We validate this algorithm on an analytical phantom as well as conventional CT and differential phase contrast measurements from two real objects. Compared to the slice-by-slice approach, our algorithm provides a more accurate reconstruction of the analytical phantom and better qualitative appearance on one of the two real datasets.

Amyloid-β plaque deposition measured using propagation-based X-ray phase contrast CT imaging.

Amyloid beta accumulation into insoluble plaques (Aβp) is known to play a significant role in the pathological process in Alzheimer's disease (AD). The presence of Aβp is also one of the neuropathological hallmarks for the disease. AD final diagnosis is generally acknowledged after the evaluation of Aβp deposition in the brain. Insoluble Aβp accumulation may also concur to cause AD as postulated in the so-called amyloid hypothesis. Therefore, the visualization, evaluation and quantification of Aβp are nowadays the keys for a better understanding of the disease, which may point to a possible cure for AD in the near future. Synchrotron-based X-ray phase contrast (XPC) has been demonstrated as the only imaging method that can retrieve the Aβp signal with high spatial resolution (up to 10 µm), high sensitivity and three-dimensional information at the same time. Although at the moment XPC is suitable for exvivo samples only, it may develop into an alternative to positron emission tomography and magnetic resonance imaging in Aβp imaging. In this contribution the possibility of using synchrotron-based X-ray phase propagation computed tomography to visualize and measure Aβp on mouse brains is presented. A careful setup optimization for this application leads to a significant improvement of spatial resolution (∼1 µm), data acquisition speed (five times faster), X-ray dose (five times lower) and setup complexity, without a substantial loss in sensitivity when compared with the classic implementation of grating-based X-ray interferometry.

Contrast-to-noise ratio optimization for a prototype phase-contrast computed tomography scanner.

In the field of biomedical X-ray imaging, novel techniques, such as phase-contrast and dark-field imaging, have the potential to enhance the contrast and provide complementary structural information about a specimen. In this paper, a first prototype of a preclinical X-ray phase-contrast CT scanner based on a Talbot-Lau interferometer is characterized. We present a study of the contrast-to-noise ratios for attenuation and phase-contrast images acquired with the prototype scanner. The shown results are based on a series of projection images and tomographic data sets of a plastic phantom in phase and attenuation-contrast recorded with varying acquisition settings. Subsequently, the signal and noise distribution of different regions in the phantom were determined. We present a novel method for estimation of contrast-to-noise ratios for projection images based on the cylindrical geometry of the phantom. Analytical functions, representing the expected signal in phase and attenuation-contrast for a circular object, are fitted to individual line profiles of the projection data. The free parameter of the fit function is used to estimate the contrast and the goodness of the fit is determined to assess the noise in the respective signal. The results depict the dependence of the contrast-to-noise ratios on the applied source voltages, the number of steps of the phase stepping routine, and the exposure times for an individual step. Moreover, the influence of the number of projection angles on the image quality of CT slices is investigated. Finally, the implications for future imaging purposes with the scanner are discussed.

B14-O-04X-Ray Microscopy and Microtomography at SPring-8

X-ray microscopy and microtomography have been continuously developed to realize two-/three-dimensional microimaging with a spatial resolution beyond the optical microscopy. Scanning microscopy and imaging microscopy using a Fresnel zone plate (FZP) as an x-ray optical device have been achieved the spatial resolution of better than 100 nm, and high-resolution computed tomography (CT) using such x-ray optical systems are now routinely available with the spatial resolution of better then 200 nm. Figure 1 shows the x-ray CT image of the asteroid “Itokawa” sample recovered by the spacecraft “Hayabusa”[1]. A phase-contrast x-ray imaging has also been developed. In the x-ray region, sensitivity of the phase-contrast imaging is about 1000 times higher at most for the low-Z materials than that of the absorption contrast imaging. Therefore, the phase-contrast microscope CT is frequently used for the biological samples and organic. Figure 2 shows the phase contrast x-ray CT image of human hair [2]. A novel system combining the scanning microscope and the imaging microscope has been developed for the purpose of a 3D multimodal imaging of the phase and absorption contrast x-ray imaging. In the conference, present status and some applications of x-ray microscopy at the SPring-8 public beamlines will be presented. [1] A. Tsuchiyama et al, Science 333 (2011) 1125-1128. [2] A. Takeuchi et al, AIP Conf. Proc. 1266 (2010) 42-46. Fig. 1. CT image of

Microdissection of Human Esophagogastric Junction Wall with Phase-contrast X-ray CT Imaging.

Phase-contrast x-ray imaging using an x-ray interferometer has great potential to reveal the structures inside soft tissues, because the sensitivity of this method to hydrogen, carbon, nitrogen, and oxygen is about 1000 times higher than that of the absorption-contrast x-ray method. In this study, we used phase-contrast X-ray CT to investigate human resected esophagogastric junction. This technology revealed the three-layer structure of the esophagogastric junction wall—mucous, submucosa and muscular layers. The mucous and muscular layers were clearly separated by a loose submucosa layer with a honeycomb appearance. The shape of the mucous and muscular layers was intact. The boundary between the mucous and submucosa layers was distinct, as was the border of the muscular and submucosa layers. The surface of the esophagogastric junction was displayed clearly through 3D reconstruction. The technology might be helpful in the diagnosis of esophagogastric junction lesion, especially for the early adenocarcinoma.